From 5d618886570e98e6745593701246b877998a5367 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Mon, 23 Nov 2015 16:51:16 -0500
Subject: [PATCH 001/144] Correct Spack cc script

---
 lib/spack/env/cc | 34 +++++++++++++++++++++++++++++++++-
 1 file changed, 33 insertions(+), 1 deletion(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 75a63f6fac..f3fadfcf45 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -126,6 +126,11 @@ if [ -z "$mode" ]; then
         elif [ "$arg" = -c ]; then
             mode=cc
             break
+        elif [ "$arg" = -S ]; then
+            mode=as
+	    echo "spac cc mode as" "$@"
+	    exit 1
+            break
         fi
     done
 fi
@@ -155,6 +160,7 @@ libraries=()
 libs=()
 rpaths=()
 other_args=()
+all_args=("$@")
 
 while [ -n "$1" ]; do
     case "$1" in
@@ -178,6 +184,8 @@ while [ -n "$1" ]; do
             if [ -z "$arg" ]; then shift; arg="$1"; fi
             if [[ "$arg" = -rpath=* ]]; then
                 rpaths+=("${arg#-rpath=}")
+            elif [[ "$arg" = -rpath,* ]]; then
+                rpaths+=("${arg#-rpath,}")
             elif [[ "$arg" = -rpath ]]; then
                 shift; arg="$1"
                 if [[ "$arg" != -Wl,* ]]; then
@@ -193,6 +201,8 @@ while [ -n "$1" ]; do
             if [ -z "$arg" ]; then shift; arg="$1"; fi
             if [[ "$arg" = -rpath=* ]]; then
                 rpaths+=("${arg#-rpath=}")
+            elif [[ "$arg" = -rpath,* ]]; then
+                rpaths+=("${arg#-rpath,}")
             elif [[ "$arg" = -rpath ]]; then
                 shift; arg="$1"
                 if [[ "$arg" != -Xlinker,* ]]; then
@@ -247,25 +257,46 @@ IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
     if [ -d "$dep/include" ]; then
         includes+=("$dep/include")
+	all_args=("-I$dep/include" ${all_args[@]})
     fi
 
     if [ -d "$dep/lib" ]; then
         libraries+=("$dep/lib")
         rpaths+=("$dep/lib")
+	if [ "$mode" = ccld ]; then
+	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
+	elif [ "$mode" = ld ]; then
+	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
+	fi
     fi
 
     if [ -d "$dep/lib64" ]; then
         libraries+=("$dep/lib64")
         rpaths+=("$dep/lib64")
+        if [ "$mode" = ccld ]; then
+	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
+        elif [ "$mode" = ld ]; then
+	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
+	fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
 for dir in "${libraries[@]}"; do
     [[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir")
+    if [ "$mode" = ccld ]; then
+	[[ dir = $SPACK_INSTALL* ]] && all_args=("-Wl,-rpath,$dir" ${all_args[@]})
+    elif [ "$mode" = ld ]; then
+	[[ dir = $SPACK_INSTALL* ]] && all_args=("-rpath" "$dir" ${all_args[@]})
+    fi
 done
 rpaths+=("$SPACK_PREFIX/lib")
 rpaths+=("$SPACK_PREFIX/lib64")
+if [ "$mode" = ccld ]; then
+    all_args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${all_args[@]})
+elif [ "$mode" = ld ]; then
+    all_args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${all_args[@]})
+fi
 
 # Put the arguments together
 args=()
@@ -317,7 +348,8 @@ done
 export PATH
 
 full_command=("$command")
-full_command+=("${args[@]}")
+# full_command+=("${args[@]}")
+full_command+=("${all_args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.

From ba22fc8b78841728500966d471db7b5bfd26cf56 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Mon, 21 Dec 2015 10:21:33 -0500
Subject: [PATCH 002/144] Simplify Spack cc script

---
 lib/spack/env/cc | 289 ++++++++++++++++++++++-------------------------
 1 file changed, 133 insertions(+), 156 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index f3fadfcf45..053295f42d 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -65,7 +65,7 @@ function die {
 }
 
 for param in $parameters; do
-    if [ -z "${!param}" ]; then
+    if [[ -z ${!param} ]]; then
         die "Spack compiler must be run from spack!  Input $param was missing!"
     fi
 done
@@ -114,114 +114,118 @@ case "$command" in
 esac
 
 # Finish setting up the mode.
-if [ -z "$mode" ]; then
+if [[ -z $mode ]]; then
     mode=ccld
     for arg in "$@"; do
-        if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
-            mode=vcheck
-            break
-        elif [ "$arg" = -E ]; then
-            mode=cpp
-            break
-        elif [ "$arg" = -c ]; then
-            mode=cc
-            break
-        elif [ "$arg" = -S ]; then
-            mode=as
-	    echo "spac cc mode as" "$@"
-	    exit 1
-            break
-        fi
+        case "$arg" in
+            -v|-V|--version|-dumpversion)
+                mode=vcheck
+                break
+                ;;
+            -E)
+                mode=cpp
+                break
+                ;;
+            -c)
+                mode=cc
+                break
+                ;;
+            -S)
+                mode=as
+                break
+                ;;
+        esac
     done
 fi
 
 # Dump the version and exist if we're in testing mode.
-if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
+if [[ $SPACK_TEST_COMMAND = dump-mode ]]; then
     echo "$mode"
     exit
 fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [ -z "$command" ]; then
+if [[ -z $command ]]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
 # Save original command for debug logging
 input_command="$@"
-
-#
-# Now do real parsing of the command line args, trying hard to keep
-# non-rpath linker arguments in the proper order w.r.t. other command
-# line arguments.  This is important for things like groups.
-#
-includes=()
-libraries=()
-libs=()
-rpaths=()
-other_args=()
-all_args=("$@")
-
-while [ -n "$1" ]; do
-    case "$1" in
-        -I*)
-            arg="${1#-I}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            includes+=("$arg")
-            ;;
-        -L*)
-            arg="${1#-L}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libraries+=("$arg")
-            ;;
-        -l*)
-            arg="${1#-l}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libs+=("$arg")
-            ;;
-        -Wl,*)
-            arg="${1#-Wl,}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            if [[ "$arg" = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ "$arg" = -rpath,* ]]; then
-                rpaths+=("${arg#-rpath,}")
-            elif [[ "$arg" = -rpath ]]; then
-                shift; arg="$1"
-                if [[ "$arg" != -Wl,* ]]; then
-                    die "-Wl,-rpath was not followed by -Wl,*"
-                fi
-                rpaths+=("${arg#-Wl,}")
-            else
-                other_args+=("-Wl,$arg")
-            fi
-            ;;
-        -Xlinker,*)
-            arg="${1#-Xlinker,}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            if [[ "$arg" = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ "$arg" = -rpath,* ]]; then
-                rpaths+=("${arg#-rpath,}")
-            elif [[ "$arg" = -rpath ]]; then
-                shift; arg="$1"
-                if [[ "$arg" != -Xlinker,* ]]; then
-                    die "-Xlinker,-rpath was not followed by -Xlinker,*"
-                fi
-                rpaths+=("${arg#-Xlinker,}")
-            else
-                other_args+=("-Xlinker,$arg")
-            fi
-            ;;
-        *)
-            other_args+=("$1")
-            ;;
-    esac
-    shift
-done
+args=("$@")
 
 # Dump parsed values for unit testing if asked for
-if [ -n "$SPACK_TEST_COMMAND" ]; then
+if [[ -n $SPACK_TEST_COMMAND ]]; then
+
+    #
+    # Now do real parsing of the command line args, trying hard to keep
+    # non-rpath linker arguments in the proper order w.r.t. other command line
+    # arguments.  This is important for things like groups.
+    #
+    includes=()
+    libraries=()
+    libs=()
+    rpaths=()
+    other_args=()
+
+    while [[ -n $1 ]]; do
+        case "$1" in
+            -I*)
+                arg="${1#-I}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                includes+=("$arg")
+                ;;
+            -L*)
+                arg="${1#-L}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                libraries+=("$arg")
+                ;;
+            -l*)
+                arg="${1#-l}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                libs+=("$arg")
+                ;;
+            -Wl,*)
+                arg="${1#-Wl,}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [[ $arg = -rpath=* ]]; then
+                    rpaths+=("${arg#-rpath=}")
+                elif [[ $arg = -rpath,* ]]; then
+                    rpaths+=("${arg#-rpath,}")
+                elif [[ $arg = -rpath ]]; then
+                    shift; arg="$1"
+                    if [[ $arg != -Wl,* ]]; then
+                        die "-Wl,-rpath was not followed by -Wl,*"
+                    fi
+                    rpaths+=("${arg#-Wl,}")
+                else
+                    other_args+=("-Wl,$arg")
+                fi
+                ;;
+            -Xlinker,*)
+                arg="${1#-Xlinker,}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [[ $arg = -rpath=* ]]; then
+                    rpaths+=("${arg#-rpath=}")
+                elif [[ $arg = -rpath,* ]]; then
+                    rpaths+=("${arg#-rpath,}")
+                elif [[ $arg = -rpath ]]; then
+                    shift; arg="$1"
+                    if [[ $arg != -Xlinker,* ]]; then
+                        die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                    fi
+                    rpaths+=("${arg#-Xlinker,}")
+                else
+                    other_args+=("-Xlinker,$arg")
+                fi
+                ;;
+            *)
+                other_args+=("$1")
+                ;;
+        esac
+        shift
+    done
+
     IFS=$'\n'
     case "$SPACK_TEST_COMMAND" in
         dump-includes)   echo "${includes[*]}";;
@@ -246,8 +250,8 @@ if [ -n "$SPACK_TEST_COMMAND" ]; then
             echo "${other_args[*]}"
             ;;
         *)
-            echo "ERROR: Unknown test command"
-            exit 1 ;;
+            die "ERROR: Unknown test command"
+            ;;
     esac
     exit
 fi
@@ -255,66 +259,44 @@ fi
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [ -d "$dep/include" ]; then
-        includes+=("$dep/include")
-	all_args=("-I$dep/include" ${all_args[@]})
+    if [[ -d $dep/include ]]; then
+        args=("-I$dep/include" "${args[@]}")
     fi
 
-    if [ -d "$dep/lib" ]; then
-        libraries+=("$dep/lib")
-        rpaths+=("$dep/lib")
-	if [ "$mode" = ccld ]; then
-	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
-	elif [ "$mode" = ld ]; then
-	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
-	fi
+    if [[ -d $dep/lib ]]; then
+        # libraries+=("$dep/lib")
+	    if [[ $mode = ccld ]]; then
+            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+        elif [[ $mode = ld ]]; then
+            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib64" ]; then
-        libraries+=("$dep/lib64")
-        rpaths+=("$dep/lib64")
-        if [ "$mode" = ccld ]; then
-	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
-        elif [ "$mode" = ld ]; then
-	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
-	fi
+    if [[ -d $dep/lib64 ]]; then
+        # libraries+=("$dep/lib64")
+        if [[ $mode = ccld ]]; then
+            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+        elif [[ $mode = ld ]]; then
+            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+        fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
-for dir in "${libraries[@]}"; do
-    [[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir")
-    if [ "$mode" = ccld ]; then
-	[[ dir = $SPACK_INSTALL* ]] && all_args=("-Wl,-rpath,$dir" ${all_args[@]})
-    elif [ "$mode" = ld ]; then
-	[[ dir = $SPACK_INSTALL* ]] && all_args=("-rpath" "$dir" ${all_args[@]})
-    fi
-done
-rpaths+=("$SPACK_PREFIX/lib")
-rpaths+=("$SPACK_PREFIX/lib64")
-if [ "$mode" = ccld ]; then
-    all_args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${all_args[@]})
-elif [ "$mode" = ld ]; then
-    all_args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${all_args[@]})
-fi
-
-# Put the arguments together
-args=()
-for dir in "${includes[@]}";  do args+=("-I$dir"); done
-args+=("${other_args[@]}")
-for dir in "${libraries[@]}"; do args+=("-L$dir"); done
-for lib in "${libs[@]}";      do args+=("-l$lib"); done
-
-if [ "$mode" = ccld ]; then
-    for dir in "${rpaths[@]}"; do
-        args+=("-Wl,-rpath")
-        args+=("-Wl,$dir");
-    done
-elif [ "$mode" = ld ]; then
-    for dir in "${rpaths[@]}"; do
-        args+=("-rpath")
-        args+=("$dir");
-    done
+if [[ $mode = ccld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-Wl,-rpath,$dir" "${args[@]}")
+    #     fi
+    # done
+    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${args[@]})
+elif [[ $mode = ld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-rpath" "$dir" "${args[@]}")
+    #     fi
+    # done
+    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${args[@]})
 fi
 
 #
@@ -330,34 +312,29 @@ unset DYLD_LIBRARY_PATH
 #
 IFS=':' read -ra env_path <<< "$PATH"
 IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH"
-spack_env_dirs+=(".")
+spack_env_dirs+=("" ".")
 PATH=""
 for dir in "${env_path[@]}"; do
     remove=""
     for rm_dir in "${spack_env_dirs[@]}"; do
-        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
+        if [[ $dir = $rm_dir ]]; then remove=True; fi
     done
-    if [ -z "$remove" ]; then
-        if [ -z "$PATH" ]; then
-            PATH="$dir"
-        else
-            PATH="$PATH:$dir"
-        fi
+    if [[ -z $remove ]]; then
+        PATH="${PATH:+$PATH:}$dir"
     fi
 done
 export PATH
 
 full_command=("$command")
-# full_command+=("${args[@]}")
-full_command+=("${all_args[@]}")
+full_command+=("${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [ "$SPACK_DEBUG" = "TRUE" ]; then
+if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command"     >> $input_log
+    echo "$input_command" >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 

From 3427174eb065a6e74fc279076423c2c5c5e8e737 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 22 Dec 2015 15:49:14 -0500
Subject: [PATCH 003/144] Correct quoting

---
 lib/spack/env/cc | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 565f959ca4..4ac8f2e7f4 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -265,7 +265,7 @@ for dep in "${deps[@]}"; do
 
     if [[ -d $dep/lib ]]; then
         # libraries+=("$dep/lib")
-	    if [[ $mode = ccld ]]; then
+        if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
             args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
@@ -289,14 +289,14 @@ if [[ $mode = ccld ]]; then
     #         args=("-Wl,-rpath,$dir" "${args[@]}")
     #     fi
     # done
-    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${args[@]})
+    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
     # for dir in "${libraries[@]}"; do
     #     if [[ dir = $SPACK_INSTALL* ]]; then
     #         args=("-rpath" "$dir" "${args[@]}")
     #     fi
     # done
-    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${args[@]})
+    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
 #
@@ -325,8 +325,7 @@ for dir in "${env_path[@]}"; do
 done
 export PATH
 
-full_command=("$command")
-full_command+=("${args[@]}")
+full_command=("$command" "${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.

From 981cefe8d3f4f73461789713726a9658498a5f14 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Sun, 17 Jan 2016 10:54:12 -0500
Subject: [PATCH 004/144] Make Boost build with MPI on OS X

Boost does not build on OS X with either gold or binutils. The gold linker does not exist on Darwin, and binutils on Darwin provides an assembler that doesn't work for Boost.

- Introduce a variant that specifies whether to build with binutils, defaulting to true for backward compatibility
- Auto-detect whether we build on Darwin; in this case, set the gold and binutils variant defaults to false
- Clean up configure flags for as and ld
---
 var/spack/packages/boost/package.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/var/spack/packages/boost/package.py b/var/spack/packages/boost/package.py
index 3427b74ad6..894af9edd1 100644
--- a/var/spack/packages/boost/package.py
+++ b/var/spack/packages/boost/package.py
@@ -1,5 +1,8 @@
 from spack import *
 
+import os
+import sys
+
 class Boost(Package):
     """Boost provides free peer-reviewed portable C++ source
        libraries, emphasizing libraries that work well with the C++
@@ -127,6 +130,16 @@ def determine_b2_options(self, spec, options):
             '--layout=tagged'])
 
     def install(self, spec, prefix):
+        # On Darwin, Boost expects the Darwin libtool. However, one of the
+        # dependencies may have pulled in Spack's GNU libtool, and these two are
+        # not compatible. We thus create a symlink to Darwin's libtool and add
+        # it at the beginning of PATH.
+        if sys.platform == 'darwin':
+            newdir = os.path.abspath('darwin-libtool')
+            mkdirp(newdir)
+            force_symlink('/usr/bin/libtool', join_path(newdir, 'libtool'))
+            env['PATH'] = newdir + ':' + env['PATH']
+
         # to make Boost find the user-config.jam
         env['BOOST_BUILD_PATH'] = './'
 

From 77c17e1d92ac1c98a5c43247d6582876bc7d14d4 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 12 Feb 2016 12:51:43 -0500
Subject: [PATCH 005/144] Since my last patch didn't get traction, here is a
 new approach to building gcc on Darwin:

- Add a variant specifying whether to build with binutils, defaulting to true
- Auto-detect whether this is Darwin; if so, set binutils and gold defaults to false, as they don't work on Darwin
- Disable Go, which doesn't build on Darwin
- Clean up handling configure options
---
 .../repos/builtin/packages/gcc/package.py     | 29 ++++++++++---------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 3e5895cfb8..eb2129c4da 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -26,6 +26,7 @@
 
 from contextlib import closing
 from glob import glob
+import sys
 
 class Gcc(Package):
     """The GNU Compiler Collection includes front ends for C, C++,
@@ -49,13 +50,14 @@ class Gcc(Package):
     version('4.6.4', 'b407a3d1480c11667f293bfb1f17d1a4')
     version('4.5.4', '27e459c2566b8209ab064570e1b378f7')
 
-    variant('gold', default=True, description="Build the gold linker plugin for ld-based LTO")
+    variant('binutils', default=sys.platform != 'darwin', description="Build via binutils")
+    variant('gold', default=sys.platform != 'darwin', description="Build the gold linker plugin for ld-based LTO")
 
     depends_on("mpfr")
     depends_on("gmp")
     depends_on("mpc")     # when @4.5:
-    depends_on("binutils~libiberty", when='~gold')
-    depends_on("binutils~libiberty+gold", when='+gold')
+    depends_on("binutils~libiberty", when='+binutils ~gold')
+    depends_on("binutils~libiberty+gold", when='+binutils +gold')
 
     # Save these until we can do optional deps.
     depends_on("isl", when=DEPENDS_ON_ISL_PREDICATE)
@@ -67,7 +69,7 @@ def install(self, spec, prefix):
         filter_file(r"'@.*@'", "'@[[:alnum:]]*@'", 'libjava/configure', string=True)
 
         enabled_languages = set(('c', 'c++', 'fortran', 'java', 'objc'))
-        if spec.satisfies("@4.7.1:"):
+        if spec.satisfies("@4.7.1:") and sys.platform != 'darwin':
             enabled_languages.add('go')
 
         # Generic options to compile GCC
@@ -79,17 +81,18 @@ def install(self, spec, prefix):
                    "--with-mpfr=%s"   % spec['mpfr'].prefix,
                    "--with-gmp=%s"    % spec['gmp'].prefix,
                    "--enable-lto",
-                   "--with-gnu-ld",
-                   "--with-gnu-as",
                    "--with-quad"]
         # Binutils
-        static_bootstrap_flags = "-static-libstdc++ -static-libgcc"
-        binutils_options = ["--with-sysroot=/",
-                            "--with-stage1-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags),
-                            "--with-boot-ldflags=%s %s"   % (self.rpath_args, static_bootstrap_flags),
-                            "--with-ld=%s/bin/ld" % spec['binutils'].prefix,
-                            "--with-as=%s/bin/as" % spec['binutils'].prefix]
-        options.extend(binutils_options)
+        if spec.satisfies('+binutils'):
+            static_bootstrap_flags = "-static-libstdc++ -static-libgcc"
+            binutils_options = ["--with-sysroot=/",
+                                "--with-stage1-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags),
+                                "--with-boot-ldflags=%s %s"   %     (self.rpath_args, static_bootstrap_flags),
+                                "--with-gnu-ld",
+                                "--with-ld=%s/bin/ld" % spec['binutils'].prefix,
+                                "--with-gnu-as",
+                                "--with-as=%s/bin/as" % spec['binutils'].prefix]
+            options.extend(binutils_options)
         # Isl
         if spec.satisfies(Gcc.DEPENDS_ON_ISL_PREDICATE):
             isl_options = ["--with-isl=%s" % spec['isl'].prefix]

From ff81aff2540f9eadd8d0ce123ae3143ebcb68789 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 12 Feb 2016 13:05:42 -0500
Subject: [PATCH 006/144] Remove source-code optimization and cleanup

---
 lib/spack/env/cc | 106 ++++++++++++++++++++---------------------------
 1 file changed, 44 insertions(+), 62 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index b83731404b..ac8f717cc7 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -65,7 +65,7 @@ function die {
 }
 
 for param in $parameters; do
-    if [[ -z ${!param} ]]; then
+    if [ -z "${!param}" ]; then
         die "Spack compiler must be run from spack!  Input $param was missing!"
     fi
 done
@@ -114,39 +114,31 @@ case "$command" in
 esac
 
 # Finish setting up the mode.
-if [[ -z $mode ]]; then
+if [ -z "$mode" ]; then
     mode=ccld
     for arg in "$@"; do
-        case "$arg" in
-            -v|-V|--version|-dumpversion)
-                mode=vcheck
-                break
-                ;;
-            -E)
-                mode=cpp
-                break
-                ;;
-            -c)
-                mode=cc
-                break
-                ;;
-            -S)
-                mode=as
-                break
-                ;;
-        esac
+        if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
+            mode=vcheck
+            break
+        elif [ "$arg" = -E ]; then
+            mode=cpp
+            break
+        elif [ "$arg" = -c ]; then
+            mode=cc
+            break
+        fi
     done
 fi
 
 # Dump the version and exist if we're in testing mode.
-if [[ $SPACK_TEST_COMMAND = dump-mode ]]; then
+if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
     echo "$mode"
     exit
 fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [[ -z $command ]]; then
+if [ -z "$command" ]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
@@ -159,8 +151,8 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
 
     #
     # Now do real parsing of the command line args, trying hard to keep
-    # non-rpath linker arguments in the proper order w.r.t. other command line
-    # arguments.  This is important for things like groups.
+    # non-rpath linker arguments in the proper order w.r.t. other command
+    # line arguments.  This is important for things like groups.
     #
     includes=()
     libraries=()
@@ -168,33 +160,31 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
     rpaths=()
     other_args=()
 
-    while [[ -n $1 ]]; do
+    while [ -n "$1" ]; do
         case "$1" in
             -I*)
                 arg="${1#-I}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
                 includes+=("$arg")
                 ;;
             -L*)
                 arg="${1#-L}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
                 libraries+=("$arg")
                 ;;
             -l*)
                 arg="${1#-l}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
                 libs+=("$arg")
                 ;;
             -Wl,*)
                 arg="${1#-Wl,}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
-                if [[ $arg = -rpath=* ]]; then
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
+                if [[ "$arg" = -rpath=* ]]; then
                     rpaths+=("${arg#-rpath=}")
-                elif [[ $arg = -rpath,* ]]; then
-                    rpaths+=("${arg#-rpath,}")
-                elif [[ $arg = -rpath ]]; then
+                elif [[ "$arg" = -rpath ]]; then
                     shift; arg="$1"
-                    if [[ $arg != -Wl,* ]]; then
+                    if [[ "$arg" != -Wl,* ]]; then
                         die "-Wl,-rpath was not followed by -Wl,*"
                     fi
                     rpaths+=("${arg#-Wl,}")
@@ -204,14 +194,12 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
                 ;;
             -Xlinker,*)
                 arg="${1#-Xlinker,}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
-                if [[ $arg = -rpath=* ]]; then
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
+                if [[ "$arg" = -rpath=* ]]; then
                     rpaths+=("${arg#-rpath=}")
-                elif [[ $arg = -rpath,* ]]; then
-                    rpaths+=("${arg#-rpath,}")
-                elif [[ $arg = -rpath ]]; then
+                elif [[ "$arg" = -rpath ]]; then
                     shift; arg="$1"
-                    if [[ $arg != -Xlinker,* ]]; then
+                    if [[ "$arg" != -Xlinker,* ]]; then
                         die "-Xlinker,-rpath was not followed by -Xlinker,*"
                     fi
                     rpaths+=("${arg#-Xlinker,}")
@@ -250,8 +238,8 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
             echo "${other_args[*]}"
             ;;
         *)
-            die "ERROR: Unknown test command"
-            ;;
+            echo "ERROR: Unknown test command"
+            exit 1 ;;
     esac
     exit
 fi
@@ -259,12 +247,11 @@ fi
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [[ -d $dep/include ]]; then
+    if [ -d "$dep/include" ]; then
         args=("-I$dep/include" "${args[@]}")
     fi
 
-    if [[ -d $dep/lib ]]; then
-        # libraries+=("$dep/lib")
+    if [ -d "$dep/lib" ]; then
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -272,7 +259,7 @@ for dep in "${deps[@]}"; do
         fi
     fi
 
-    if [[ -d $dep/lib64 ]]; then
+    if [ -d "$dep/lib64" ]; then
         # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
@@ -284,18 +271,8 @@ done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-Wl,-rpath,$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-rpath" "$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
@@ -317,23 +294,28 @@ PATH=""
 for dir in "${env_path[@]}"; do
     remove=""
     for rm_dir in "${spack_env_dirs[@]}"; do
-        if [[ $dir = $rm_dir ]]; then remove=True; fi
+        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
     done
-    if [[ -z $remove ]]; then
-        PATH="${PATH:+$PATH:}$dir"
+    if [ -z "$remove" ]; then
+        if [ -z "$PATH" ]; then
+            PATH="$dir"
+        else
+            PATH="$PATH:$dir"
+        fi
     fi
 done
 export PATH
 
-full_command=("$command" "${args[@]}")
+full_command=("$command")
+full_command+=("${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [[ $SPACK_DEBUG = TRUE ]]; then
+if [ "$SPACK_DEBUG" = "TRUE" ]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command" >> $input_log
+    echo "$input_command"     >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 

From 8e33cc1ae118b138aadc3c354b622c045dd81009 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 12 Feb 2016 13:11:45 -0500
Subject: [PATCH 007/144] Properly wrap all long lines

---
 .../repos/builtin/packages/gcc/package.py     | 27 ++++++++++++-------
 1 file changed, 17 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index eb2129c4da..8292670de0 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -50,8 +50,10 @@ class Gcc(Package):
     version('4.6.4', 'b407a3d1480c11667f293bfb1f17d1a4')
     version('4.5.4', '27e459c2566b8209ab064570e1b378f7')
 
-    variant('binutils', default=sys.platform != 'darwin', description="Build via binutils")
-    variant('gold', default=sys.platform != 'darwin', description="Build the gold linker plugin for ld-based LTO")
+    variant('binutils', default=sys.platform != 'darwin',
+        description="Build via binutils")
+    variant('gold', default=sys.platform != 'darwin',
+        description="Build the gold linker plugin for ld-based LTO")
 
     depends_on("mpfr")
     depends_on("gmp")
@@ -66,7 +68,8 @@ class Gcc(Package):
 
     def install(self, spec, prefix):
         # libjava/configure needs a minor fix to install into spack paths.
-        filter_file(r"'@.*@'", "'@[[:alnum:]]*@'", 'libjava/configure', string=True)
+        filter_file(r"'@.*@'", "'@[[:alnum:]]*@'", 'libjava/configure',
+            string=True)
 
         enabled_languages = set(('c', 'c++', 'fortran', 'java', 'objc'))
         if spec.satisfies("@4.7.1:") and sys.platform != 'darwin':
@@ -77,17 +80,19 @@ def install(self, spec, prefix):
                    "--libdir=%s/lib64" % prefix,
                    "--disable-multilib",
                    "--enable-languages=" + ','.join(enabled_languages),
-                   "--with-mpc=%s"    % spec['mpc'].prefix,
-                   "--with-mpfr=%s"   % spec['mpfr'].prefix,
-                   "--with-gmp=%s"    % spec['gmp'].prefix,
+                   "--with-mpc=%s" % spec['mpc'].prefix,
+                   "--with-mpfr=%s" % spec['mpfr'].prefix,
+                   "--with-gmp=%s" % spec['gmp'].prefix,
                    "--enable-lto",
                    "--with-quad"]
         # Binutils
         if spec.satisfies('+binutils'):
             static_bootstrap_flags = "-static-libstdc++ -static-libgcc"
             binutils_options = ["--with-sysroot=/",
-                                "--with-stage1-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags),
-                                "--with-boot-ldflags=%s %s"   %     (self.rpath_args, static_bootstrap_flags),
+                                "--with-stage1-ldflags=%s %s" %
+                                    (self.rpath_args, static_bootstrap_flags),
+                                "--with-boot-ldflags=%s %s" %
+                                    (self.rpath_args, static_bootstrap_flags),
                                 "--with-gnu-ld",
                                 "--with-ld=%s/bin/ld" % spec['binutils'].prefix,
                                 "--with-gnu-as",
@@ -120,7 +125,8 @@ def write_rpath_specs(self):
         """Generate a spec file so the linker adds a rpath to the libs
            the compiler used to build the executable."""
         if not self.spec_dir:
-            tty.warn("Could not install specs for %s." % self.spec.format('$_$@'))
+            tty.warn("Could not install specs for %s." %
+                self.spec.format('$_$@'))
             return
 
         gcc = Executable(join_path(self.prefix.bin, 'gcc'))
@@ -130,5 +136,6 @@ def write_rpath_specs(self):
             for line in lines:
                 out.write(line + "\n")
                 if line.startswith("*link:"):
-                    out.write("-rpath %s/lib:%s/lib64 \\\n"% (self.prefix, self.prefix))
+                    out.write("-rpath %s/lib:%s/lib64 \\\n" %
+                        (self.prefix, self.prefix))
         set_install_permissions(specs_file)

From 63ae40716908ee8c19d49de83accff482d921331 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 3 Mar 2016 16:39:21 +0100
Subject: [PATCH 008/144] netlib-lapack : unified build with netlib-blas
 openssl : updated version py-numpy : updated dependencies

---
 .../builtin/packages/netlib-blas/package.py   | 46 ---------------
 .../builtin/packages/netlib-lapack/package.py | 57 +++++++------------
 .../repos/builtin/packages/openssl/package.py |  1 +
 .../builtin/packages/py-numpy/package.py      |  3 +-
 4 files changed, 21 insertions(+), 86 deletions(-)
 delete mode 100644 var/spack/repos/builtin/packages/netlib-blas/package.py

diff --git a/var/spack/repos/builtin/packages/netlib-blas/package.py b/var/spack/repos/builtin/packages/netlib-blas/package.py
deleted file mode 100644
index 85e97323d3..0000000000
--- a/var/spack/repos/builtin/packages/netlib-blas/package.py
+++ /dev/null
@@ -1,46 +0,0 @@
-from spack import *
-import os
-
-
-class NetlibBlas(Package):
-    """Netlib reference BLAS"""
-    homepage = "http://www.netlib.org/lapack/"
-    url      = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
-
-    version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
-
-    variant('fpic', default=False, description="Build with -fpic compiler option")
-
-    # virtual dependency
-    provides('blas')
-
-    # Doesn't always build correctly in parallel
-    parallel = False
-
-    def patch(self):
-        os.symlink('make.inc.example', 'make.inc')
-
-        mf = FileFilter('make.inc')
-        mf.filter('^FORTRAN.*', 'FORTRAN = f90')
-        mf.filter('^LOADER.*',  'LOADER = f90')
-        mf.filter('^CC =.*',  'CC = cc')
-
-        if '+fpic' in self.spec:
-            mf.filter('^OPTS.*=.*',  'OPTS = -O2 -frecursive -fpic')
-            mf.filter('^CFLAGS =.*',  'CFLAGS = -O3 -fpic')
-
-
-    def install(self, spec, prefix):
-        make('blaslib')
-
-        # Tests that blas builds correctly
-        make('blas_testing')
-
-        # No install provided
-        mkdirp(prefix.lib)
-        install('librefblas.a', prefix.lib)
-
-        # Blas virtual package should provide blas.a and libblas.a
-        with working_dir(prefix.lib):
-            symlink('librefblas.a', 'blas.a')
-            symlink('librefblas.a', 'libblas.a')
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index fb6b99e27c..1bb77919d5 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -1,16 +1,15 @@
 from spack import *
 
+
 class NetlibLapack(Package):
     """
-    LAPACK version 3.X is a comprehensive FORTRAN library that does
-    linear algebra operations including matrix inversions, least
-    squared solutions to linear sets of equations, eigenvector
-    analysis, singular value decomposition, etc. It is a very
-    comprehensive and reputable package that has found extensive
-    use in the scientific community.
+    LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix
+    inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value
+    decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the
+    scientific community.
     """
     homepage = "http://www.netlib.org/lapack/"
-    url      = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
+    url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
 
     version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
     version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478')
@@ -18,42 +17,24 @@ class NetlibLapack(Package):
     version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
     version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
 
-    variant('shared', default=False, description="Build shared library version")
+    variant('debug', default=False, description='Activates the Debug build type')
+    variant('shared', default=True, description="Build shared library version")
+
+    variant('lapacke', default=True, description='Activates the build of the LAPACKE C interface')
 
     # virtual dependency
+    provides('blas')
     provides('lapack')
 
-    # blas is a virtual dependency.
-    depends_on('blas')
-
     depends_on('cmake')
 
-    # Doesn't always build correctly in parallel
-    parallel = False
-
-    @when('^netlib-blas')
-    def get_blas_libs(self):
-        blas = self.spec['netlib-blas']
-        return [join_path(blas.prefix.lib, 'blas.a')]
-
-
-    @when('^atlas')
-    def get_blas_libs(self):
-        blas = self.spec['atlas']
-        return [join_path(blas.prefix.lib, l)
-                for l in ('libf77blas.a', 'libatlas.a')]
-
-
     def install(self, spec, prefix):
-        blas_libs = ";".join(self.get_blas_libs())
-        cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs]
-
-        if '+shared' in spec:
-            cmake_args.append('-DBUILD_SHARED_LIBS=ON')
-
-        cmake_args += std_cmake_args
-
-        cmake(*cmake_args)
-        make()
-        make("install")
+        cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
+                      '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
+                      '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
+        cmake_args.extend(std_cmake_args)
 
+        with working_dir('spack-build', create=True):
+            cmake('..', *cmake_args)
+            make()
+            make("install")
diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index c73102f05d..70afaf4038 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -17,6 +17,7 @@ class Openssl(Package):
     version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
     version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
     version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
+    version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
 
     depends_on("zlib")
     parallel = False
diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index 0354811186..0844ff5caa 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -12,8 +12,7 @@ class PyNumpy(Package):
 
     extends('python')
     depends_on('py-nose')
-    depends_on('netlib-blas+fpic', when='+blas')
-    depends_on('netlib-lapack+shared', when='+blas')
+    depends_on('lapack+shared', when='+blas')
 
     def install(self, spec, prefix):
         if '+blas' in spec:

From 310099d88838c8e08d15fb34028263c9294b62e9 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 4 Mar 2016 09:31:03 +0100
Subject: [PATCH 009/144] atlas : provides blas and lapack

---
 .../repos/builtin/packages/atlas/package.py   | 62 +++++++++----------
 1 file changed, 30 insertions(+), 32 deletions(-)

diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py
index fc683363a7..f9b50417b0 100644
--- a/var/spack/repos/builtin/packages/atlas/package.py
+++ b/var/spack/repos/builtin/packages/atlas/package.py
@@ -1,31 +1,34 @@
 from spack import *
 from spack.util.executable import Executable
-import os
+import os.path
 
 class Atlas(Package):
     """
-    Automatically Tuned Linear Algebra Software, generic shared
-    ATLAS is an approach for the automatic generation and optimization of
-    numerical software. Currently ATLAS supplies optimized versions for the
-    complete set of linear algebra kernels known as the Basic Linear Algebra
-    Subroutines (BLAS), and a subset of the linear algebra routines in the
-    LAPACK library.
+    Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and
+    optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear
+    algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines
+    in the LAPACK library.
     """
     homepage = "http://math-atlas.sourceforge.net/"
 
+    version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da',
+            url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True)
+    resource(name='lapack',
+             url='http://www.netlib.org/lapack/lapack-3.5.0.tgz',
+             md5='b1d3e3e425b2e44a06760ff173104bdf',
+             destination='spack-resource-lapack',
+             when='@3:')
+
     version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825',
             url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2/download')
-    version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da',
-            url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2')
 
-    # TODO: make this provide BLAS once it works better.  Create a way
-    # TODO: to mark "beta" packages and require explicit invocation.
-
-    # provides('blas')
+    variant('shared', default=True, description='Builds shared library')
 
+    provides('blas')
+    provides('lapack')
 
     def patch(self):
-        # Disable thraed check.  LLNL's environment does not allow
+        # Disable thread check.  LLNL's environment does not allow
         # disabling of CPU throttling in a way that ATLAS actually
         # understands.
         filter_file(r'^\s+if \(thrchk\) exit\(1\);', 'if (0) exit(1);',
@@ -33,26 +36,21 @@ def patch(self):
         # TODO: investigate a better way to add the check back in
         # TODO: using, say, MSRs.  Or move this to a variant.
 
-    @when('@:3.10')
     def install(self, spec, prefix):
-        with working_dir('ATLAS-Build', create=True):
+
+        options = []
+        if '+shared' in spec:
+            options.append('--shared')
+
+        # Lapack resource
+        lapack_stage = self.stage[1]
+        lapack_tarfile = os.path.basename(lapack_stage.fetcher.url)
+        lapack_tarfile_path = join_path(lapack_stage.path, lapack_tarfile)
+        options.append('--with-netlib-lapack-tarfile=%s' % lapack_tarfile_path)
+
+        with working_dir('spack-build', create=True):
             configure = Executable('../configure')
-            configure('--prefix=%s' % prefix, '-C', 'ic', 'cc', '-C', 'if', 'f77', "--dylibs")
-            make()
-            make('check')
-            make('ptcheck')
-            make('time')
-            make("install")
-
-
-    def install(self, spec, prefix):
-        with working_dir('ATLAS-Build', create=True):
-            configure = Executable('../configure')
-            configure('--incdir=%s' % prefix.include,
-                      '--libdir=%s' % prefix.lib,
-                      '--cc=cc',
-                      "--shared")
-
+            configure('--prefix=%s' % prefix, *options)
             make()
             make('check')
             make('ptcheck')

From a2af4940aaf169f3358f19986fc94a02222a8096 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 4 Mar 2016 09:59:16 +0100
Subject: [PATCH 010/144] atlas : disabling parallel builds

---
 var/spack/repos/builtin/packages/atlas/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py
index f9b50417b0..b5504122b7 100644
--- a/var/spack/repos/builtin/packages/atlas/package.py
+++ b/var/spack/repos/builtin/packages/atlas/package.py
@@ -27,6 +27,8 @@ class Atlas(Package):
     provides('blas')
     provides('lapack')
 
+    parallel = False
+
     def patch(self):
         # Disable thread check.  LLNL's environment does not allow
         # disabling of CPU throttling in a way that ATLAS actually

From 4f14db8af214b6648da04c5c5121757ea171f18c Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 10 Mar 2016 10:34:51 +0100
Subject: [PATCH 011/144] netlib-lapack : optional dependency on external blas

---
 .../repos/builtin/packages/netlib-lapack/package.py  | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index 1bb77919d5..a208929d08 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -19,19 +19,29 @@ class NetlibLapack(Package):
 
     variant('debug', default=False, description='Activates the Debug build type')
     variant('shared', default=True, description="Build shared library version")
+    variant('external-blas', default=False, description='Build lapack with an external blas')
 
     variant('lapacke', default=True, description='Activates the build of the LAPACKE C interface')
 
     # virtual dependency
-    provides('blas')
+    provides('blas', when='~external-blas')
     provides('lapack')
 
     depends_on('cmake')
+    depends_on('blas', when='+external-blas')
 
     def install(self, spec, prefix):
         cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
                       '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
                       '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
+        if '+external-blas' in spec:
+            # TODO : the mechanism to specify the library should be more general,
+            # TODO : but this allows to have an hook to an external blas
+            cmake_args.extend([
+                '-DUSE_OPTIMIZED_BLAS:BOOL=ON',
+                '-DBLAS_LIBRARIES:PATH=%s' % join_path(spec['blas'].prefix.lib, 'libblas.a')
+            ])
+
         cmake_args.extend(std_cmake_args)
 
         with working_dir('spack-build', create=True):

From f3ea0420f80f418a0f3e628479c782f197e6a43e Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Thu, 17 Mar 2016 21:53:13 -0400
Subject: [PATCH 012/144] Import recent changes

---
 lib/spack/env/cc | 185 +++++++++++++++++------------------------------
 1 file changed, 65 insertions(+), 120 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index df6795c264..c6a09724e9 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -65,7 +65,7 @@ function die {
 }
 
 for param in $parameters; do
-    if [ -z "${!param}" ]; then
+    if [[ -z ${!param} ]]; then
         die "Spack compiler must be run from spack!  Input $param was missing!"
     fi
 done
@@ -78,10 +78,11 @@ done
 # 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90]
 #
 # 'mode' is set to one of:
+#    cpp     preprocess
 #    cc      compile
+#    as      assemble
 #    ld      link
 #    ccld    compile & link
-#    cpp     preprocessor
 #    vcheck  version check
 #
 command=$(basename "$0")
@@ -131,6 +132,9 @@ if [ -z "$mode" ]; then
         if [ "$arg" = -E ]; then
             mode=cpp
             break
+        elif [ "$arg" = -S ]; then
+            mode=as
+            break
         elif [ "$arg" = -c ]; then
             mode=cc
             break
@@ -146,22 +150,25 @@ fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [ -z "$command" ]; then
+if [[ -z $command ]]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
+if [ "$mode" == vcheck ] ; then
+    exec ${command} "$@"
+fi
+
 # Save original command for debug logging
 input_command="$@"
 args=("$@")
 
-<<<<<<< HEAD
 # Dump parsed values for unit testing if asked for
 if [[ -n $SPACK_TEST_COMMAND ]]; then
 
     #
     # Now do real parsing of the command line args, trying hard to keep
-    # non-rpath linker arguments in the proper order w.r.t. other command
-    # line arguments.  This is important for things like groups.
+    # non-rpath linker arguments in the proper order w.r.t. other command line
+    # arguments.  This is important for things like groups.
     #
     includes=()
     libraries=()
@@ -188,32 +195,44 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
                 ;;
             -Wl,*)
                 arg="${1#-Wl,}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                if [[ "$arg" = -rpath=* ]]; then
-                    rpaths+=("${arg#-rpath=}")
-                elif [[ "$arg" = -rpath ]]; then
+                # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
+                if [[ $arg == -rpath=* ]]; then
+                    arg="${arg#-rpath=}"
+                    for rpath in ${arg//,/ }; do
+                        rpaths+=("$rpath")
+                    done
+                elif [[ $arg == -rpath,* ]]; then
+                    arg="${arg#-rpath,}"
+                    for rpath in ${arg//,/ }; do
+                        rpaths+=("$rpath")
+                    done
+                elif [[ $arg == -rpath ]]; then
                     shift; arg="$1"
-                    if [[ "$arg" != -Wl,* ]]; then
+                    if [[ $arg != '-Wl,'* ]]; then
                         die "-Wl,-rpath was not followed by -Wl,*"
                     fi
-                    rpaths+=("${arg#-Wl,}")
+                    arg="${arg#-Wl,}"
+                    for rpath in ${arg//,/ }; do
+                        rpaths+=("$rpath")
+                    done
                 else
                     other_args+=("-Wl,$arg")
                 fi
                 ;;
-            -Xlinker,*)
-                arg="${1#-Xlinker,}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                if [[ "$arg" = -rpath=* ]]; then
+            -Xlinker)
+                shift; arg="$1";
+                if [[ $arg = -rpath=* ]]; then
                     rpaths+=("${arg#-rpath=}")
-                elif [[ "$arg" = -rpath ]]; then
+                elif [[ $arg = -rpath ]]; then
                     shift; arg="$1"
-                    if [[ "$arg" != -Xlinker,* ]]; then
-                        die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                    if [[ $arg != -Xlinker ]]; then
+                        die "-Xlinker -rpath was not followed by -Xlinker <arg>"
                     fi
-                    rpaths+=("${arg#-Xlinker,}")
+                    shift; arg="$1"
+                    rpaths+=("$arg")
                 else
-                    other_args+=("-Xlinker,$arg")
+                    other_args+=("-Xlinker")
+                    other_args+=("$arg")
                 fi
                 ;;
             *)
@@ -222,88 +241,6 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
         esac
         shift
     done
-=======
-if [ "$mode" == vcheck ] ; then
-    exec ${command} "$@"
-fi
-
-#
-# Now do real parsing of the command line args, trying hard to keep
-# non-rpath linker arguments in the proper order w.r.t. other command
-# line arguments.  This is important for things like groups.
-#
-includes=()
-libraries=()
-libs=()
-rpaths=()
-other_args=()
-
-while [ -n "$1" ]; do
-    case "$1" in
-        -I*)
-            arg="${1#-I}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            includes+=("$arg")
-            ;;
-        -L*)
-            arg="${1#-L}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libraries+=("$arg")
-            ;;
-        -l*)
-            arg="${1#-l}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libs+=("$arg")
-            ;;
-        -Wl,*)
-            arg="${1#-Wl,}"
-            # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
-            if [[ $arg == -rpath=* ]]; then
-                arg="${arg#-rpath=}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            elif [[ $arg == -rpath,* ]]; then
-                arg="${arg#-rpath,}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            elif [[ $arg == -rpath ]]; then
-                shift; arg="$1"
-                if [[ $arg != '-Wl,'* ]]; then
-                    die "-Wl,-rpath was not followed by -Wl,*"
-                fi
-                arg="${arg#-Wl,}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            else
-                other_args+=("-Wl,$arg")
-            fi
-            ;;
-        -Xlinker)
-            shift; arg="$1";
-            if [[ $arg = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ $arg = -rpath ]]; then
-                shift; arg="$1"
-                if [[ $arg != -Xlinker ]]; then
-                    die "-Xlinker -rpath was not followed by -Xlinker <arg>"
-                fi
-                shift; arg="$1"
-                rpaths+=("$arg")
-            else
-                other_args+=("-Xlinker")
-                other_args+=("$arg")
-            fi
-            ;;
-        *)
-            other_args+=("$1")
-            ;;
-    esac
-    shift
-done
->>>>>>> develop
 
     IFS=$'\n'
     case "$SPACK_TEST_COMMAND" in
@@ -329,8 +266,8 @@ done
             echo "${other_args[*]}"
             ;;
         *)
-            echo "ERROR: Unknown test command"
-            exit 1 ;;
+            die "ERROR: Unknown test command"
+            ;;
     esac
     exit
 fi
@@ -338,11 +275,14 @@ fi
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [ -d "$dep/include" ]; then
-        args=("-I$dep/include" "${args[@]}")
+    if [[ -d $dep/include ]]; then
+        if [[ $mode = cpp || $mode = cc || $mode = as || $mode = ccld ]]; then
+            args=("-I$dep/include" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib" ]; then
+    if [[ -d $dep/lib ]]; then
+        # libraries+=("$dep/lib")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -350,7 +290,7 @@ for dep in "${deps[@]}"; do
         fi
     fi
 
-    if [ -d "$dep/lib64" ]; then
+    if [[ -d $dep/lib64 ]]; then
         # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
@@ -362,8 +302,18 @@ done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-Wl,-rpath,$dir" "${args[@]}")
+    #     fi
+    # done
     args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-rpath" "$dir" "${args[@]}")
+    #     fi
+    # done
     args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
@@ -385,28 +335,23 @@ PATH=""
 for dir in "${env_path[@]}"; do
     remove=""
     for rm_dir in "${spack_env_dirs[@]}"; do
-        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
+        if [[ $dir = $rm_dir ]]; then remove=True; fi
     done
-    if [ -z "$remove" ]; then
-        if [ -z "$PATH" ]; then
-            PATH="$dir"
-        else
-            PATH="$PATH:$dir"
-        fi
+    if [[ -z $remove ]]; then
+        PATH="${PATH:+$PATH:}$dir"
     fi
 done
 export PATH
 
-full_command=("$command")
-full_command+=("${args[@]}")
+full_command=("$command" "${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [ "$SPACK_DEBUG" = "TRUE" ]; then
+if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command"     >> $input_log
+    echo "$input_command" >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 

From 3b24db92b5ea64814b1294fc6c9c982bbaa9b3c6 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Thu, 17 Mar 2016 13:43:40 -0400
Subject: [PATCH 013/144] Update PAPI to 5.4.3

---
 var/spack/repos/builtin/packages/papi/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py
index 910e0aa9f9..53d69e28d9 100644
--- a/var/spack/repos/builtin/packages/papi/package.py
+++ b/var/spack/repos/builtin/packages/papi/package.py
@@ -13,6 +13,7 @@ class Papi(Package):
     homepage = "http://icl.cs.utk.edu/papi/index.html"
 
     url      = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz"
+    version('5.4.3', '3211b5a5bb389fe692370f5cf4cc2412')
     version('5.4.1', '9134a99219c79767a11463a76b0b01a2')
     version('5.3.0', '367961dd0ab426e5ae367c2713924ffb')
 

From ed0b5e649dd6bc480e3faa6ffcca121eb9e264b8 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Fri, 18 Mar 2016 15:54:26 -0600
Subject: [PATCH 014/144] + Provide fpic variant for netlib-lapack.

---
 var/spack/repos/builtin/packages/netlib-lapack/package.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index 741f4af421..78c5a053fe 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -20,13 +20,13 @@ class NetlibLapack(Package):
     version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
 
     variant('shared', default=False, description="Build shared library version")
+    variant('fpic', default=False, description="Build with -fpic compiler option")
 
     # virtual dependency
     provides('lapack')
 
     # blas is a virtual dependency.
     depends_on('blas')
-
     depends_on('cmake')
 
     # Doesn't always build correctly in parallel
@@ -37,24 +37,23 @@ def get_blas_libs(self):
         blas = self.spec['netlib-blas']
         return [join_path(blas.prefix.lib, 'blas.a')]
 
-
     @when('^atlas')
     def get_blas_libs(self):
         blas = self.spec['atlas']
         return [join_path(blas.prefix.lib, l)
                 for l in ('libf77blas.a', 'libatlas.a')]
 
-
     def install(self, spec, prefix):
         blas_libs = ";".join(self.get_blas_libs())
         cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs]
 
         if '+shared' in spec:
             cmake_args.append('-DBUILD_SHARED_LIBS=ON')
+        if '+fpic' in spec:
+            cmake_args.append('-DCMAKE_POSITION_INDEPENDENT_CODE=ON')
 
         cmake_args += std_cmake_args
 
         cmake(*cmake_args)
         make()
         make("install")
-

From db61a09cf14cc791d7692aac0329e8958b228fb6 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 18 Mar 2016 16:28:36 +0100
Subject: [PATCH 015/144] fix mumps: when installed with parmetis has to be
 linked with metis

---
 .../repos/builtin/packages/mumps/package.py   | 28 +++++++++++--------
 1 file changed, 16 insertions(+), 12 deletions(-)

diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 44a37903cc..5c120c37df 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -20,10 +20,10 @@ class Mumps(Package):
     variant('complex', default=True, description='Activate the compilation of cmumps and/or zmumps')
     variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
 
-    
+
     depends_on('scotch + esmumps', when='~ptscotch+scotch')
     depends_on('scotch + esmumps + mpi', when='+ptscotch')
-    depends_on('metis', when='~parmetis+metis')
+    depends_on('metis', when='+metis')
     depends_on('parmetis', when="+parmetis")
     depends_on('blas')
     depends_on('lapack')
@@ -38,11 +38,11 @@ class Mumps(Package):
     def write_makefile_inc(self):
         if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec:
             raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')
-        
+
         makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib]
 
         orderings = ['-Dpord']
-        
+
         if '+ptscotch' in self.spec or '+scotch' in self.spec:
             join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '')
             makefile_conf.extend(
@@ -54,15 +54,19 @@ def write_makefile_inc(self):
             if '+ptscotch' in self.spec:
                 orderings.append('-Dptscotch')
 
-        if '+parmetis' in self.spec or '+metis' in self.spec:
+        if '+parmetis' in self.spec and '+metis' in self.spec:
             libname = 'parmetis' if '+parmetis' in self.spec else 'metis'
             makefile_conf.extend(
-                ["IMETIS = -I%s" % self.spec[libname].prefix.include,
-                 "LMETIS = -L%s -l%s" % (self.spec[libname].prefix.lib, libname)])
+                ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
+                 "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')])
+
+            orderings.append('-Dparmetis')
+        elif '+metis' in self.spec:
+            makefile_conf.extend(
+                ["IMETIS = -I%s" % self.spec['metis'].prefix.include,
+                 "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')])
 
             orderings.append('-Dmetis')
-            if '+parmetis' in self.spec:
-                orderings.append('-Dparmetis')
 
         makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
 
@@ -101,12 +105,12 @@ def write_makefile_inc(self):
         # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER
         makefile_conf.append("CDEFS   = -DAdd_")
 
-        
+
         makefile_inc_template = join_path(os.path.dirname(self.module.__file__),
                                           'Makefile.inc')
         with open(makefile_inc_template, "r") as fh:
             makefile_conf.extend(fh.read().split('\n'))
-        
+
         with working_dir('.'):
             with open("Makefile.inc", "w") as fh:
                 makefile_inc = '\n'.join(makefile_conf)
@@ -130,7 +134,7 @@ def install(self, spec, prefix):
                 make_libs.append('zexamples')
 
         self.write_makefile_inc()
-                
+
         make(*make_libs)
 
         install_tree('lib', prefix.lib)

From d493658a583231eeb778613cf7b6c8c8641c63a0 Mon Sep 17 00:00:00 2001
From: Cyrus Harrison <cyrush@llnl.gov>
Date: Sun, 20 Mar 2016 15:18:36 -0700
Subject: [PATCH 016/144] cmake package: add variant for openssl support

The openssl variant defaults to true to preserve spack's
current CMake configuration, which is using OpenSSL.

Signed-off-by: Cyrus Harrison <cyrush@llnl.gov>
---
 var/spack/repos/builtin/packages/cmake/package.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index cc93c7067c..be930a90ab 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -38,6 +38,7 @@ class Cmake(Package):
     version('2.8.10.2', '097278785da7182ec0aea8769d06860c')
 
     variant('ncurses', default=True, description='Enables the build of the ncurses gui')
+    variant('openssl', default=True, description="Enables CMake's OpenSSL features")
     variant('qt', default=False, description='Enables the build of cmake-gui')
     variant('doc', default=False, description='Enables the generation of html and man page documentation')
 
@@ -77,8 +78,9 @@ def install(self, spec, prefix):
             options.append('--sphinx-html')
             options.append('--sphinx-man')
 
-        options.append('--')
-        options.append('-DCMAKE_USE_OPENSSL=ON')
+        if '+openssl' in spec:
+            options.append('--')
+            options.append('-DCMAKE_USE_OPENSSL=ON')
 
         configure(*options)
         make()

From bba66cbe2836e364b58a611a5a5f5ae0d9692df4 Mon Sep 17 00:00:00 2001
From: Cyrus Harrison <cyrush@llnl.gov>
Date: Sun, 20 Mar 2016 19:27:22 -0700
Subject: [PATCH 017/144] cmake: depend on openssl when openssl variant=true

---
 var/spack/repos/builtin/packages/cmake/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index be930a90ab..1f93d39769 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -43,6 +43,7 @@ class Cmake(Package):
     variant('doc', default=False, description='Enables the generation of html and man page documentation')
 
     depends_on('ncurses', when='+ncurses')
+    depends_on('openssl', when='+openssl')
     depends_on('qt', when='+qt')
     depends_on('python@2.7.11:', when='+doc')
     depends_on('py-sphinx', when='+doc')

From 7b283bfaffa5509915d91392878203bba8a8d2cb Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 21 Mar 2016 07:48:17 +0100
Subject: [PATCH 018/144] fix petsc on osx

---
 .../repos/builtin/packages/petsc/package.py   | 20 ++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index efe172fc08..7239baaf7f 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -61,14 +61,24 @@ def mpi_dependent_options(self):
                 errors = ['incompatible variants given'] + errors
                 raise RuntimeError('\n'.join(errors))
         else:
-            compiler_opts = [
-                '--with-mpi=1',
-                '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
-            ]
+            if self.compiler.name == "clang":
+                compiler_opts = [
+                    '--with-mpi=1',
+                    '--with-cc=%s  -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # Avoid confusing PETSc config by clang: warning: argument unused during compilation
+                    '--with-cxx=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
+                    '--with-fc=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
+                    '--with-f77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'),
+                ]
+            else:
+                compiler_opts = [
+                    '--with-mpi=1',
+                    '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
+                ]
         return compiler_opts
 
     def install(self, spec, prefix):
-        options = []
+        options = ['--with-debugging=0',
+                   '--with-ssl=0']
         options.extend(self.mpi_dependent_options())
         options.extend([
             '--with-precision=%s' % ('double' if '+double' in spec else 'single'),

From b926d8a0cdcf47de029e372cf15e281266930378 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 21 Mar 2016 14:33:00 +0100
Subject: [PATCH 019/144] build parmetis against external metis

---
 .../parmetis/enable_external_metis.patch      | 13 ++++++++++
 .../builtin/packages/parmetis/package.py      | 24 ++++---------------
 2 files changed, 17 insertions(+), 20 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch

diff --git a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
new file mode 100644
index 0000000000..514781b8b8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
@@ -0,0 +1,13 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index ca945dd..1bf94e9 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -33,7 +33,7 @@ include_directories(${GKLIB_PATH})
+ include_directories(${METIS_PATH}/include)
+
+ # List of directories that cmake will look for CMakeLists.txt
+-add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
++#add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
+ add_subdirectory(include)
+ add_subdirectory(libparmetis)
+ add_subdirectory(programs)
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index c897dec7e4..3f18dd76b8 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -25,9 +25,6 @@
 
 from spack import *
 
-# FIXME : lot of code is duplicated from packages/metis/package.py . Inheriting from there may reduce
-# FIXME : the installation rules to just a few lines
-
 
 class Parmetis(Package):
     """
@@ -43,13 +40,11 @@ class Parmetis(Package):
     variant('debug', default=False, description='Builds the library in debug mode')
     variant('gdb', default=False, description='Enables gdb support')
 
-    variant('idx64', default=False, description='Use int64_t as default index type')
-    variant('double', default=False, description='Use double precision floating point types')
-
     depends_on('cmake @2.8:')  # build dependency
     depends_on('mpi')
 
-    # FIXME : this should conflict with metis as it builds its own version internally
+    patch('enable_external_metis.patch')
+    depends_on('metis')
 
     depends_on('gdb', when='+gdb')
 
@@ -63,8 +58,8 @@ def install(self, spec, prefix):
 
         # FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
         # FIXME : they use a non-standard name
-        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source),
-                        '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=metis_source),
+        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), # still need headers from METIS source, and they are not installed with METIS. shame...
+                        '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix),
                         '-DCMAKE_C_COMPILER:STRING=mpicc',
                         '-DCMAKE_CXX_COMPILER:STRING=mpicxx'])
 
@@ -78,18 +73,7 @@ def install(self, spec, prefix):
         if '+gdb' in spec:
             options.append('-DGDB:BOOL=ON')
 
-        metis_header = join_path(metis_source, 'include', 'metis.h')
-
-        if '+idx64' in spec:
-            filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header)
-
-        if '+double' in spec:
-            filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
-
         with working_dir(build_directory, create=True):
             cmake(source_directory, *options)
             make()
             make("install")
-            # Parmetis build system doesn't allow for an external metis to be used, but doesn't copy the required
-            # metis header either
-            install(metis_header, self.prefix.include)

From 3fcaf5b9031c3d55b152844b97cd432078340f4b Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Mon, 21 Mar 2016 14:47:05 +0100
Subject: [PATCH 020/144] llvm : update to 3.8.0

---
 var/spack/repos/builtin/packages/llvm/package.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index 280e400f69..5c38b5b88c 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -132,6 +132,21 @@ class Llvm(Package):
                         'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk',
                         }
                   },
+                  {
+                    'version' : '3.8.0',
+                    'md5':'07a7a74f3c6bd65de4702bf941b511a0',
+                    'resources' : {
+                        'compiler-rt' : 'd6fcbe14352ffb708e4d1ac2e48bb025',
+                        'openmp' : '8fd7cc35d48051613cf1e750e9f22e40',
+                        'polly' : '1b3b20f52d34a4024e21a4ea7112caa7',
+                        'libcxx' : 'd6e0bdbbee39f7907ad74fd56d03b88a',
+                        'libcxxabi' : 'bbe6b4d72c7c5978550d370af529bcf7',
+                        'clang' : 'cc99e7019bb74e6459e80863606250c5',
+                        'clang-tools-extra' : 'c2344f50e0eea0b402f0092a80ddc036',
+                        'lldb' : 'a5da35ed9cc8c8817ee854e3dbfba00e',
+                        'llvm-libunwind' : '162ade468607f153cca12be90b5194fa',
+                        }
+                  },
                   {
                     'version' : '3.7.1',
                     'md5':'bf8b3a2c79e61212c5409041dfdbd319',

From 3a3443dff63167fc0331672871af4c0cc1fe5903 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 21 Mar 2016 15:14:48 +0100
Subject: [PATCH 021/144] parmetis patches by PETSc developers

---
 .../builtin/packages/parmetis/package.py      |  6 ++
 ...9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch | 77 +++++++++++++++++++
 ...9d68aa1d6cbc70740d0f35024aae17f7d5cb.patch | 35 +++++++++
 3 files changed, 118 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch
 create mode 100644 var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch

diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index 3f18dd76b8..c691cf4191 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -46,6 +46,12 @@ class Parmetis(Package):
     patch('enable_external_metis.patch')
     depends_on('metis')
 
+    # bug fixes from PETSc developers
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/
+    patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch')
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
+    patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
+
     depends_on('gdb', when='+gdb')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch
new file mode 100644
index 0000000000..e6b8056c21
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch
@@ -0,0 +1,77 @@
+From 1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b Mon Sep 17 00:00:00 2001
+From: Jed Brown <jed@59A2.org>
+Date: Fri, 12 Oct 2012 15:45:10 -0500
+Subject: [PATCH] ParMetis bug fixes reported by John Fettig [petsc-maint
+ #133631]
+
+'''
+I have also reported to to Karypis but have received zero
+response and he hasn't released any updates to the original release
+either.  At least he approved my forum posting so that other people
+can see the bug and the fix.
+http://glaros.dtc.umn.edu/gkhome/node/837
+'''
+
+Hg-commit: 1c2b9fe39201d404b493885093b5992028b9b8d4
+---
+ libparmetis/xyzpart.c | 12 ++++++------
+ 1 file changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c
+index 3a2c289..63abfcb 100644
+--- a/libparmetis/xyzpart.c
++++ b/libparmetis/xyzpart.c
+@@ -104,7 +104,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+ 
+     for (i=0; i<nbins; i++)
+       emarkers[i] = gmin + (gmax-gmin)*i/nbins;
+-    emarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON);
++    emarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON);
+ 
+     /* get into a iterative backet boundary refinement */
+     for (l=0; l<5; l++) {
+@@ -152,7 +152,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+         }
+       }
+       nemarkers[0]     = gmin;
+-      nemarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON);
++      nemarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON);
+       rcopy(nbins+1, nemarkers, emarkers);
+     }
+ 
+@@ -218,7 +218,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+ 
+     emarkers[0] = gmin;
+     emarkers[1] = gsum/gnvtxs;
+-    emarkers[2] = gmax*(1.0+2.0*REAL_EPSILON);
++    emarkers[2] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON);
+     cnbins = 2;
+ 
+     /* get into a iterative backet boundary refinement */
+@@ -227,7 +227,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+       iset(cnbins, 0, lcounts);
+       rset(cnbins, 0, lsums);
+       for (j=0, i=0; i<nvtxs;) {
+-        if (cand[i].key < emarkers[j+1]) {
++        if (cand[i].key <= emarkers[j+1]) {
+           lcounts[j]++;
+           lsums[j] += cand[i].key;
+           i++;
+@@ -272,12 +272,12 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+       
+       rsorti(cnbins, nemarkers);
+       rcopy(cnbins, nemarkers, emarkers);
+-      emarkers[cnbins] = gmax*(1.0+2.0*REAL_EPSILON);
++      emarkers[cnbins] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON);
+     }
+ 
+     /* assign the coordinate to the appropriate bin */
+     for (j=0, i=0; i<nvtxs;) {
+-      if (cand[i].key < emarkers[j+1]) {
++      if (cand[i].key <= emarkers[j+1]) {
+         bxyz[cand[i].val*ndims+k] = j;
+         i++;
+       }
+-- 
+2.1.1.1.g1fb337f
+
diff --git a/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch
new file mode 100644
index 0000000000..9651d55347
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch
@@ -0,0 +1,35 @@
+From 82409d68aa1d6cbc70740d0f35024aae17f7d5cb Mon Sep 17 00:00:00 2001
+From: Sean Farley <sean@mcs.anl.gov>
+Date: Tue, 20 Mar 2012 11:59:44 -0500
+Subject: [PATCH] parmetis: fix bug reported by jfettig; '<' to '<=' in xyzpart
+
+Hg-commit: 2dd2eae596acaabbc80e0ef875182616f868dbc2
+---
+ libparmetis/xyzpart.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c
+index 307aed9..3a2c289 100644
+--- a/libparmetis/xyzpart.c
++++ b/libparmetis/xyzpart.c
+@@ -111,7 +111,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+       /* determine bucket counts */
+       iset(nbins, 0, lcounts);
+       for (j=0, i=0; i<nvtxs;) {
+-        if (cand[i].key < emarkers[j+1]) {
++        if (cand[i].key <= emarkers[j+1]) {
+           lcounts[j]++;
+           i++;
+         }
+@@ -158,7 +158,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+ 
+     /* assign the coordinate to the appropriate bin */
+     for (j=0, i=0; i<nvtxs;) {
+-      if (cand[i].key < emarkers[j+1]) {
++      if (cand[i].key <= emarkers[j+1]) {
+         bxyz[cand[i].val*ndims+k] = j;
+         i++;
+       }
+-- 
+2.1.1.1.g1fb337f
+

From 7569204a53076f763cc713123b5e92551f647d7f Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Mon, 21 Mar 2016 16:18:02 +0100
Subject: [PATCH 022/144] llvm : does not support python 3

---
 var/spack/repos/builtin/packages/llvm/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index 5c38b5b88c..1d25d59e50 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -52,7 +52,7 @@ class Llvm(Package):
     depends_on('cmake @2.8.12.2:')
 
     # Universal dependency
-    depends_on('python@2.7:')
+    depends_on('python@2.7:2.8')  # Seems not to support python 3.X.Y
 
     # lldb dependencies
     depends_on('ncurses', when='+lldb')

From 7ec450912dc71915205857da75bb418ffc3d0904 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Mon, 21 Mar 2016 21:14:03 -0600
Subject: [PATCH 023/144] + Provide subversion and required packages apr and
 apr-util. + Installation of subversion may need to be modified to include
 python and perl   bindings. I have provided comments to this end, but the
 code is not active.

---
 .../packages/apr-util/apr-util.new/package.py | 44 ++++++++++++++
 .../builtin/packages/apr/apr.new/package.py   | 51 ++++++++++++++++
 .../subversion/subversion.new/package.py      | 59 +++++++++++++++++++
 .../repos/builtin/packages/swig/package.py    |  5 +-
 4 files changed, 158 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py
 create mode 100644 var/spack/repos/builtin/packages/apr/apr.new/package.py
 create mode 100644 var/spack/repos/builtin/packages/subversion/subversion.new/package.py

diff --git a/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py b/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py
new file mode 100644
index 0000000000..8f19c84d22
--- /dev/null
+++ b/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class AprUtil(Package):
+    """Apache Portable Runtime Utility"""
+    homepage  = 'https://apr.apache.org/'
+    url       = 'http://archive.apache.org/dist/apr/apr-util-1.5.4.tar.gz'
+
+    version('1.5.4',    '866825c04da827c6e5f53daff5569f42')
+
+    depends_on('apr')
+
+    def install(self, spec, prefix):
+
+        # configure, build, install:
+        options = ['--prefix=%s' % prefix]
+        options.append('--with-apr=%s' % spec['apr'].prefix)
+
+        configure(*options)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/apr/apr.new/package.py b/var/spack/repos/builtin/packages/apr/apr.new/package.py
new file mode 100644
index 0000000000..5cbbad350b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/apr/apr.new/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class Apr(Package):
+    """Apache portable runtime."""
+    homepage  = 'https://apr.apache.org/'
+    url       = 'http://archive.apache.org/dist/apr/apr-1.5.2.tar.gz'
+
+    version('1.5.2',    '98492e965963f852ab29f9e61b2ad700')
+
+    #variant('ncurses', default=True, description='Enables the build of the ncurses gui')
+    #variant('qt', default=False, description='Enables the build of cmake-gui')
+    #variant('doc', default=False, description='Enables the generation of html and man page documentation')
+
+    #depends_on('ncurses', when='+ncurses')
+    #depends_on('qt', when='+qt')
+    #depends_on('python@2.7.11:', when='+doc')
+    #depends_on('py-sphinx', when='+doc')
+
+    #def url_for_version(self, version):
+    #    """Handle CMake's version-based custom URLs."""
+    #    return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % (version.up_to(2), version)
+
+    def install(self, spec, prefix):
+        options = ['--prefix=%s' % prefix]
+        configure(*options)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/subversion/subversion.new/package.py b/var/spack/repos/builtin/packages/subversion/subversion.new/package.py
new file mode 100644
index 0000000000..b1c3380238
--- /dev/null
+++ b/var/spack/repos/builtin/packages/subversion/subversion.new/package.py
@@ -0,0 +1,59 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+#import os
+
+class Subversion(Package):
+    """Apache Subversion - an open source version control system."""
+    homepage  = 'https://subversion.apache.org/'
+    url       = 'http://archive.apache.org/dist/subversion/subversion-1.8.13.tar.gz'
+
+    version('1.8.13',    '8065b3698d799507fb72dd7926ed32b6')
+    version('1.9.3',     'a92bcfaec4e5038f82c74a7b5bbd2f46')
+
+    depends_on('apr')
+    depends_on('apr-util')
+    depends_on('zlib')
+    depends_on('sqlite')
+    #depends_on('swig')
+
+    def install(self, spec, prefix):
+
+        # configure, build, install:
+        # Ref: http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html
+        options = ['--prefix=%s' % prefix]
+        options.append('--with-apr=%s' % spec['apr'].prefix)
+        options.append('--with-apr-util=%s' % spec['apr-util'].prefix)
+        options.append('--with-zlib=%s' % spec['zlib'].prefix)
+        options.append('--with-sqlite=%s' % spec['sqlite'].prefix)
+        #options.append('--with-swig=%s' % spec['swig'].prefix)
+
+        configure(*options)
+        make()
+        make('install')
+        #make('swig-py') # python bindings
+        #make('install-swig-py')
+        #make('swig-pl') # perl bindings
+        #make('install-swig-pl')
diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py
index 8d46c4fe46..de6055e965 100644
--- a/var/spack/repos/builtin/packages/swig/package.py
+++ b/var/spack/repos/builtin/packages/swig/package.py
@@ -36,11 +36,14 @@ class Swig(Package):
     homepage = "http://www.swig.org"
     url      = "http://prdownloads.sourceforge.net/swig/swig-3.0.2.tar.gz"
 
-    version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41')
+    version('3.0.8',  'c96a1d5ecb13d38604d7e92148c73c97')
+    version('3.0.2',  '62f9b0d010cef36a13a010dc530d0d41')
+    version('2.0.12', 'c3fb0b2d710cc82ed0154b91e43085a4')
 
     depends_on('pcre')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
+
         make()
         make("install")

From 23bf70296e4a02f49c301b1b744055802b1e8dc1 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 09:22:42 +0100
Subject: [PATCH 024/144] arpack: add a patch for 3.3

---
 .../repos/builtin/packages/arpack-ng/package.py   |  4 ++++
 .../builtin/packages/arpack-ng/pdlamch10.patch    | 15 +++++++++++++++
 2 files changed, 19 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch

diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index 0b49d14202..614071cf53 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -35,6 +35,10 @@ class ArpackNg(Package):
     variant('shared', default=True, description='Enables the build of shared libraries')
     variant('mpi', default=False, description='Activates MPI support')
 
+    # The function pdlamch10 does not set the return variable. This is fixed upstream
+    # see https://github.com/opencollab/arpack-ng/issues/34
+    patch('pdlamch10.patch', when='@3.3:')
+
     depends_on('blas')
     depends_on('lapack')
     depends_on('mpi', when='+mpi')
diff --git a/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch b/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch
new file mode 100644
index 0000000000..922828909f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch
@@ -0,0 +1,15 @@
+diff --git a/PARPACK/SRC/MPI/pdlamch10.f b/PARPACK/SRC/MPI/pdlamch10.f
+index 6571da9..2882c2e 100644
+--- a/PARPACK/SRC/MPI/pdlamch10.f
++++ b/PARPACK/SRC/MPI/pdlamch10.f
+@@ -86,8 +86,8 @@
+           TEMP = TEMP1
+       END IF
+ *
+-      PDLAMCH = TEMP
++      PDLAMCH10 = TEMP
+ *
+-*     End of PDLAMCH
++*     End of PDLAMCH10
+ *
+       END

From aca8b5c89de7058ab58f2eb3392e8b023b16fe8a Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 09:27:00 +0100
Subject: [PATCH 025/144] move suite sparse to a proper folder

---
 .../builtin/packages/{SuiteSparse => suite-sparse}/package.py     | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename var/spack/repos/builtin/packages/{SuiteSparse => suite-sparse}/package.py (100%)

diff --git a/var/spack/repos/builtin/packages/SuiteSparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
similarity index 100%
rename from var/spack/repos/builtin/packages/SuiteSparse/package.py
rename to var/spack/repos/builtin/packages/suite-sparse/package.py

From 3c5a1605d5e3cba881b743bf561f0966b1a3ad8b Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 09:27:39 +0100
Subject: [PATCH 026/144] adjust the class name for suite sparse

---
 var/spack/repos/builtin/packages/suite-sparse/package.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index 6e130d118f..b57f9967c3 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -1,7 +1,7 @@
 from spack import *
 
 
-class Suitesparse(Package):
+class SuiteSparse(Package):
     """
     SuiteSparse is a suite of sparse matrix algorithms
     """
@@ -24,4 +24,3 @@ def install(self, spec, prefix):
         # FIXME : this actually uses the current workaround
         # FIXME : (blas / lapack always provide libblas and liblapack as aliases)
         make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack')
-

From cb97e8dd9301e5bbc6752caed2f4861a2a06f494 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 09:43:10 +0100
Subject: [PATCH 027/144] adjust eigen and octave to use new names of suite
 sparse

---
 var/spack/repos/builtin/packages/eigen/package.py  | 2 +-
 var/spack/repos/builtin/packages/octave/package.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py
index e40046b452..8d6e672f86 100644
--- a/var/spack/repos/builtin/packages/eigen/package.py
+++ b/var/spack/repos/builtin/packages/eigen/package.py
@@ -48,7 +48,7 @@ class Eigen(Package):
     depends_on('metis', when='+metis')
     depends_on('scotch', when='+scotch')
     depends_on('fftw', when='+fftw')
-    depends_on('SuiteSparse', when='+suitesparse')
+    depends_on('suite-sparse', when='+suitesparse')
     depends_on('mpfr@2.3.0:')  # Eigen 3.2.7 requires at least 2.3.0
     depends_on('gmp')
 
diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py
index 38b355159d..6e99c23652 100644
--- a/var/spack/repos/builtin/packages/octave/package.py
+++ b/var/spack/repos/builtin/packages/octave/package.py
@@ -62,7 +62,7 @@ class Octave(Package):
     depends_on('qrupdate',    when='+qrupdate')
     #depends_on('qscintilla',  when='+qscintilla) # TODO: add package
     depends_on('qt',          when='+qt')
-    depends_on('SuiteSparse', when='+suitesparse')
+    depends_on('suite-sparse',when='+suitesparse')
     depends_on('zlib',        when='+zlib')
 
 

From a26992ef55fed958c15b45b989fc0a4d57f02251 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 22 Mar 2016 01:56:16 -0700
Subject: [PATCH 028/144] Change from PR #552: rename
 setup_dependent_python_module -> setup_dependent_package

- Fixed in package.py
- Fixed wrong prototypes in packages that use it.
- Fixed build_environment to set module variables properly
  - added hacky fix to ensure spec/package consistency in build processes.
  - Need to think about defensive spec copy done by `Repo.get`.  May be
    time to think about an immutable spec implementation.
---
 lib/spack/spack/build_environment.py          | 52 ++++++++++++++-----
 lib/spack/spack/package.py                    |  2 +-
 .../repos/builtin/packages/mpich/package.py   |  2 +-
 .../packages/netlib-scalapack/package.py      | 22 ++++----
 4 files changed, 52 insertions(+), 26 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index fc5b7d6207..119a255a34 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -225,7 +225,7 @@ def set_module_variables_for_package(pkg, module):
     m.spack_cc  = join_path(link_dir, pkg.compiler.link_paths['cc'])
     m.spack_cxx = join_path(link_dir, pkg.compiler.link_paths['cxx'])
     m.spack_f77 = join_path(link_dir, pkg.compiler.link_paths['f77'])
-    m.spack_f90 = join_path(link_dir, pkg.compiler.link_paths['fc'])
+    m.spack_fc  = join_path(link_dir, pkg.compiler.link_paths['fc'])
 
     # Emulate some shell commands for convenience
     m.pwd          = os.getcwd
@@ -270,32 +270,56 @@ def parent_class_modules(cls):
     return result
 
 
+def setup_module_variables_for_dag(pkg):
+    """Set module-scope variables for all packages in the DAG."""
+    for spec in pkg.spec.traverse(order='post'):
+        # If a user makes their own package repo, e.g.
+        # spack.repos.mystuff.libelf.Libelf, and they inherit from
+        # an existing class like spack.repos.original.libelf.Libelf,
+        # then set the module variables for both classes so the
+        # parent class can still use them if it gets called.
+        spkg = spec.package
+        modules = parent_class_modules(spkg.__class__)
+        for mod in modules:
+            set_module_variables_for_package(spkg, mod)
+        set_module_variables_for_package(spkg, spkg.module)
+
+
 def setup_package(pkg):
     """Execute all environment setup routines."""
     spack_env = EnvironmentModifications()
     run_env   = EnvironmentModifications()
 
+    # Before proceeding, ensure that specs and packages are consistent
+    #
+    # This is a confusing behavior due to how packages are
+    # constructed.  `setup_dependent_package` may set attributes on
+    # specs in the DAG for use by other packages' install
+    # method. However, spec.package will look up a package via
+    # spack.repo, which defensively copies specs into packages.  This
+    # code ensures that all packages in the DAG have pieces of the
+    # same spec object at build time.
+    #
+    # This is safe for the build process, b/c the build process is a
+    # throwaway environment, but it is kind of dirty.
+    #
+    # TODO: Think about how to avoid this fix and do something cleaner.
+    for s in pkg.spec.traverse(): s.package.spec = s
+
     set_compiler_environment_variables(pkg, spack_env)
     set_build_environment_variables(pkg, spack_env)
-
-    # If a user makes their own package repo, e.g.
-    # spack.repos.mystuff.libelf.Libelf, and they inherit from
-    # an existing class like spack.repos.original.libelf.Libelf,
-    # then set the module variables for both classes so the
-    # parent class can still use them if it gets called.
-    modules = parent_class_modules(pkg.__class__)
-    for mod in modules:
-        set_module_variables_for_package(pkg, mod)
+    setup_module_variables_for_dag(pkg)
 
     # Allow dependencies to modify the module
-    for dependency_spec in pkg.spec.traverse(root=False):
+    spec = pkg.spec
+    for dependency_spec in spec.traverse(root=False):
         dpkg = dependency_spec.package
-        dpkg.setup_dependent_python_module(pkg.module, pkg.spec)
+        dpkg.setup_dependent_package(pkg.module, spec)
 
     # Allow dependencies to set up environment as well
-    for dependency_spec in pkg.spec.traverse(root=False):
+    for dependency_spec in spec.traverse(root=False):
         dpkg = dependency_spec.package
-        dpkg.setup_dependent_environment(spack_env, run_env, pkg.spec)
+        dpkg.setup_dependent_environment(spack_env, run_env, spec)
 
     # Allow the package to apply some settings.
     pkg.setup_environment(spack_env, run_env)
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 9d8ac87bd7..9af3221837 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -1075,7 +1075,7 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         self.setup_environment(spack_env, run_env)
 
 
-    def setup_dependent_python_module(self, module, dependent_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         """Set up Python module-scope variables for dependent packages.
 
         Called before the install() method of dependents.
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index c4d9940bb7..b20dc8dd60 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -54,7 +54,7 @@ def setup_dependent_environment(self, env, dependent_spec):
         env.set('MPICH_F90', spack_f90)
         env.set('MPICH_FC', spack_fc)
 
-    def setup_dependent_python_module(self, module, spec, dep_spec):
+    def setup_dependent_package(self, module, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
         # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers?
         module.mpicc = join_path(self.prefix.bin, 'mpicc')
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 62abfcc48e..c3e6822cdf 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import sys
 
 class NetlibScalapack(Package):
     """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines"""
@@ -11,16 +12,16 @@ class NetlibScalapack(Package):
     version('2.0.0', '9e76ae7b291be27faaad47cfc256cbfe')
     # versions before 2.0.0 are not using cmake and requires blacs as
     # a separated package
-    
+
     variant('shared', default=True, description='Build the shared library version')
     variant('fpic', default=False, description="Build with -fpic compiler option")
-    
+
     provides('scalapack')
-    
+
     depends_on('mpi')
     depends_on('lapack')
-    
-    def install(self, spec, prefix):       
+
+    def install(self, spec, prefix):
         options = [
             "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'),
             "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else 'ON'),
@@ -40,10 +41,11 @@ def install(self, spec, prefix):
             make()
             make("install")
 
-    def setup_dependent_python_module(self, module, spec, dependent_spec):
+    def setup_dependent_package(self, module, dependent_spec):
+        spec = self.spec
         lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
-        lib_suffix = lib_dsuffix if '+shared' in spec['scalapack'] else '.a'
+        lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
 
-        spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib
-        spec['scalapack'].cc_link = spec['scalapack'].fc_link
-        spec['scalapack'].libraries = [join_path(spec['scalapack'].prefix.lib, 'libscalapack%s' % lib_suffix)]
+        spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib
+        spec.cc_link = spec.fc_link
+        spec.libraries = [join_path(spec.prefix.lib, 'libscalapack%s' % lib_suffix)]

From 6eb97a30a36f0a0f072826d473a641dd143345ed Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 14:24:27 +0100
Subject: [PATCH 029/144] arpack: fix for +mpi variant

---
 var/spack/repos/builtin/packages/arpack-ng/package.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index 614071cf53..dd86b17a53 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -50,7 +50,10 @@ def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix]
 
         if '+mpi' in spec:
-            options.append('--enable-mpi')
+            options.extend([
+                '--enable-mpi',
+                'F77=mpif77' #FIXME: avoid hardcoding MPI wrapper names
+            ])
 
         if '~shared' in spec:
             options.append('--enable-shared=no')

From d25026b74936f9988cdaf701258c937b3965c106 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 16:26:16 +0100
Subject: [PATCH 030/144] add OCE package

---
 .../repos/builtin/packages/oce/package.py     | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/oce/package.py

diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py
new file mode 100644
index 0000000000..06acb96736
--- /dev/null
+++ b/var/spack/repos/builtin/packages/oce/package.py
@@ -0,0 +1,47 @@
+from spack import *
+import platform
+
+class Oce(Package):
+    """
+    Open CASCADE Community Edition:
+    patches/improvements/experiments contributed by users over the official Open CASCADE library.
+    """
+    homepage = "https://github.com/tpaviot/oce"
+    url      = "https://github.com/tpaviot/oce/archive/OCE-0.17.tar.gz"
+
+    version('0.17.1', '36c67b87093c675698b483454258af91')
+    version('0.17'  , 'f1a89395c4b0d199bea3db62b85f818d')
+    version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3')
+    version('0.16'  , '7a4b4df5a104d75a537e25e7dd387eca')
+    version('0.15'  , '7ec541a1c350ca8a684f74980e48801c')
+
+    depends_on('cmake@2.8:')
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+        options.extend([
+            '-DOCE_INSTALL_PREFIX=%s' % prefix,
+            '-DOCE_BUILD_SHARED_LIB:BOOL=ON',
+            '-DOCE_BUILD_TYPE:STRING=Release',
+            '-DOCE_DATAEXCHANGE:BOOL=ON',
+            '-DOCE_DISABLE_X11:BOOL=ON',
+            '-DOCE_DRAW:BOOL=OFF',
+            '-DOCE_MODEL:BOOL=ON',
+            '-DOCE_MULTITHREAD_LIBRARY:STRING=NONE', # FIXME: add tbb
+            '-DOCE_OCAF:BOOL=ON',
+            '-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF',
+            '-DOCE_VISUALISATION:BOOL=OFF',
+            '-DOCE_WITH_FREEIMAGE:BOOL=OFF',
+            '-DOCE_WITH_GL2PS:BOOL=OFF',
+            '-DOCE_WITH_OPENCL:BOOL=OFF'
+        ])
+
+        if platform.system() == 'Darwin':
+            options.extend([
+                '-DOCE_OSX_USE_COCOA:BOOL=ON',
+            ])
+
+        cmake('.', *options)
+
+        make("install/strip")

From 7618dc504cb58e115a0a95b130bcfc485cd8341d Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 22 Mar 2016 19:17:39 +0100
Subject: [PATCH 031/144] temporary fix Hypre for OSX by building static lib by
 default

---
 var/spack/repos/builtin/packages/hypre/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 242ee100d7..8d93d48d1f 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -1,5 +1,5 @@
 from spack import *
-import os
+import os, sys
 
 class Hypre(Package):
     """Hypre is a library of high performance preconditioners that
@@ -12,7 +12,8 @@ class Hypre(Package):
     version('2.10.1', 'dc048c4cabb3cd549af72591474ad674')
     version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
 
-    variant('shared', default=True, description="Build shared library version (disables static library)")
+    # hypre does not know how to build shared libraries on Darwin
+    variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)")
 
     depends_on("mpi")
     depends_on("blas")

From e56f5c4d6b4626a428b3c209f00eff59cd37b22f Mon Sep 17 00:00:00 2001
From: Cyrus Harrison <cyrush@llnl.gov>
Date: Tue, 22 Mar 2016 16:59:40 +0100
Subject: [PATCH 032/144] add Intel TBB package

---
 .../repos/builtin/packages/tbb/package.py     | 79 +++++++++++++++++++
 1 file changed, 79 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/tbb/package.py

diff --git a/var/spack/repos/builtin/packages/tbb/package.py b/var/spack/repos/builtin/packages/tbb/package.py
new file mode 100644
index 0000000000..56ffe4c27c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tbb/package.py
@@ -0,0 +1,79 @@
+from spack import *
+import os
+import glob
+
+class Tbb(Package):
+    """Widely used C++ template library for task parallelism.
+    Intel Threading Building Blocks (Intel TBB) lets you easily write parallel
+    C++ programs that take full advantage of multicore performance, that are
+    portable and composable, and that have future-proof scalability.
+    """
+    homepage = "http://www.threadingbuildingblocks.org/"
+
+    # Only version-specific URL's work for TBB
+    version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz')
+
+    def coerce_to_spack(self,tbb_build_subdir):
+        for compiler in ["icc","gcc","clang"]:
+              fs = glob.glob(join_path(tbb_build_subdir,"*.%s.inc" % compiler ))
+              for f in fs:
+                  lines = open(f).readlines()
+                  of = open(f,"w")
+                  for l in lines:
+                      if l.strip().startswith("CPLUS ="):
+                        of.write("# coerced to spack\n")
+                        of.write("CPLUS = $(CXX)\n")
+                      elif l.strip().startswith("CPLUS ="):
+                        of.write("# coerced to spack\n")
+                        of.write("CONLY = $(CC)\n")
+                      else:
+                        of.write(l);
+
+    def install(self, spec, prefix):
+        #
+        # we need to follow TBB's compiler selection logic to get the proper build + link flags
+        # but we still need to use spack's compiler wrappers
+        # to accomplish this, we do two things:
+        #
+        # * Look at the spack spec to determine which compiler we should pass to tbb's Makefile
+        #
+        # * patch tbb's build system to use the compiler wrappers (CC, CXX) for
+        #    icc, gcc, clang
+        #    (see coerce_to_spack())
+        #
+        self.coerce_to_spack("build")
+
+        if spec.satisfies('%clang'):
+            tbb_compiler = "clang"
+        elif spec.satisfies('%intel'):
+            tbb_compiler = "icc"
+        else:
+            tbb_compiler = "gcc"
+
+
+        mkdirp(prefix)
+        mkdirp(prefix.lib)
+
+        #
+        # tbb does not have a configure script or make install target
+        # we simply call make, and try to put the pieces together
+        #
+        make("compiler=%s"  %(tbb_compiler))
+
+        # install headers to {prefix}/include
+        install_tree('include',prefix.include)
+
+        # install libs to {prefix}/lib
+        tbb_lib_names = ["libtbb",
+                         "libtbbmalloc",
+                         "libtbbmalloc_proxy"]
+
+        for lib_name in tbb_lib_names:
+            # install release libs
+            fs = glob.glob(join_path("build","*release",lib_name + ".*"))
+            for f in fs:
+                install(f, prefix.lib)
+            # install debug libs if they exist
+            fs = glob.glob(join_path("build","*debug",lib_name + "_debug.*"))
+            for f in fs:
+                install(f, prefix.lib)

From 5f68e14d3bd90e4a71f6366a328dcc97fc6e8a92 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 19:41:31 +0100
Subject: [PATCH 033/144] add gettext package

---
 .../repos/builtin/packages/gettext/package.py | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/gettext/package.py

diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py
new file mode 100644
index 0000000000..05712d7392
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gettext/package.py
@@ -0,0 +1,30 @@
+from spack import *
+
+class Gettext(Package):
+    """GNU internationalization (i18n) and localization (l10n) library."""
+    homepage = "https://www.gnu.org/software/gettext/"
+    url      = "http://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz"
+
+    version('0.19.7', 'f81e50556da41b44c1d59ac93474dca5')
+
+    def install(self, spec, prefix):
+        options = ['--disable-dependency-tracking',
+                   '--disable-silent-rules',
+                   '--disable-debug',
+                   '--prefix=%s' % prefix,
+                   '--with-included-gettext',
+                   '--with-included-glib',
+                   '--with-included-libcroco',
+                   '--with-included-libunistring',
+                   '--with-emacs',
+                   '--with-lispdir=%s/emacs/site-lisp/gettext' % prefix.share,
+                   '--disable-java',
+                   '--disable-csharp',
+                   '--without-git', # Don't use VCS systems to create these archives
+                   '--without-cvs',
+                   '--without-xz']
+
+        configure(*options)
+
+        make()
+        make("install")

From fd1784369a20650c3fc6f84d57ed4e6be59afc44 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 19:50:15 +0100
Subject: [PATCH 034/144] add muparser package

---
 .../repos/builtin/packages/muparser/package.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/muparser/package.py

diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py
new file mode 100644
index 0000000000..a1a9ff90e5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/muparser/package.py
@@ -0,0 +1,18 @@
+from spack import *
+
+class Muparser(Package):
+    """C++ math expression parser library."""
+    homepage = "http://muparser.beltoforion.de/"
+    url      = "https://github.com/beltoforion/muparser/archive/v2.2.5.tar.gz"
+
+    version('2.2.5', '02dae671aa5ad955fdcbcd3fee313fb7')
+
+    def install(self, spec, prefix):
+        options = ['--disable-debug',
+                   '--disable-dependency-tracking',
+                   '--prefix=%s' % prefix]
+
+        configure(*options)
+
+        make()
+        make("install")

From d05e4581c9d249c0736d8d58b394860ca05f8402 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 22 Mar 2016 12:31:26 -0700
Subject: [PATCH 035/144] Added the '+silex' variant to the Silo package. Added
 a number of different versions to the Silo package.

---
 .../repos/builtin/packages/silo/package.py    | 23 ++++++++++++++-----
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py
index d1aed78e0e..b7894e4d2b 100644
--- a/var/spack/repos/builtin/packages/silo/package.py
+++ b/var/spack/repos/builtin/packages/silo/package.py
@@ -5,24 +5,35 @@ class Silo(Package):
        data to binary, disk files."""
 
     homepage = "http://wci.llnl.gov/simulation/computer-codes/silo"
-    url      = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.8/silo-4.8.tar.gz"
+    base_url = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo"
 
+    version('4.10.2', '9ceac777a2f2469ac8cef40f4fab49c8')
+    version('4.9', 'a83eda4f06761a86726e918fc55e782a')
     version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9')
 
     variant('fortran', default=True, description='Enable Fortran support')
+    variant('silex', default=False, description='Builds Silex, a GUI for viewing Silo files')
 
-    depends_on("hdf5")
+    depends_on('hdf5')
+    depends_on('qt', when='+silex')
 
     def install(self, spec, prefix):
         config_args = [
             '--enable-fortran' if '+fortran' in spec else '--disable-fortran',
+            '--enable-silex' if '+silex' in spec else '--disable-silex',
         ]
 
+        if '+silex' in spec:
+            config_args.append('--with-Qt-dir=%s' % spec['qt'].prefix)
+
         configure(
-            "--prefix=%s" % prefix,
-            "--with-hdf5=%s,%s" % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib),
-            "--with-zlib=%s,%s" % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib),
+            '--prefix=%s' % prefix,
+            '--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib),
+            '--with-zlib=%s,%s' % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib),
             *config_args)
 
         make()
-        make("install")
+        make('install')
+
+    def url_for_version(self, version):
+        return '%s/silo-%s/silo-%s.tar.gz' % (Silo.base_url, version, version)

From 1728a0c3e60d55d1181f14ef5a677b1652a0680b Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 22 Mar 2016 12:33:11 -0700
Subject: [PATCH 036/144] Updated the 'crypto++' package to use an improved URL
 formation scheme (inspired by changes made to the 'Silo' package).

---
 var/spack/repos/builtin/packages/cryptopp/package.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py
index 1693c4b160..743a3ac70f 100644
--- a/var/spack/repos/builtin/packages/cryptopp/package.py
+++ b/var/spack/repos/builtin/packages/cryptopp/package.py
@@ -8,8 +8,8 @@ class Cryptopp(Package):
        public-key encryption (RSA, DSA), and a few obsolete/historical encryption
        algorithms (MD5, Panama)."""
 
-    homepage = "http://www.cryptopp.com/"
-    url      = "http://www.cryptopp.com/cryptopp563.zip"
+    homepage = "http://www.cryptopp.com"
+    base_url = "http://www.cryptopp.com"
 
     version('5.6.3', '3c5b70e2ec98b7a24988734446242d07')
     version('5.6.2', '7ed022585698df48e65ce9218f6c6a67')
@@ -28,4 +28,4 @@ def url_for_version(self, version):
         version_tuple = tuple(v for v in iter(version))
         version_string = reduce(lambda vs, nv: vs + str(nv), version_tuple, "")
 
-        return "%scryptopp%s.zip" % (Cryptopp.homepage, version_string)
+        return '%s/cryptopp%s.zip' % (Cryptopp.base_url, version_string)

From 27f337aa11104a6e625db6e40f8d9414954123ee Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 11:44:38 +0100
Subject: [PATCH 037/144] petsc: set PETSC_DIR in dependent_env

---
 var/spack/repos/builtin/packages/petsc/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 7239baaf7f..3dd117eed1 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -100,3 +100,7 @@ def install(self, spec, prefix):
         # PETSc has its own way of doing parallel make.
         make('MAKE_NP=%s' % make_jobs, parallel=False)
         make("install")
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        # set up PETSC_DIR for everyone using PETSc package
+        spack_env.set('PETSC_DIR', self.prefix)

From 24264eb00e4f4e3661ea1a28e9cbe3a97cd69580 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 11:45:18 +0100
Subject: [PATCH 038/144] add slepc package

---
 .../repos/builtin/packages/slepc/package.py   | 49 +++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/slepc/package.py

diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py
new file mode 100644
index 0000000000..8b5f24394f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/slepc/package.py
@@ -0,0 +1,49 @@
+import os
+from spack import *
+
+
+class Slepc(Package):
+    """
+    Scalable Library for Eigenvalue Computations.
+    """
+
+    homepage = "http://www.grycap.upv.es/slepc"
+    url = "http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz"
+
+    version('3.6.2', '2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df')
+
+    variant('arpack', default=False, description='Enables Arpack wrappers')
+
+    depends_on('petsc')
+    depends_on('arpack-ng~mpi',when='+arpack^petsc~mpi')
+    depends_on('arpack-ng+mpi',when='+arpack^petsc+mpi')
+
+    def install(self, spec, prefix):
+        # set SLEPC_DIR for installation
+        os.environ['SLEPC_DIR'] = self.stage.source_path
+
+        options = []
+
+        if '+arpack' in spec:
+            options.extend([
+                '--with-arpack-dir=%s' % spec['arpack-ng'].prefix.lib,
+            ])
+            if 'arpack-ng~mpi' in spec:
+                options.extend([
+                    '--with-arpack-flags=-larpack'
+                ])
+            else:
+                options.extend([
+                    '--with-arpack-flags=-lparpack,-larpack'
+                ])
+
+        configure('--prefix=%s' % prefix, *options)
+
+        make('MAKE_NP=%s' % make_jobs, parallel=False)
+        #FIXME:
+        # make('test')
+        make('install')
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        # set up SLEPC_DIR for everyone using SLEPc package
+        spack_env.set('SLEPC_DIR', self.prefix)

From 6c8d51f403213cf3a49373d4dca03fac565a73b4 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 22:58:14 +0100
Subject: [PATCH 039/144] add p4est package

---
 .../repos/builtin/packages/p4est/package.py   | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/p4est/package.py

diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py
new file mode 100644
index 0000000000..1e2969fe64
--- /dev/null
+++ b/var/spack/repos/builtin/packages/p4est/package.py
@@ -0,0 +1,34 @@
+from spack import *
+
+class P4est(Package):
+    """Dynamic management of a collection (a forest) of adaptive octrees in parallel"""
+    homepage = "http://www.p4est.org"
+    url      = "http://p4est.github.io/release/p4est-1.1.tar.gz"
+
+    version('1.1', '37ba7f4410958cfb38a2140339dbf64f')
+
+    # disable by default to make it work on frontend of clusters
+    variant('tests', default=False, description='Run small tests')
+
+    depends_on('mpi')
+
+    def install(self, spec, prefix):
+        options = ['--enable-mpi',
+                   '--enable-shared',
+                   '--disable-vtk-binary',
+                   '--without-blas',
+                   'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL',
+                   'CFLAGS=-O2',
+                   'CC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # TODO: use ENV variables or MPI class wrappers
+                   'CXX=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
+                   'FC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
+                   'F77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'),
+                  ]
+
+        configure('--prefix=%s' % prefix, *options)
+
+        make()
+        if '+tests' in self.spec:
+            make("check")
+
+        make("install")

From 474db2085e223b8226a6ae799232bb2fede3efde Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 22 Mar 2016 15:55:54 -0700
Subject: [PATCH 040/144] Simplified the 'url_for_version' function for the
 'Crypto++' package.

---
 var/spack/repos/builtin/packages/cryptopp/package.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py
index 743a3ac70f..bc83cb2b65 100644
--- a/var/spack/repos/builtin/packages/cryptopp/package.py
+++ b/var/spack/repos/builtin/packages/cryptopp/package.py
@@ -25,7 +25,5 @@ def install(self, spec, prefix):
         install('libcryptopp.a', prefix.lib)
 
     def url_for_version(self, version):
-        version_tuple = tuple(v for v in iter(version))
-        version_string = reduce(lambda vs, nv: vs + str(nv), version_tuple, "")
-
+        version_string = str(version).replace('.', '')
         return '%s/cryptopp%s.zip' % (Cryptopp.base_url, version_string)

From 5b3c96a9bb0ba6501512c93dcdb26510e796314e Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 08:07:45 +0100
Subject: [PATCH 041/144] fix superlu-dist lib installation

---
 var/spack/repos/builtin/packages/superlu-dist/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index c4c76909b3..9a94de8ba5 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -54,6 +54,7 @@ def install(self, spec, prefix):
         # need to install by hand
         headers_location = join_path(self.prefix.include,'superlu_dist')
         mkdirp(headers_location)
+        mkdirp(prefix.lib)
         # FIXME: fetch all headers in the folder automatically
         for header in ['Cnames.h','cublas_utils.h','dcomplex.h','html_mainpage.h','machines.h','old_colamd.h','psymbfact.h','superlu_ddefs.h','superlu_defs.h','superlu_enum_consts.h','superlu_zdefs.h','supermatrix.h','util_dist.h']:
             superludist_header = join_path(self.stage.source_path, 'SRC/',header)

From c4134ee71e43a6a2a38822e25cc72ca73efdcfea Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 23 Mar 2016 00:36:32 -0700
Subject: [PATCH 042/144] Fix #608: broken numpy build.

- Failed to catch all instances of modify_module when it was renamed
  to setup_dependent_package.

- Refactored remaining modify_module calls.

- Also modified Python's setup_dependent_package slightly: only
  creates empty site-packages directory for Python extensions now, not
  for all dependents.
---
 lib/spack/spack/modules.py                         |  4 ++--
 lib/spack/spack/preferred_packages.py              |  4 +++-
 var/spack/repos/builtin/packages/python/package.py | 11 ++++++-----
 var/spack/repos/builtin/packages/ruby/package.py   |  6 +++---
 4 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 05c93cd3e6..8ed98e5d38 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -160,8 +160,8 @@ def write(self):
         # package-specific modifications
         for extendee in self.pkg.extendees:
             extendee_spec = self.spec[extendee]
-            extendee_spec.package.modify_module(
-                self.pkg.module, extendee_spec, self.spec)
+            extendee_spec.package.setup_dependent_package(
+                self.pkg.module, self.spec)
 
         # Package-specific environment modifications
         spack_env = EnvironmentModifications()
diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py
index 4d8526c75f..f0a5382dc9 100644
--- a/lib/spack/spack/preferred_packages.py
+++ b/lib/spack/spack/preferred_packages.py
@@ -150,7 +150,9 @@ def spec_has_preferred_provider(self, pkgname, provider_str):
     def version_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if version a of pkgname is
            respecively less-than, equal-to, or greater-than version b of pkgname.
-           One version is less-than another if it is preferred over the other."""
+           Versions marked 'preferred=True' in package.py take precedence over any
+           versions not marked preferred.
+        """
         return self._spec_compare(pkgname, 'version', a, b, True, None)
 
 
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 4f55bc803e..6d9030805b 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -108,7 +108,7 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
         run_env.set('PYTHONPATH', pythonpath)
 
 
-    def modify_module(self, module, spec, ext_spec):
+    def setup_dependent_package(self, module, ext_spec):
         """
         Called before python modules' install() methods.
 
@@ -118,17 +118,18 @@ def modify_module(self, module, spec, ext_spec):
         """
         # Python extension builds can have a global python executable function
         if self.version >= Version("3.0.0") and self.version < Version("4.0.0"):
-            module.python = Executable(join_path(spec.prefix.bin, 'python3'))
+            module.python = Executable(join_path(self.spec.prefix.bin, 'python3'))
         else:
-            module.python = Executable(join_path(spec.prefix.bin, 'python'))
+            module.python = Executable(join_path(self.spec.prefix.bin, 'python'))
 
         # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
         module.python_lib_dir     = os.path.join(ext_spec.prefix, self.python_lib_dir)
         module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir)
         module.site_packages_dir  = os.path.join(ext_spec.prefix, self.site_packages_dir)
 
-        # Make the site packages directory if it does not exist already.
-        mkdirp(module.site_packages_dir)
+        # Make the site packages directory for extensions, if it does not exist already.
+        if ext_spec.package.is_extension:
+            mkdirp(module.site_packages_dir)
 
     # ========================================================================
     # Handle specifics of activating and deactivating python modules.
diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index 7ff1898ce9..e13677e4d2 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -30,7 +30,7 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
         # The actual installation path for this gem
         spack_env.set('GEM_HOME', extension_spec.prefix)
 
-    def modify_module(self, module, spec, ext_spec):
+    def setup_dependent_package(self, module, ext_spec):
         """Called before ruby modules' install() methods.  Sets GEM_HOME
         and GEM_PATH to values appropriate for the package being built.
 
@@ -39,5 +39,5 @@ def modify_module(self, module, spec, ext_spec):
             gem('install', '<gem-name>.gem')
         """
         # Ruby extension builds have global ruby and gem functions
-        module.ruby = Executable(join_path(spec.prefix.bin, 'ruby'))
-        module.gem = Executable(join_path(spec.prefix.bin, 'gem'))
+        module.ruby = Executable(join_path(self.spec.prefix.bin, 'ruby'))
+        module.gem = Executable(join_path(self.spec.prefix.bin, 'gem'))

From 01918a6f4891ab985b8619daaadc1bf484e4db17 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 05:26:51 +0100
Subject: [PATCH 043/144] fix MUMPS build on OSX (set parallel=False)

---
 var/spack/repos/builtin/packages/mumps/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 5c120c37df..5a254dfd00 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -135,7 +135,8 @@ def install(self, spec, prefix):
 
         self.write_makefile_inc()
 
-        make(*make_libs)
+        # Build fails in parallel, at least on OS-X
+        make(*make_libs, parallel=False)
 
         install_tree('lib', prefix.lib)
         install_tree('include', prefix.include)

From 38350ae33d29e108803cebdf13b90b6898947328 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 23 Mar 2016 01:32:54 -0700
Subject: [PATCH 044/144] resurrect preferred=True option for packages lost in
 merge of externals support.

- Pyton 2.7.11 is preferred again.
---
 lib/spack/spack/concretize.py         | 4 ++++
 lib/spack/spack/preferred_packages.py | 4 +---
 lib/spack/spack/test/concretize.py    | 9 +++++++++
 3 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index 2e576743ec..ed9bf79868 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -159,6 +159,10 @@ def concretize_version(self, spec):
              if any(v.satisfies(sv) for sv in spec.versions)],
             cmp=cmp_versions)
 
+        def prefer_key(v):
+            return pkg.versions.get(Version(v)).get('preferred', False)
+        valid_versions.sort(key=prefer_key, reverse=True)
+
         if valid_versions:
             spec.versions = ver([valid_versions[0]])
         else:
diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py
index f0a5382dc9..4d8526c75f 100644
--- a/lib/spack/spack/preferred_packages.py
+++ b/lib/spack/spack/preferred_packages.py
@@ -150,9 +150,7 @@ def spec_has_preferred_provider(self, pkgname, provider_str):
     def version_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if version a of pkgname is
            respecively less-than, equal-to, or greater-than version b of pkgname.
-           Versions marked 'preferred=True' in package.py take precedence over any
-           versions not marked preferred.
-        """
+           One version is less-than another if it is preferred over the other."""
         return self._spec_compare(pkgname, 'version', a, b, True, None)
 
 
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index 08cce09674..9cd8c969ae 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -24,6 +24,7 @@
 ##############################################################################
 import spack
 from spack.spec import Spec, CompilerSpec
+from spack.version import ver
 from spack.concretize import find_spec
 from spack.test.mock_packages_test import *
 
@@ -77,6 +78,14 @@ def test_concretize_variant(self):
         self.check_concretize('mpich')
 
 
+    def test_concretize_preferred_version(self):
+        spec = self.check_concretize('python')
+        self.assertEqual(spec.versions, ver('2.7.11'))
+
+        spec = self.check_concretize('python@3.5.1')
+        self.assertEqual(spec.versions, ver('3.5.1'))
+
+
     def test_concretize_with_virtual(self):
         self.check_concretize('mpileaks ^mpi')
         self.check_concretize('mpileaks ^mpi@:1.1')

From cc582dd4b435ba06dc140b1ca96b688871e36abb Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 23 Mar 2016 02:02:49 -0700
Subject: [PATCH 045/144] Add mock python package.

---
 .../builtin.mock/packages/python/package.py   | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 var/spack/repos/builtin.mock/packages/python/package.py

diff --git a/var/spack/repos/builtin.mock/packages/python/package.py b/var/spack/repos/builtin.mock/packages/python/package.py
new file mode 100644
index 0000000000..c5fed52f53
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/python/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class Python(Package):
+    """Dummy Python package to demonstrate preferred versions."""
+    homepage = "http://www.python.org"
+    url      = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz"
+
+    extendable = True
+
+    version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe')
+    version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36')
+    version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True)
+    version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521')
+    version('2.7.9', '5eebcaa0030dc4061156d3429657fb83')
+    version('2.7.8', 'd4bca0159acb0b44a781292b5231936f')
+
+    def install(self, spec, prefix):
+        pass
+

From 0fbdb3f65d234d6ed8f77d3732c134962ad47b35 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 15:43:16 +0100
Subject: [PATCH 046/144] modules : added configuration file with disable
 keyword

---
 lib/spack/spack/config.py  | 28 +++++++++++++++++++++++++---
 lib/spack/spack/modules.py | 12 ++++++++++--
 2 files changed, 35 insertions(+), 5 deletions(-)

diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 6afd69b3ac..6ef79c70b1 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -237,7 +237,29 @@
                                 'type' : 'object',
                                 'default' : {},
                             }
-                        },},},},},}
+                        },},},},},},
+    'modules': {
+        '$schema': 'http://json-schema.org/schema#',
+        'title': 'Spack module file configuration file schema',
+        'type': 'object',
+        'additionalProperties': False,
+        'patternProperties': {
+            r'modules:?': {
+                'type': 'object',
+                'default': {},
+                'additionalProperties': False,
+                'properties': {
+                    'disable': {
+                        'type': 'array',
+                        'default': [],
+                        'items': {
+                            'type': 'string'
+                        }
+                    }
+                }
+            },
+        },
+    },
 }
 
 """OrderedDict of config scopes keyed by name.
@@ -405,11 +427,11 @@ def _read_config_file(filename, schema):
             validate_section(data, schema)
         return data
 
-    except MarkedYAMLError, e:
+    except MarkedYAMLError as e:
         raise ConfigFileError(
             "Error parsing yaml%s: %s" % (str(e.context_mark), e.problem))
 
-    except IOError, e:
+    except IOError as e:
         raise ConfigFileError(
             "Error reading configuration file %s: %s" % (filename, str(e)))
 
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 8ed98e5d38..639f1101b8 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -48,6 +48,7 @@
 
 import llnl.util.tty as tty
 import spack
+import spack.config
 from llnl.util.filesystem import join_path, mkdirp
 from spack.environment import *
 
@@ -57,6 +58,13 @@
 module_types = {}
 
 
+def read_configuration_file():
+    f = spack.config.get_config('modules')
+    f.setdefault('disable', [])  # Default : disable nothing
+    return f
+
+CONFIGURATION = read_configuration_file()
+
 def print_help():
     """For use by commands to tell user how to activate shell support."""
 
@@ -115,8 +123,8 @@ class EnvModule(object):
     class __metaclass__(type):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
-            if cls.name != 'env_module':
-                module_types[cls.name] = cls
+            if cls.name != 'env_module' and cls.name not in CONFIGURATION['disable']:
+                    module_types[cls.name] = cls
 
     def __init__(self, spec=None):
         self.spec = spec

From d93f2b335d5a5198b943cc6293a1d24d614c979b Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 16:04:36 +0100
Subject: [PATCH 047/144] modules : fixed annoying indent

---
 lib/spack/spack/modules.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 639f1101b8..d354c8bb71 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -124,7 +124,7 @@ class __metaclass__(type):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
             if cls.name != 'env_module' and cls.name not in CONFIGURATION['disable']:
-                    module_types[cls.name] = cls
+                module_types[cls.name] = cls
 
     def __init__(self, spec=None):
         self.spec = spec

From 34a8f0c96bc50870f20f094d95b403b2bb19487d Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 17:01:52 +0100
Subject: [PATCH 048/144] espresso : fixes #454

---
 var/spack/repos/builtin/packages/espresso/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index a2bf58f585..59f362ab46 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -32,6 +32,10 @@ def check_variants(self, spec):
         if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec):
             raise RuntimeError(error.format(variant='elpa'))
 
+    def setup_environment(self, spack_env, run_env):
+        # Espresso copies every executable in prefix without creating sub-folders
+        run_env.prepend_path('PATH', self.prefix)
+
     def install(self, spec, prefix):
         self.check_variants(spec)
 

From 4e5dfc8b18ed30e261fe6b6dd014c8991937934d Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 19:40:16 +0100
Subject: [PATCH 049/144] fix missing (depricated) _dggsvd_ and _sggsvd_ in
 Openblas 0.2.16

---
 var/spack/repos/builtin/packages/openblas/package.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 781a1e2ec8..1d10f217c4 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -6,6 +6,7 @@ class Openblas(Package):
     homepage = "http://www.openblas.net"
     url      = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz"
 
+    version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1')
     version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc')
     version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9')
 
@@ -14,7 +15,14 @@ class Openblas(Package):
     provides('lapack')
 
     def install(self, spec, prefix):
-        make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77')
+        extra=[]
+        if spec.satisfies('@0.2.16'):
+            extra.extend([
+                'BUILD_LAPACK_DEPRECATED=1' # fix missing _dggsvd_ and _sggsvd_
+            ])
+
+        make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77',*extra)
+        make("tests")
         make('install', "PREFIX='%s'" % prefix)
 
         lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so'

From f095e619b985a9271ff96cd469086d4654edf489 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 24 Mar 2016 09:31:28 +0100
Subject: [PATCH 050/144] module files configuration : enable/disable logic is
 now positive

---
 lib/spack/spack/config.py  | 2 +-
 lib/spack/spack/modules.py | 9 ++-------
 2 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 6ef79c70b1..14e5aaf4fb 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -249,7 +249,7 @@
                 'default': {},
                 'additionalProperties': False,
                 'properties': {
-                    'disable': {
+                    'enable': {
                         'type': 'array',
                         'default': [],
                         'items': {
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index d354c8bb71..6c32937c3c 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -57,13 +57,8 @@
 # Registry of all types of modules.  Entries created by EnvModule's metaclass
 module_types = {}
 
+CONFIGURATION = spack.config.get_config('modules')
 
-def read_configuration_file():
-    f = spack.config.get_config('modules')
-    f.setdefault('disable', [])  # Default : disable nothing
-    return f
-
-CONFIGURATION = read_configuration_file()
 
 def print_help():
     """For use by commands to tell user how to activate shell support."""
@@ -123,7 +118,7 @@ class EnvModule(object):
     class __metaclass__(type):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
-            if cls.name != 'env_module' and cls.name not in CONFIGURATION['disable']:
+            if cls.name != 'env_module' and cls.name in CONFIGURATION['enable']:
                 module_types[cls.name] = cls
 
     def __init__(self, spec=None):

From e4adc675e58222f3082f167e709e3819beafd474 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 24 Mar 2016 10:04:02 +0100
Subject: [PATCH 051/144] module files configuration : added default
 configuration

---
 etc/spack/modules.yaml | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 etc/spack/modules.yaml

diff --git a/etc/spack/modules.yaml b/etc/spack/modules.yaml
new file mode 100644
index 0000000000..aa2a2c3fe2
--- /dev/null
+++ b/etc/spack/modules.yaml
@@ -0,0 +1,8 @@
+# -------------------------------------------------------------------------
+# This is the default spack module files generation configuration.
+#
+# Changes to this file will affect all users of this spack install,
+# although users can override these settings in their ~/.spack/modules.yaml.
+# -------------------------------------------------------------------------
+modules:
+  enable: ['tcl', 'dotkit']

From 9b8b17b6f1ec22ce4ac2115e5f7687beba21dd19 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 10:36:02 +0100
Subject: [PATCH 052/144] fix parmetis on Ubuntu with GNU compilers by linking
 to lm

---
 .../builtin/packages/parmetis/link-to-lm.patch     | 14 ++++++++++++++
 .../repos/builtin/packages/parmetis/package.py     |  2 ++
 2 files changed, 16 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/parmetis/link-to-lm.patch

diff --git a/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch b/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch
new file mode 100644
index 0000000000..faa809231e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch
@@ -0,0 +1,14 @@
+diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt
+index 9cfc8a7..dfc0125 100644
+--- a/libparmetis/CMakeLists.txt
++++ b/libparmetis/CMakeLists.txt
+@@ -5,7 +5,7 @@ file(GLOB parmetis_sources *.c)
+ # Create libparmetis
+ add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources})
+ # Link with metis and MPI libraries.
+-target_link_libraries(parmetis metis ${MPI_LIBRARIES})
++target_link_libraries(parmetis metis ${MPI_LIBRARIES} "-lm")
+ set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}")
+
+ install(TARGETS parmetis
+
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index c691cf4191..bc71fb7299 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -52,6 +52,8 @@ class Parmetis(Package):
     # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
     patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
 
+    patch('link-to-lm.patch')
+
     depends_on('gdb', when='+gdb')
 
     def install(self, spec, prefix):

From 758a9c9096bd6c306f2dba0e40b46544dcec1992 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 11:18:11 +0100
Subject: [PATCH 053/144] python extensions : create PYTHONPATH in module files

---
 lib/spack/spack/modules.py                         | 10 +++++-----
 var/spack/repos/builtin/packages/python/package.py |  5 ++++-
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 6c32937c3c..d45fdde703 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -161,13 +161,13 @@ def write(self):
 
         # Let the extendee modify their extensions before asking for
         # package-specific modifications
-        for extendee in self.pkg.extendees:
-            extendee_spec = self.spec[extendee]
-            extendee_spec.package.setup_dependent_package(
-                self.pkg.module, self.spec)
+        spack_env = EnvironmentModifications()
+        for item in self.pkg.extendees:
+            package = self.spec[item].package
+            package.setup_dependent_package(self.pkg.module, self.spec)
+            package.setup_dependent_environment(spack_env, env, self.spec)
 
         # Package-specific environment modifications
-        spack_env = EnvironmentModifications()
         self.spec.package.setup_environment(spack_env, env)
 
         # TODO : implement site-specific modifications and filters
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 6d9030805b..f5237c3b57 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -105,7 +105,10 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
 
         pythonpath = ':'.join(python_paths)
         spack_env.set('PYTHONPATH', pythonpath)
-        run_env.set('PYTHONPATH', pythonpath)
+
+        # For run time environment set only the path for extension_spec and prepend it to PYTHONPATH
+        if extension_spec.package.extends(self.spec):
+            run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))
 
 
     def setup_dependent_package(self, module, ext_spec):

From 8643e2191357dd6f53bfafdfd51f43b770e2137c Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 24 Mar 2016 12:34:58 -0500
Subject: [PATCH 054/144] Simplified NumPy dependencies

---
 .../builtin/packages/py-numpy/package.py      | 37 ++++++++++++++-----
 .../builtin/packages/py-scipy/package.py      |  5 ++-
 2 files changed, 31 insertions(+), 11 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index 0354811186..a08e612df6 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -1,24 +1,43 @@
 from spack import *
 
 class PyNumpy(Package):
-    """array processing for numbers, strings, records, and objects."""
-    homepage = "https://pypi.python.org/pypi/numpy"
+    """NumPy is the fundamental package for scientific computing with Python.
+    It contains among other things: a powerful N-dimensional array object,
+    sophisticated (broadcasting) functions, tools for integrating C/C++ and
+    Fortran code, and useful linear algebra, Fourier transform, and random
+    number capabilities"""
+    homepage = "http://www.numpy.org/"
     url      = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz"
 
-    version('1.9.1', '78842b73560ec378142665e712ae4ad9')
-    version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645')
+    version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad')
+    version('1.9.2',  'a1ed53432dbcd256398898d35bc8e645')
+    version('1.9.1',  '78842b73560ec378142665e712ae4ad9')
 
-    variant('blas', default=True)
+
+    variant('blas',   default=True)
+    variant('lapack', default=True)
 
     extends('python')
     depends_on('py-nose')
-    depends_on('netlib-blas+fpic', when='+blas')
-    depends_on('netlib-lapack+shared', when='+blas')
+    depends_on('blas',   when='+blas')
+    depends_on('lapack', when='+lapack')
 
     def install(self, spec, prefix):
+        libraries    = []
+        library_dirs = []
+
         if '+blas' in spec:
+            libraries.append('blas')
+            library_dirs.append(spec['blas'].prefix.lib)
+        if '+lapack' in spec:
+            libraries.append('lapack')
+            library_dirs.append(spec['lapack'].prefix.lib)
+
+        if '+blas' in spec or '+lapack' in spec:
             with open('site.cfg', 'w') as f:
                 f.write('[DEFAULT]\n')
-                f.write('libraries=lapack,blas\n')
-                f.write('library_dirs=%s/lib:%s/lib\n' % (spec['blas'].prefix, spec['lapack'].prefix))
+                f.write('libraries=%s\n'    % ','.join(libraries))
+                f.write('library_dirs=%s\n' % ':'.join(library_dirs))
+
         python('setup.py', 'install', '--prefix=%s' % prefix)
+
diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index 3a1124cc15..c2161c90c4 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -2,11 +2,12 @@
 
 class PyScipy(Package):
     """Scientific Library for Python."""
-    homepage = "https://pypi.python.org/pypi/scipy"
+    homepage = "http://www.scipy.org/"
     url      = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
 
-    version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
+    version('0.17.0', '5ff2971e1ce90e762c59d2cd84837224')
     version('0.15.1', 'be56cd8e60591d6332aac792a5880110')
+    version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
 
     extends('python')
     depends_on('py-nose')

From 254f65f2994de32da8681c24838beb32bbbc5fe1 Mon Sep 17 00:00:00 2001
From: Alfredo Gimenez <gimenez1@llnl.gov>
Date: Thu, 24 Mar 2016 10:48:38 -0700
Subject: [PATCH 055/144] Remove incorrect sanity check for libelf

---
 var/spack/repos/builtin/packages/libelf/package.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py
index 9f16708af5..29bc21b65c 100644
--- a/var/spack/repos/builtin/packages/libelf/package.py
+++ b/var/spack/repos/builtin/packages/libelf/package.py
@@ -38,8 +38,6 @@ class Libelf(Package):
 
     provides('elf')
 
-    sanity_check_is_file = 'include/libelf.h'
-
     def install(self, spec, prefix):
         configure("--prefix=" + prefix,
                   "--enable-shared",

From 9985816642bad10008f45583a7d715761a6ae03d Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 24 Mar 2016 14:49:41 -0500
Subject: [PATCH 056/144] Fix spack info indentation

---
 lib/spack/spack/cmd/info.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py
index e7abe7f4a5..c93db55c63 100644
--- a/lib/spack/spack/cmd/info.py
+++ b/lib/spack/spack/cmd/info.py
@@ -52,7 +52,7 @@ def print_text_info(pkg):
     print "Safe versions:  "
 
     if not pkg.versions:
-        print("None")
+        print("    None")
     else:
         pad = padder(pkg.versions, 4)
         for v in reversed(sorted(pkg.versions)):
@@ -62,7 +62,7 @@ def print_text_info(pkg):
     print
     print "Variants:"
     if not pkg.variants:
-        print "None"
+        print "    None"
     else:
         pad = padder(pkg.variants, 4)
 

From 7fb463abb9b912f9a5bcb6e810b733f0b8bc1672 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 20:23:13 +0100
Subject: [PATCH 057/144] install GKlib headers along with METIS

---
 .../metis/install_gklib_defs_rename.patch     | 22 +++++++++++++++++++
 .../repos/builtin/packages/metis/package.py   | 13 +++++++++--
 2 files changed, 33 insertions(+), 2 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch

diff --git a/var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch b/var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch
new file mode 100644
index 0000000000..b182b167b9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch
@@ -0,0 +1,22 @@
+# HG changeset patch
+# User Sean Farley <sean@mcs.anl.gov>
+# Date 1332269671 18000
+#      Tue Mar 20 13:54:31 2012 -0500
+# Node ID b95c0c2e1d8bf8e3273f7d45e856f0c0127d998e
+# Parent  88049269953c67c3fdcc4309bf901508a875f0dc
+cmake: add gklib headers to install into include
+
+diff -r 88049269953c -r b95c0c2e1d8b libmetis/CMakeLists.txt
+Index: libmetis/CMakeLists.txt
+===================================================================
+--- a/libmetis/CMakeLists.txt Tue Mar 20 13:54:29 2012 -0500
++++ b/libmetis/CMakeLists.txt Tue Mar 20 13:54:31 2012 -0500
+@@ -12,6 +12,8 @@ endif()
+ if(METIS_INSTALL)
+   install(TARGETS metis
+     LIBRARY DESTINATION lib
+     RUNTIME DESTINATION lib
+     ARCHIVE DESTINATION lib)
++  install(FILES gklib_defs.h DESTINATION include)
++  install(FILES gklib_rename.h DESTINATION include)
+ endif()
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index bbfc4de7d1..68b9f6fd30 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-
+import glob
 
 class Metis(Package):
     """
@@ -49,6 +49,8 @@ class Metis(Package):
 
     depends_on('gdb', when='+gdb')
 
+    patch('install_gklib_defs_rename.patch')
+
     def install(self, spec, prefix):
 
         options = []
@@ -80,4 +82,11 @@ def install(self, spec, prefix):
         with working_dir(build_directory, create=True):
             cmake(source_directory, *options)
             make()
-            make("install")
\ No newline at end of file
+            make("install")
+
+            # install GKlib headers, which will be needed for ParMETIS
+            GKlib_dist = join_path(prefix.include,'GKlib')
+            mkdirp(GKlib_dist)
+            fs = glob.glob(join_path(source_directory,'GKlib',"*.h"))
+            for f in fs:
+                install(f, GKlib_dist)

From 0d4d201b70c57359f041807df0a2f58b47be78d6 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 21:22:58 +0100
Subject: [PATCH 058/144] patch parmetis to use external GKlib

---
 .../parmetis/enable_external_metis.patch      | 48 +++++++++++++++++--
 .../builtin/packages/parmetis/package.py      |  2 +-
 2 files changed, 46 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
index 514781b8b8..8b05ecc872 100644
--- a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
+++ b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
@@ -1,13 +1,55 @@
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index ca945dd..1bf94e9 100644
+index ca945dd..5995e42 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
+@@ -23,7 +23,7 @@ else()
+   set(ParMETIS_LIBRARY_TYPE STATIC)
+ endif()
+ 
+-include(${GKLIB_PATH}/GKlibSystem.cmake)
++include_directories(${GKLIB_PATH})
+ 
+ # List of paths that the compiler will search for header files.
+ # i.e., the -I equivalent
 @@ -33,7 +33,7 @@ include_directories(${GKLIB_PATH})
  include_directories(${METIS_PATH}/include)
-
+ 
  # List of directories that cmake will look for CMakeLists.txt
 -add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
-+#add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
++# add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
  add_subdirectory(include)
  add_subdirectory(libparmetis)
  add_subdirectory(programs)
+diff --git a/libparmetis/parmetislib.h b/libparmetis/parmetislib.h
+index c1daeeb..07511f6 100644
+--- a/libparmetis/parmetislib.h
++++ b/libparmetis/parmetislib.h
+@@ -20,13 +20,12 @@
+ 
+ #include <parmetis.h>
+ 
+-#include "../metis/libmetis/gklib_defs.h"
++#include <gklib_defs.h>
+ 
+-#include <mpi.h> 
++#include <mpi.h>
+ 
+ #include <rename.h>
+ #include <defs.h>
+ #include <struct.h>
+ #include <macros.h>
+ #include <proto.h>
+-
+diff --git a/programs/parmetisbin.h b/programs/parmetisbin.h
+index e26cd2d..d156480 100644
+--- a/programs/parmetisbin.h
++++ b/programs/parmetisbin.h
+@@ -19,7 +19,7 @@
+ #include <GKlib.h>
+ #include <parmetis.h>
+ 
+-#include "../metis/libmetis/gklib_defs.h"
++#include <gklib_defs.h>
+ #include "../libparmetis/rename.h"
+ #include "../libparmetis/defs.h"
+ #include "../libparmetis/struct.h"
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index bc71fb7299..5c97a836f9 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -66,7 +66,7 @@ def install(self, spec, prefix):
 
         # FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
         # FIXME : they use a non-standard name
-        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), # still need headers from METIS source, and they are not installed with METIS. shame...
+        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=spec['metis'].prefix.include),
                         '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix),
                         '-DCMAKE_C_COMPILER:STRING=mpicc',
                         '-DCMAKE_CXX_COMPILER:STRING=mpicxx'])

From 03c8a91f6a647849f0251496f361da9574a98c22 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 22:33:10 +0100
Subject: [PATCH 059/144] parmetis: avoid hardcoding -lm; use same approach as
 in METIS

---
 .../parmetis/enable_external_metis.patch      | 20 +++++++++++++++++--
 .../packages/parmetis/link-to-lm.patch        | 14 -------------
 .../builtin/packages/parmetis/package.py      |  2 --
 3 files changed, 18 insertions(+), 18 deletions(-)
 delete mode 100644 var/spack/repos/builtin/packages/parmetis/link-to-lm.patch

diff --git a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
index 8b05ecc872..e4f2729483 100644
--- a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
+++ b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
@@ -1,5 +1,5 @@
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index ca945dd..5995e42 100644
+index ca945dd..aff8b5f 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
 @@ -23,7 +23,7 @@ else()
@@ -16,10 +16,26 @@ index ca945dd..5995e42 100644
  
  # List of directories that cmake will look for CMakeLists.txt
 -add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
-+# add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
++find_library(METIS_LIBRARY metis PATHS ${METIS_PATH}/lib)
  add_subdirectory(include)
  add_subdirectory(libparmetis)
  add_subdirectory(programs)
+diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt
+index 9cfc8a7..e0c4de7 100644
+--- a/libparmetis/CMakeLists.txt
++++ b/libparmetis/CMakeLists.txt
+@@ -5,7 +5,10 @@ file(GLOB parmetis_sources *.c)
+ # Create libparmetis
+ add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources})
+ # Link with metis and MPI libraries.
+-target_link_libraries(parmetis metis ${MPI_LIBRARIES})
++target_link_libraries(parmetis ${METIS_LIBRARY} ${MPI_LIBRARIES})
++if(UNIX)
++  target_link_libraries(parmetis m)
++endif()
+ set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}")
+ 
+ install(TARGETS parmetis
 diff --git a/libparmetis/parmetislib.h b/libparmetis/parmetislib.h
 index c1daeeb..07511f6 100644
 --- a/libparmetis/parmetislib.h
diff --git a/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch b/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch
deleted file mode 100644
index faa809231e..0000000000
--- a/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt
-index 9cfc8a7..dfc0125 100644
---- a/libparmetis/CMakeLists.txt
-+++ b/libparmetis/CMakeLists.txt
-@@ -5,7 +5,7 @@ file(GLOB parmetis_sources *.c)
- # Create libparmetis
- add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources})
- # Link with metis and MPI libraries.
--target_link_libraries(parmetis metis ${MPI_LIBRARIES})
-+target_link_libraries(parmetis metis ${MPI_LIBRARIES} "-lm")
- set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}")
-
- install(TARGETS parmetis
-
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index 5c97a836f9..f5b8b6de91 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -52,8 +52,6 @@ class Parmetis(Package):
     # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
     patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
 
-    patch('link-to-lm.patch')
-
     depends_on('gdb', when='+gdb')
 
     def install(self, spec, prefix):

From fdd7e91ba078bea4f0fec1859124baaa8261fa2c Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 12:49:56 +0100
Subject: [PATCH 060/144] add shared variant to mumps (needed for Trilinos)
 plus tests

---
 .../repos/builtin/packages/mumps/Makefile.inc |  5 +--
 .../repos/builtin/packages/mumps/package.py   | 45 ++++++++++++++++---
 2 files changed, 41 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/mumps/Makefile.inc b/var/spack/repos/builtin/packages/mumps/Makefile.inc
index 2e6a041878..22d8f5518a 100644
--- a/var/spack/repos/builtin/packages/mumps/Makefile.inc
+++ b/var/spack/repos/builtin/packages/mumps/Makefile.inc
@@ -8,12 +8,9 @@ IORDERINGSF = $(ISCOTCH)
 IORDERINGSC = $(IMETIS) $(IPORD) $(ISCOTCH)
 
 PLAT    =
-LIBEXT  = .a
-OUTC    = -o 
+OUTC    = -o
 OUTF    = -o
 RM = /bin/rm -f
-AR = ar vr 
-RANLIB = ranlib
 
 INCSEQ  = -I$(topdir)/libseq
 LIBSEQ  = -L$(topdir)/libseq -lmpiseq
diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 5a254dfd00..2801d4194d 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -1,6 +1,5 @@
 from spack import *
-import os
-
+import os, sys
 
 class Mumps(Package):
     """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@@ -19,6 +18,7 @@ class Mumps(Package):
     variant('float', default=True, description='Activate the compilation of smumps')
     variant('complex', default=True, description='Activate the compilation of cmumps and/or zmumps')
     variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
+    variant('shared', default=True, description='Build shared libraries')
 
 
     depends_on('scotch + esmumps', when='~ptscotch+scotch')
@@ -105,6 +105,27 @@ def write_makefile_inc(self):
         # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER
         makefile_conf.append("CDEFS   = -DAdd_")
 
+        if '+shared' in self.spec:
+            if sys.platform == 'darwin':
+                # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew)
+                makefile_conf.extend([
+                    'LIBEXT=.dylib',
+                    'AR=%s -dynamiclib -undefined dynamic_lookup -o ' % os.environ['FC'],
+                    'RANLIB=echo'
+                ])
+            else:
+                makefile_conf.extend([
+                    'LIBEXT=.so',
+                    'AR=$(FL) -shared -o',
+                    'RANLIB=echo'
+                ])
+        else:
+            makefile_conf.extend([
+                'LIBEXT  = .a',
+                'AR = ar vr',
+                'RANLIB = ranlib'
+            ])
+
 
         makefile_inc_template = join_path(os.path.dirname(self.module.__file__),
                                           'Makefile.inc')
@@ -121,7 +142,7 @@ def write_makefile_inc(self):
     def install(self, spec, prefix):
         make_libs = []
 
-        # the coice to compile ?examples is to have kind of a sanity
+        # the choice to compile ?examples is to have kind of a sanity
         # check on the libraries generated.
         if '+float' in spec:
             make_libs.append('sexamples')
@@ -135,10 +156,24 @@ def install(self, spec, prefix):
 
         self.write_makefile_inc()
 
-        # Build fails in parallel, at least on OS-X
+        # Build fails in parallel
         make(*make_libs, parallel=False)
 
         install_tree('lib', prefix.lib)
         install_tree('include', prefix.include)
         if '~mpi' in spec:
-            install('libseq/libmpiseq.a', prefix.lib)
+            lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
+            lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
+            install('libseq/libmpiseq%s' % lib_suffix, prefix.lib)
+
+        # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI
+        # FIXME: use something like numdiff to compare blessed output with the current
+        with working_dir('examples'):
+            if '+float' in spec:
+                os.system('./ssimpletest < input_simpletest_real')
+                if '+complex' in spec:
+                    os.system('./csimpletest < input_simpletest_real')
+            if '+double' in spec:
+                os.system('./dsimpletest < input_simpletest_real')
+                if '+complex' in spec:
+                    os.system('./zsimpletest < input_simpletest_cmplx')

From 540e57f02686bad7125a951d14784e8fcc896e26 Mon Sep 17 00:00:00 2001
From: Josh Sixsmith <josh.sixsmith@gmail.com>
Date: Fri, 25 Mar 2016 18:27:02 +1100
Subject: [PATCH 061/144] Upload of GDAL, kealib, openjpeg, py-tuiview package
 builds.

---
 .../repos/builtin/packages/gdal/package.py    | 69 +++++++++++++++++++
 .../repos/builtin/packages/kealib/package.py  | 35 ++++++++++
 .../builtin/packages/openjpeg/package.py      | 26 +++++++
 .../builtin/packages/py-tuiview/package.py    | 19 +++++
 4 files changed, 149 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/gdal/package.py
 create mode 100644 var/spack/repos/builtin/packages/kealib/package.py
 create mode 100644 var/spack/repos/builtin/packages/openjpeg/package.py
 create mode 100644 var/spack/repos/builtin/packages/py-tuiview/package.py

diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py
new file mode 100644
index 0000000000..4f1f1ec2dd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gdal/package.py
@@ -0,0 +1,69 @@
+from spack import *
+
+class Gdal(Package):
+    """
+    GDAL is a translator library for raster and vector geospatial
+    data formats that is released under an X/MIT style Open Source
+    license by the Open Source Geospatial Foundation. As a library,
+    it presents a single raster abstract data model and vector
+    abstract data model to the calling application for all supported
+    formats. It also comes with a variety of useful command line
+    utilities for data translation and processing
+    """
+
+    homepage   = "http://www.gdal.org/"
+    url        = "http://download.osgeo.org/gdal/2.0.2/gdal-2.0.2.tar.gz"
+    list_url   = "http://download.osgeo.org/gdal/"
+    list_depth = 2
+
+    version('2.0.2', '573865f3f59ba7b4f8f4cddf223b52a5')
+
+    extends('python')
+
+    variant('hdf5', default=False, description='Enable HDF5 support')
+    variant('hdf', default=False, description='Enable HDF4 support')
+    variant('openjpeg', default=False, description='Enable JPEG2000 support')
+    variant('geos', default=False, description='Enable GEOS support')
+    variant('kea', default=False, description='Enable KEA support')
+    variant('netcdf', default=False, description='Enable netcdf support')
+
+    depends_on('swig')
+    depends_on("hdf5", when='+hdf5')
+    depends_on("hdf", when='+hdf')
+    depends_on("openjpeg", when='+openjpeg')
+    depends_on("geos", when='+geos')
+    depends_on("kealib", when='+kea')
+    depends_on("netcdf", when='+netcdf')
+    depends_on("libtiff")
+    depends_on("libpng")
+    depends_on("zlib")
+    depends_on("proj")
+    depends_on("py-numpy")
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        args = []
+        args.append("--prefix=%s" % prefix)
+        args.append("--with-liblzma=yes")
+        args.append("--with-zlib=%s" % spec['zlib'].prefix)
+        args.append("--with-python=%s" % spec['python'].prefix.bin + "/python")
+        args.append("--without-libtool")
+
+        if '+geos' in spec:
+            args.append('--with-geos=yes')
+        if '+hdf' in spec:
+            args.append('--with-hdf4=%s' % spec['hdf'].prefix)
+        if '+hdf5' in spec:
+            args.append('--with-hdf5=%s' % spec['hdf5'].prefix)
+        if '+openjpeg' in spec:
+            args.append('--with-openjpeg=%s' % spec['openjpeg'].prefix)
+        if '+kea' in spec:
+            args.append('--with-kea=yes')
+        if '+netcdf' in spec:
+            args.append('--with-netcdf=%s' % spec['netcdf'].prefix)
+
+        configure(*args)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/kealib/package.py b/var/spack/repos/builtin/packages/kealib/package.py
new file mode 100644
index 0000000000..475d21e1d8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kealib/package.py
@@ -0,0 +1,35 @@
+from spack import *
+
+class Kealib(Package):
+    """An HDF5 Based Raster File Format
+    
+    KEALib provides an implementation of the GDAL data model.
+    The format supports raster attribute tables, image pyramids,
+    meta-data and in-built statistics while also handling very
+    large files and compression throughout.
+    
+    Based on the HDF5 standard, it also provides a base from which
+    other formats can be derived and is a good choice for long
+    term data archiving. An independent software library (libkea)
+    provides complete access to the KEA image format and a GDAL
+    driver allowing KEA images to be used from any GDAL supported software.
+    
+    Development work on this project has been funded by Landcare Research.
+    """
+    homepage = "http://kealib.org/"
+    url      = "https://bitbucket.org/chchrsc/kealib/get/kealib-1.4.5.tar.gz"
+
+    version('1.4.5', '112e9c42d980b2d2987a3c15d0833a5d')
+
+    depends_on("hdf5")
+
+    def install(self, spec, prefix):
+        with working_dir('trunk', create=False):
+            cmake_args = []
+            cmake_args.append("-DCMAKE_INSTALL_PREFIX=%s" % prefix)
+            cmake_args.append("-DHDF5_INCLUDE_DIR=%s" % spec['hdf5'].prefix.include)
+            cmake_args.append("-DHDF5_LIB_PATH=%s" % spec['hdf5'].prefix.lib)
+            cmake('.', *cmake_args)
+
+            make()
+            make("install")
diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py
new file mode 100644
index 0000000000..afec197d11
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openjpeg/package.py
@@ -0,0 +1,26 @@
+from spack import *
+
+class Openjpeg(Package):
+    """
+    OpenJPEG is an open-source JPEG 2000 codec written in C language.
+    It has been developed in order to promote the use of JPEG 2000, a
+    still-image compression standard from the Joint Photographic
+    Experts Group (JPEG).
+    Since April 2015, it is officially recognized by ISO/IEC and
+    ITU-T as a JPEG 2000 Reference Software.
+    """
+    homepage = "https://github.com/uclouvain/openjpeg"
+    url      = "https://github.com/uclouvain/openjpeg/archive/version.2.1.tar.gz"
+
+    version('2.1'  , '3e1c451c087f8462955426da38aa3b3d')
+    version('2.0.1', '105876ed43ff7dbb2f90b41b5a43cfa5')
+    version('2.0'  , 'cdf266530fee8af87454f15feb619609')
+    version('1.5.2', '545f98923430369a6b046ef3632ef95c')
+    version('1.5.1', 'd774e4b5a0db5f0f171c4fc0aabfa14e')
+
+
+    def install(self, spec, prefix):
+        cmake('.', *std_cmake_args)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py
new file mode 100644
index 0000000000..984b4196b1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-tuiview/package.py
@@ -0,0 +1,19 @@
+from spack import *
+
+class PyTuiview(Package):
+    """
+       TuiView is a lightweight raster GIS with powerful raster attribute
+       table manipulation abilities.
+    """
+    homepage = "https://bitbucket.org/chchrsc/tuiview"
+    url      = "https://bitbucket.org/chchrsc/tuiview/get/tuiview-1.1.7.tar.gz"
+
+    version('1.1.7', '4b3b38a820cc239c8ab4a181ac5d4c30')
+
+    extends("python")
+    depends_on("py-pyqt")
+    depends_on("py-numpy")
+    depends_on("gdal")
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

From fd67da607e5476b767071dc37af66af6fd492452 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 08:32:14 +0100
Subject: [PATCH 062/144] make netcdf link against Spack's curl

---
 var/spack/repos/builtin/packages/netcdf/package.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index 227362399a..b60a2c4e9a 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -43,6 +43,13 @@ def install(self, spec, prefix):
             "--enable-dap"
         ]
 
+        # Make sure Netcdf links against Spack's curl
+        # Otherwise it may pick up system's curl, which could lead to link errors:
+        # /usr/lib/x86_64-linux-gnu/libcurl.so: undefined reference to `SSL_CTX_use_certificate_chain_file@OPENSSL_1.0.0'
+        LIBS.append("-lcurl")
+        CPPFLAGS.append("-I%s" % spec['curl'].prefix.include)
+        LDFLAGS.append ("-L%s" % spec['curl'].prefix.lib)
+
         if '+mpi' in spec:
             config_args.append('--enable-parallel4')
 

From 3e39daeb12aa13a3f3f975ff315143bc3f13a2b4 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 09:56:24 +0100
Subject: [PATCH 063/144] add fPIC to MUMPS when building shared libs

---
 var/spack/repos/builtin/packages/mumps/package.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 2801d4194d..b295857ab5 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -70,6 +70,9 @@ def write_makefile_inc(self):
 
         makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
 
+        # when building shared libs need -fPIC, otherwise
+        # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
+        fpic = '-fPIC' if '+shared' in self.spec else ''
         # TODO: test this part, it needs a full blas, scalapack and
         # partitionning environment with 64bit integers
         if '+idx64' in self.spec:
@@ -77,14 +80,14 @@ def write_makefile_inc(self):
                 # the fortran compilation flags most probably are
                 # working only for intel and gnu compilers this is
                 # perhaps something the compiler should provide
-                ['OPTF    = -O  -DALLOW_NON_INIT %s' % '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8',
-                 'OPTL    = -O ',
-                 'OPTC    = -O -DINTSIZE64'])
+                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),
+                 'OPTL    = %s -O ' % fpic,
+                 'OPTC    = %s -O -DINTSIZE64' % fpic])
         else:
             makefile_conf.extend(
-                ['OPTF    = -O  -DALLOW_NON_INIT',
-                 'OPTL    = -O ',
-                 'OPTC    = -O '])
+                ['OPTF    = %s -O  -DALLOW_NON_INIT' % fpic,
+                 'OPTL    = %s -O ' % fpic,
+                 'OPTC    = %s -O ' % fpic])
 
 
         if '+mpi' in self.spec:

From 83fea631f1765d4641cde8af2c5c931b22e4ee33 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 23:04:17 +0100
Subject: [PATCH 064/144] extend trilinos

---
 .../builtin/packages/trilinos/package.py      | 32 ++++++++++++++++---
 1 file changed, 28 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index edc40476e3..22c7ab6d61 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -1,5 +1,5 @@
 from spack import *
-
+import os
 
 class Trilinos(Package):
     """
@@ -10,6 +10,7 @@ class Trilinos(Package):
     homepage = "https://trilinos.org/"
     url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz"
 
+    version('12.6.1', 'adcf2d3aab74cdda98f88fee19cd1442604199b0515ee3da4d80cbe8f37d00e4')
     version('12.4.2', '7c830f7f0f68b8ad324690603baf404e')
     version('12.2.1', '6161926ea247863c690e927687f83be9')
     version('12.0.1', 'bd99741d047471e127b8296b2ec08017')
@@ -39,15 +40,38 @@ def install(self, spec, prefix):
         options.extend(std_cmake_args)
 
         options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
+                        '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
                         '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
                         '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
                         '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
                         '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
-                        '-DTPL_ENABLE_MPI:STRING=ON',
-                        '-DBLAS_LIBRARY_DIRS:PATH=%s' % spec['blas'].prefix,
-                        '-DLAPACK_LIBRARY_DIRS:PATH=%s' % spec['lapack'].prefix
+                        '-DTPL_ENABLE_MPI:BOOL=ON',
+                        '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
+                        '-DTPL_ENABLE_BLAS=ON',
+                        '-DBLAS_LIBRARY_NAMES=blas',
+                        '-DBLAS_LIBRARY_DIRS=/usr/lib', # % spec['blas'].prefix,
+                        '-DTPL_ENABLE_LAPACK=ON',
+                        '-DLAPACK_LIBRARY_NAMES=lapack',
+                        '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix,
+                        '-DTPL_ENABLE_Boost:BOOL=ON',
+                        '-DBOOST_BASE_DIR:PATH=%s' % spec['boost'].prefix,
+                        '-DTrilinos_ENABLE_Fortran=OFF',
+                        '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
+                        '-DTrilinos_ENABLE_CXX11:BOOL=ON',
+                        '-DTrilinos_CXX11_FLAGS=-std=c++11'
                         ])
 
+        # disable due to compiler / config errors:
+        options.extend(['-DTrilinos_ENABLE_SEACAS=OFF',
+                        '-DTrilinos_ENABLE_Pike=OFF',
+                        '-DTrilinos_ENABLE_STK=OFF'
+                        ])
+
+        if self.compiler.name == "clang":
+            os.environ['CPPFLAGS']="-Qunused-arguments"
+
+        #os.environ['LDFLAGS']="lgfortran"
+
         with working_dir('spack-build', create=True):
             cmake('..', *options)
             make()

From 30ba96e58fe699e92902ce53a87b5e1cfb756d6f Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 23:56:18 +0100
Subject: [PATCH 065/144] same

---
 .../builtin/packages/trilinos/package.py      | 84 ++++++++++++++++---
 1 file changed, 74 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 22c7ab6d61..7b913031e3 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -2,8 +2,7 @@
 import os
 
 class Trilinos(Package):
-    """
-    The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
+    """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
     software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.
     A unique design feature of Trilinos is its focus on packages.
     """
@@ -28,10 +27,19 @@ class Trilinos(Package):
     depends_on('matio')
     depends_on('glm')
     depends_on('swig')
+    depends_on('metis')
+    depends_on('suite-sparse')
+    depends_on('tbb')
 
     # MPI related dependencies
     depends_on('mpi')
     depends_on('netcdf+mpi')
+    depends_on('parmetis')
+    depends_on('mumps+metis+parmetis')
+    depends_on('scalapack')
+    depends_on('superlu-dist')
+    depends_on('hypre')
+    depends_on('hdf5+mpi')
 
     depends_on('python') #  Needs py-numpy activated
 
@@ -49,23 +57,79 @@ def install(self, spec, prefix):
                         '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
                         '-DTPL_ENABLE_BLAS=ON',
                         '-DBLAS_LIBRARY_NAMES=blas',
-                        '-DBLAS_LIBRARY_DIRS=/usr/lib', # % spec['blas'].prefix,
+                        '-DBLAS_LIBRARY_DIRS=/usr/lib', # % spec['blas'].prefix, #FIXME
                         '-DTPL_ENABLE_LAPACK=ON',
                         '-DLAPACK_LIBRARY_NAMES=lapack',
-                        '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix,
+                        '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, #FIXME
                         '-DTPL_ENABLE_Boost:BOOL=ON',
                         '-DBOOST_BASE_DIR:PATH=%s' % spec['boost'].prefix,
-                        '-DTrilinos_ENABLE_Fortran=OFF',
+                        '-DTrilinos_ENABLE_Fortran=OFF', # FIXME
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
-                        '-DTrilinos_CXX11_FLAGS=-std=c++11'
+                        '-DTrilinos_CXX11_FLAGS=-std=c++11',
+                        '-DTPL_ENABLE_Netcdf:BOOL=ON',
+                        '-DTPL_ENABLE_HYPRE:BOOL=ON',
+                        '-DTPL_ENABLE_HDF5:BOOL=ON',
+                        '-DTPL_ENABLE_TBB:BOOL=ON'
                         ])
 
+        # Amesos, conflicting types of double and complex SLU_D
+        # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
+        # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
+        options.extend([
+            '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
+            '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
+        ])
+
+        # suite-sparse related
+        options.extend([
+            '-DTPL_ENABLE_Cholmod:BOOL=ON',
+            '-DTPL_ENABLE_UMFPACK:BOOL=ON',
+            '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
+        ])
+
+        # metis / parmetis
+        options.extend([
+            '-DTPL_ENABLE_METIS:BOOL=ON',
+            '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib,
+            '-DMETIS_LIBRARY_NAMES=metis',
+            '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include,
+            '-DTPL_ENABLE_ParMETIS:BOOL=ON',
+            '-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib),
+            '-DParMETIS_LIBRARY_NAMES=parmetis;metis',
+            '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include
+        ])
+
+        # mumps
+        options.extend([
+            '-DTPL_ENABLE_MUMPS:BOOL=ON"',
+            '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
+            '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
+        ])
+
+        # scalapack
+        options.extend([
+            '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
+            '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
+        ])
+
+        # superlu_dist
+        options.extend([
+            '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
+            '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu_dist'].prefix.include
+        ])
+        if spec.satisfies('^superlu-dist@4.0:'):
+            options.extend([
+                '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
+            ])
+
+
         # disable due to compiler / config errors:
-        options.extend(['-DTrilinos_ENABLE_SEACAS=OFF',
-                        '-DTrilinos_ENABLE_Pike=OFF',
-                        '-DTrilinos_ENABLE_STK=OFF'
-                        ])
+        options.extend([
+            '-DTrilinos_ENABLE_SEACAS=OFF',
+            '-DTrilinos_ENABLE_Pike=OFF',
+            '-DTrilinos_ENABLE_STK=OFF'
+        ])
 
         if self.compiler.name == "clang":
             os.environ['CPPFLAGS']="-Qunused-arguments"

From 76006fc346c7880b03356c1cf9d00bab2fdeac45 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 05:30:48 +0100
Subject: [PATCH 066/144] fix typo

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 7b913031e3..7d7613d2b5 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -116,7 +116,7 @@ def install(self, spec, prefix):
         # superlu_dist
         options.extend([
             '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
-            '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu_dist'].prefix.include
+            '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
         ])
         if spec.satisfies('^superlu-dist@4.0:'):
             options.extend([

From 18db930866b2024b242ea7c825851d7a56b27247 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 07:09:58 +0100
Subject: [PATCH 067/144] rearrange

---
 .../repos/builtin/packages/trilinos/package.py | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 7d7613d2b5..063d179c7e 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -73,14 +73,6 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_TBB:BOOL=ON'
                         ])
 
-        # Amesos, conflicting types of double and complex SLU_D
-        # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
-        # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
-        options.extend([
-            '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
-            '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
-        ])
-
         # suite-sparse related
         options.extend([
             '-DTPL_ENABLE_Cholmod:BOOL=ON',
@@ -113,7 +105,14 @@ def install(self, spec, prefix):
             '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
         ])
 
-        # superlu_dist
+        # superlu_dist:
+        # Amesos, conflicting types of double and complex SLU_D
+        # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
+        # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
+        options.extend([
+            '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
+            '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
+        ])
         options.extend([
             '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
             '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
@@ -123,7 +122,6 @@ def install(self, spec, prefix):
                 '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
             ])
 
-
         # disable due to compiler / config errors:
         options.extend([
             '-DTrilinos_ENABLE_SEACAS=OFF',

From b91a155e8d996c9e51da7f75d4e106469ba488e6 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 07:10:31 +0100
Subject: [PATCH 068/144] more specific about dependencies

---
 var/spack/repos/builtin/packages/trilinos/package.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 063d179c7e..2937ed4c38 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -62,7 +62,7 @@ def install(self, spec, prefix):
                         '-DLAPACK_LIBRARY_NAMES=lapack',
                         '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, #FIXME
                         '-DTPL_ENABLE_Boost:BOOL=ON',
-                        '-DBOOST_BASE_DIR:PATH=%s' % spec['boost'].prefix,
+                        '-DBoost_BASE_DIR:PATH=%s' % spec['boost'].prefix,
                         '-DTrilinos_ENABLE_Fortran=OFF', # FIXME
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
@@ -76,7 +76,9 @@ def install(self, spec, prefix):
         # suite-sparse related
         options.extend([
             '-DTPL_ENABLE_Cholmod:BOOL=ON',
+            '-DCholmod_BASE_DIR:PATH=%s' % spec['suite-sparse'].prefix,
             '-DTPL_ENABLE_UMFPACK:BOOL=ON',
+            '-D_UMFPACK_BASE_DIR:PATH=%s' % spec['suite-sparse'].prefix,
             '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
         ])
 
@@ -94,7 +96,7 @@ def install(self, spec, prefix):
 
         # mumps
         options.extend([
-            '-DTPL_ENABLE_MUMPS:BOOL=ON"',
+            '-DTPL_ENABLE_MUMPS:BOOL=ON',
             '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
             '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
         ])
@@ -115,6 +117,7 @@ def install(self, spec, prefix):
         ])
         options.extend([
             '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
+            '-DSuperLUDist_BASE_DIR:PATH=%s' % spec['superlu-dist'].prefix,
             '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
         ])
         if spec.satisfies('^superlu-dist@4.0:'):

From b6a35716ce3e02e1a3661e2433986ad637b65d0c Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 07:33:28 +0100
Subject: [PATCH 069/144] same

---
 var/spack/repos/builtin/packages/trilinos/package.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 2937ed4c38..b31cf880bc 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -43,6 +43,8 @@ class Trilinos(Package):
 
     depends_on('python') #  Needs py-numpy activated
 
+    patch('umfpack_from_suitesparse.patch')
+
     def install(self, spec, prefix):
         options = []
         options.extend(std_cmake_args)
@@ -76,9 +78,11 @@ def install(self, spec, prefix):
         # suite-sparse related
         options.extend([
             '-DTPL_ENABLE_Cholmod:BOOL=ON',
-            '-DCholmod_BASE_DIR:PATH=%s' % spec['suite-sparse'].prefix,
+            '-DCholmod_LIBRARY_DIRS=%s' % spec['suite-sparse'].prefix.lib,
+            '-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
             '-DTPL_ENABLE_UMFPACK:BOOL=ON',
-            '-D_UMFPACK_BASE_DIR:PATH=%s' % spec['suite-sparse'].prefix,
+            '-D_UMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
+            '-D_UMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
             '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
         ])
 
@@ -117,7 +121,7 @@ def install(self, spec, prefix):
         ])
         options.extend([
             '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
-            '-DSuperLUDist_BASE_DIR:PATH=%s' % spec['superlu-dist'].prefix,
+            '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib,
             '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
         ])
         if spec.satisfies('^superlu-dist@4.0:'):

From 45b4895888a2abb3cf11ecf2b26b7940a9f89b5a Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 07:34:22 +0100
Subject: [PATCH 070/144] patch

---
 .../packages/trilinos/umfpack_from_suitesparse.patch | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch

diff --git a/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch b/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch
new file mode 100644
index 0000000000..9defc55527
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch
@@ -0,0 +1,12 @@
+diff --git a/cmake/TPLs/FindTPLUMFPACK.cmake b/cmake/TPLs/FindTPLUMFPACK.cmake
+index 963eb71..998cd02 100644
+--- a/cmake/TPLs/FindTPLUMFPACK.cmake
++++ b/cmake/TPLs/FindTPLUMFPACK.cmake
+@@ -55,6 +55,6 @@
+
+
+ TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( UMFPACK
+-  REQUIRED_HEADERS umfpack.h amd.h UFconfig.h
++  REQUIRED_HEADERS umfpack.h amd.h SuiteSparse_config.h
+   REQUIRED_LIBS_NAMES umfpack amd
+   )

From bc3314a57d43963416f709a94967ae8e1758c458 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 08:05:18 +0100
Subject: [PATCH 071/144] more and more

---
 .../repos/builtin/packages/trilinos/package.py     | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index b31cf880bc..77ae6f818d 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -64,7 +64,8 @@ def install(self, spec, prefix):
                         '-DLAPACK_LIBRARY_NAMES=lapack',
                         '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, #FIXME
                         '-DTPL_ENABLE_Boost:BOOL=ON',
-                        '-DBoost_BASE_DIR:PATH=%s' % spec['boost'].prefix,
+                        '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include,
+                        '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib,
                         '-DTrilinos_ENABLE_Fortran=OFF', # FIXME
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
@@ -77,12 +78,13 @@ def install(self, spec, prefix):
 
         # suite-sparse related
         options.extend([
-            '-DTPL_ENABLE_Cholmod:BOOL=ON',
-            '-DCholmod_LIBRARY_DIRS=%s' % spec['suite-sparse'].prefix.lib,
-            '-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
+            '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file?
+            #'-DTPL_ENABLE_Cholmod:BOOL=ON',
+            #'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
+            #'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
             '-DTPL_ENABLE_UMFPACK:BOOL=ON',
-            '-D_UMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
-            '-D_UMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
+            '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
+            '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
             '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
         ])
 

From 2162627f35f98dc7f07cd34a6593f71d74095955 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 08:13:19 +0100
Subject: [PATCH 072/144] more

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 77ae6f818d..532db69cc2 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -124,7 +124,7 @@ def install(self, spec, prefix):
         options.extend([
             '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
             '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib,
-            '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
+            '-DSuperLUDist_INCLUDE_DIRS=%s/superlu_dist' % spec['superlu-dist'].prefix.include # superlu_dist and superlu have the same header names :-( In order to avoid conflicts, try to keep "dist" version headers in a subfolder
         ])
         if spec.satisfies('^superlu-dist@4.0:'):
             options.extend([

From 88a7a23132a379e526220324b8493d3be870f7e6 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 08:46:23 +0100
Subject: [PATCH 073/144] even more

---
 .../repos/builtin/packages/trilinos/package.py   | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 532db69cc2..13794ae930 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -36,7 +36,7 @@ class Trilinos(Package):
     depends_on('netcdf+mpi')
     depends_on('parmetis')
     depends_on('mumps+metis+parmetis')
-    depends_on('scalapack')
+    # depends_on('scalapack') # see FIXME below
     depends_on('superlu-dist')
     depends_on('hypre')
     depends_on('hdf5+mpi')
@@ -49,6 +49,7 @@ def install(self, spec, prefix):
         options = []
         options.extend(std_cmake_args)
 
+        mpi_bin = spec['mpi'].prefix.bin
         options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
                         '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
                         '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
@@ -73,7 +74,12 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_Netcdf:BOOL=ON',
                         '-DTPL_ENABLE_HYPRE:BOOL=ON',
                         '-DTPL_ENABLE_HDF5:BOOL=ON',
-                        '-DTPL_ENABLE_TBB:BOOL=ON'
+                        '-DTPL_ENABLE_TBB:BOOL=ON',
+                        # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS
+                        '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
+                        '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
+                        '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
+                        '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran'
                         ])
 
         # suite-sparse related
@@ -109,8 +115,8 @@ def install(self, spec, prefix):
 
         # scalapack
         options.extend([
-            '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
-            '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
+            '-DTPL_ENABLE_SCALAPACK:BOOL=OFF', #FIXME: Undefined symbols for architecture x86_64: "_blacs_gridinfo__", referenced from: Amesos_Scalapack::RedistributeA() in Amesos_Scalapack.cpp.o
+            #'-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
         ])
 
         # superlu_dist:
@@ -141,8 +147,6 @@ def install(self, spec, prefix):
         if self.compiler.name == "clang":
             os.environ['CPPFLAGS']="-Qunused-arguments"
 
-        #os.environ['LDFLAGS']="lgfortran"
-
         with working_dir('spack-build', create=True):
             cmake('..', *options)
             make()

From 7e4e2c988ab4e5163469395ace204d9f332a9675 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 08:48:25 +0100
Subject: [PATCH 074/144] minor

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 13794ae930..c915d8eb1a 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -78,7 +78,7 @@ def install(self, spec, prefix):
                         # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS
                         '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
                         '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
-                        '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
+                        '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90'),
                         '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran'
                         ])
 

From 50e4b609c688b573ef882a079e2d45a83966f94c Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 09:11:26 +0100
Subject: [PATCH 075/144] minor

---
 var/spack/repos/builtin/packages/trilinos/package.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index c915d8eb1a..3622548ece 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -52,6 +52,7 @@ def install(self, spec, prefix):
         mpi_bin = spec['mpi'].prefix.bin
         options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
                         '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
+                        '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF',
                         '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
                         '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
                         '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
@@ -145,7 +146,9 @@ def install(self, spec, prefix):
         ])
 
         if self.compiler.name == "clang":
-            os.environ['CPPFLAGS']="-Qunused-arguments"
+            options.extend([
+                '-DCMAKE_EXE_LINKER_FLAGS:STRING=-Qunused-arguments'
+            ])
 
         with working_dir('spack-build', create=True):
             cmake('..', *options)

From 2fb599ea86c82e3395d8402db116a3a25fed0c73 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 09:16:51 +0100
Subject: [PATCH 076/144] minor

---
 var/spack/repos/builtin/packages/trilinos/package.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 3622548ece..82681e004c 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -55,7 +55,7 @@ def install(self, spec, prefix):
                         '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF',
                         '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
                         '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
-                        '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
+                        '-DCMAKE_BUILD_TYPE:STRING=%s' % ('DEBUG' if '+debug' in spec else 'RELEASE'),
                         '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
                         '-DTPL_ENABLE_MPI:BOOL=ON',
                         '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
@@ -83,6 +83,11 @@ def install(self, spec, prefix):
                         '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran'
                         ])
 
+        # for build-debug only:
+        options.extend([
+            '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
+        ])
+
         # suite-sparse related
         options.extend([
             '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file?

From eb5b0767aa20b46932c36203595c124b7463a444 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 09:45:33 +0100
Subject: [PATCH 077/144] remove gfortran as we have libnotfound...

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 82681e004c..bb6f095190 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -80,7 +80,7 @@ def install(self, spec, prefix):
                         '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
                         '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
                         '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90'),
-                        '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran'
+                        # '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran' # FIXME 
                         ])
 
         # for build-debug only:

From 7897f10126f0f8389326c9e723d73021f654ea6a Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 13:04:43 +0100
Subject: [PATCH 078/144] fiddle with fortran

---
 .../builtin/packages/trilinos/package.py      | 21 ++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index bb6f095190..f6f24e967e 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -68,7 +68,7 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_Boost:BOOL=ON',
                         '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include,
                         '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib,
-                        '-DTrilinos_ENABLE_Fortran=OFF', # FIXME
+                        # '-DTrilinos_ENABLE_Fortran=OFF', # FIXME
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
                         '-DTrilinos_CXX11_FLAGS=-std=c++11',
@@ -79,10 +79,17 @@ def install(self, spec, prefix):
                         # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS
                         '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
                         '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
-                        '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90'),
-                        # '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran' # FIXME 
+                        '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90')
                         ])
 
+        # Fortran lib
+        libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read())
+        #os.environ['LDFLAGS'] = '-L%s -lgfortran' % libgfortran
+        options.extend([
+            '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran',
+            '-DCMAKE_EXE_LINKER_FLAGS:STRING=-L%s -lgfortran' % libgfortran
+        ])
+
         # for build-debug only:
         options.extend([
             '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
@@ -150,10 +157,10 @@ def install(self, spec, prefix):
             '-DTrilinos_ENABLE_STK=OFF'
         ])
 
-        if self.compiler.name == "clang":
-            options.extend([
-                '-DCMAKE_EXE_LINKER_FLAGS:STRING=-Qunused-arguments'
-            ])
+        #if self.compiler.name == "clang":
+        #    options.extend([
+        #        '-DCMAKE_EXE_LINKER_FLAGS:STRING=-Qunused-arguments'
+        #    ])
 
         with working_dir('spack-build', create=True):
             cmake('..', *options)

From fade526ae4e748a9454fd56c07ef7bc1fca38423 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 16:58:59 +0100
Subject: [PATCH 079/144] remove tbb

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index f6f24e967e..12212360a0 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -29,7 +29,6 @@ class Trilinos(Package):
     depends_on('swig')
     depends_on('metis')
     depends_on('suite-sparse')
-    depends_on('tbb')
 
     # MPI related dependencies
     depends_on('mpi')
@@ -75,7 +74,6 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_Netcdf:BOOL=ON',
                         '-DTPL_ENABLE_HYPRE:BOOL=ON',
                         '-DTPL_ENABLE_HDF5:BOOL=ON',
-                        '-DTPL_ENABLE_TBB:BOOL=ON',
                         # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS
                         '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
                         '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),

From e51fe2934e0189aa5c33c8663819d23e7706f809 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 17:38:36 +0100
Subject: [PATCH 080/144] fiddle more

---
 var/spack/repos/builtin/packages/trilinos/package.py | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 12212360a0..fb14e1f36c 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -67,7 +67,6 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_Boost:BOOL=ON',
                         '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include,
                         '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib,
-                        # '-DTrilinos_ENABLE_Fortran=OFF', # FIXME
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
                         '-DTrilinos_CXX11_FLAGS=-std=c++11',
@@ -82,10 +81,9 @@ def install(self, spec, prefix):
 
         # Fortran lib
         libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read())
-        #os.environ['LDFLAGS'] = '-L%s -lgfortran' % libgfortran
         options.extend([
-            '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran',
-            '-DCMAKE_EXE_LINKER_FLAGS:STRING=-L%s -lgfortran' % libgfortran
+            '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
+            '-DTrilinos_ENABLE_Fortran=OFF' # FIXME: otherwise VerifyFortranC fails as it does not contain -lgfortran , issues with IMPLICIT_LINK_LIBRARIES in CMakeFiles/CMake(C|CXX|Fortran)Compiler.cmake?
         ])
 
         # for build-debug only:
@@ -155,11 +153,6 @@ def install(self, spec, prefix):
             '-DTrilinos_ENABLE_STK=OFF'
         ])
 
-        #if self.compiler.name == "clang":
-        #    options.extend([
-        #        '-DCMAKE_EXE_LINKER_FLAGS:STRING=-Qunused-arguments'
-        #    ])
-
         with working_dir('spack-build', create=True):
             cmake('..', *options)
             make()

From 3f12a51759fcdd3b11867cb849fc2aa81a4941ef Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 19:35:49 +0100
Subject: [PATCH 081/144] keep fiddling

---
 .../repos/builtin/packages/trilinos/package.py  | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index fb14e1f36c..cdc2bf2379 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -1,6 +1,11 @@
 from spack import *
 import os
 
+# Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it:
+# https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111
+# https://github.com/koecher/candi/blob/master/deal.II-toolchain/packages/trilinos.package
+# https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh
+# https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb
 class Trilinos(Package):
     """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
     software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.
@@ -59,11 +64,11 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_MPI:BOOL=ON',
                         '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
                         '-DTPL_ENABLE_BLAS=ON',
-                        '-DBLAS_LIBRARY_NAMES=blas',
-                        '-DBLAS_LIBRARY_DIRS=/usr/lib', # % spec['blas'].prefix, #FIXME
+                        '-DBLAS_LIBRARY_NAMES=blas', # FIXME: for Intel, Clang+GNU, GNU; easybuild add gfortran here...
+                        '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
                         '-DTPL_ENABLE_LAPACK=ON',
                         '-DLAPACK_LIBRARY_NAMES=lapack',
-                        '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, #FIXME
+                        '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
                         '-DTPL_ENABLE_Boost:BOOL=ON',
                         '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include,
                         '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib,
@@ -74,9 +79,9 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_HYPRE:BOOL=ON',
                         '-DTPL_ENABLE_HDF5:BOOL=ON',
                         # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS
-                        '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
-                        '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
-                        '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90')
+                        #'-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
+                        #'-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
+                        #'-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90')
                         ])
 
         # Fortran lib

From 8c9f88761384d16c77aa9cbee55cc501712c7b12 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 12:45:43 +0100
Subject: [PATCH 082/144] finally builds

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index cdc2bf2379..b80123838a 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -39,7 +39,7 @@ class Trilinos(Package):
     depends_on('mpi')
     depends_on('netcdf+mpi')
     depends_on('parmetis')
-    depends_on('mumps+metis+parmetis')
+    depends_on('mumps+metis+parmetis+shared') # build errors with static libs
     # depends_on('scalapack') # see FIXME below
     depends_on('superlu-dist')
     depends_on('hypre')

From df995c4ef850338823b3a5a5c2ee3b12e05a33b1 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 12:57:22 +0100
Subject: [PATCH 083/144] minor cleanup

---
 .../repos/builtin/packages/trilinos/package.py     | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index b80123838a..f2e9c37caa 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -77,24 +77,20 @@ def install(self, spec, prefix):
                         '-DTrilinos_CXX11_FLAGS=-std=c++11',
                         '-DTPL_ENABLE_Netcdf:BOOL=ON',
                         '-DTPL_ENABLE_HYPRE:BOOL=ON',
-                        '-DTPL_ENABLE_HDF5:BOOL=ON',
-                        # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS
-                        #'-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
-                        #'-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
-                        #'-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90')
+                        '-DTPL_ENABLE_HDF5:BOOL=ON'
                         ])
 
         # Fortran lib
         libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read())
         options.extend([
             '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
-            '-DTrilinos_ENABLE_Fortran=OFF' # FIXME: otherwise VerifyFortranC fails as it does not contain -lgfortran , issues with IMPLICIT_LINK_LIBRARIES in CMakeFiles/CMake(C|CXX|Fortran)Compiler.cmake?
+            '-DTrilinos_ENABLE_Fortran=OFF' # FIXME: otherwise CMake's VerifyFortranC fails as it does not contain -lgfortran
         ])
 
         # for build-debug only:
-        options.extend([
-            '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
-        ])
+        # options.extend([
+        #    '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
+        # ])
 
         # suite-sparse related
         options.extend([

From 0fc9326a4cc742e7a06cc1bb4192d0dfd008880d Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 13:23:56 +0100
Subject: [PATCH 084/144] add variants

---
 .../builtin/packages/trilinos/package.py      | 111 +++++++++++-------
 1 file changed, 69 insertions(+), 42 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index f2e9c37caa..2e119581e1 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -22,8 +22,15 @@ class Trilinos(Package):
     version('11.14.2', 'a43590cf896c677890d75bfe75bc6254')
     version('11.14.1', '40febc57f76668be8b6a77b7607bb67f')
 
-    variant('shared', default=True, description='Enables the build of shared libraries')
-    variant('debug', default=False, description='Builds a debug version of the libraries')
+    variant('metis',        default=True,  description='Compile with METIS')
+    variant('parmetis',     default=True,  description='Compile with ParMETIS')
+    variant('mumps',        default=True,  description='Compile with support for MUMPS solvers')
+    variant('superlu-dist', default=True,  description='Compile with SuperluDist solvers')
+    variant('hypre',        default=True,  description='Compile with Hypre preconditioner')
+    variant('hdf5',         default=True,  description='Compile with HDF5')
+    variant('suite-sparse', default=True,  description='Compile with SuiteSparse solvers')
+    variant('shared',       default=True,  description='Enables the build of shared libraries')
+    variant('debug',        default=False, description='Builds a debug version of the libraries')
 
     # Everything should be compiled with -fpic
     depends_on('blas')
@@ -49,7 +56,23 @@ class Trilinos(Package):
 
     patch('umfpack_from_suitesparse.patch')
 
+    # check that the combination of variants makes sense
+    def variants_check(self):
+        if '+parmetis' in self.spec and '+metis' not in self.spec:
+            raise RuntimeError('You cannot use the variant parmetis without metis')
+
+        if '+mumps' in self.spec and '+parmetis' not in self.spec:
+            raise RuntimeError('You cannot use the variant mumps without parmetis')
+
+        if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'):
+            # For Trilinos v11 we need to force SuperLUDist=OFF,
+            # since only the deprecated SuperLUDist v3.3 together with an Amesos patch
+            # is working.
+            raise RuntimeError('The superlu-dist variant can only be used with Trilinos @12.0.1:')
+
     def install(self, spec, prefix):
+        self.variants_check()
+
         options = []
         options.extend(std_cmake_args)
 
@@ -93,35 +116,38 @@ def install(self, spec, prefix):
         # ])
 
         # suite-sparse related
-        options.extend([
-            '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file?
-            #'-DTPL_ENABLE_Cholmod:BOOL=ON',
-            #'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
-            #'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
-            '-DTPL_ENABLE_UMFPACK:BOOL=ON',
-            '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
-            '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
-            '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
-        ])
+        if '+suite-sparse' in spec:
+            options.extend([
+                '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file?
+                #'-DTPL_ENABLE_Cholmod:BOOL=ON',
+                #'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
+                #'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
+                '-DTPL_ENABLE_UMFPACK:BOOL=ON',
+                '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
+                '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
+                '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
+            ])
 
         # metis / parmetis
-        options.extend([
-            '-DTPL_ENABLE_METIS:BOOL=ON',
-            '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib,
-            '-DMETIS_LIBRARY_NAMES=metis',
-            '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include,
-            '-DTPL_ENABLE_ParMETIS:BOOL=ON',
-            '-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib),
-            '-DParMETIS_LIBRARY_NAMES=parmetis;metis',
-            '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include
-        ])
+        if '+parmetis' in spec: # metis is required, see variants_check()
+            options.extend([
+                '-DTPL_ENABLE_METIS:BOOL=ON',
+                '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib,
+                '-DMETIS_LIBRARY_NAMES=metis',
+                '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include,
+                '-DTPL_ENABLE_ParMETIS:BOOL=ON',
+                '-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib),
+                '-DParMETIS_LIBRARY_NAMES=parmetis;metis',
+                '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include
+            ])
 
         # mumps
-        options.extend([
-            '-DTPL_ENABLE_MUMPS:BOOL=ON',
-            '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
-            '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
-        ])
+        if '+mumps' in spec:
+            options.extend([
+                '-DTPL_ENABLE_MUMPS:BOOL=ON',
+                '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
+                '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
+            ])
 
         # scalapack
         options.extend([
@@ -129,23 +155,24 @@ def install(self, spec, prefix):
             #'-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
         ])
 
-        # superlu_dist:
-        # Amesos, conflicting types of double and complex SLU_D
-        # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
-        # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
-        options.extend([
-            '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
-            '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
-        ])
-        options.extend([
-            '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
-            '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib,
-            '-DSuperLUDist_INCLUDE_DIRS=%s/superlu_dist' % spec['superlu-dist'].prefix.include # superlu_dist and superlu have the same header names :-( In order to avoid conflicts, try to keep "dist" version headers in a subfolder
-        ])
-        if spec.satisfies('^superlu-dist@4.0:'):
+        # superlu-dist:
+        if '+superlu-dist' in spec:
+            # Amesos, conflicting types of double and complex SLU_D
+            # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
+            # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
             options.extend([
-                '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
+                '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
+                '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
             ])
+            options.extend([
+                '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
+                '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib,
+                '-DSuperLUDist_INCLUDE_DIRS=%s/superlu_dist' % spec['superlu-dist'].prefix.include # superlu_dist and superlu have the same header names :-( In order to avoid conflicts, try to keep "dist" version headers in a subfolder
+            ])
+            if spec.satisfies('^superlu-dist@4.0:'):
+                options.extend([
+                    '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
+                ])
 
         # disable due to compiler / config errors:
         options.extend([

From 416fcd081013afa8349d311909d50b21d9685674 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 13:33:00 +0100
Subject: [PATCH 085/144] same

---
 .../repos/builtin/packages/trilinos/package.py  | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 2e119581e1..3beadeb798 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -29,6 +29,7 @@ class Trilinos(Package):
     variant('hypre',        default=True,  description='Compile with Hypre preconditioner')
     variant('hdf5',         default=True,  description='Compile with HDF5')
     variant('suite-sparse', default=True,  description='Compile with SuiteSparse solvers')
+    variant('python',       default=True,  description='Build python wrappers')
     variant('shared',       default=True,  description='Enables the build of shared libraries')
     variant('debug',        default=False, description='Builds a debug version of the libraries')
 
@@ -39,20 +40,20 @@ class Trilinos(Package):
     depends_on('matio')
     depends_on('glm')
     depends_on('swig')
-    depends_on('metis')
-    depends_on('suite-sparse')
+    depends_on('metis',when='+metis')
+    depends_on('suite-sparse',when='+suite-sparse')
 
     # MPI related dependencies
     depends_on('mpi')
     depends_on('netcdf+mpi')
-    depends_on('parmetis')
-    depends_on('mumps+metis+parmetis+shared') # build errors with static libs
+    depends_on('parmetis',when='+parmetis')
+    depends_on('mumps+metis+parmetis+shared',when='+mumps') # build errors with static libs
     # depends_on('scalapack') # see FIXME below
-    depends_on('superlu-dist')
-    depends_on('hypre')
-    depends_on('hdf5+mpi')
+    depends_on('superlu-dist',when='+superlu-dist')
+    depends_on('hypre',when='+hypre')
+    depends_on('hdf5+mpi',when='+hdf5')
 
-    depends_on('python') #  Needs py-numpy activated
+    depends_on('python',when='+python') #  Needs py-numpy activated
 
     patch('umfpack_from_suitesparse.patch')
 

From c33a63cabc8dcd8c71fc87de60a883cef4a4dae2 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 13:47:07 +0100
Subject: [PATCH 086/144] fix python installation

---
 var/spack/repos/builtin/packages/trilinos/package.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 3beadeb798..886893b639 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -186,3 +186,14 @@ def install(self, spec, prefix):
             cmake('..', *options)
             make()
             make('install')
+
+            # When trilinos is built with Python, libpytrilinos is included through
+            # cmake configure files. Namely, Trilinos_LIBRARIES in TrilinosConfig.cmake
+            # contains pytrilinos. This leads to a run-time error:
+            # Symbol not found: _PyBool_Type
+            # and prevents Trilinos to be used in any C++ code, which links executable
+            # against the libraries listed in Trilinos_LIBRARIES.
+            # See https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509
+            # A workaround it to remove PyTrilinos from the COMPONENTS_LIST :
+            if '+python' in self.spec:
+                filter_file(r'(?:SET\(COMPONENTS_LIST.*)(PyTrilinos;)(?:.*)',  '',  '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib)

From d096b155f45d97775affa2bdda640a22823cb73e Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 19:41:37 +0100
Subject: [PATCH 087/144] fix filter_file

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 886893b639..3967d0ef0e 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -196,4 +196,4 @@ def install(self, spec, prefix):
             # See https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509
             # A workaround it to remove PyTrilinos from the COMPONENTS_LIST :
             if '+python' in self.spec:
-                filter_file(r'(?:SET\(COMPONENTS_LIST.*)(PyTrilinos;)(?:.*)',  '',  '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib)
+                filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)',  (r'\1\3'),  '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib)

From 7f2db8c26793abb1977dbccd2ae8a3a1b5a46568 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 11:54:51 +0100
Subject: [PATCH 088/144] fix w GCC 4.8 on Ubuntu but broke w GCC 5.3/Clang on
 OSX

---
 .../builtin/packages/trilinos/package.py      | 26 ++++++++++++++-----
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 3967d0ef0e..1f1601e537 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -48,7 +48,7 @@ class Trilinos(Package):
     depends_on('netcdf+mpi')
     depends_on('parmetis',when='+parmetis')
     depends_on('mumps+metis+parmetis+shared',when='+mumps') # build errors with static libs
-    # depends_on('scalapack') # see FIXME below
+    depends_on('scalapack')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre',when='+hypre')
     depends_on('hdf5+mpi',when='+hdf5')
@@ -108,13 +108,13 @@ def install(self, spec, prefix):
         libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read())
         options.extend([
             '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
-            '-DTrilinos_ENABLE_Fortran=OFF' # FIXME: otherwise CMake's VerifyFortranC fails as it does not contain -lgfortran
+            '-DTrilinos_ENABLE_Fortran=ON' # FIXME: otherwise CMake's VerifyFortranC fails as it does not contain -lgfortran
         ])
 
         # for build-debug only:
-        # options.extend([
-        #    '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
-        # ])
+        options.extend([
+           '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
+        ])
 
         # suite-sparse related
         if '+suite-sparse' in spec:
@@ -144,16 +144,22 @@ def install(self, spec, prefix):
 
         # mumps
         if '+mumps' in spec:
+            # FIXME:
+            # since we use mumps with MPI, it will certainly be build against Scalapack.
+            # Add scalapack lib here as well. 
+            # This likely won't be need if Trilinos would compile with Scalapack
             options.extend([
                 '-DTPL_ENABLE_MUMPS:BOOL=ON',
                 '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
                 '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
+#                '-DMUMPS_LIBRARY_DIRS=%s;%s' % (spec['mumps'].prefix.lib,spec['scalapack'].prefix.lib),
+#                '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord;scalapack' # order is important!
             ])
 
         # scalapack
         options.extend([
-            '-DTPL_ENABLE_SCALAPACK:BOOL=OFF', #FIXME: Undefined symbols for architecture x86_64: "_blacs_gridinfo__", referenced from: Amesos_Scalapack::RedistributeA() in Amesos_Scalapack.cpp.o
-            #'-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
+            '-DTPL_ENABLE_SCALAPACK:BOOL=ON', #FIXME: Undefined symbols for architecture x86_64: "_blacs_gridinfo__", referenced from: Amesos_Scalapack::RedistributeA() in Amesos_Scalapack.cpp.o
+            '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
         ])
 
         # superlu-dist:
@@ -175,6 +181,12 @@ def install(self, spec, prefix):
                     '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
                 ])
 
+        # python
+        if '~python' in spec:
+            options.extend([
+                '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF'
+            ])
+
         # disable due to compiler / config errors:
         options.extend([
             '-DTrilinos_ENABLE_SEACAS=OFF',

From 828aeefb1d4e09deb0694c61397a3097bda85ccb Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 12:01:00 +0100
Subject: [PATCH 089/144] minor cleanup

---
 var/spack/repos/builtin/packages/trilinos/package.py | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 1f1601e537..1dba2b8db3 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -88,7 +88,7 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_MPI:BOOL=ON',
                         '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
                         '-DTPL_ENABLE_BLAS=ON',
-                        '-DBLAS_LIBRARY_NAMES=blas', # FIXME: for Intel, Clang+GNU, GNU; easybuild add gfortran here...
+                        '-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names
                         '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
                         '-DTPL_ENABLE_LAPACK=ON',
                         '-DLAPACK_LIBRARY_NAMES=lapack',
@@ -108,7 +108,7 @@ def install(self, spec, prefix):
         libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read())
         options.extend([
             '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
-            '-DTrilinos_ENABLE_Fortran=ON' # FIXME: otherwise CMake's VerifyFortranC fails as it does not contain -lgfortran
+            '-DTrilinos_ENABLE_Fortran=ON'
         ])
 
         # for build-debug only:
@@ -144,21 +144,15 @@ def install(self, spec, prefix):
 
         # mumps
         if '+mumps' in spec:
-            # FIXME:
-            # since we use mumps with MPI, it will certainly be build against Scalapack.
-            # Add scalapack lib here as well. 
-            # This likely won't be need if Trilinos would compile with Scalapack
             options.extend([
                 '-DTPL_ENABLE_MUMPS:BOOL=ON',
                 '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
                 '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
-#                '-DMUMPS_LIBRARY_DIRS=%s;%s' % (spec['mumps'].prefix.lib,spec['scalapack'].prefix.lib),
-#                '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord;scalapack' # order is important!
             ])
 
         # scalapack
         options.extend([
-            '-DTPL_ENABLE_SCALAPACK:BOOL=ON', #FIXME: Undefined symbols for architecture x86_64: "_blacs_gridinfo__", referenced from: Amesos_Scalapack::RedistributeA() in Amesos_Scalapack.cpp.o
+            '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
             '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
         ])
 

From 21e81e92a9ac88bd498bd65aa9b77a43c27da881 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 12:05:48 +0100
Subject: [PATCH 090/144] try to disable VerifyFortranC tests on Darwin

---
 var/spack/repos/builtin/packages/trilinos/package.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 1dba2b8db3..0c7d8a7967 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -110,6 +110,13 @@ def install(self, spec, prefix):
             '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
             '-DTrilinos_ENABLE_Fortran=ON'
         ])
+        # FIXME:
+        # VerifyFortranC test of CMake does not contain -lgfortran and thus fails.
+        # This could be GCC/CMake related, but appears at least on OSX with Clang@7.0.2 and GNU Fortran@5.3.0
+        if sys.platform == 'darwin':
+            options.extend([
+                '-DTrilinos_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=TRUE'
+            ])
 
         # for build-debug only:
         options.extend([

From 26a72619aed8684019ab331889b276b8883b76c8 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 12:42:26 +0100
Subject: [PATCH 091/144] add missing sys

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 0c7d8a7967..e077dfbbfd 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -1,5 +1,5 @@
 from spack import *
-import os
+import os, sys
 
 # Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it:
 # https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111

From 5172f09b9f966a3f1be438bab972a0267cccc73b Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 16:47:48 +0100
Subject: [PATCH 092/144] builds on OSX again (modulo CC wrappers are solved)

---
 .../builtin/packages/trilinos/package.py      | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index e077dfbbfd..3003b4ab53 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -113,15 +113,15 @@ def install(self, spec, prefix):
         # FIXME:
         # VerifyFortranC test of CMake does not contain -lgfortran and thus fails.
         # This could be GCC/CMake related, but appears at least on OSX with Clang@7.0.2 and GNU Fortran@5.3.0
-        if sys.platform == 'darwin':
-            options.extend([
-                '-DTrilinos_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=TRUE'
-            ])
+        #if sys.platform == 'darwin':
+        #    options.extend([
+        #        '-DTrilinos_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=TRUE'
+        #    ])
 
         # for build-debug only:
-        options.extend([
-           '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
-        ])
+        #options.extend([
+        #   '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
+        #])
 
         # suite-sparse related
         if '+suite-sparse' in spec:
@@ -194,6 +194,11 @@ def install(self, spec, prefix):
             '-DTrilinos_ENABLE_Pike=OFF',
             '-DTrilinos_ENABLE_STK=OFF'
         ])
+        if sys.platform == 'darwin':
+            options.extend([
+                '-DTrilinos_ENABLE_FEI=OFF'
+            ])
+
 
         with working_dir('spack-build', create=True):
             cmake('..', *options)

From eec50b524bdf9e04f9e3536bc389ce633133373b Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 16:58:14 +0100
Subject: [PATCH 093/144] minor cleanup

---
 .../builtin/packages/trilinos/package.py      | 46 ++++++++++++++-----
 1 file changed, 35 insertions(+), 11 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 3003b4ab53..b1caca96ff 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -28,6 +28,7 @@ class Trilinos(Package):
     variant('superlu-dist', default=True,  description='Compile with SuperluDist solvers')
     variant('hypre',        default=True,  description='Compile with Hypre preconditioner')
     variant('hdf5',         default=True,  description='Compile with HDF5')
+    variant('scalapack',    default=True,  description='Compile with Scalapack')
     variant('suite-sparse', default=True,  description='Compile with SuiteSparse solvers')
     variant('python',       default=True,  description='Build python wrappers')
     variant('shared',       default=True,  description='Enables the build of shared libraries')
@@ -110,13 +111,6 @@ def install(self, spec, prefix):
             '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
             '-DTrilinos_ENABLE_Fortran=ON'
         ])
-        # FIXME:
-        # VerifyFortranC test of CMake does not contain -lgfortran and thus fails.
-        # This could be GCC/CMake related, but appears at least on OSX with Clang@7.0.2 and GNU Fortran@5.3.0
-        #if sys.platform == 'darwin':
-        #    options.extend([
-        #        '-DTrilinos_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=TRUE'
-        #    ])
 
         # for build-debug only:
         #options.extend([
@@ -135,6 +129,11 @@ def install(self, spec, prefix):
                 '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
                 '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
             ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_Cholmod:BOOL=OFF',
+                '-DTPL_ENABLE_UMFPACK:BOOL=OFF',
+            ])
 
         # metis / parmetis
         if '+parmetis' in spec: # metis is required, see variants_check()
@@ -148,6 +147,11 @@ def install(self, spec, prefix):
                 '-DParMETIS_LIBRARY_NAMES=parmetis;metis',
                 '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include
             ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_METIS:BOOL=OFF',
+                '-DTPL_ENABLE_ParMETIS:BOOL=OFF',
+            ])
 
         # mumps
         if '+mumps' in spec:
@@ -156,12 +160,22 @@ def install(self, spec, prefix):
                 '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
                 '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
             ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_MUMPS:BOOL=OFF',
+            ])
 
         # scalapack
-        options.extend([
-            '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
-            '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
-        ])
+        if '+scalapack' in spec:
+            options.extend([
+                '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
+                '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
+            ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_SCALAPACK:BOOL=OFF',
+            ])
+
 
         # superlu-dist:
         if '+superlu-dist' in spec:
@@ -181,12 +195,22 @@ def install(self, spec, prefix):
                 options.extend([
                     '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
                 ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_SuperLUDist:BOOL=OFF',
+            ])
+
 
         # python
         if '~python' in spec:
             options.extend([
                 '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF'
             ])
+        else:
+            options.extend([
+                '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON'
+            ])
+
 
         # disable due to compiler / config errors:
         options.extend([

From 6699399e5191004ed924b9a8916ec1ae61223000 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 17:00:42 +0100
Subject: [PATCH 094/144] add when to depends_on scalapack

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index b1caca96ff..8b66405137 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -49,7 +49,7 @@ class Trilinos(Package):
     depends_on('netcdf+mpi')
     depends_on('parmetis',when='+parmetis')
     depends_on('mumps+metis+parmetis+shared',when='+mumps') # build errors with static libs
-    depends_on('scalapack')
+    depends_on('scalapack',when='+scalapack')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre',when='+hypre')
     depends_on('hdf5+mpi',when='+hdf5')

From 497adc3b42191c000323c55aae5da32fab901265 Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Fri, 25 Mar 2016 22:45:19 -0400
Subject: [PATCH 095/144] Added new version; old versions don't work with
 Python3.

---
 var/spack/repos/builtin/packages/py-cython/package.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py
index 68eb735ad9..4d728fa8fb 100644
--- a/var/spack/repos/builtin/packages/py-cython/package.py
+++ b/var/spack/repos/builtin/packages/py-cython/package.py
@@ -3,10 +3,13 @@
 class PyCython(Package):
     """The Cython compiler for writing C extensions for the Python language."""
     homepage = "https://pypi.python.org/pypi/cython"
-    url      = "https://pypi.python.org/packages/source/C/Cython/cython-0.22.tar.gz"
+    url      = "https://pypi.python.org/packages/source/C/Cython/Cython-0.22.tar.gz"
 
-    version('0.21.2', 'd21adb870c75680dc857cd05d41046a4')
+    version('0.23.4', '157df1f69bcec6b56fd97e0f2e057f6e')
+
+    # These versions contain illegal Python3 code...
     version('0.22', '1ae25add4ef7b63ee9b4af697300d6b6')
+    version('0.21.2', 'd21adb870c75680dc857cd05d41046a4')
 
     extends('python')
 

From f603c82e814ebc59ba03b0b83be86f1a4bfcbd94 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sat, 26 Mar 2016 18:43:55 +0100
Subject: [PATCH 096/144] qualify Amesos link errors

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 8b66405137..0ba7a51b8b 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -48,7 +48,7 @@ class Trilinos(Package):
     depends_on('mpi')
     depends_on('netcdf+mpi')
     depends_on('parmetis',when='+parmetis')
-    depends_on('mumps+metis+parmetis+shared',when='+mumps') # build errors with static libs
+    depends_on('mumps+metis+parmetis+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
     depends_on('scalapack',when='+scalapack')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre',when='+hypre')

From 965ce633c311e2bcb765f5e9900f0da6205f9c23 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sat, 26 Mar 2016 18:51:59 +0100
Subject: [PATCH 097/144] cleanup variants

---
 .../builtin/packages/trilinos/package.py      | 40 ++++++-------------
 1 file changed, 13 insertions(+), 27 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 0ba7a51b8b..48bffc65e0 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -22,13 +22,11 @@ class Trilinos(Package):
     version('11.14.2', 'a43590cf896c677890d75bfe75bc6254')
     version('11.14.1', '40febc57f76668be8b6a77b7607bb67f')
 
-    variant('metis',        default=True,  description='Compile with METIS')
-    variant('parmetis',     default=True,  description='Compile with ParMETIS')
+    variant('metis',        default=True,  description='Compile with METIS and ParMETIS')
     variant('mumps',        default=True,  description='Compile with support for MUMPS solvers')
     variant('superlu-dist', default=True,  description='Compile with SuperluDist solvers')
     variant('hypre',        default=True,  description='Compile with Hypre preconditioner')
     variant('hdf5',         default=True,  description='Compile with HDF5')
-    variant('scalapack',    default=True,  description='Compile with Scalapack')
     variant('suite-sparse', default=True,  description='Compile with SuiteSparse solvers')
     variant('python',       default=True,  description='Build python wrappers')
     variant('shared',       default=True,  description='Enables the build of shared libraries')
@@ -47,9 +45,9 @@ class Trilinos(Package):
     # MPI related dependencies
     depends_on('mpi')
     depends_on('netcdf+mpi')
-    depends_on('parmetis',when='+parmetis')
-    depends_on('mumps+metis+parmetis+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
-    depends_on('scalapack',when='+scalapack')
+    depends_on('parmetis',when='+metis')
+    depends_on('mumps+mpi+metis+parmetis+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
+    depends_on('scalapack',when='+mumps')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre',when='+hypre')
     depends_on('hdf5+mpi',when='+hdf5')
@@ -60,11 +58,8 @@ class Trilinos(Package):
 
     # check that the combination of variants makes sense
     def variants_check(self):
-        if '+parmetis' in self.spec and '+metis' not in self.spec:
-            raise RuntimeError('You cannot use the variant parmetis without metis')
-
-        if '+mumps' in self.spec and '+parmetis' not in self.spec:
-            raise RuntimeError('You cannot use the variant mumps without parmetis')
+        if '+mumps' in self.spec and '+metis' not in self.spec:
+            raise RuntimeError('You cannot use the variant mumps without metis')
 
         if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'):
             # For Trilinos v11 we need to force SuperLUDist=OFF,
@@ -136,7 +131,7 @@ def install(self, spec, prefix):
             ])
 
         # metis / parmetis
-        if '+parmetis' in spec: # metis is required, see variants_check()
+        if '+metis' in spec:
             options.extend([
                 '-DTPL_ENABLE_METIS:BOOL=ON',
                 '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib,
@@ -153,30 +148,21 @@ def install(self, spec, prefix):
                 '-DTPL_ENABLE_ParMETIS:BOOL=OFF',
             ])
 
-        # mumps
+        # mumps / scalapack
         if '+mumps' in spec:
             options.extend([
                 '-DTPL_ENABLE_MUMPS:BOOL=ON',
                 '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
-                '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
-            ])
-        else:
-            options.extend([
-                '-DTPL_ENABLE_MUMPS:BOOL=OFF',
-            ])
-
-        # scalapack
-        if '+scalapack' in spec:
-            options.extend([
+                '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord', # order is important!
                 '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
                 '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
             ])
         else:
             options.extend([
+                '-DTPL_ENABLE_MUMPS:BOOL=OFF',
                 '-DTPL_ENABLE_SCALAPACK:BOOL=OFF',
             ])
 
-
         # superlu-dist:
         if '+superlu-dist' in spec:
             # Amesos, conflicting types of double and complex SLU_D
@@ -202,13 +188,13 @@ def install(self, spec, prefix):
 
 
         # python
-        if '~python' in spec:
+        if '+python' in spec:
             options.extend([
-                '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF'
+                '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON'
             ])
         else:
             options.extend([
-                '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON'
+                '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF'
             ])
 
 

From 11ca06b1045283e2c89dc84a91ceb88fcadb6163 Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Sat, 26 Mar 2016 20:35:34 -0400
Subject: [PATCH 098/144] Added new py-cython version

---
 var/spack/repos/builtin/packages/py-cython/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py
index 4d728fa8fb..072355026e 100644
--- a/var/spack/repos/builtin/packages/py-cython/package.py
+++ b/var/spack/repos/builtin/packages/py-cython/package.py
@@ -5,6 +5,7 @@ class PyCython(Package):
     homepage = "https://pypi.python.org/pypi/cython"
     url      = "https://pypi.python.org/packages/source/C/Cython/Cython-0.22.tar.gz"
 
+    version('0.23.5', '66b62989a67c55af016c916da36e7514')
     version('0.23.4', '157df1f69bcec6b56fd97e0f2e057f6e')
 
     # These versions contain illegal Python3 code...

From 9b130e1d199bcff10903e981bd7592ed941d0107 Mon Sep 17 00:00:00 2001
From: citibeth <rpf2116@columbia.edu>
Date: Sat, 26 Mar 2016 20:42:35 -0400
Subject: [PATCH 099/144] Added googletest package.

---
 .../builtin/packages/googletest/package.py    | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/googletest/package.py

diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py
new file mode 100644
index 0000000000..ed27afa10c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/googletest/package.py
@@ -0,0 +1,40 @@
+# FIXME:
+# This is a template package file for Spack.  We've conveniently
+# put "FIXME" labels next to all the things you'll want to change.
+#
+# Once you've edited all the FIXME's, delete this whole message,
+# save this file, and test out your package like this:
+#
+#     spack install googletest
+#
+# You can always get back here to change things with:
+#
+#     spack edit googletest
+#
+# See the spack documentation for more information on building
+# packages.
+#
+from spack import *
+
+class Googletest(Package):
+    """Google test framework for C++.  Also called gtest."""
+    homepage = "https://github.com/google/googletest"
+    url      = "https://github.com/google/googletest/tarball/release-1.7.0"
+
+    version('1.7.0', '5eaf03ed925a47b37c8e1d559eb19bc4')
+
+    depends_on("cmake")
+
+    def install(self, spec, prefix):
+        which('cmake')('.', *std_cmake_args)
+
+        make()
+
+        # Google Test doesn't have a make install
+        # We have to do our own install here.
+	install_tree('include', prefix.include)
+
+        mkdirp(prefix.lib)
+	install('./libgtest.a', '%s' % prefix.lib)
+	install('./libgtest_main.a', '%s' % prefix.lib)
+

From a82a587b3298ffec0c11ddf1c9639c6de228fa6a Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 06:17:43 +0200
Subject: [PATCH 100/144] lower requirement on mumps

---
 var/spack/repos/builtin/packages/trilinos/package.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 48bffc65e0..e8c4bcd7e2 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -46,7 +46,7 @@ class Trilinos(Package):
     depends_on('mpi')
     depends_on('netcdf+mpi')
     depends_on('parmetis',when='+metis')
-    depends_on('mumps+mpi+metis+parmetis+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
+    depends_on('mumps+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
     depends_on('scalapack',when='+mumps')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre',when='+hypre')
@@ -58,9 +58,6 @@ class Trilinos(Package):
 
     # check that the combination of variants makes sense
     def variants_check(self):
-        if '+mumps' in self.spec and '+metis' not in self.spec:
-            raise RuntimeError('You cannot use the variant mumps without metis')
-
         if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'):
             # For Trilinos v11 we need to force SuperLUDist=OFF,
             # since only the deprecated SuperLUDist v3.3 together with an Amesos patch

From 9cff241ad52ba628a0bdad47cee98bbbf6ba5511 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 10:39:09 +0200
Subject: [PATCH 101/144] fix install name on Darwin

---
 var/spack/repos/builtin/packages/trilinos/package.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index e8c4bcd7e2..72f904d8aa 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -1,5 +1,5 @@
 from spack import *
-import os, sys
+import os, sys, glob
 
 # Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it:
 # https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111
@@ -222,3 +222,10 @@ def install(self, spec, prefix):
             # A workaround it to remove PyTrilinos from the COMPONENTS_LIST :
             if '+python' in self.spec:
                 filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)',  (r'\1\3'),  '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib)
+
+            # The shared libraries are not installed correctly on Darwin; correct this
+            if (sys.platform == 'darwin') and ('+shared' in spec):
+                fs = glob.glob(join_path(prefix.lib,"*.dylib"))
+                install_name_tool = which('install_name_tool')
+                for f in fs:
+                    install_name_tool('-id',f,f)

From 69ebc8173e1843ea570d78ac27465b0ea32c753d Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 16:04:13 +0200
Subject: [PATCH 102/144] use global tool to fix install_name

---
 var/spack/repos/builtin/packages/trilinos/package.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 72f904d8aa..6608f64ea7 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -225,7 +225,4 @@ def install(self, spec, prefix):
 
             # The shared libraries are not installed correctly on Darwin; correct this
             if (sys.platform == 'darwin') and ('+shared' in spec):
-                fs = glob.glob(join_path(prefix.lib,"*.dylib"))
-                install_name_tool = which('install_name_tool')
-                for f in fs:
-                    install_name_tool('-id',f,f)
+                fix_darwin_install_name(prefix.lib)

From cc42391e0fa6eda490c4aeffcbfbae584f077db3 Mon Sep 17 00:00:00 2001
From: citibeth <rpf2116@columbia.edu>
Date: Sun, 27 Mar 2016 11:06:10 -0400
Subject: [PATCH 103/144] Added py-netcdf

---
 .../repos/builtin/packages/py-netcdf/package.py  | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-netcdf/package.py

diff --git a/var/spack/repos/builtin/packages/py-netcdf/package.py b/var/spack/repos/builtin/packages/py-netcdf/package.py
new file mode 100644
index 0000000000..7faa15ad25
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-netcdf/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class PyNetcdf(Package):
+    """Python interface to the netCDF Library."""
+    homepage = "http://unidata.github.io/netcdf4-python"
+    url      = "https://github.com/Unidata/netcdf4-python/tarball/v1.2.3.1rel"
+
+    version('1.2.3.1', '4fc4320d4f2a77b894ebf8da1c9895af')
+
+    extends('python')
+    depends_on('py-numpy')
+    depends_on('py-cython')
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

From 439d3b3ddb4e53721b216bd19bec1e8fa16faf89 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 17:38:25 +0200
Subject: [PATCH 104/144] mumps: add install_name / soname

---
 var/spack/repos/builtin/packages/mumps/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index b295857ab5..26440ab7c8 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -113,13 +113,13 @@ def write_makefile_inc(self):
                 # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew)
                 makefile_conf.extend([
                     'LIBEXT=.dylib',
-                    'AR=%s -dynamiclib -undefined dynamic_lookup -o ' % os.environ['FC'],
+                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib),
                     'RANLIB=echo'
                 ])
             else:
                 makefile_conf.extend([
                     'LIBEXT=.so',
-                    'AR=$(FL) -shared -o',
+                    'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,
                     'RANLIB=echo'
                 ])
         else:

From b0b882cbb3d903a85413acb0439a02d6ac9e26fc Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 26 Mar 2016 00:56:19 -0700
Subject: [PATCH 105/144] Speed up directives  by skipping debug info in stack
 traversal.

- `caller_locals()` doesn't need debug info, only frame locals.
- `get_calling_module()` doesn't either.

- Changed calls to `inspect.stack()` -> `inspect.stack(0)`
---
 lib/spack/llnl/util/lang.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py
index 13d301f84e..3b4e2c8352 100644
--- a/lib/spack/llnl/util/lang.py
+++ b/lib/spack/llnl/util/lang.py
@@ -117,7 +117,8 @@ def caller_locals():
        scope.  Yes, this is some black magic, and yes it's useful
        for implementing things like depends_on and provides.
     """
-    stack = inspect.stack()
+    # Passing zero here skips line context for speed.
+    stack = inspect.stack(0)
     try:
         return stack[2][0].f_locals
     finally:
@@ -128,7 +129,8 @@ def get_calling_module_name():
     """Make sure that the caller is a class definition, and return the
        enclosing module's name.
     """
-    stack = inspect.stack()
+    # Passing zero here skips line context for speed.
+    stack = inspect.stack(0)
     try:
         # Make sure locals contain __module__
         caller_locals = stack[2][0].f_locals

From 5695e4c03d6c98fc187ec405923cd1dcf2fbdff6 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Sun, 27 Mar 2016 15:37:52 -0500
Subject: [PATCH 106/144] Wrap the long description of an environment module so
 it is more readable.

---
 lib/spack/spack/modules.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index d45fdde703..f6a11c92e3 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -278,6 +278,6 @@ def write_header(self, module_file):
         # Long description
         if self.long_description:
             module_file.write('proc ModulesHelp { } {\n')
-            doc = re.sub(r'"', '\"', self.long_description)
-            module_file.write("puts stderr \"%s\"\n" % doc)
+            for line in textwrap.wrap(self.long_description, 72):
+                module_file.write("puts stderr \"%s\"\n" % line)
             module_file.write('}\n\n')

From ccd155572fc8ef066b93424e90a74f9bb8fcf435 Mon Sep 17 00:00:00 2001
From: citibeth <rpf2116@columbia.edu>
Date: Sun, 27 Mar 2016 18:18:54 -0400
Subject: [PATCH 107/144] Removed redundant package py-libxml2.  Use libxml2
 instead.

---
 .../repos/builtin/packages/py-libxml2/package.py  | 15 ---------------
 1 file changed, 15 deletions(-)
 delete mode 100644 var/spack/repos/builtin/packages/py-libxml2/package.py

diff --git a/var/spack/repos/builtin/packages/py-libxml2/package.py b/var/spack/repos/builtin/packages/py-libxml2/package.py
deleted file mode 100644
index 59005428e4..0000000000
--- a/var/spack/repos/builtin/packages/py-libxml2/package.py
+++ /dev/null
@@ -1,15 +0,0 @@
-from spack import *
-
-class PyLibxml2(Package):
-    """A Python wrapper around libxml2."""
-    homepage = "https://xmlsoft.org/python.html"
-    url      = "ftp://xmlsoft.org/libxml2/python/libxml2-python-2.6.21.tar.gz"
-
-    version('2.6.21', '229dd2b3d110a77defeeaa73af83f7f3')
-
-    extends('python')
-    depends_on('libxml2')
-    depends_on('libxslt')
-
-    def install(self, spec, prefix):
-        python('setup.py', 'install', '--prefix=%s' % prefix)

From 7eca1284c81c3efc5a87b8a174a0974811656b3e Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 08:59:25 +0200
Subject: [PATCH 108/144] metis/parmetis/boost/oce/scalapack: correct
 install_name on Darwin via a global function.

---
 lib/spack/llnl/util/filesystem.py             | 30 ++++++++++-
 .../repos/builtin/packages/boost/package.py   | 50 ++++++++++---------
 .../repos/builtin/packages/metis/package.py   |  6 ++-
 .../packages/netlib-scalapack/package.py      |  5 ++
 .../repos/builtin/packages/oce/package.py     |  6 ++-
 .../builtin/packages/parmetis/package.py      |  6 ++-
 6 files changed, 76 insertions(+), 27 deletions(-)

diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index c4665c284c..46ca03bec4 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -27,9 +27,10 @@
            'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file',
            'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
            'set_executable', 'copy_mode', 'unset_executable_mode',
-           'remove_dead_links', 'remove_linked_tree']
+           'remove_dead_links', 'remove_linked_tree', 'fix_darwin_install_name']
 
 import os
+import glob
 import sys
 import re
 import shutil
@@ -38,6 +39,7 @@
 import getpass
 from contextlib import contextmanager, closing
 from tempfile import NamedTemporaryFile
+import subprocess
 
 import llnl.util.tty as tty
 from spack.util.compression import ALLOWED_ARCHIVE_TYPES
@@ -392,3 +394,29 @@ def remove_linked_tree(path):
             os.unlink(path)
         else:
             shutil.rmtree(path, True)
+
+def fix_darwin_install_name(path):
+    """
+    Fix install name of dynamic libraries on Darwin to have full path.
+    There are two parts of this task:
+    (i) use install_name('-id',...) to change install name of a single lib;
+    (ii) use install_name('-change',...) to change the cross linking between libs.
+    The function assumes that all libraries are in one folder and currently won't
+    follow subfolders.
+
+    Args:
+        path: directory in which .dylib files are alocated
+
+    """
+    libs = glob.glob(join_path(path,"*.dylib"))
+    for lib in libs:
+        # fix install name first:
+        subprocess.Popen(["install_name_tool", "-id",lib,lib], stdout=subprocess.PIPE).communicate()[0]
+        long_deps = subprocess.Popen(["otool", "-L",lib], stdout=subprocess.PIPE).communicate()[0].split('\n')
+        deps = [dep.partition(' ')[0][1::] for dep in long_deps[2:-1]]
+        # fix all dependencies:
+        for dep in deps:
+            for loc in libs:
+                if dep == os.path.basename(loc):
+                    subprocess.Popen(["install_name_tool", "-change",dep,loc,lib], stdout=subprocess.PIPE).communicate()[0]
+                    break
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index fb1f5daee7..82ce6fbb74 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -1,5 +1,6 @@
 from spack import *
 import spack
+import sys
 
 class Boost(Package):
     """Boost provides free peer-reviewed portable C++ source
@@ -45,34 +46,34 @@ class Boost(Package):
     version('1.34.1', '2d938467e8a448a2c9763e0a9f8ca7e5')
     version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0')
 
-    default_install_libs = set(['atomic', 
-        'chrono', 
-        'date_time', 
-        'filesystem', 
+    default_install_libs = set(['atomic',
+        'chrono',
+        'date_time',
+        'filesystem',
         'graph',
         'iostreams',
         'locale',
         'log',
-        'math', 
+        'math',
         'program_options',
-        'random', 
-        'regex', 
-        'serialization', 
-        'signals', 
-        'system', 
-        'test', 
-        'thread', 
+        'random',
+        'regex',
+        'serialization',
+        'signals',
+        'system',
+        'test',
+        'thread',
         'wave'])
 
-    # mpi/python are not installed by default because they pull in many 
-    # dependencies and/or because there is a great deal of customization 
+    # mpi/python are not installed by default because they pull in many
+    # dependencies and/or because there is a great deal of customization
     # possible (and it would be difficult to choose sensible defaults)
     default_noinstall_libs = set(['mpi', 'python'])
 
     all_libs = default_install_libs | default_noinstall_libs
 
     for lib in all_libs:
-        variant(lib, default=(lib not in default_noinstall_libs), 
+        variant(lib, default=(lib not in default_noinstall_libs),
             description="Compile with {0} library".format(lib))
 
     variant('debug', default=False, description='Switch to the debug version of Boost')
@@ -124,9 +125,9 @@ def determine_bootstrap_options(self, spec, withLibs, options):
 
         with open('user-config.jam', 'w') as f:
             compiler_wrapper = join_path(spack.build_env_path, 'c++')
-            f.write("using {0} : : {1} ;\n".format(boostToolsetId, 
+            f.write("using {0} : : {1} ;\n".format(boostToolsetId,
                 compiler_wrapper))
-            
+
             if '+mpi' in spec:
                 f.write('using mpi : %s ;\n' %
                     join_path(spec['mpi'].prefix.bin, 'mpicxx'))
@@ -155,7 +156,7 @@ def determine_b2_options(self, spec, options):
         linkTypes = ['static']
         if '+shared' in spec:
             linkTypes.append('shared')
-        
+
         threadingOpts = []
         if '+multithreaded' in spec:
             threadingOpts.append('multi')
@@ -163,12 +164,12 @@ def determine_b2_options(self, spec, options):
             threadingOpts.append('single')
         if not threadingOpts:
             raise RuntimeError("At least one of {singlethreaded, multithreaded} must be enabled")
-        
+
         options.extend([
             'toolset=%s' % self.determine_toolset(spec),
             'link=%s' % ','.join(linkTypes),
             '--layout=tagged'])
-        
+
         return threadingOpts
 
     def install(self, spec, prefix):
@@ -177,14 +178,14 @@ def install(self, spec, prefix):
             if "+{0}".format(lib) in spec:
                 withLibs.append(lib)
         if not withLibs:
-            # if no libraries are specified for compilation, then you dont have 
+            # if no libraries are specified for compilation, then you dont have
             # to configure/build anything, just copy over to the prefix directory.
             src = join_path(self.stage.source_path, 'boost')
             mkdirp(join_path(prefix, 'include'))
             dst = join_path(prefix, 'include', 'boost')
             install_tree(src, dst)
             return
-    
+
         # to make Boost find the user-config.jam
         env['BOOST_BUILD_PATH'] = './'
 
@@ -207,4 +208,7 @@ def install(self, spec, prefix):
         # Boost.MPI if the threading options are not separated.
         for threadingOpt in threadingOpts:
             b2('install', 'threading=%s' % threadingOpt, *b2_options)
-        
+
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin') and ('+shared' in spec):
+            fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index 68b9f6fd30..9301135f9f 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-import glob
+import glob,sys
 
 class Metis(Package):
     """
@@ -90,3 +90,7 @@ def install(self, spec, prefix):
             fs = glob.glob(join_path(source_directory,'GKlib',"*.h"))
             for f in fs:
                 install(f, GKlib_dist)
+
+            # The shared library is not installed correctly on Darwin; correct this
+            if (sys.platform == 'darwin') and ('+shared' in spec):
+                fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index c3e6822cdf..d59f8e41fe 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -41,6 +41,11 @@ def install(self, spec, prefix):
             make()
             make("install")
 
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin') and ('+shared' in spec):
+            fix_darwin_install_name(prefix.lib)
+
+
     def setup_dependent_package(self, module, dependent_spec):
         spec = self.spec
         lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py
index 06acb96736..4d5081ac9d 100644
--- a/var/spack/repos/builtin/packages/oce/package.py
+++ b/var/spack/repos/builtin/packages/oce/package.py
@@ -1,5 +1,5 @@
 from spack import *
-import platform
+import platform, sys
 
 class Oce(Package):
     """
@@ -45,3 +45,7 @@ def install(self, spec, prefix):
         cmake('.', *options)
 
         make("install/strip")
+
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin'):
+            fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index f5b8b6de91..ff4370aa4b 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-
+import sys
 
 class Parmetis(Package):
     """
@@ -83,3 +83,7 @@ def install(self, spec, prefix):
             cmake(source_directory, *options)
             make()
             make("install")
+
+            # The shared library is not installed correctly on Darwin; correct this
+            if (sys.platform == 'darwin') and ('+shared' in spec):
+                fix_darwin_install_name(prefix.lib)

From 3bd550d6a2ceb279743aae626c6a3a614519d2f5 Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Sun, 27 Mar 2016 18:27:06 -0400
Subject: [PATCH 109/144] GEOS Python extension did not compile with Python3.

---
 .../repos/builtin/packages/geos/package.py    | 24 +++++++++++++++----
 1 file changed, 20 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py
index 4a2657e32f..030703f286 100644
--- a/var/spack/repos/builtin/packages/geos/package.py
+++ b/var/spack/repos/builtin/packages/geos/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import os
 
 class Geos(Package):
     """GEOS (Geometry Engine - Open Source) is a C++ port of the Java
@@ -10,6 +11,10 @@ class Geos(Package):
     homepage = "http://trac.osgeo.org/geos/"
     url      = "http://download.osgeo.org/geos/geos-3.4.2.tar.bz2"
 
+    # Verison 3.5.0 supports Autotools and CMake
+    version('3.5.0', '136842690be7f504fba46b3c539438dd')
+
+    # Versions through 3.4.2 have CMake, but only Autotools is supported
     version('3.4.2', 'fc5df2d926eb7e67f988a43a92683bae')
     version('3.4.1', '4c930dec44c45c49cd71f3e0931ded7e')
     version('3.4.0', 'e41318fc76b5dc764a69d43ac6b18488')
@@ -21,11 +26,22 @@ class Geos(Package):
     version('3.3.4', '1bb9f14d57ef06ffa41cb1d67acb55a1')
     version('3.3.3', '8454e653d7ecca475153cc88fd1daa26')
 
-    extends('python')
-    depends_on('swig')
+#    # Python3 is not supported.
+#    variant('python', default=False, description='Enable Python support')
+
+#    extends('python', when='+python')
+#    depends_on('python', when='+python')
+#    depends_on('swig', when='+python')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix,
-                  "--enable-python")
+        args = ["--prefix=%s" % prefix]
+#        if '+python' in spec:
+#            os.environ['PYTHON'] = join_path(spec['python'].prefix, 'bin',
+#                'python' if spec['python'].version[:1][0] <= 2 else 'python3')
+#            os.environ['SWIG'] = join_path(spec['swig'].prefix, 'bin', 'swig')
+#
+#            args.append("--enable-python")
+
+        configure(*args)
         make()
         make("install")

From 9c894f59354bafd9cd45e874be599dc8535e426e Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 10:19:25 +0200
Subject: [PATCH 110/144] new package: netcdf-cxx

---
 .../repos/builtin/packages/netcdf-cxx/package.py  | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/netcdf-cxx/package.py

diff --git a/var/spack/repos/builtin/packages/netcdf-cxx/package.py b/var/spack/repos/builtin/packages/netcdf-cxx/package.py
new file mode 100644
index 0000000000..5334dfb853
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netcdf-cxx/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class NetcdfCxx(Package):
+    """C++ compatibility bindings for NetCDF"""
+    homepage = "http://www.unidata.ucar.edu/software/netcdf"
+    url      = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx-4.2.tar.gz"
+
+    version('4.2', 'd32b20c00f144ae6565d9e98d9f6204c')
+
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make("install")

From f3dd889d4462d14c9f0233540bccbf6a9720bcf0 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 28 Mar 2016 03:51:05 -0700
Subject: [PATCH 111/144] Fix bug with lib64 RPATH setting in cc.

---
 lib/spack/env/cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index c6a09724e9..17740250d1 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -293,9 +293,9 @@ for dep in "${deps[@]}"; do
     if [[ -d $dep/lib64 ]]; then
         # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
-            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+            args=("-L$dep/lib64" "-Wl,-rpath,$dep/lib64" "${args[@]}")
         elif [[ $mode = ld ]]; then
-            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+            args=("-L$dep/lib64" "-rpath" "$dep/lib64" "${args[@]}")
         fi
     fi
 done

From d8579a5b80efd8b09e5332a922dee533f2a0a55e Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 28 Mar 2016 03:51:41 -0700
Subject: [PATCH 112/144] Simplify cc: Remove old logic and add better tests.

- removed a lot of old logic that was only still needed for tests.

- Added better unit tests for dependency RPATH, -L, and -I args

- tests now check whether the compiler omits -I args in link mode.
---
 lib/spack/env/cc           | 138 ++++---------------------------------
 lib/spack/spack/test/cc.py | 127 +++++++++++++++++++++++++++++-----
 2 files changed, 123 insertions(+), 142 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 17740250d1..4217159a25 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -114,7 +114,9 @@ case "$command" in
         ;;
 esac
 
-# If any of the arguments below is present then the mode is vcheck. In vcheck mode nothing is added in terms of extra search paths or libraries
+# If any of the arguments below is present then the mode is vcheck. In
+# vcheck mode nothing is added in terms of extra search paths or
+# libraries
 if [ -z "$mode" ]; then
     for arg in "$@"; do
         if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
@@ -125,7 +127,6 @@ if [ -z "$mode" ]; then
 fi
 
 # Finish setting up the mode.
-
 if [ -z "$mode" ]; then
     mode=ccld
     for arg in "$@"; do
@@ -162,127 +163,18 @@ fi
 input_command="$@"
 args=("$@")
 
-# Dump parsed values for unit testing if asked for
-if [[ -n $SPACK_TEST_COMMAND ]]; then
-
-    #
-    # Now do real parsing of the command line args, trying hard to keep
-    # non-rpath linker arguments in the proper order w.r.t. other command line
-    # arguments.  This is important for things like groups.
-    #
-    includes=()
-    libraries=()
-    libs=()
-    rpaths=()
-    other_args=()
-
-    while [ -n "$1" ]; do
-        case "$1" in
-            -I*)
-                arg="${1#-I}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                includes+=("$arg")
-                ;;
-            -L*)
-                arg="${1#-L}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                libraries+=("$arg")
-                ;;
-            -l*)
-                arg="${1#-l}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                libs+=("$arg")
-                ;;
-            -Wl,*)
-                arg="${1#-Wl,}"
-                # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
-                if [[ $arg == -rpath=* ]]; then
-                    arg="${arg#-rpath=}"
-                    for rpath in ${arg//,/ }; do
-                        rpaths+=("$rpath")
-                    done
-                elif [[ $arg == -rpath,* ]]; then
-                    arg="${arg#-rpath,}"
-                    for rpath in ${arg//,/ }; do
-                        rpaths+=("$rpath")
-                    done
-                elif [[ $arg == -rpath ]]; then
-                    shift; arg="$1"
-                    if [[ $arg != '-Wl,'* ]]; then
-                        die "-Wl,-rpath was not followed by -Wl,*"
-                    fi
-                    arg="${arg#-Wl,}"
-                    for rpath in ${arg//,/ }; do
-                        rpaths+=("$rpath")
-                    done
-                else
-                    other_args+=("-Wl,$arg")
-                fi
-                ;;
-            -Xlinker)
-                shift; arg="$1";
-                if [[ $arg = -rpath=* ]]; then
-                    rpaths+=("${arg#-rpath=}")
-                elif [[ $arg = -rpath ]]; then
-                    shift; arg="$1"
-                    if [[ $arg != -Xlinker ]]; then
-                        die "-Xlinker -rpath was not followed by -Xlinker <arg>"
-                    fi
-                    shift; arg="$1"
-                    rpaths+=("$arg")
-                else
-                    other_args+=("-Xlinker")
-                    other_args+=("$arg")
-                fi
-                ;;
-            *)
-                other_args+=("$1")
-                ;;
-        esac
-        shift
-    done
-
-    IFS=$'\n'
-    case "$SPACK_TEST_COMMAND" in
-        dump-includes)   echo "${includes[*]}";;
-        dump-libraries)  echo "${libraries[*]}";;
-        dump-libs)       echo "${libs[*]}";;
-        dump-rpaths)     echo "${rpaths[*]}";;
-        dump-other-args) echo "${other_args[*]}";;
-        dump-all)
-            echo "INCLUDES:"
-            echo "${includes[*]}"
-            echo
-            echo "LIBRARIES:"
-            echo "${libraries[*]}"
-            echo
-            echo "LIBS:"
-            echo "${libs[*]}"
-            echo
-            echo "RPATHS:"
-            echo "${rpaths[*]}"
-            echo
-            echo "ARGS:"
-            echo "${other_args[*]}"
-            ;;
-        *)
-            die "ERROR: Unknown test command"
-            ;;
-    esac
-    exit
-fi
-
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
+    # Prepend include directories
     if [[ -d $dep/include ]]; then
         if [[ $mode = cpp || $mode = cc || $mode = as || $mode = ccld ]]; then
             args=("-I$dep/include" "${args[@]}")
         fi
     fi
 
+    # Prepend lib and RPATH directories
     if [[ -d $dep/lib ]]; then
-        # libraries+=("$dep/lib")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -290,8 +182,8 @@ for dep in "${deps[@]}"; do
         fi
     fi
 
+    # Prepend lib64 and RPATH directories
     if [[ -d $dep/lib64 ]]; then
-        # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib64" "-Wl,-rpath,$dep/lib64" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -302,18 +194,8 @@ done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-Wl,-rpath,$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-rpath" "$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
@@ -345,6 +227,14 @@ export PATH
 
 full_command=("$command" "${args[@]}")
 
+# In test command mode, write out full command for Spack tests.
+if [[ $SPACK_TEST_COMMAND = dump-args ]]; then
+    echo "${full_command[@]}"
+    exit
+elif [[ -n $SPACK_TEST_COMMAND ]]; then
+    die "ERROR: Unknown test command"
+fi
+
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py
index f3f6d4a22e..0b1aeb2a8f 100644
--- a/lib/spack/spack/test/cc.py
+++ b/lib/spack/spack/test/cc.py
@@ -28,6 +28,8 @@
 """
 import os
 import unittest
+import tempfile
+import shutil
 
 from llnl.util.filesystem import *
 import spack
@@ -55,13 +57,40 @@ def setUp(self):
         self.ld = Executable(join_path(spack.build_env_path, "ld"))
         self.cpp = Executable(join_path(spack.build_env_path, "cpp"))
 
-        os.environ['SPACK_CC'] = "/bin/mycc"
-        os.environ['SPACK_PREFIX'] = "/usr"
+        self.realcc = "/bin/mycc"
+        self.prefix = "/spack-test-prefix"
+
+        os.environ['SPACK_CC'] = self.realcc
+        os.environ['SPACK_PREFIX'] = self.prefix
         os.environ['SPACK_ENV_PATH']="test"
         os.environ['SPACK_DEBUG_LOG_DIR'] = "."
         os.environ['SPACK_COMPILER_SPEC'] = "gcc@4.4.7"
         os.environ['SPACK_SHORT_SPEC'] = "foo@1.2"
 
+        # Make some fake dependencies
+        self.tmp_deps = tempfile.mkdtemp()
+        self.dep1 = join_path(self.tmp_deps, 'dep1')
+        self.dep2 = join_path(self.tmp_deps, 'dep2')
+        self.dep3 = join_path(self.tmp_deps, 'dep3')
+        self.dep4 = join_path(self.tmp_deps, 'dep4')
+
+        mkdirp(join_path(self.dep1, 'include'))
+        mkdirp(join_path(self.dep1, 'lib'))
+
+        mkdirp(join_path(self.dep2, 'lib64'))
+
+        mkdirp(join_path(self.dep3, 'include'))
+        mkdirp(join_path(self.dep3, 'lib64'))
+
+        mkdirp(join_path(self.dep4, 'include'))
+
+        if 'SPACK_DEPENDENCIES' in os.environ:
+            del os.environ['SPACK_DEPENDENCIES']
+
+
+    def tearDown(self):
+        shutil.rmtree(self.tmp_deps, True)
+
 
     def check_cc(self, command, args, expected):
         os.environ['SPACK_TEST_COMMAND'] = command
@@ -92,6 +121,10 @@ def test_cpp_mode(self):
         self.check_cpp('dump-mode', [], "cpp")
 
 
+    def test_as_mode(self):
+        self.check_cc('dump-mode', ['-S'], "as")
+
+
     def test_ccld_mode(self):
         self.check_cc('dump-mode', [], "ccld")
         self.check_cc('dump-mode', ['foo.c', '-o', 'foo'], "ccld")
@@ -104,27 +137,85 @@ def test_ld_mode(self):
         self.check_ld('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ld")
 
 
-    def test_includes(self):
-        self.check_cc('dump-includes', test_command,
-                      "\n".join(["/test/include", "/other/include"]))
+    def test_dep_rpath(self):
+        """Ensure RPATHs for root package are added."""
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      ' '.join(test_command))
 
 
-    def test_libraries(self):
-        self.check_cc('dump-libraries', test_command,
-                      "\n".join(["/test/lib", "/other/lib"]))
+    def test_dep_include(self):
+        """Ensure a single dependency include directory is added."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep4
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-I' + self.dep4 + '/include ' +
+                      ' '.join(test_command))
 
 
-    def test_libs(self):
-        self.check_cc('dump-libs', test_command,
-                      "\n".join(["lib1", "lib2", "lib3", "lib4"]))
+    def test_dep_lib(self):
+        """Ensure a single dependency RPATH is added."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep2
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
+                      ' '.join(test_command))
 
 
-    def test_rpaths(self):
-        self.check_cc('dump-rpaths', test_command,
-                      "\n".join(["/first/rpath", "/second/rpath", "/third/rpath", "/fourth/rpath"]))
+    def test_all_deps(self):
+        """Ensure includes and RPATHs for all deps are added. """
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
+
+        # This is probably more constrained than it needs to be; it
+        # checks order within prepended args and doesn't strictly have
+        # to.  We could loosen that if it becomes necessary
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+
+                      '-I' + self.dep4 + '/include ' +
+
+                      '-L' + self.dep3 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep3 + '/lib64 ' +
+                      '-I' + self.dep3 + '/include ' +
+
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
+
+                      '-L' + self.dep1 + '/lib ' +
+                      '-Wl,-rpath,' + self.dep1 + '/lib ' +
+                      '-I' + self.dep1 + '/include ' +
+
+                      ' '.join(test_command))
 
 
-    def test_other_args(self):
-        self.check_cc('dump-other-args', test_command,
-                      "\n".join(["arg1", "-Wl,--start-group", "arg2", "arg3", "arg4",
-                                 "-Wl,--end-group", "arg5", "arg6"]))
+    def test_ld_deps(self):
+        """Ensure no (extra) -I args or -Wl, are passed in ld mode."""
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
+
+        self.check_ld('dump-args', test_command,
+                      'ld ' +
+                      '-rpath ' + self.prefix + '/lib ' +
+                      '-rpath ' + self.prefix + '/lib64 ' +
+
+                      '-L' + self.dep3 + '/lib64 ' +
+                      '-rpath ' + self.dep3 + '/lib64 ' +
+
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-rpath ' + self.dep2 + '/lib64 ' +
+
+                      '-L' + self.dep1 + '/lib ' +
+                      '-rpath ' + self.dep1 + '/lib ' +
+
+                      ' '.join(test_command))
+

From 0da545ecac1c57a04abf814c9fed4f9929726ff5 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 13:16:08 +0200
Subject: [PATCH 113/144] tell amesos that we use mumps 5

---
 .../repos/builtin/packages/trilinos/package.py    | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 6608f64ea7..90b7bff149 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -6,6 +6,9 @@
 # https://github.com/koecher/candi/blob/master/deal.II-toolchain/packages/trilinos.package
 # https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh
 # https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb
+# and some relevant documentation/examples:
+# https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html
+# https://github.com/trilinos/Trilinos/issues/175
 class Trilinos(Package):
     """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
     software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.
@@ -46,7 +49,7 @@ class Trilinos(Package):
     depends_on('mpi')
     depends_on('netcdf+mpi')
     depends_on('parmetis',when='+metis')
-    depends_on('mumps+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
+    depends_on('mumps@5.0:+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
     depends_on('scalapack',when='+mumps')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre',when='+hypre')
@@ -67,6 +70,7 @@ def variants_check(self):
     def install(self, spec, prefix):
         self.variants_check()
 
+        cxx_flags = []
         options = []
         options.extend(std_cmake_args)
 
@@ -91,7 +95,6 @@ def install(self, spec, prefix):
                         '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib,
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
-                        '-DTrilinos_CXX11_FLAGS=-std=c++11',
                         '-DTPL_ENABLE_Netcdf:BOOL=ON',
                         '-DTPL_ENABLE_HYPRE:BOOL=ON',
                         '-DTPL_ENABLE_HDF5:BOOL=ON'
@@ -154,6 +157,10 @@ def install(self, spec, prefix):
                 '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
                 '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
             ])
+            # see https://github.com/trilinos/Trilinos/blob/master/packages/amesos/README-MUMPS
+            cxx_flags.extend([
+                '-DMUMPS_5_0'
+            ])
         else:
             options.extend([
                 '-DTPL_ENABLE_MUMPS:BOOL=OFF',
@@ -194,6 +201,10 @@ def install(self, spec, prefix):
                 '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF'
             ])
 
+        # collect CXX flags:
+        options.extend([
+            '-DCMAKE_CXX_FLAGS:STRING=%s' % (' '.join(cxx_flags)),
+        ])
 
         # disable due to compiler / config errors:
         options.extend([

From 5eefca43e75d2df1c2f859d199f7bb37e7142993 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 14:35:01 +0200
Subject: [PATCH 114/144] petsc: extend variants by mumps, complex and debug

---
 .../repos/builtin/packages/petsc/package.py   | 31 ++++++++++++-------
 1 file changed, 19 insertions(+), 12 deletions(-)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 3dd117eed1..dd3d2aa162 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -17,14 +17,17 @@ class Petsc(Package):
     version('3.5.1', 'a557e029711ebf425544e117ffa44d8f')
     version('3.4.4', '7edbc68aa6d8d6a3295dd5f6c2f6979d')
 
-    variant('shared', default=True, description='Enables the build of shared libraries')
-    variant('mpi', default=True, description='Activates MPI support')
-    variant('double', default=True, description='Switches between single and double precision')
+    variant('shared',  default=True,  description='Enables the build of shared libraries')
+    variant('mpi',     default=True,  description='Activates MPI support')
+    variant('double',  default=True,  description='Switches between single and double precision')
+    variant('complex', default=False, description='Build with complex numbers')
+    variant('debug',   default=False, description='Compile in debug mode')
 
-    variant('metis', default=True, description='Activates support for metis and parmetis')
-    variant('hdf5', default=True, description='Activates support for HDF5 (only parallel)')
-    variant('boost', default=True, description='Activates support for Boost')
-    variant('hypre', default=True, description='Activates support for Hypre')
+    variant('metis',   default=True,  description='Activates support for metis and parmetis')
+    variant('hdf5',    default=True,  description='Activates support for HDF5 (only parallel)')
+    variant('boost',   default=True,  description='Activates support for Boost')
+    variant('hypre',   default=True,  description='Activates support for Hypre (only parallel)')
+    variant('mumps',   default=True,  description='Activates support for MUMPS (only parallel)')
 
     # Virtual dependencies
     depends_on('blas')
@@ -40,7 +43,10 @@ class Petsc(Package):
 
     depends_on('hdf5+mpi', when='+hdf5+mpi')
     depends_on('parmetis', when='+metis+mpi')
-    depends_on('hypre',    when='+hypre+mpi')
+    depends_on('hypre',    when='+hypre+mpi~complex') # Hypre does not support complex numbers
+
+    depends_on('mumps+mpi', when='+mumps+mpi')
+    depends_on('scalapack', when='+mumps+mpi')
 
     def mpi_dependent_options(self):
         if '~mpi' in self.spec:
@@ -55,7 +61,7 @@ def mpi_dependent_options(self):
             # If mpi is disabled (~mpi), it's an error to have any of these enabled.
             # This generates a list of any such errors.
             errors = [error_message_fmt.format(library=x)
-                      for x in ('hdf5', 'hypre', 'parmetis')
+                      for x in ('hdf5', 'hypre', 'parmetis','mumps')
                       if ('+'+x) in self.spec]
             if errors:
                 errors = ['incompatible variants given'] + errors
@@ -77,16 +83,17 @@ def mpi_dependent_options(self):
         return compiler_opts
 
     def install(self, spec, prefix):
-        options = ['--with-debugging=0',
-                   '--with-ssl=0']
+        options = ['--with-ssl=0']
         options.extend(self.mpi_dependent_options())
         options.extend([
             '--with-precision=%s' % ('double' if '+double' in spec else 'single'),
+            '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'),
             '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
+            '--with-debugging=%s' % ('1' if '+debug' in spec else '0'),
             '--with-blas-lapack-dir=%s' % spec['lapack'].prefix
         ])
         # Activates library support if needed
-        for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis'):
+        for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis','mumps','scalapack'):
             options.append(
                 '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))
             )

From dd60cc326c12bfa8434b68afec72f4b68c18a94c Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 17:52:22 +0200
Subject: [PATCH 115/144] adopt modifed superlu and hypre

---
 var/spack/repos/builtin/packages/trilinos/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 90b7bff149..b2dc8df0ea 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -52,7 +52,7 @@ class Trilinos(Package):
     depends_on('mumps@5.0:+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
     depends_on('scalapack',when='+mumps')
     depends_on('superlu-dist',when='+superlu-dist')
-    depends_on('hypre',when='+hypre')
+    depends_on('hypre~internal-superlu',when='+hypre')
     depends_on('hdf5+mpi',when='+hdf5')
 
     depends_on('python',when='+python') #  Needs py-numpy activated
@@ -179,7 +179,7 @@ def install(self, spec, prefix):
             options.extend([
                 '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
                 '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib,
-                '-DSuperLUDist_INCLUDE_DIRS=%s/superlu_dist' % spec['superlu-dist'].prefix.include # superlu_dist and superlu have the same header names :-( In order to avoid conflicts, try to keep "dist" version headers in a subfolder
+                '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
             ])
             if spec.satisfies('^superlu-dist@4.0:'):
                 options.extend([

From 207215980b05e4916e05ded8b05044b3edbe92c0 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 17:54:27 +0200
Subject: [PATCH 116/144] make hypre and hdf5 be ON/OFF

---
 var/spack/repos/builtin/packages/trilinos/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index b2dc8df0ea..eb3bd1e0ee 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -96,8 +96,8 @@ def install(self, spec, prefix):
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
                         '-DTPL_ENABLE_Netcdf:BOOL=ON',
-                        '-DTPL_ENABLE_HYPRE:BOOL=ON',
-                        '-DTPL_ENABLE_HDF5:BOOL=ON'
+                        '-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'),,
+                        '-DTPL_ENABLE_HDF5:BOOL=%s' % ('ON' if '+hdf5' in spec else 'OFF'),
                         ])
 
         # Fortran lib

From 4e87cf9d7492133d30675a64703b91ec6992ca00 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 18:00:34 +0200
Subject: [PATCH 117/144] fix extra comma

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index eb3bd1e0ee..71c0be61c3 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -96,7 +96,7 @@ def install(self, spec, prefix):
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
                         '-DTPL_ENABLE_Netcdf:BOOL=ON',
-                        '-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'),,
+                        '-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'),
                         '-DTPL_ENABLE_HDF5:BOOL=%s' % ('ON' if '+hdf5' in spec else 'OFF'),
                         ])
 

From 09e77812b67d92094bea8dae54617e3e02ebaa61 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 17:49:20 +0200
Subject: [PATCH 118/144] fix installation of superlu_dist headers and add it
 as a dependency to petsc; add a variant to hypre to disable internal superlu

---
 .../repos/builtin/packages/hypre/package.py   |  5 +++++
 .../repos/builtin/packages/petsc/package.py   | 21 ++++++++++++++++---
 .../builtin/packages/superlu-dist/package.py  | 11 +++++-----
 3 files changed, 29 insertions(+), 8 deletions(-)

diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 8d93d48d1f..0e99553293 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -14,6 +14,8 @@ class Hypre(Package):
 
     # hypre does not know how to build shared libraries on Darwin
     variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)")
+    # SuperluDist have conflicting headers with those in Hypre
+    variant('internal-superlu', default=True, description="Use internal Superlu routines")
 
     depends_on("mpi")
     depends_on("blas")
@@ -38,6 +40,9 @@ def install(self, spec, prefix):
         if '+shared' in self.spec:
             configure_args.append("--enable-shared")
 
+        if '~internal-superlu' in self.spec:
+            configure_args.append("--without-superlu")
+
         # Hypre's source is staged under ./src so we'll have to manually
         # cd into it.
         with working_dir("src"):
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index dd3d2aa162..e9b7c8a732 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -28,6 +28,7 @@ class Petsc(Package):
     variant('boost',   default=True,  description='Activates support for Boost')
     variant('hypre',   default=True,  description='Activates support for Hypre (only parallel)')
     variant('mumps',   default=True,  description='Activates support for MUMPS (only parallel)')
+    variant('superlu-dist', default=True, description='Activates support for SuperluDist (only parallel)')
 
     # Virtual dependencies
     depends_on('blas')
@@ -43,8 +44,11 @@ class Petsc(Package):
 
     depends_on('hdf5+mpi', when='+hdf5+mpi')
     depends_on('parmetis', when='+metis+mpi')
-    depends_on('hypre',    when='+hypre+mpi~complex') # Hypre does not support complex numbers
-
+    # Hypre does not support complex numbers.
+    # Also PETSc prefer to build it without internal superlu, likely due to conflict in headers
+    # see https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py
+    depends_on('hypre~internal-superlu', when='+hypre+mpi~complex')
+    depends_on('superlu-dist', when='+superlu-dist+mpi')
     depends_on('mumps+mpi', when='+mumps+mpi')
     depends_on('scalapack', when='+mumps+mpi')
 
@@ -61,7 +65,7 @@ def mpi_dependent_options(self):
             # If mpi is disabled (~mpi), it's an error to have any of these enabled.
             # This generates a list of any such errors.
             errors = [error_message_fmt.format(library=x)
-                      for x in ('hdf5', 'hypre', 'parmetis','mumps')
+                      for x in ('hdf5', 'hypre', 'parmetis','mumps','superlu-dist')
                       if ('+'+x) in self.spec]
             if errors:
                 errors = ['incompatible variants given'] + errors
@@ -101,6 +105,17 @@ def install(self, spec, prefix):
                 options.append(
                     '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix)
                 )
+        # PETSc does not pick up SuperluDist from the dir as they look for superlu_dist_4.1.a
+        if 'superlu-dist' in spec:
+            options.extend([
+                '--with-superlu_dist-include=%s' % spec['superlu-dist'].prefix.include,
+                '--with-superlu_dist-lib=%s' % join_path(spec['superlu-dist'].prefix.lib, 'libsuperlu_dist.a'),
+                '--with-superlu_dist=1'
+            ])
+        else:
+            options.append(
+                '--with-superlu_dist=0'
+            )
 
         configure('--prefix=%s' % prefix, *options)
 
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index 9a94de8ba5..ddcb7f9225 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import glob
 
 class SuperluDist(Package):
     """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines."""
@@ -52,13 +53,13 @@ def install(self, spec, prefix):
         # system "make"
 
         # need to install by hand
-        headers_location = join_path(self.prefix.include,'superlu_dist')
+        headers_location = self.prefix.include
         mkdirp(headers_location)
         mkdirp(prefix.lib)
-        # FIXME: fetch all headers in the folder automatically
-        for header in ['Cnames.h','cublas_utils.h','dcomplex.h','html_mainpage.h','machines.h','old_colamd.h','psymbfact.h','superlu_ddefs.h','superlu_defs.h','superlu_enum_consts.h','superlu_zdefs.h','supermatrix.h','util_dist.h']:
-            superludist_header = join_path(self.stage.source_path, 'SRC/',header)
-            install(superludist_header, headers_location)
+
+        headers = glob.glob(join_path(self.stage.source_path, 'SRC','*.h'))
+        for h in headers:
+            install(h,headers_location)
 
         superludist_lib = join_path(self.stage.source_path, 'lib/libsuperlu_dist.a')
         install(superludist_lib,self.prefix.lib)

From a14527ec0619151d6defc909a46aefd2a9378cb7 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 28 Mar 2016 15:34:25 -0700
Subject: [PATCH 119/144] Add command to compiler input log.

---
 lib/spack/env/cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 4217159a25..68cd8514f4 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -241,7 +241,7 @@ fi
 if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command" >> $input_log
+    echo "$command $input_command" >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 

From f9bcce6a683b1d948190b9927254e3ee29d3606c Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 29 Mar 2016 09:19:24 +0200
Subject: [PATCH 120/144] turn off python by default

---
 var/spack/repos/builtin/packages/trilinos/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 71c0be61c3..0ab4addd52 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -31,7 +31,8 @@ class Trilinos(Package):
     variant('hypre',        default=True,  description='Compile with Hypre preconditioner')
     variant('hdf5',         default=True,  description='Compile with HDF5')
     variant('suite-sparse', default=True,  description='Compile with SuiteSparse solvers')
-    variant('python',       default=True,  description='Build python wrappers')
+    # not everyone has py-numpy activated, keep it disabled by default to avoid configure errors
+    variant('python',       default=False, description='Build python wrappers')
     variant('shared',       default=True,  description='Enables the build of shared libraries')
     variant('debug',        default=False, description='Builds a debug version of the libraries')
 
@@ -55,7 +56,7 @@ class Trilinos(Package):
     depends_on('hypre~internal-superlu',when='+hypre')
     depends_on('hdf5+mpi',when='+hdf5')
 
-    depends_on('python',when='+python') #  Needs py-numpy activated
+    depends_on('python',when='+python')
 
     patch('umfpack_from_suitesparse.patch')
 

From 7753d823cbe1d1983957fb948bf095d624d76b7c Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 29 Mar 2016 09:27:55 +0200
Subject: [PATCH 121/144] add a comment on static mumps

---
 var/spack/repos/builtin/packages/trilinos/package.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 0ab4addd52..6223848c68 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -7,7 +7,6 @@
 # https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh
 # https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb
 # and some relevant documentation/examples:
-# https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html
 # https://github.com/trilinos/Trilinos/issues/175
 class Trilinos(Package):
     """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
@@ -50,7 +49,14 @@ class Trilinos(Package):
     depends_on('mpi')
     depends_on('netcdf+mpi')
     depends_on('parmetis',when='+metis')
-    depends_on('mumps@5.0:+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
+    # Trilinos' Tribits config system is limited which makes it
+    # very tricky to link Amesos with static MUMPS, see
+    # https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html
+    # One could work it out by getting linking flags from mpif90 --showme:link (or alike)
+    # and adding results to -DTrilinos_EXTRA_LINK_FLAGS
+    # together with Blas and Lapack and ScaLAPACK and Blacs and -lgfortran and
+    # it may work at the end. But let's avoid all this by simply using shared libs
+    depends_on('mumps@5.0:+mpi+shared',when='+mumps')
     depends_on('scalapack',when='+mumps')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre~internal-superlu',when='+hypre')

From 63c3feb79e7e4022e5565deb9f2749fa9732e7d2 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 29 Mar 2016 09:41:57 +0200
Subject: [PATCH 122/144] minor fixes to hypre and muparser on Linux

---
 var/spack/repos/builtin/packages/hypre/package.py    | 3 +++
 var/spack/repos/builtin/packages/muparser/package.py | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 0e99553293..4b915daa68 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -42,6 +42,9 @@ def install(self, spec, prefix):
 
         if '~internal-superlu' in self.spec:
             configure_args.append("--without-superlu")
+            # MLI and FEI do not build without superlu on Linux
+            configure_args.append("--without-mli")
+            configure_args.append("--without-fei")
 
         # Hypre's source is staged under ./src so we'll have to manually
         # cd into it.
diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py
index a1a9ff90e5..19ca8ce287 100644
--- a/var/spack/repos/builtin/packages/muparser/package.py
+++ b/var/spack/repos/builtin/packages/muparser/package.py
@@ -14,5 +14,5 @@ def install(self, spec, prefix):
 
         configure(*options)
 
-        make()
+        make(parallel=False)
         make("install")

From f80e839ff48809a5ba8b7343d2378133a3fbce82 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 29 Mar 2016 02:58:05 -0700
Subject: [PATCH 123/144] Handle Darwin's ld -r option properly

- ld -r doesn't work with RPATH on OS X.

- for GNU ld, the -r option only means 'relocatable',
  and doesn't affect RPATH.

- This adds special handling to omit RPATHs for ld -r on OS X
---
 lib/spack/env/cc | 35 +++++++++++++++++++++++++++--------
 1 file changed, 27 insertions(+), 8 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 68cd8514f4..2eb6f46afe 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -85,6 +85,10 @@ done
 #    ccld    compile & link
 #    vcheck  version check
 #
+# Depending on the mode, we may or may not add extra rpaths.
+# This variable controls whether they are added.
+add_rpaths=true
+
 command=$(basename "$0")
 case "$command" in
     cc|c89|c99|gcc|clang|icc|pgcc|xlc)
@@ -108,6 +112,17 @@ case "$command" in
         ;;
     ld)
         mode=ld
+
+        # Darwin's linker has a -r argument that merges object files
+        # together. It doesn't work with -rpath.
+        if [[ $OSTYPE = darwin* ]]; then
+            for arg in "$@"; do
+                if [ "$arg" = -r ]; then
+                    add_rpaths=false
+                    break
+	            fi
+            done
+        fi
         ;;
     *)
         die "Unkown compiler: $command"
@@ -176,27 +191,31 @@ for dep in "${deps[@]}"; do
     # Prepend lib and RPATH directories
     if [[ -d $dep/lib ]]; then
         if [[ $mode = ccld ]]; then
-            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+            $add_rpaths && args=("-Wl,-rpath,$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
-            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+            $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
         fi
     fi
 
     # Prepend lib64 and RPATH directories
     if [[ -d $dep/lib64 ]]; then
         if [[ $mode = ccld ]]; then
-            args=("-L$dep/lib64" "-Wl,-rpath,$dep/lib64" "${args[@]}")
+            $add_rpaths && args=("-Wl,-rpath,$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
         elif [[ $mode = ld ]]; then
-            args=("-L$dep/lib64" "-rpath" "$dep/lib64" "${args[@]}")
+            $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
         fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
-    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
+    $add_rpaths && args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
-    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
+    $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
 #
@@ -241,8 +260,8 @@ fi
 if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$command $input_command" >> $input_log
-    echo "$mode       ${full_command[@]}" >> $output_log
+    echo "[$mode] $command $input_command" >> $input_log
+    echo "[$mode] ${full_command[@]}" >> $output_log
 fi
 
 exec "${full_command[@]}"

From ccc1b23bea57a9c8a31ab1f4e9b739b54440466b Mon Sep 17 00:00:00 2001
From: Patrick Gartung <gartung@fnal.gov>
Date: Mon, 28 Mar 2016 16:28:29 -0500
Subject: [PATCH 124/144] this allows gcc4.9.3 to build on OSX10

---
 .../packages/gcc/darwin/gcc-4.9.patch1        | 42 +++++++++++++++++++
 .../packages/gcc/darwin/gcc-4.9.patch2        | 28 +++++++++++++
 .../repos/builtin/packages/gcc/package.py     | 12 +++++-
 3 files changed, 81 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1
 create mode 100644 var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2

diff --git a/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1 b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1
new file mode 100644
index 0000000000..444e292786
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1
@@ -0,0 +1,42 @@
+diff --git a/gcc/configure b/gcc/configure
+index 9523773..52b0bf7 100755
+--- a/gcc/configure
++++ b/gcc/configure
+@@ -24884,7 +24884,7 @@ if test "${gcc_cv_as_ix86_filds+set}" = set; then :
+ else
+   gcc_cv_as_ix86_filds=no
+   if test x$gcc_cv_as != x; then
+-    $as_echo 'filds mem; fists mem' > conftest.s
++    $as_echo 'filds (%ebp); fists (%ebp)' > conftest.s
+     if { ac_try='$gcc_cv_as $gcc_cv_as_flags  -o conftest.o conftest.s >&5'
+   { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5
+   (eval $ac_try) 2>&5
+@@ -24915,7 +24915,7 @@ if test "${gcc_cv_as_ix86_fildq+set}" = set; then :
+ else
+   gcc_cv_as_ix86_fildq=no
+   if test x$gcc_cv_as != x; then
+-    $as_echo 'fildq mem; fistpq mem' > conftest.s
++    $as_echo 'fildq (%ebp); fistpq (%ebp)' > conftest.s
+     if { ac_try='$gcc_cv_as $gcc_cv_as_flags  -o conftest.o conftest.s >&5'
+   { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5
+   (eval $ac_try) 2>&5
+diff --git a/gcc/configure.ac b/gcc/configure.ac
+index 68b0ee8..bd53978 100644
+--- a/gcc/configure.ac
++++ b/gcc/configure.ac
+@@ -3869,13 +3869,13 @@ foo:	nop
+ 
+     gcc_GAS_CHECK_FEATURE([filds and fists mnemonics],
+        gcc_cv_as_ix86_filds,,,
+-       [filds mem; fists mem],,
++       [filds (%ebp); fists (%ebp)],,
+        [AC_DEFINE(HAVE_AS_IX86_FILDS, 1,
+          [Define if your assembler uses filds and fists mnemonics.])])
+ 
+     gcc_GAS_CHECK_FEATURE([fildq and fistpq mnemonics],
+        gcc_cv_as_ix86_fildq,,,
+-       [fildq mem; fistpq mem],,
++       [fildq (%ebp); fistpq (%ebp)],,
+        [AC_DEFINE(HAVE_AS_IX86_FILDQ, 1,
+          [Define if your assembler uses fildq and fistq mnemonics.])])
+ 
diff --git a/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2 b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2
new file mode 100644
index 0000000000..b065997f45
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2
@@ -0,0 +1,28 @@
+From 82f81877458ea372176eabb5de36329431dce99b Mon Sep 17 00:00:00 2001
+From: Iain Sandoe <iain@codesourcery.com>
+Date: Sat, 21 Dec 2013 00:30:18 +0000
+Subject: [PATCH] don't try to mark local symbols as no-dead-strip
+
+---
+ gcc/config/darwin.c | 5 +++++
+ 1 file changed, 5 insertions(+)
+
+diff --git a/gcc/config/darwin.c b/gcc/config/darwin.c
+index 40804b8..0080299 100644
+--- a/gcc/config/darwin.c
++++ b/gcc/config/darwin.c
+@@ -1259,6 +1259,11 @@ darwin_encode_section_info (tree decl, rtx rtl, int first ATTRIBUTE_UNUSED)
+ void
+ darwin_mark_decl_preserved (const char *name)
+ {
++  /* Actually we shouldn't mark any local symbol this way, but for now
++     this only happens with ObjC meta-data.  */
++  if (darwin_label_is_anonymous_local_objc_name (name))
++    return;
++
+   fprintf (asm_out_file, "\t.no_dead_strip ");
+   assemble_name (asm_out_file, name);
+   fputc ('\n', asm_out_file);
+-- 
+2.2.1
+
diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 232d0020df..6043b62279 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -27,6 +27,7 @@
 from contextlib import closing
 from glob import glob
 import sys
+import os
 
 class Gcc(Package):
     """The GNU Compiler Collection includes front ends for C, C++,
@@ -63,6 +64,9 @@ class Gcc(Package):
     # TODO: integrate these libraries.
     #depends_on("ppl")
     #depends_on("cloog")
+    if sys.platform == 'darwin':
+        patch('darwin/gcc-4.9.patch1', when='@4.9.3')
+        patch('darwin/gcc-4.9.patch2', when='@4.9.3')
 
     def install(self, spec, prefix):
         # libjava/configure needs a minor fix to install into spack paths.
@@ -70,6 +74,7 @@ def install(self, spec, prefix):
             string=True)
 
         enabled_languages = set(('c', 'c++', 'fortran', 'java', 'objc'))
+
         if spec.satisfies("@4.7.1:") and sys.platform != 'darwin':
             enabled_languages.add('go')
 
@@ -101,12 +106,17 @@ def install(self, spec, prefix):
             isl_options = ["--with-isl=%s" % spec['isl'].prefix]
             options.extend(isl_options)
 
+        if sys.platform == 'darwin' :
+            darwin_options = [ "--with-build-config=bootstrap-debug" ]
+            options.extend(darwin_options)
+
         build_dir = join_path(self.stage.path, 'spack-build')
         configure = Executable( join_path(self.stage.source_path, 'configure') )
         with working_dir(build_dir, create=True):
             # Rest of install is straightforward.
             configure(*options)
-            make()
+            if sys.platform == 'darwin' : make("bootstrap")
+            else: make()
             make("install")
 
         self.write_rpath_specs()

From dfc5cf288c1017ef62390489cb534848aef5a9a6 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 29 Mar 2016 04:35:41 -0700
Subject: [PATCH 125/144] Fix bug in restage

- Restage previously only removed the source directory from the stage.
- Now removes any other directories in stage as well.
---
 lib/spack/spack/fetch_strategy.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index 0d0a7db8a9..4ea87bea7e 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -289,8 +289,14 @@ def reset(self):
         if not self.archive_file:
             raise NoArchiveFileError("Tried to reset URLFetchStrategy before fetching",
                                      "Failed on reset() for URL %s" % self.url)
-        if self.stage.source_path:
-            shutil.rmtree(self.stage.source_path, ignore_errors=True)
+
+        # Remove everythigng but the archive from the stage
+        for filename in os.listdir(self.stage.path):
+            abspath = os.path.join(self.stage.path, filename)
+            if abspath != self.archive_file:
+                shutil.rmtree(abspath, ignore_errors=True)
+
+        # Expand the archive again
         self.expand()
 
     def __repr__(self):

From ad402ff85bc4150aa49fb394929b062b40b27604 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 21 Mar 2016 22:36:31 +0100
Subject: [PATCH 126/144] astyle@2.04: add new package

---
 .../repos/builtin/packages/astyle/package.py    | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/astyle/package.py

diff --git a/var/spack/repos/builtin/packages/astyle/package.py b/var/spack/repos/builtin/packages/astyle/package.py
new file mode 100644
index 0000000000..7260fd74a1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/astyle/package.py
@@ -0,0 +1,17 @@
+from spack import *
+import os
+
+class Astyle(Package):
+    """A Free, Fast, and Small Automatic Formatter for C, C++, C++/CLI, Objective-C, C#, and Java Source Code."""
+    homepage = "http://astyle.sourceforge.net/"
+    url      = "http://downloads.sourceforge.net/project/astyle/astyle/astyle%202.04/astyle_2.04_linux.tar.gz"
+
+    version('2.04', '30b1193a758b0909d06e7ee8dd9627f6')
+
+    def install(self, spec, prefix):
+
+        with working_dir('src'):
+            make('-f',
+                join_path(self.stage.source_path,'build','clang','Makefile'),
+                parallel=False)
+            install(join_path(self.stage.source_path, 'src','bin','astyle'), self.prefix.bin)

From abee9c83b440b8341be6df1f07c7c5f1bef9dd89 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <rpf2116@columbia.edu>
Date: Tue, 29 Mar 2016 17:26:34 -0400
Subject: [PATCH 127/144] Removed googletest FIXME...

---
 .../repos/builtin/packages/googletest/package.py | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py
index ed27afa10c..663b758747 100644
--- a/var/spack/repos/builtin/packages/googletest/package.py
+++ b/var/spack/repos/builtin/packages/googletest/package.py
@@ -1,19 +1,3 @@
-# FIXME:
-# This is a template package file for Spack.  We've conveniently
-# put "FIXME" labels next to all the things you'll want to change.
-#
-# Once you've edited all the FIXME's, delete this whole message,
-# save this file, and test out your package like this:
-#
-#     spack install googletest
-#
-# You can always get back here to change things with:
-#
-#     spack edit googletest
-#
-# See the spack documentation for more information on building
-# packages.
-#
 from spack import *
 
 class Googletest(Package):

From a4eff6de3faa3624a529015ea4cf5ebb1af41484 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Tue, 29 Mar 2016 17:10:49 -0600
Subject: [PATCH 128/144] + New version of cmake (3.5.1).

---
 var/spack/repos/builtin/packages/cmake/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index 1f93d39769..91a4e3b415 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -30,6 +30,7 @@ class Cmake(Package):
     homepage  = 'https://www.cmake.org'
     url       = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
 
+    version('3.5.1',    'ca051f4a66375c89d1a524e726da0296')
     version('3.5.0',    '33c5d09d4c33d4ffcc63578a6ba8777e')
     version('3.4.3',    '4cb3ff35b2472aae70f542116d616e63')
     version('3.4.0',    'cd3034e0a44256a0917e254167217fc8')

From 98bb151d85fc35389e0b76eaac90448fa688aa6c Mon Sep 17 00:00:00 2001
From: "Gregory L. Lee" <lee218@surface86.llnl.gov>
Date: Tue, 29 Mar 2016 20:25:56 -0700
Subject: [PATCH 129/144] updated geos version

---
 var/spack/repos/builtin/packages/dbus/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/dbus/package.py b/var/spack/repos/builtin/packages/dbus/package.py
index 294b0de54e..422f5a19eb 100644
--- a/var/spack/repos/builtin/packages/dbus/package.py
+++ b/var/spack/repos/builtin/packages/dbus/package.py
@@ -13,6 +13,7 @@ class Dbus(Package):
     homepage = "http://dbus.freedesktop.org/"
     url      = "http://dbus.freedesktop.org/releases/dbus/dbus-1.8.8.tar.gz"
 
+    version('1.11.2', '957a07f066f3730d2bb3ea0932f0081b')
     version('1.9.0', 'ec6895a4d5c0637b01f0d0e7689e2b36')
     version('1.8.8', 'b9f4a18ee3faa1e07c04aa1d83239c43')
     version('1.8.6', '6a08ba555d340e9dfe2d623b83c0eea8')

From 5b1ef64e31a56877f6859820ca7a79dd51f6fe84 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Wed, 30 Mar 2016 09:33:00 -0600
Subject: [PATCH 130/144] + Provide basic instructions for providing subversion
 w/o additional language bindings.

---
 .../apr-util/{apr-util.new => }/package.py    |  0
 .../packages/apr/{apr.new => }/package.py     | 13 ----------
 .../{subversion.new => }/package.py           | 24 ++++++++++++++++---
 3 files changed, 21 insertions(+), 16 deletions(-)
 rename var/spack/repos/builtin/packages/apr-util/{apr-util.new => }/package.py (100%)
 rename var/spack/repos/builtin/packages/apr/{apr.new => }/package.py (71%)
 rename var/spack/repos/builtin/packages/subversion/{subversion.new => }/package.py (78%)

diff --git a/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py b/var/spack/repos/builtin/packages/apr-util/package.py
similarity index 100%
rename from var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py
rename to var/spack/repos/builtin/packages/apr-util/package.py
diff --git a/var/spack/repos/builtin/packages/apr/apr.new/package.py b/var/spack/repos/builtin/packages/apr/package.py
similarity index 71%
rename from var/spack/repos/builtin/packages/apr/apr.new/package.py
rename to var/spack/repos/builtin/packages/apr/package.py
index 5cbbad350b..8a440766ec 100644
--- a/var/spack/repos/builtin/packages/apr/apr.new/package.py
+++ b/var/spack/repos/builtin/packages/apr/package.py
@@ -31,19 +31,6 @@ class Apr(Package):
 
     version('1.5.2',    '98492e965963f852ab29f9e61b2ad700')
 
-    #variant('ncurses', default=True, description='Enables the build of the ncurses gui')
-    #variant('qt', default=False, description='Enables the build of cmake-gui')
-    #variant('doc', default=False, description='Enables the generation of html and man page documentation')
-
-    #depends_on('ncurses', when='+ncurses')
-    #depends_on('qt', when='+qt')
-    #depends_on('python@2.7.11:', when='+doc')
-    #depends_on('py-sphinx', when='+doc')
-
-    #def url_for_version(self, version):
-    #    """Handle CMake's version-based custom URLs."""
-    #    return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % (version.up_to(2), version)
-
     def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix]
         configure(*options)
diff --git a/var/spack/repos/builtin/packages/subversion/subversion.new/package.py b/var/spack/repos/builtin/packages/subversion/package.py
similarity index 78%
rename from var/spack/repos/builtin/packages/subversion/subversion.new/package.py
rename to var/spack/repos/builtin/packages/subversion/package.py
index b1c3380238..5db1c3eb92 100644
--- a/var/spack/repos/builtin/packages/subversion/subversion.new/package.py
+++ b/var/spack/repos/builtin/packages/subversion/package.py
@@ -37,7 +37,13 @@ class Subversion(Package):
     depends_on('apr-util')
     depends_on('zlib')
     depends_on('sqlite')
+
+    # Optional: We need swig if we want the Perl, Python or Ruby
+    # bindings.
     #depends_on('swig')
+    #depends_on('python')
+    #depends_on('perl')
+    #depends_on('ruby')
 
     def install(self, spec, prefix):
 
@@ -53,7 +59,19 @@ def install(self, spec, prefix):
         configure(*options)
         make()
         make('install')
-        #make('swig-py') # python bindings
-        #make('install-swig-py')
-        #make('swig-pl') # perl bindings
+
+        # python bindings
+        #make('swig-py',
+        #     'swig-pydir=/usr/lib/python2.7/site-packages/libsvn',
+        #     'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn')
+        #make('install-swig-py',
+        #     'swig-pydir=/usr/lib/python2.7/site-packages/libsvn',
+        #     'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn')
+
+        # perl bindings
+        #make('swig-pl')
         #make('install-swig-pl')
+
+        # ruby bindings
+        #make('swig-rb')
+        #make('isntall-swig-rb')

From a7ceacb991b2a3b0caba8da41a39e045912f9e22 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Wed, 30 Mar 2016 09:47:31 -0600
Subject: [PATCH 131/144] + Changes to swig are not needed with this PR.

---
 var/spack/repos/builtin/packages/swig/package.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py
index de6055e965..8d46c4fe46 100644
--- a/var/spack/repos/builtin/packages/swig/package.py
+++ b/var/spack/repos/builtin/packages/swig/package.py
@@ -36,14 +36,11 @@ class Swig(Package):
     homepage = "http://www.swig.org"
     url      = "http://prdownloads.sourceforge.net/swig/swig-3.0.2.tar.gz"
 
-    version('3.0.8',  'c96a1d5ecb13d38604d7e92148c73c97')
-    version('3.0.2',  '62f9b0d010cef36a13a010dc530d0d41')
-    version('2.0.12', 'c3fb0b2d710cc82ed0154b91e43085a4')
+    version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41')
 
     depends_on('pcre')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
-
         make()
         make("install")

From bc309e42d8f4d5c536ea43dc01a8356bf0aba3f2 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:00:18 -0500
Subject: [PATCH 132/144] New package, py-bottleneck.

---
 .../builtin/packages/py-bottleneck/package.py      | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-bottleneck/package.py

diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py
new file mode 100644
index 0000000000..0aa4208b4d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyBottleneck(Package):
+    """Bottleneck is a collection of fast NumPy array functions written in Cython."""
+    homepage = "https://pypi.python.org/pypi/Bottleneck/1.0.0"
+    url      = "https://pypi.python.org/packages/source/B/Bottleneck/Bottleneck-1.0.0.tar.gz"
+
+    version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2')
+
+    extends('python', ignore=r'bin/f2py$')
+    depends_on('py-numpy')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

From 5c95977dccef17a3cceb741d39f94aa075a0a9c4 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:06:04 -0500
Subject: [PATCH 133/144] Added version 15.0.1

---
 var/spack/repos/builtin/packages/py-virtualenv/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py
index 037a6fc59f..09303d37b4 100644
--- a/var/spack/repos/builtin/packages/py-virtualenv/package.py
+++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py
@@ -8,6 +8,7 @@ class PyVirtualenv(Package):
 
     version('1.11.6', 'f61cdd983d2c4e6aeabb70b1060d6f49')
     version('13.0.1', '1ffc011bde6667f0e37ecd976f4934db')
+    version('15.0.1', '28d76a0d9cbd5dc42046dd14e76a6ecc')
 
     extends('python')
     depends_on('py-setuptools')

From 3b19cc303fae89eed11581d7cdfe2ab8e9d469ef Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:08:28 -0500
Subject: [PATCH 134/144] Added version 1.10.0.

---
 var/spack/repos/builtin/packages/py-six/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-six/package.py b/var/spack/repos/builtin/packages/py-six/package.py
index 05c5bd00a9..df277100f7 100644
--- a/var/spack/repos/builtin/packages/py-six/package.py
+++ b/var/spack/repos/builtin/packages/py-six/package.py
@@ -6,6 +6,7 @@ class PySix(Package):
     url      = "https://pypi.python.org/packages/source/s/six/six-1.9.0.tar.gz"
 
     version('1.9.0', '476881ef4012262dfc8adc645ee786c4')
+    version('1.10.0', '34eed507548117b2ab523ab14b2f8b55')
 
     extends('python')
     depends_on('py-setuptools')

From 9153e03e5ce5bdd5161aa4b493854208040fcf3d Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:09:47 -0500
Subject: [PATCH 135/144] Added version 20.5.

---
 var/spack/repos/builtin/packages/py-setuptools/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py
index 26c048bfd4..c6d9be1add 100644
--- a/var/spack/repos/builtin/packages/py-setuptools/package.py
+++ b/var/spack/repos/builtin/packages/py-setuptools/package.py
@@ -9,6 +9,7 @@ class PySetuptools(Package):
     version('16.0', '0ace0b96233516fc5f7c857d086aa3ad')
     version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06')
     version('19.2', '78353b1f80375ca5e088f4b4627ffe03')
+    version('20.5', 'fadc1e1123ddbe31006e5e43e927362b')
 
     extends('python')
 

From 42729d9cceafaf2382455f9e765cbc261dc41578 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:10:32 -0500
Subject: [PATCH 136/144] Added version 2016.3.

---
 var/spack/repos/builtin/packages/py-pytz/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-pytz/package.py b/var/spack/repos/builtin/packages/py-pytz/package.py
index da6311a784..060cf0cde4 100644
--- a/var/spack/repos/builtin/packages/py-pytz/package.py
+++ b/var/spack/repos/builtin/packages/py-pytz/package.py
@@ -7,6 +7,7 @@ class PyPytz(Package):
 
     version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7')
     version('2015.4', '417a47b1c432d90333e42084a605d3d8')
+    version('2016.3', 'abae92c3301b27bd8a9f56b14f52cb29')
 
     extends('python')
 

From 17075736a0ff4f8f677527664e37d55b39cbfe93 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:16:11 -0500
Subject: [PATCH 137/144] Add version 2.5.2.

---
 var/spack/repos/builtin/packages/py-dateutil/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-dateutil/package.py b/var/spack/repos/builtin/packages/py-dateutil/package.py
index 0a17f2f2d2..b67e91ace6 100644
--- a/var/spack/repos/builtin/packages/py-dateutil/package.py
+++ b/var/spack/repos/builtin/packages/py-dateutil/package.py
@@ -7,6 +7,7 @@ class PyDateutil(Package):
 
     version('2.4.0', '75714163bb96bedd07685cdb2071b8bc')
     version('2.4.2', '4ef68e1c485b09e9f034e10473e5add2')
+    version('2.5.2', 'eafe168e8f404bf384514f5116eedbb6')
 
     extends('python')
     depends_on('py-setuptools')

From 8948cb100be21034b7e4bc78b7383fa73005a03a Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:16:35 -0500
Subject: [PATCH 138/144] Add version 1.3.7.

---
 var/spack/repos/builtin/packages/py-nose/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py
index 4fee99098e..c2c2b52e03 100644
--- a/var/spack/repos/builtin/packages/py-nose/package.py
+++ b/var/spack/repos/builtin/packages/py-nose/package.py
@@ -10,6 +10,7 @@ class PyNose(Package):
 
     version('1.3.4', '6ed7169887580ddc9a8e16048d38274d')
     version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16')
+    version('1.3.7', '4d3ad0ff07b61373d2cefc89c5d0b20b')
 
     extends('python', ignore=r'bin/nosetests.*$')
     depends_on('py-setuptools')

From f3b353f5f95c21641d4bee274393879e3a068c3c Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:17:24 -0500
Subject: [PATCH 139/144] Add 'bin/f2py' to ignore so activation works.

---
 var/spack/repos/builtin/packages/py-matplotlib/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py
index 2167735fb8..45e77dd631 100644
--- a/var/spack/repos/builtin/packages/py-matplotlib/package.py
+++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py
@@ -12,7 +12,7 @@ class PyMatplotlib(Package):
     variant('gui', default=False, description='Enable GUI')
     variant('ipython', default=False, description='Enable ipython support')
 
-    extends('python', ignore=r'bin/nosetests.*$|bin/pbr$')
+    extends('python', ignore=r'bin/nosetests.*$|bin/pbr$|bin/f2py$')
 
     depends_on('py-pyside', when='+gui')
     depends_on('py-ipython', when='+ipython')

From e7ae983b41943939a20ca4964824b166833c282b Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:20:27 -0500
Subject: [PATCH 140/144] Added version 2.5. Added 'bin/f2py' to ignore so that
 activation works.

---
 var/spack/repos/builtin/packages/py-numexpr/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py
index 89f8a525b1..081a79dec6 100644
--- a/var/spack/repos/builtin/packages/py-numexpr/package.py
+++ b/var/spack/repos/builtin/packages/py-numexpr/package.py
@@ -7,8 +7,9 @@ class PyNumexpr(Package):
     url      = "https://pypi.python.org/packages/source/n/numexpr/numexpr-2.4.6.tar.gz"
 
     version('2.4.6', '17ac6fafc9ea1ce3eb970b9abccb4fbd')
+    version('2.5', '84f66cced45ba3e30dcf77a937763aaa')
 
-    extends('python')
+    extends('python', ignore=r'bin/f2py$')
     depends_on('py-numpy')
 
     def install(self, spec, prefix):

From 78be85c84f89d861086c04e4fcc4fa70c21d0a5f Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:21:17 -0500
Subject: [PATCH 141/144] Added version 1.11.0.

---
 var/spack/repos/builtin/packages/py-numpy/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index a08e612df6..40988fb44a 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -9,6 +9,7 @@ class PyNumpy(Package):
     homepage = "http://www.numpy.org/"
     url      = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz"
 
+    version('1.11.0', 'bc56fb9fc2895aa4961802ffbdb31d0b')
     version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad')
     version('1.9.2',  'a1ed53432dbcd256398898d35bc8e645')
     version('1.9.1',  '78842b73560ec378142665e712ae4ad9')

From 8ae84cfabaf22e52b01911c909b2d2342b75f3d9 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:21:38 -0500
Subject: [PATCH 142/144] This commit updates pandas and fixes dependencies.
 Added version 0.18.0. Added 'bin/f2py' to ignore so that activation works.

Removed unneccessary dependencies on
- libdrm
- libpciaccess
- llvm
- mesa

Added recommended dependencies from the pandas project site.
http://pandas.pydata.org/pandas-docs/stable/install.html
- py-numexpr
- py-bottleneck

The py-bottleneck is a new package that is also in this branch.

Removed optional dependencies
- py-scipy
- py-matplotlib

While those are most likely desired to be in the same python stack as
pandas they are not required by pandas.
---
 var/spack/repos/builtin/packages/py-pandas/package.py | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py
index 5b9997faa9..2320b1f92f 100644
--- a/var/spack/repos/builtin/packages/py-pandas/package.py
+++ b/var/spack/repos/builtin/packages/py-pandas/package.py
@@ -8,18 +8,15 @@ class PyPandas(Package):
 
     version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73')
     version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8')
+    version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6')
 
-    extends('python')
+    extends('python', ignore=r'bin/f2py$')
     depends_on('py-dateutil')
     depends_on('py-numpy')
-    depends_on('py-matplotlib')
-    depends_on('py-scipy')
     depends_on('py-setuptools')
     depends_on('py-pytz')
-    depends_on('libdrm')
-    depends_on('libpciaccess')
-    depends_on('llvm')
-    depends_on('mesa')
+    depends_on('py-numexpr')
+    depends_on('py-bottleneck')
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)

From b909da759d7b6d0443a97c13ba1c97118acd3e7a Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 30 Mar 2016 19:26:03 +0200
Subject: [PATCH 143/144] petsc: remove no longer needed -Qunused-arguments
 hack

---
 .../repos/builtin/packages/petsc/package.py     | 17 ++++-------------
 1 file changed, 4 insertions(+), 13 deletions(-)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index e9b7c8a732..5c1fc6cc92 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -71,19 +71,10 @@ def mpi_dependent_options(self):
                 errors = ['incompatible variants given'] + errors
                 raise RuntimeError('\n'.join(errors))
         else:
-            if self.compiler.name == "clang":
-                compiler_opts = [
-                    '--with-mpi=1',
-                    '--with-cc=%s  -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # Avoid confusing PETSc config by clang: warning: argument unused during compilation
-                    '--with-cxx=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
-                    '--with-fc=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
-                    '--with-f77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'),
-                ]
-            else:
-                compiler_opts = [
-                    '--with-mpi=1',
-                    '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
-                ]
+            compiler_opts = [
+                '--with-mpi=1',
+                '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
+            ]
         return compiler_opts
 
     def install(self, spec, prefix):

From 01657e6991197c999180c2fec367fc75e59fba15 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 30 Mar 2016 11:41:25 -0700
Subject: [PATCH 144/144] Make suite-sparse use spack compilers.

---
 .../repos/builtin/packages/suite-sparse/package.py   | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index b57f9967c3..c2196dcec4 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -23,4 +23,14 @@ def install(self, spec, prefix):
 
         # FIXME : this actually uses the current workaround
         # FIXME : (blas / lapack always provide libblas and liblapack as aliases)
-        make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack')
+        make('install', 'INSTALL=%s' % prefix,
+
+             # inject Spack compiler wrappers
+             'AUTOCC=no',
+             'CC=cc',
+             'CXX=c++',
+             'F77=f77',
+
+             # BLAS arguments require path to libraries
+             'BLAS=-lblas',
+             'LAPACK=-llapack')