Merge branch 'develop' of https://github.com/LLNL/spack into qa/coding_standard

README.md

@@ -59,7 +59,8 @@ can join it here:
 
 At the moment, contributing to Spack is relatively simple.  Just send us
 a [pull request](https://help.github.com/articles/using-pull-requests/).
-When you send your request, make ``develop`` the destination branch.
+When you send your request, make ``develop`` the destination branch on the
+[Spack repository](https://github.com/LLNL/spack).
 
 Spack is using a rough approximation of the [Git
 Flow](http://nvie.com/posts/a-successful-git-branching-model/)

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']

lib/spack/docs/basic_usage.rst

@@ -149,26 +149,46 @@ customize an installation in :ref:`sec-specs`.
 ``spack uninstall``
 ~~~~~~~~~~~~~~~~~~~~~
 
-To uninstall a package, type ``spack uninstall <package>``.  This will
+To uninstall a package, type ``spack uninstall <package>``.  This will ask the user for
-completely remove the directory in which the package was installed.
+confirmation, and in case will completely remove the directory in which the package was installed.
 
 .. code-block:: sh
 
    spack uninstall mpich
 
 If there are still installed packages that depend on the package to be
-uninstalled, spack will refuse to uninstall it. You can override this
+uninstalled, spack will refuse to uninstall it.
-behavior with ``spack uninstall -f <package>``, but you risk breaking
-other installed packages. In general, it is safer to remove dependent
-packages *before* removing their dependencies.
 
-A line like ``spack uninstall mpich`` may be ambiguous, if multiple
+To uninstall a package and every package that depends on it, you may give the
-``mpich`` configurations are installed.  For example, if both
+`--dependents` option.
+
+.. code-block:: sh
+
+   spack uninstall --dependents mpich
+
+will display a list of all the packages that depends on `mpich` and, upon confirmation,
+will uninstall them in the right order.
+
+A line like
+
+.. code-block:: sh
+
+   spack uninstall mpich
+
+may be ambiguous, if multiple ``mpich`` configurations are installed.  For example, if both
 ``mpich@3.0.2`` and ``mpich@3.1`` are installed, ``mpich`` could refer
 to either one. Because it cannot determine which one to uninstall,
-Spack will ask you to provide a version number to remove the
+Spack will ask you either to provide a version number to remove the
-ambiguity.  As an example, ``spack uninstall mpich@3.1`` is
+ambiguity or use the ``--all`` option to uninstall all of the matching packages.
-unambiguous in this scenario.
+
+You may force uninstall a package with the `--force` option
+
+.. code-block:: sh
+
+   spack uninstall --force mpich
+
+but you risk breaking other installed packages. In general, it is safer to remove dependent
+packages *before* removing their dependencies or use the `--dependents` option.
 
 
 Seeing installed packages
@@ -774,6 +794,34 @@ Environment modules
 Spack provides some limited integration with environment module
 systems to make it easier to use the packages it provides.
 
+
+Installing Environment Modules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In order to use Spack's generated environment modules, you must have
+installed the *Environment Modules* package.  On many Linux
+distributions, this can be installed from the vendor's repository.
+For example: ```yum install environment-modules``
+(Fedora/RHEL/CentOS).  If your Linux distribution does not have
+Environment Modules, you can get it with Spack:
+
+1. Install with::
+
+    spack install environment-modules
+
+2. Activate with::
+
+    MODULES_HOME=`spack location -i environment-modules`
+     MODULES_VERSION=`ls -1 $MODULES_HOME/Modules | head -1`
+     ${MODULES_HOME}/Modules/${MODULES_VERSION}/bin/add.modules
+
+This adds to your ``.bashrc`` (or similar) files, enabling Environment
+Modules when you log in.  It will ask your permission before changing
+any files.
+
+Spack and Environment Modules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
 You can enable shell support by sourcing some files in the
 ``/share/spack`` directory.
 

lib/spack/env/cc

@@ -39,7 +39,7 @@
 #
 
 # This is the list of environment variables that need to be set before
-# the script runs.  They are set by routines in spack.build_environment
+# the script runs. They are set by routines in spack.build_environment
 # as part of spack.package.Package.do_install().
 parameters="
 SPACK_PREFIX
@@ -50,7 +50,7 @@ SPACK_SHORT_SPEC"
 
 # The compiler input variables are checked for sanity later:
 #   SPACK_CC, SPACK_CXX, SPACK_F77, SPACK_FC
-# Debug flag is optional; set to true for debug logging:
+# Debug flag is optional; set to "TRUE" for debug logging:
 #   SPACK_DEBUG
 # Test command is used to unit test the compiler script.
 #   SPACK_TEST_COMMAND
@@ -65,12 +65,11 @@ function die {
 }
 
 for param in $parameters; do
-    if [ -z "${!param}" ]; then
+    if [[ -z ${!param} ]]; then
-        die "Spack compiler must be run from spack!  Input $param was missing!"
+        die "Spack compiler must be run from Spack! Input '$param' is missing."
     fi
 done
 
-#
 # Figure out the type of compiler, the language, and the mode so that
 # the compiler script knows what to do.
 #
@@ -78,14 +77,18 @@ done
 # 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90]
 #
 # 'mode' is set to one of:
+#    vcheck  version check
+#    cpp     preprocess
 #    cc      compile
+#    as      assemble
 #    ld      link
 #    ccld    compile & link
-#    cpp     preprocessor
+
-#    vcheck  version check
-#
 command=$(basename "$0")
 case "$command" in
+    cpp)
+        mode=cpp
+        ;;
     cc|c89|c99|gcc|clang|icc|pgcc|xlc)
         command="$SPACK_CC"
         language="C"
@@ -102,9 +105,6 @@ case "$command" in
         command="$SPACK_F77"
         language="Fortran 77"
         ;;
-    cpp)
-        mode=cpp
-        ;;
     ld)
         mode=ld
         ;;
@@ -113,10 +113,12 @@ case "$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 are present, then the mode is vcheck.
-if [ -z "$mode" ]; then
+# 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
+        if [[ $arg == -v || $arg == -V || $arg == --version || $arg == -dumpversion ]]; then
             mode=vcheck
             break
     fi
@@ -124,14 +126,16 @@ if [ -z "$mode" ]; then
 fi
 
 # Finish setting up the mode.
-
+if [[ -z $mode ]]; then
-if [ -z "$mode" ]; then
     mode=ccld
     for arg in "$@"; do
-        if [ "$arg" = -E ]; then
+        if [[ $arg == -E ]]; then
             mode=cpp
             break
-        elif [ "$arg" = -c ]; then
+        elif [[ $arg == -S ]]; then
+            mode=as
+            break
+        elif [[ $arg == -c ]]; then
             mode=cc
             break
         fi
@@ -139,175 +143,76 @@ if [ -z "$mode" ]; then
 fi
 
 # Dump the version and exit 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
 
+if [[ $mode == vcheck ]]; then
+    exec ${command} "$@"
+fi
+
+# Darwin's linker has a -r argument that merges object files together.
+# It doesn't work with -rpath.
+# This variable controls whether they are added.
+add_rpaths=true
+if [[ mode == ld && $OSTYPE == darwin* ]]; then
+    for arg in "$@"; do
+        if [[ $arg == -r ]]; then
+            add_rpaths=false
+            break
+        fi
+    done
+fi
+
 # Save original command for debug logging
 input_command="$@"
-
+args=("$@")
-if [ "$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+=("$1")
-            ;;
-    esac
-    shift
-done
-
-# Dump parsed values for unit testing if asked for
-if [ -n "$SPACK_TEST_COMMAND" ]; then
-    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[*]}"
-            ;;
-        *)
-            echo "ERROR: Unknown test command"
-            exit 1 ;;
-    esac
-    exit
-fi
 
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [ -d "$dep/include" ]; then
+    # Prepend include directories
-        includes+=("$dep/include")
+    if [[ -d $dep/include ]]; then
+        if [[ $mode == cpp || $mode == cc || $mode == as || $mode == ccld ]]; then
+            args=("-I$dep/include" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib" ]; then
+    # Prepend lib and RPATH directories
-        libraries+=("$dep/lib")
+    if [[ -d $dep/lib ]]; then
-        rpaths+=("$dep/lib")
+        if [[ $mode == ccld ]]; then
+            $add_rpaths && args=("-Wl,-rpath,$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
+        elif [[ $mode == ld ]]; then
+            $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib64" ]; then
+    # Prepend lib64 and RPATH directories
-        libraries+=("$dep/lib64")
+    if [[ -d $dep/lib64 ]]; then
-        rpaths+=("$dep/lib64")
+        if [[ $mode == ccld ]]; then
+            $add_rpaths && args=("-Wl,-rpath,$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
+        elif [[ $mode == ld ]]; then
+            $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
+        fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
-for dir in "${libraries[@]}"; do
+if [[ $mode == ccld ]]; then
-    [[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir")
+    $add_rpaths && args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
-done
+elif [[ $mode == ld ]]; then
-rpaths+=("$SPACK_PREFIX/lib")
+    $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
-rpaths+=("$SPACK_PREFIX/lib64")
-
-# Put the arguments together
-args=()
-for dir in "${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
 fi
 
 #
@@ -323,34 +228,40 @@ 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 "${env_path[@]}"; do
-    remove=""
+    addpath=true
-    for rm_dir in "${spack_env_dirs[@]}"; do
+    for env_dir in "${spack_env_dirs[@]}"; do
-        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
+        if [[ $dir == $env_dir ]]; then
-    done
+            addpath=false
-    if [ -z "$remove" ]; then
+            break
-        if [ -z "$PATH" ]; then
-            PATH="$dir"
-        else
-            PATH="$PATH:$dir"
         fi
+    done
+    if $addpath; then
+        PATH="${PATH:+$PATH:}$dir"
     fi
 done
 export PATH
 
-full_command=("$command")
+full_command=("$command" "${args[@]}")
-full_command+=("${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.
 #
-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"     >> $input_log
+    echo "[$mode] $command $input_command" >> $input_log
-    echo "$mode       ${full_command[@]}" >> $output_log
+    echo "[$mode] ${full_command[@]}" >> $output_log
 fi
 
 exec "${full_command[@]}"

lib/spack/llnl/util/filesystem.py

@@ -27,9 +27,11 @@
            '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', 'find_library_path',
+           'fix_darwin_install_name']
 
 import os
+import glob
 import sys
 import re
 import shutil
@@ -38,6 +40,7 @@
 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 +395,44 @@ 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
+
+
+def find_library_path(libname, *paths):
+    """Searches for a file called <libname> in each path.
+
+    Return:
+      directory where the library was found, if found.  None otherwise.
+
+    """
+    for path in paths:
+        library = join_path(path, libname)
+        if os.path.exists(library):
+            return path
+    return None

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

lib/spack/spack/__init__.py

@@ -136,9 +136,7 @@
     # don't add a second username if it's already unique by user.
     if not _tmp_user in path:
         tmp_dirs.append(join_path(path, '%u', 'spack-stage'))
-
+    else:
-for path in _tmp_candidates:
-    if not path in tmp_dirs:
         tmp_dirs.append(join_path(path, 'spack-stage'))
 
 # Whether spack should allow installation of unsafe versions of

lib/spack/spack/build_environment.py

@@ -59,6 +59,11 @@
 SPACK_DEBUG_LOG_DIR    = 'SPACK_DEBUG_LOG_DIR'
 
 
+# Platform-specific library suffix.
+dso_suffix = 'dylib' if sys.platform == 'darwin' else 'so'
+
+
+
 class MakeExecutable(Executable):
     """Special callable executable object for make so the user can
        specify parallel or not on a per-invocation basis.  Using
@@ -208,7 +213,7 @@ def set_module_variables_for_package(pkg, module):
     # TODO: of build dependencies, as opposed to link dependencies.
     # TODO: Currently, everything is a link dependency, but tools like
     # TODO: this shouldn't be.
-    m.cmake = which("cmake")
+    m.cmake = Executable('cmake')
 
     # standard CMake arguments
     m.std_cmake_args = ['-DCMAKE_INSTALL_PREFIX=%s' % pkg.prefix,
@@ -246,6 +251,9 @@ def set_module_variables_for_package(pkg, module):
     # a Prefix object.
     m.prefix  = pkg.prefix
 
+    # Platform-specific library suffix.
+    m.dso_suffix = dso_suffix
+
 
 def get_rpaths(pkg):
     """Get a list of all the rpaths for a package."""
@@ -270,21 +278,6 @@ 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()
@@ -308,20 +301,27 @@ def setup_package(pkg):
 
     set_compiler_environment_variables(pkg, spack_env)
     set_build_environment_variables(pkg, spack_env)
-    setup_module_variables_for_dag(pkg)
 
-    # Allow dependencies to modify the module
+    # traverse in postorder so package can use vars from its dependencies
     spec = pkg.spec
-    for dependency_spec in spec.traverse(root=False):
+    for dspec in pkg.spec.traverse(order='post', root=False):
-        dpkg = dependency_spec.package
+        # If a user makes their own package repo, e.g.
-        dpkg.setup_dependent_package(pkg.module, spec)
+        # 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 = dspec.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)
 
-    # Allow dependencies to set up environment as well
+        # Allow dependencies to modify the module
-    for dependency_spec in spec.traverse(root=False):
+        dpkg = dspec.package
-        dpkg = dependency_spec.package
+        dpkg.setup_dependent_package(pkg.module, spec)
         dpkg.setup_dependent_environment(spack_env, run_env, spec)
 
-    # Allow the package to apply some settings.
+    set_module_variables_for_package(pkg, pkg.module)
     pkg.setup_environment(spack_env, run_env)
 
     # Make sure nothing's strange about the Spack environment.

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)
 

lib/spack/spack/cmd/module.py

@@ -22,21 +22,16 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
 import os
 import shutil
-import argparse
+import sys
 
 import llnl.util.tty as tty
-from llnl.util.lang import partition_list
-from llnl.util.filesystem import mkdirp
-
 import spack.cmd
+from llnl.util.filesystem import mkdirp
 from spack.modules import module_types
 from spack.util.string import *
 
-from spack.spec import Spec
-
 description ="Manipulate modules and dotkits."
 
 
@@ -98,7 +93,6 @@ def module_refresh():
             cls(spec).write()
 
 
-
 def module(parser, args):
     if args.module_command == 'refresh':
         module_refresh()

lib/spack/spack/cmd/pkg.py

@@ -77,7 +77,8 @@ def get_git():
 
 def list_packages(rev):
     git = get_git()
-    relpath = spack.packages_path[len(spack.prefix + os.path.sep):] + os.path.sep
+    pkgpath = os.path.join(spack.packages_path, 'packages')
+    relpath = pkgpath[len(spack.prefix + os.path.sep):] + os.path.sep
     output = git('ls-tree', '--full-tree', '--name-only', rev, relpath,
                  output=str)
     return sorted(line[len(relpath):] for line in output.split('\n') if line)

lib/spack/spack/cmd/stage.py

@@ -35,6 +35,9 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-n', '--no-checksum', action='store_true', dest='no_checksum',
         help="Do not check downloaded packages against checksum")
+    subparser.add_argument(
+        '-p', '--path', dest='path',
+        help="Path to stage package, does not add to spack tree")
 
     subparser.add_argument(
         'specs', nargs=argparse.REMAINDER, help="specs of packages to stage")
@@ -50,4 +53,6 @@ def stage(parser, args):
     specs = spack.cmd.parse_specs(args.specs, concretize=True)
     for spec in specs:
         package = spack.repo.get(spec)
+        if args.path:
+            package.path = args.path
         package.do_stage()

lib/spack/spack/cmd/uninstall.py

@@ -23,19 +23,33 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from __future__ import print_function
-import sys
+
 import argparse
 
 import llnl.util.tty as tty
-from llnl.util.tty.colify import colify
-
 import spack
 import spack.cmd
 import spack.repository
 from spack.cmd.find import display_specs
-from spack.package import PackageStillNeededError
 
-description="Remove an installed package"
+description = "Remove an installed package"
+
+error_message = """You can either:
+    a) Use a more specific spec, or
+    b) use spack uninstall -a to uninstall ALL matching specs.
+"""
+
+
+def ask_for_confirmation(message):
+    while True:
+        tty.msg(message + '[y/n]')
+        choice = raw_input().lower()
+        if choice == 'y':
+            break
+        elif choice == 'n':
+            raise SystemExit('Operation aborted')
+        tty.warn('Please reply either "y" or "n"')
+
 
 def setup_parser(subparser):
     subparser.add_argument(
@@ -44,10 +58,101 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-a', '--all', action='store_true', dest='all',
         help="USE CAREFULLY. Remove ALL installed packages that match each " +
-        "supplied spec. i.e., if you say uninstall libelf, ALL versions of " +
+             "supplied spec. i.e., if you say uninstall libelf, ALL versions of " +
-        "libelf are uninstalled. This is both useful and dangerous, like rm -r.")
+             "libelf are uninstalled. This is both useful and dangerous, like rm -r.")
     subparser.add_argument(
-        'packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
+        '-d', '--dependents', action='store_true', dest='dependents',
+        help='Also uninstall any packages that depend on the ones given via command line.'
+    )
+    subparser.add_argument(
+        '-y', '--yes-to-all', action='store_true', dest='yes_to_all',
+        help='Assume "yes" is the answer to every confirmation asked to the user.'
+
+    )
+    subparser.add_argument('packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
+
+
+def concretize_specs(specs, allow_multiple_matches=False, force=False):
+    """
+    Returns a list of specs matching the non necessarily concretized specs given from cli
+
+    Args:
+        specs: list of specs to be matched against installed packages
+        allow_multiple_matches : boolean (if True multiple matches for each item in specs are admitted)
+
+    Return:
+        list of specs
+    """
+    specs_from_cli = []  # List of specs that match expressions given via command line
+    has_errors = False
+    for spec in specs:
+        matching = spack.installed_db.query(spec)
+        # For each spec provided, make sure it refers to only one package.
+        # Fail and ask user to be unambiguous if it doesn't
+        if not allow_multiple_matches and len(matching) > 1:
+            tty.error("%s matches multiple packages:" % spec)
+            print()
+            display_specs(matching, long=True)
+            print()
+            has_errors = True
+
+        # No installed package matches the query
+        if len(matching) == 0 and not force:
+            tty.error("%s does not match any installed packages." % spec)
+            has_errors = True
+
+        specs_from_cli.extend(matching)
+    if has_errors:
+        tty.die(error_message)
+
+    return specs_from_cli
+
+
+def installed_dependents(specs):
+    """
+    Returns a dictionary that maps a spec with a list of its installed dependents
+
+    Args:
+        specs: list of specs to be checked for dependents
+
+    Returns:
+        dictionary of installed dependents
+    """
+    dependents = {}
+    for item in specs:
+        lst = [x for x in item.package.installed_dependents if x not in specs]
+        if lst:
+            lst = list(set(lst))
+            dependents[item] = lst
+    return dependents
+
+
+def do_uninstall(specs, force):
+    """
+    Uninstalls all the specs in a list.
+
+    Args:
+        specs: list of specs to be uninstalled
+        force: force uninstallation (boolean)
+    """
+    packages = []
+    for item in specs:
+        try:
+            # should work if package is known to spack
+            packages.append(item.package)
+        except spack.repository.UnknownPackageError as e:
+            # The package.py file has gone away -- but still
+            # want to uninstall.
+            spack.Package(item).do_uninstall(force=True)
+
+    # Sort packages to be uninstalled by the number of installed dependents
+    # This ensures we do things in the right order
+    def num_installed_deps(pkg):
+        return len(pkg.installed_dependents)
+
+    packages.sort(key=num_installed_deps)
+    for item in packages:
+        item.do_uninstall(force=force)
 
 
 def uninstall(parser, args):
@@ -56,50 +161,34 @@ def uninstall(parser, args):
 
     with spack.installed_db.write_transaction():
         specs = spack.cmd.parse_specs(args.packages)
+        # Gets the list of installed specs that match the ones give via cli
+        uninstall_list = concretize_specs(specs, args.all, args.force)  # takes care of '-a' is given in the cli
+        dependent_list = installed_dependents(uninstall_list)  # takes care of '-d'
 
-        # For each spec provided, make sure it refers to only one package.
+        # Process dependent_list and update uninstall_list
-        # Fail and ask user to be unambiguous if it doesn't
+        has_error = False
-        pkgs = []
+        if dependent_list and not args.dependents and not args.force:
-        for spec in specs:
+            for spec, lst in dependent_list.items():
-            matching_specs = spack.installed_db.query(spec)
+                tty.error("Will not uninstall %s" % spec.format("$_$@$%@$#", color=True))
-            if not args.all and len(matching_specs) > 1:
-                tty.error("%s matches multiple packages:" % spec)
-                print()
-                display_specs(matching_specs, long=True)
-                print()
-                print("You can either:")
-                print("  a) Use a more specific spec, or")
-                print("  b) use spack uninstall -a to uninstall ALL matching specs.")
-                sys.exit(1)
-
-            if len(matching_specs) == 0:
-                if args.force: continue
-                tty.die("%s does not match any installed packages." % spec)
-
-            for s in matching_specs:
-                try:
-                    # should work if package is known to spack
-                    pkgs.append(s.package)
-                except spack.repository.UnknownPackageError as e:
-                    # The package.py file has gone away -- but still
-                    # want to uninstall.
-                    spack.Package(s).do_uninstall(force=True)
-
-        # Sort packages to be uninstalled by the number of installed dependents
-        # This ensures we do things in the right order
-        def num_installed_deps(pkg):
-            return len(pkg.installed_dependents)
-        pkgs.sort(key=num_installed_deps)
-
-        # Uninstall packages in order now.
-        for pkg in pkgs:
-            try:
-                pkg.do_uninstall(force=args.force)
-            except PackageStillNeededError as e:
-                tty.error("Will not uninstall %s" % e.spec.format("$_$@$%@$#", color=True))
                 print('')
                 print("The following packages depend on it:")
-                display_specs(e.dependents, long=True)
+                display_specs(lst, long=True)
                 print('')
-                print("You can use spack uninstall -f to force this action.")
+                has_error = True
-                sys.exit(1)
+        elif args.dependents:
+            for key, lst in dependent_list.items():
+                uninstall_list.extend(lst)
+            uninstall_list = list(set(uninstall_list))
+
+        if has_error:
+            tty.die('You can use spack uninstall --dependents to uninstall these dependencies as well')
+
+        if not args.yes_to_all:
+            tty.msg("The following packages will be uninstalled : ")
+            print('')
+            display_specs(uninstall_list, long=True)
+            print('')
+            ask_for_confirmation('Do you want to proceed ? ')
+
+        # Uninstall everything on the list
+        do_uninstall(uninstall_list, args.force)

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:

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': {
+                    'enable': {
+                        '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)))
 

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):

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 *
 
@@ -56,6 +57,8 @@
 # Registry of all types of modules.  Entries created by EnvModule's metaclass
 module_types = {}
 
+CONFIGURATION = spack.config.get_config('modules')
+
 
 def print_help():
     """For use by commands to tell user how to activate shell support."""
@@ -115,7 +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':
+            if cls.name != 'env_module' and cls.name in CONFIGURATION['enable']:
                 module_types[cls.name] = cls
 
     def __init__(self, spec=None):
@@ -158,13 +161,18 @@ def write(self):
 
         # Let the extendee modify their extensions before asking for
         # package-specific modifications
-        for extendee in self.pkg.extendees:
+        spack_env = EnvironmentModifications()
-            extendee_spec = self.spec[extendee]
+        for item in self.pkg.extendees:
-            extendee_spec.package.modify_module(
+            try:
-                self.pkg.module, extendee_spec, self.spec)
+                package = self.spec[item].package
+                package.setup_dependent_package(self.pkg.module, self.spec)
+                package.setup_dependent_environment(spack_env, env, self.spec)
+            except:
+                # The extends was conditional, so it doesn't count here
+                # eg: extends('python', when='+python')
+                pass
 
         # Package-specific environment modifications
-        spack_env = EnvironmentModifications()
         self.spec.package.setup_environment(spack_env, env)
 
         # TODO : implement site-specific modifications and filters
@@ -203,7 +211,11 @@ def use_name(self):
     def remove(self):
         mod_file = self.file_name
         if os.path.exists(mod_file):
-            shutil.rmtree(mod_file, ignore_errors=True)
+            try:
+                os.remove(mod_file)  # Remove the module file
+                os.removedirs(os.path.dirname(mod_file))  # Remove all the empty directories from the leaf up
+            except OSError:
+                pass  # removedirs throws OSError on first non-empty directory found
 
 
 class Dotkit(EnvModule):
@@ -275,6 +287,6 @@ 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)
+            for line in textwrap.wrap(self.long_description, 72):
-            module_file.write("puts stderr \"%s\"\n" % doc)
+                module_file.write("puts stderr \"%s\"\n" % line)
             module_file.write('}\n\n')

lib/spack/spack/package.py

@@ -335,6 +335,9 @@ def __init__(self, spec):
         if '.' in self.name:
             self.name = self.name[self.name.rindex('.') + 1:]
 
+        # Allow custom staging paths for packages
+        self.path=None
+
         # Sanity check attributes required by Spack directives.
         spack.directives.ensure_dicts(type(self))
 
@@ -445,7 +448,8 @@ def _make_resource_stage(self, root_stage, fetcher, resource):
         resource_stage_folder = self._resource_stage(resource)
         resource_mirror = join_path(self.name, os.path.basename(fetcher.url))
         stage = ResourceStage(resource.fetcher, root=root_stage, resource=resource,
-                              name=resource_stage_folder, mirror_path=resource_mirror)
+                              name=resource_stage_folder, mirror_path=resource_mirror,
+                              path=self.path)
         return stage
 
     def _make_root_stage(self, fetcher):
@@ -455,7 +459,7 @@ def _make_root_stage(self, fetcher):
         s = self.spec
         stage_name = "%s-%s-%s" % (s.name, s.version, s.dag_hash())
         # Build the composite stage
-        stage = Stage(fetcher, mirror_path=mp, name=stage_name)
+        stage = Stage(fetcher, mirror_path=mp, name=stage_name, path=self.path)
         return stage
 
     def _make_stage(self):
@@ -709,7 +713,6 @@ def do_fetch(self, mirror_only=False):
         if spack.do_checksum and self.version in self.versions:
             self.stage.check()
 
-
     def do_stage(self, mirror_only=False):
         """Unpacks the fetched tarball, then changes into the expanded tarball
            directory."""
@@ -926,6 +929,9 @@ def build_process():
                      install(env_path, env_install_path)
                      dump_packages(self.spec, packages_dir)
 
+                # Run post install hooks before build stage is removed.
+                spack.hooks.post_install(self)
+
             # Stop timer.
             self._total_time = time.time() - start_time
             build_time = self._total_time - self._fetch_time
@@ -954,9 +960,6 @@ def build_process():
         # the database, so that we don't need to re-read from file.
         spack.installed_db.add(self.spec, self.prefix)
 
-        # Once everything else is done, run post install hooks
-        spack.hooks.post_install(self)
-
 
     def sanity_check_prefix(self):
         """This function checks whether install succeeded."""

lib/spack/spack/stage.py

@@ -89,7 +89,7 @@ class Stage(object):
     """
 
     def __init__(self, url_or_fetch_strategy,
-                 name=None, mirror_path=None, keep=False):
+                 name=None, mirror_path=None, keep=False, path=None):
         """Create a stage object.
            Parameters:
              url_or_fetch_strategy
@@ -135,7 +135,10 @@ def __init__(self, url_or_fetch_strategy,
 
         # Try to construct here a temporary name for the stage directory
         # If this is a named stage, then construct a named path.
-        self.path = join_path(spack.stage_path, self.name)
+        if path is not None:
+            self.path = path
+        else:
+            self.path = join_path(spack.stage_path, self.name)
 
         # Flag to decide whether to delete the stage folder on exit or not
         self.keep = keep

lib/spack/spack/test/__init__.py

@@ -67,7 +67,8 @@
               'namespace_trie',
               'yaml',
               'sbang',
-              'environment']
+              'environment',
+              'cmd.uninstall']
 
 
 def list_tests():

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"
+        self.realcc = "/bin/mycc"
-        os.environ['SPACK_PREFIX'] = "/usr"
+        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):
+    def test_dep_rpath(self):
-        self.check_cc('dump-includes', test_command,
+        """Ensure RPATHs for root package are added."""
-                      "\n".join(["/test/include", "/other/include"]))
+        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):
+    def test_dep_include(self):
-        self.check_cc('dump-libraries', test_command,
+        """Ensure a single dependency include directory is added."""
-                      "\n".join(["/test/lib", "/other/lib"]))
+        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):
+    def test_dep_lib(self):
-        self.check_cc('dump-libs', test_command,
+        """Ensure a single dependency RPATH is added."""
-                      "\n".join(["lib1", "lib2", "lib3", "lib4"]))
+        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):
+    def test_all_deps(self):
-        self.check_cc('dump-rpaths', test_command,
+        """Ensure includes and RPATHs for all deps are added. """
-                      "\n".join(["/first/rpath", "/second/rpath", "/third/rpath", "/fourth/rpath"]))
+        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):
+    def test_ld_deps(self):
-        self.check_cc('dump-other-args', test_command,
+        """Ensure no (extra) -I args or -Wl, are passed in ld mode."""
-                      "\n".join(["arg1", "-Wl,--start-group", "arg2", "arg3", "arg4",
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
-                                 "-Wl,--end-group", "arg5", "arg6"]))
+            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))
+

lib/spack/spack/test/cmd/uninstall.py

@@ -0,0 +1,37 @@
+import spack.test.mock_database
+
+from spack.cmd.uninstall import uninstall
+
+
+class MockArgs(object):
+    def __init__(self, packages, all=False, force=False, dependents=False):
+        self.packages = packages
+        self.all = all
+        self.force = force
+        self.dependents = dependents
+        self.yes_to_all = True
+
+
+class TestUninstall(spack.test.mock_database.MockDatabase):
+    def test_uninstall(self):
+        parser = None
+        # Multiple matches
+        args = MockArgs(['mpileaks'])
+        self.assertRaises(SystemExit, uninstall, parser, args)
+        # Installed dependents
+        args = MockArgs(['libelf'])
+        self.assertRaises(SystemExit, uninstall, parser, args)
+        # Recursive uninstall
+        args = MockArgs(['callpath'], all=True, dependents=True)
+        uninstall(parser, args)
+
+        all_specs = spack.install_layout.all_specs()
+        self.assertEqual(len(all_specs), 7)
+        # query specs with multiple configurations
+        mpileaks_specs = [s for s in all_specs if s.satisfies('mpileaks')]
+        callpath_specs = [s for s in all_specs if s.satisfies('callpath')]
+        mpi_specs = [s for s in all_specs if s.satisfies('mpi')]
+
+        self.assertEqual(len(mpileaks_specs), 0)
+        self.assertEqual(len(callpath_specs), 0)
+        self.assertEqual(len(mpi_specs),      3)

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')

lib/spack/spack/test/database.py

@@ -28,16 +28,12 @@
 """
 import os.path
 import multiprocessing
-import shutil
-import tempfile
 
 import spack
 from llnl.util.filesystem import join_path
 from llnl.util.lock import *
 from llnl.util.tty.colify import colify
-from spack.database import Database
+from spack.test.mock_database import MockDatabase
-from spack.directory_layout import YamlDirectoryLayout
-from spack.test.mock_packages_test import *
 
 
 def _print_ref_counts():
@@ -75,80 +71,7 @@ def add_rec(spec):
     colify(recs, cols=3)
 
 
-class DatabaseTest(MockPackagesTest):
+class DatabaseTest(MockDatabase):
-
-    def _mock_install(self, spec):
-        s = Spec(spec)
-        s.concretize()
-        pkg = spack.repo.get(s)
-        pkg.do_install(fake=True)
-
-
-    def _mock_remove(self, spec):
-        specs = spack.installed_db.query(spec)
-        assert(len(specs) == 1)
-        spec = specs[0]
-        spec.package.do_uninstall(spec)
-
-
-    def setUp(self):
-        super(DatabaseTest, self).setUp()
-        #
-        # TODO: make the mockup below easier.
-        #
-
-        # Make a fake install directory
-        self.install_path = tempfile.mkdtemp()
-        self.spack_install_path = spack.install_path
-        spack.install_path = self.install_path
-
-        self.install_layout = YamlDirectoryLayout(self.install_path)
-        self.spack_install_layout = spack.install_layout
-        spack.install_layout = self.install_layout
-
-        # Make fake database and fake install directory.
-        self.installed_db = Database(self.install_path)
-        self.spack_installed_db = spack.installed_db
-        spack.installed_db = self.installed_db
-
-        # make a mock database with some packages installed note that
-        # the ref count for dyninst here will be 3, as it's recycled
-        # across each install.
-        #
-        # Here is what the mock DB looks like:
-        #
-        # o  mpileaks     o  mpileaks'    o  mpileaks''
-        # |\              |\              |\
-        # | o  callpath   | o  callpath'  | o  callpath''
-        # |/|             |/|             |/|
-        # o |  mpich      o |  mpich2     o |  zmpi
-        #   |               |             o |  fake
-        #   |               |               |
-        #   |               |______________/
-        #   | .____________/
-        #   |/
-        #   o  dyninst
-        #   |\
-        #   | o  libdwarf
-        #   |/
-        #   o  libelf
-        #
-
-        # Transaction used to avoid repeated writes.
-        with spack.installed_db.write_transaction():
-            self._mock_install('mpileaks ^mpich')
-            self._mock_install('mpileaks ^mpich2')
-            self._mock_install('mpileaks ^zmpi')
-
-
-    def tearDown(self):
-        super(DatabaseTest, self).tearDown()
-        shutil.rmtree(self.install_path)
-        spack.install_path = self.spack_install_path
-        spack.install_layout = self.spack_install_layout
-        spack.installed_db = self.spack_installed_db
-
-
     def test_005_db_exists(self):
         """Make sure db cache file exists after creating."""
         index_file = join_path(self.install_path, '.spack-db', 'index.yaml')
@@ -157,7 +80,6 @@ def test_005_db_exists(self):
         self.assertTrue(os.path.exists(index_file))
         self.assertTrue(os.path.exists(lock_file))
 
-
     def test_010_all_install_sanity(self):
         """Ensure that the install layout reflects what we think it does."""
         all_specs = spack.install_layout.all_specs()

lib/spack/spack/test/install.py

@@ -64,7 +64,14 @@ def tearDown(self):
         shutil.rmtree(self.tmpdir, ignore_errors=True)
 
 
-    def test_install_and_uninstall(self):
+    def fake_fetchify(self, pkg):
+        """Fake the URL for a package so it downloads from a file."""
+        fetcher = FetchStrategyComposite()
+        fetcher.append(URLFetchStrategy(self.repo.url))
+        pkg.fetcher = fetcher
+
+
+    def ztest_install_and_uninstall(self):
         # Get a basic concrete spec for the trivial install package.
         spec = Spec('trivial_install_test_package')
         spec.concretize()
@@ -73,11 +80,7 @@ def test_install_and_uninstall(self):
         # Get the package
         pkg = spack.repo.get(spec)
 
-        # Fake the URL for the package so it downloads from a file.
+        self.fake_fetchify(pkg)
-
-        fetcher = FetchStrategyComposite()
-        fetcher.append(URLFetchStrategy(self.repo.url))
-        pkg.fetcher = fetcher
 
         try:
             pkg.do_install()
@@ -85,3 +88,17 @@ def test_install_and_uninstall(self):
         except Exception, e:
             pkg.remove_prefix()
             raise
+
+
+    def test_install_environment(self):
+        spec = Spec('cmake-client').concretized()
+
+        for s in spec.traverse():
+            self.fake_fetchify(s.package)
+
+        pkg = spec.package
+        try:
+            pkg.do_install()
+        except Exception, e:
+            pkg.remove_prefix()
+            raise

lib/spack/spack/test/mock_database.py

@@ -0,0 +1,80 @@
+import shutil
+import tempfile
+
+import spack
+from spack.spec import Spec
+from spack.database import Database
+from spack.directory_layout import YamlDirectoryLayout
+from spack.test.mock_packages_test import MockPackagesTest
+
+
+class MockDatabase(MockPackagesTest):
+    def _mock_install(self, spec):
+        s = Spec(spec)
+        s.concretize()
+        pkg = spack.repo.get(s)
+        pkg.do_install(fake=True)
+
+    def _mock_remove(self, spec):
+        specs = spack.installed_db.query(spec)
+        assert len(specs) == 1
+        spec = specs[0]
+        spec.package.do_uninstall(spec)
+
+    def setUp(self):
+        super(MockDatabase, self).setUp()
+        #
+        # TODO: make the mockup below easier.
+        #
+
+        # Make a fake install directory
+        self.install_path = tempfile.mkdtemp()
+        self.spack_install_path = spack.install_path
+        spack.install_path = self.install_path
+
+        self.install_layout = YamlDirectoryLayout(self.install_path)
+        self.spack_install_layout = spack.install_layout
+        spack.install_layout = self.install_layout
+
+        # Make fake database and fake install directory.
+        self.installed_db = Database(self.install_path)
+        self.spack_installed_db = spack.installed_db
+        spack.installed_db = self.installed_db
+
+        # make a mock database with some packages installed note that
+        # the ref count for dyninst here will be 3, as it's recycled
+        # across each install.
+        #
+        # Here is what the mock DB looks like:
+        #
+        # o  mpileaks     o  mpileaks'    o  mpileaks''
+        # |\              |\              |\
+        # | o  callpath   | o  callpath'  | o  callpath''
+        # |/|             |/|             |/|
+        # o |  mpich      o |  mpich2     o |  zmpi
+        #   |               |             o |  fake
+        #   |               |               |
+        #   |               |______________/
+        #   | .____________/
+        #   |/
+        #   o  dyninst
+        #   |\
+        #   | o  libdwarf
+        #   |/
+        #   o  libelf
+        #
+
+        # Transaction used to avoid repeated writes.
+        with spack.installed_db.write_transaction():
+            self._mock_install('mpileaks ^mpich')
+            self._mock_install('mpileaks ^mpich2')
+            self._mock_install('mpileaks ^zmpi')
+
+    def tearDown(self):
+        for spec in spack.installed_db.query():
+            spec.package.do_uninstall(spec)
+        super(MockDatabase, self).tearDown()
+        shutil.rmtree(self.install_path)
+        spack.install_path = self.spack_install_path
+        spack.install_layout = self.spack_install_layout
+        spack.installed_db = self.spack_installed_db

var/spack/repos/builtin.mock/packages/cmake-client/package.py

@@ -0,0 +1,89 @@
+##############################################################################
+# 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
+
+def check(condition, msg):
+    """Raise an install error if condition is False."""
+    if not condition:
+        raise InstallError(msg)
+
+
+class CmakeClient(Package):
+    """A dumy package that uses cmake."""
+    homepage  = 'https://www.example.com'
+    url       = 'https://www.example.com/cmake-client-1.0.tar.gz'
+
+    version('1.0', '4cb3ff35b2472aae70f542116d616e63')
+
+    depends_on('cmake')
+
+
+    def setup_environment(self, spack_env, run_env):
+        spack_cc    # Ensure spack module-scope variable is avaiabl
+        check(from_cmake == "from_cmake",
+              "setup_environment couldn't read global set by cmake.")
+
+        check(self.spec['cmake'].link_arg == "test link arg",
+              "link arg on dependency spec not readable from setup_environment.")
+
+
+    def setup_dependent_environment(self, spack_env, run_env, dspec):
+        spack_cc    # Ensure spack module-scope variable is avaiable
+        check(from_cmake == "from_cmake",
+              "setup_dependent_environment couldn't read global set by cmake.")
+
+        check(self.spec['cmake'].link_arg == "test link arg",
+              "link arg on dependency spec not readable from setup_dependent_environment.")
+
+
+    def setup_dependent_package(self, module, dspec):
+        spack_cc    # Ensure spack module-scope variable is avaiable
+        check(from_cmake == "from_cmake",
+              "setup_dependent_package couldn't read global set by cmake.")
+
+        check(self.spec['cmake'].link_arg == "test link arg",
+              "link arg on dependency spec not readable from setup_dependent_package.")
+
+
+
+    def install(self, spec, prefix):
+        # check that cmake is in the global scope.
+        global cmake
+        check(cmake is not None, "No cmake was in environment!")
+
+        # check that which('cmake') returns the right one.
+        cmake = which('cmake')
+        check(cmake.exe[0].startswith(spec['cmake'].prefix.bin),
+              "Wrong cmake was in environment: %s" % cmake)
+
+        check(from_cmake == "from_cmake",
+              "Couldn't read global set by cmake.")
+
+        check(os.environ['from_cmake'] == 'from_cmake',
+              "Couldn't read env var set in envieonmnt by dependency")
+
+        mkdirp(prefix.bin)
+        touch(join_path(prefix.bin, 'dummy'))

var/spack/repos/builtin.mock/packages/cmake/package.py

@@ -0,0 +1,69 @@
+##############################################################################
+# 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
+
+def check(condition, msg):
+    """Raise an install error if condition is False."""
+    if not condition:
+        raise InstallError(msg)
+
+
+class Cmake(Package):
+    """A dumy package for the cmake build system."""
+    homepage  = 'https://www.cmake.org'
+    url       = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
+
+    version('3.4.3',    '4cb3ff35b2472aae70f542116d616e63',
+            url='https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz')
+
+
+    def setup_environment(self, spack_env, run_env):
+        spack_cc    # Ensure spack module-scope variable is avaiable
+        spack_env.set('for_install', 'for_install')
+
+    def setup_dependent_environment(self, spack_env, run_env, dspec):
+        spack_cc    # Ensure spack module-scope variable is avaiable
+        spack_env.set('from_cmake', 'from_cmake')
+
+
+    def setup_dependent_package(self, module, dspec):
+        spack_cc    # Ensure spack module-scope variable is avaiable
+
+        self.spec.from_cmake = "from_cmake"
+        module.from_cmake = "from_cmake"
+
+        self.spec.link_arg = "test link arg"
+
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+
+        check(os.environ['for_install'] == 'for_install',
+              "Couldn't read env var set in compile envieonmnt")
+
+        cmake_exe = join_path(prefix.bin, 'cmake')
+        touch(cmake_exe)
+        set_executable(cmake_exe)

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
+

var/spack/repos/builtin/packages/apr-util/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')

var/spack/repos/builtin/packages/apr/package.py

@@ -0,0 +1,38 @@
+##############################################################################
+# 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')
+
+    def install(self, spec, prefix):
+        options = ['--prefix=%s' % prefix]
+        configure(*options)
+        make()
+        make('install')

var/spack/repos/builtin/packages/arpack-ng/package.py

@@ -41,16 +41,26 @@ class ArpackNg(Package):
 
     depends_on('blas')
     depends_on('lapack')
+    depends_on('automake')
+    depends_on('autoconf')
+    depends_on('libtool@2.4.2:')
+
     depends_on('mpi', when='+mpi')
 
     def install(self, spec, prefix):
         # Apparently autotools are not bootstrapped
+        # TODO: switch to use the CMake build in the next version
+        # rather than bootstrapping.
+        which('libtoolize')()
         bootstrap = Executable('./bootstrap')
 
         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')

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)

var/spack/repos/builtin/packages/atlas/package.py

@@ -1,31 +1,36 @@
 from spack import *
 from spack.util.executable import Executable
-import os
+import os.path
 
 class Atlas(Package):
     """
-    Automatically Tuned Linear Algebra Software, generic shared
+    Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and
-    ATLAS is an approach for the automatic generation and optimization of
+    optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear
-    numerical software. Currently ATLAS supplies optimized versions for the
+    algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines
-    complete set of linear algebra kernels known as the Basic Linear Algebra
+    in the LAPACK library.
-    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
+    variant('shared', default=True, description='Builds shared library')
-    # TODO: to mark "beta" packages and require explicit invocation.
 
-    # provides('blas')
+    provides('blas')
+    provides('lapack')
 
+    parallel = False
 
     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 +38,21 @@ 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")
+            configure('--prefix=%s' % prefix, *options)
-            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")
-
             make()
             make('check')
             make('ptcheck')

var/spack/repos/builtin/packages/bash/package.py

@@ -0,0 +1,20 @@
+from spack import *
+
+class Bash(Package):
+    """The GNU Project's Bourne Again SHell."""
+
+    homepage = "https://www.gnu.org/software/bash/"
+    url      = "ftp://ftp.gnu.org/gnu/bash/bash-4.3.tar.gz"
+
+    version('4.3', '81348932d5da294953e15d4814c74dd1')
+
+    depends_on('readline')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix,
+                  '--with-curses',
+                  '--with-installed-readline=%s' % spec['readline'].prefix)
+
+        make()
+        make("tests")
+        make("install")

var/spack/repos/builtin/packages/binutils/package.py

@@ -12,6 +12,10 @@ class Binutils(Package):
     version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
     version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764')
 
+    depends_on('m4')
+    depends_on('flex')
+    depends_on('bison')
+
     # Add a patch that creates binutils libiberty_pic.a which is preferred by OpenSpeedShop and cbtf-krell
     variant('krellpatch', default=False, description="build with openspeedshop based patch.")
     variant('gold', default=True, description="build the gold linker")

var/spack/repos/builtin/packages/boost/package.py

@@ -1,5 +1,9 @@
 from spack import *
 import spack
+import sys
+
+import os
+import sys
 
 class Boost(Package):
     """Boost provides free peer-reviewed portable C++ source
@@ -172,6 +176,16 @@ def determine_b2_options(self, spec, options):
         return threadingOpts
 
     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']
+
         withLibs = list()
         for lib in Boost.all_libs:
             if "+{0}".format(lib) in spec:
@@ -185,6 +199,18 @@ def install(self, spec, prefix):
             install_tree(src, dst)
             return
 
+        # Remove libraries that the release version does not support
+        if not spec.satisfies('@1.54.0:'):
+            withLibs.remove('log')
+        if not spec.satisfies('@1.53.0:'):
+            withLibs.remove('atomic')
+        if not spec.satisfies('@1.48.0:'):
+            withLibs.remove('locale')
+        if not spec.satisfies('@1.47.0:'):
+            withLibs.remove('chrono')
+        if not spec.satisfies('@1.43.0:'):
+            withLibs.remove('random')
+
         # to make Boost find the user-config.jam
         env['BOOST_BUILD_PATH'] = './'
 
@@ -208,3 +234,6 @@ def install(self, spec, prefix):
         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)

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')
@@ -38,10 +39,12 @@ 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')
 
     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')
@@ -77,8 +80,9 @@ def install(self, spec, prefix):
             options.append('--sphinx-html')
             options.append('--sphinx-man')
 
-        options.append('--')
+        if '+openssl' in spec:
-        options.append('-DCMAKE_USE_OPENSSL=ON')
+            options.append('--')
+            options.append('-DCMAKE_USE_OPENSSL=ON')
 
         configure(*options)
         make()

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/"
+    homepage = "http://www.cryptopp.com"
-    url      = "http://www.cryptopp.com/cryptopp563.zip"
+    base_url = "http://www.cryptopp.com"
 
     version('5.6.3', '3c5b70e2ec98b7a24988734446242d07')
     version('5.6.2', '7ed022585698df48e65ce9218f6c6a67')
@@ -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 = str(version).replace('.', '')
-        version_string = reduce(lambda vs, nv: vs + str(nv), version_tuple, "")
+        return '%s/cryptopp%s.zip' % (Cryptopp.base_url, version_string)
-
-        return "%scryptopp%s.zip" % (Cryptopp.homepage, version_string)

var/spack/repos/builtin/packages/cuda/package.py

@@ -0,0 +1,47 @@
+from spack import *
+from glob import glob
+import os
+
+class Cuda(Package):
+    """CUDA is a parallel computing platform and programming model invented by
+    NVIDIA. It enables dramatic increases in computing performance by harnessing
+    the power of the graphics processing unit (GPU).
+
+    Note: NVIDIA does not provide a download URL for CUDA so you will need to
+    download it yourself. Go to https://developer.nvidia.com/cuda-downloads
+    and select your Operating System, Architecture, Distribution, and Version.
+    For the Installer Type, select runfile and click Download. Spack will search
+    your current directory for this file. Alternatively, add this file to a
+    mirror so that Spack can find it. For instructions on how to set up a mirror,
+    see http://software.llnl.gov/spack/mirrors.html
+
+    Note: This package does not currently install the drivers necessary to run
+    CUDA. These will need to be installed manually. See:
+    http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux for details."""
+
+    homepage = "http://www.nvidia.com/object/cuda_home_new.html"
+
+    version('7.5.18', '4b3bcecf0dfc35928a0898793cf3e4c6', expand=False,
+            url="file://%s/cuda_7.5.18_linux.run"    % os.getcwd())
+    version('6.5.14', '90b1b8f77313600cc294d9271741f4da', expand=False,
+            url="file://%s/cuda_6.5.14_linux_64.run" % os.getcwd())
+
+
+    def install(self, spec, prefix):
+        runfile = glob(os.path.join(self.stage.path, 'cuda*.run'))[0]
+        chmod = which('chmod')
+        chmod('+x', runfile)
+        runfile = which(runfile)
+
+        # Note: NVIDIA does not officially support many newer versions of compilers.
+        # For example, on CentOS 6, you must use GCC 4.4.7 or older. See:
+        # http://docs.nvidia.com/cuda/cuda-installation-guide-linux/#system-requirements
+        # for details.
+
+        runfile(
+            '--silent',   # disable interactive prompts
+            '--verbose',  # create verbose log file
+            '--toolkit',  # install CUDA Toolkit
+            '--toolkitpath=%s' % prefix
+        )
+

var/spack/repos/builtin/packages/dbus/package.py

@@ -13,12 +13,15 @@ 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')
     version('1.8.4', '4717cb8ab5b80978fcadf2b4f2f72e1b')
     version('1.8.2', 'd6f709bbec0a022a1847c7caec9d6068')
 
+    depends_on('expat')
+
     def install(self, spec, prefix):
         configure(
             "--prefix=%s" % prefix,

var/spack/repos/builtin/packages/dealii/package.py

@@ -0,0 +1,253 @@
+from spack import *
+import sys
+
+class Dealii(Package):
+    """C++ software library providing well-documented tools to build finite element codes for a broad variety of PDEs."""
+    homepage = "https://www.dealii.org"
+    url      = "https://github.com/dealii/dealii/releases/download/v8.4.0/dealii-8.4.0.tar.gz"
+
+    version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00')
+    version('dev', git='https://github.com/dealii/dealii.git')
+
+    variant('mpi',      default=True,  description='Compile with MPI')
+    variant('arpack',   default=True,  description='Compile with Arpack and PArpack (only with MPI)')
+    variant('doc',      default=False, description='Compile with documentation')
+    variant('hdf5',     default=True,  description='Compile with HDF5 (only with MPI)')
+    variant('metis',    default=True,  description='Compile with Metis')
+    variant('netcdf',   default=True,  description='Compile with Netcdf (only with MPI)')
+    variant('oce',      default=True,  description='Compile with OCE')
+    variant('p4est',    default=True,  description='Compile with P4est (only with MPI)')
+    variant('petsc',    default=True,  description='Compile with Petsc (only with MPI)')
+    variant('slepc',    default=True,  description='Compile with Slepc (only with Petsc and MPI)')
+    variant('trilinos', default=True,  description='Compile with Trilinos (only with MPI)')
+
+    # required dependencies, light version
+    depends_on ("blas")
+    # Boost 1.58 is blacklisted, see https://github.com/dealii/dealii/issues/1591
+    # require at least 1.59
+    depends_on ("boost@1.59.0:",     when='~mpi')
+    depends_on ("boost@1.59.0:+mpi", when='+mpi')
+    depends_on ("bzip2")
+    depends_on ("cmake")
+    depends_on ("lapack")
+    depends_on ("muparser")
+    depends_on ("suite-sparse")
+    depends_on ("tbb")
+    depends_on ("zlib")
+
+    # optional dependencies
+    depends_on ("mpi", when="+mpi")
+    depends_on ("arpack-ng+mpi", when='+arpack+mpi')
+    depends_on ("doxygen", when='+doc')
+    depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why?
+    depends_on ("metis@5:", when='+metis')
+    depends_on ("netcdf+mpi", when="+netcdf+mpi")
+    depends_on ("netcdf-cxx", when='+netcdf+mpi')
+    depends_on ("oce", when='+oce')
+    depends_on ("p4est", when='+p4est+mpi')
+    depends_on ("petsc+mpi", when='+petsc+mpi')
+    depends_on ("slepc", when='+slepc+petsc+mpi')
+    depends_on ("trilinos", when='+trilinos+mpi')
+
+    # developer dependnecies
+    #depends_on ("numdiff") #FIXME
+    #depends_on ("astyle") #FIXME
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+
+        # CMAKE_BUILD_TYPE should be DebugRelease | Debug | Release
+        for word in options[:]:
+            if word.startswith('-DCMAKE_BUILD_TYPE'):
+                options.remove(word)
+
+        dsuf = 'dylib' if sys.platform == 'darwin' else 'so'
+        options.extend([
+            '-DCMAKE_BUILD_TYPE=DebugRelease',
+            '-DDEAL_II_COMPONENT_EXAMPLES=ON',
+            '-DDEAL_II_WITH_THREADS:BOOL=ON',
+            '-DBOOST_DIR=%s' % spec['boost'].prefix,
+            '-DBZIP2_DIR=%s' % spec['bzip2'].prefix,
+            # CMake's FindBlas/Lapack may pickup system's blas/lapack instead of Spack's.
+            # Be more specific to avoid this.
+            # Note that both lapack and blas are provided in -DLAPACK_XYZ variables
+            '-DLAPACK_FOUND=true',
+            '-DLAPACK_INCLUDE_DIRS=%s;%s' %
+                (spec['lapack'].prefix.include,
+                 spec['blas'].prefix.include),
+            '-DLAPACK_LIBRARIES=%s;%s' %
+                (join_path(spec['lapack'].prefix.lib,'liblapack.%s' % dsuf), # FIXME don't hardcode names
+                 join_path(spec['blas'].prefix.lib,'libblas.%s' % dsuf)),    # FIXME don't hardcode names
+            '-DMUPARSER_DIR=%s ' % spec['muparser'].prefix,
+            '-DP4EST_DIR=%s' % spec['p4est'].prefix,
+            '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
+            '-DTBB_DIR=%s' % spec['tbb'].prefix,
+            '-DZLIB_DIR=%s' % spec['zlib'].prefix
+        ])
+
+        # MPI
+        if '+mpi' in spec:
+            options.extend([
+                '-DDEAL_II_WITH_MPI:BOOL=ON',
+                '-DCMAKE_C_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # FIXME: avoid hardcoding mpi wrappers names
+                '-DCMAKE_CXX_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
+                '-DCMAKE_Fortran_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
+            ])
+        else:
+            options.extend([
+                '-DDEAL_II_WITH_MPI:BOOL=OFF',
+            ])
+
+        # Optional dependencies for which librariy names are the same as CMake variables
+        for library in ('hdf5', 'p4est','petsc', 'slepc','trilinos','metis'):
+            if library in spec:
+                options.extend([
+                    '-D{library}_DIR={value}'.format(library=library.upper(), value=spec[library].prefix),
+                    '-DDEAL_II_WITH_{library}:BOOL=ON'.format(library=library.upper())
+                ])
+            else:
+                options.extend([
+                    '-DDEAL_II_WITH_{library}:BOOL=OFF'.format(library=library.upper())
+                ])
+
+        # doxygen
+        options.extend([
+            '-DDEAL_II_COMPONENT_DOCUMENTATION=%s' % ('ON' if '+doc' in spec else 'OFF'),
+        ])
+
+
+        # arpack
+        if '+arpack' in spec:
+            options.extend([
+                '-DARPACK_DIR=%s' % spec['arpack-ng'].prefix,
+                '-DDEAL_II_WITH_ARPACK=ON',
+                '-DDEAL_II_ARPACK_WITH_PARPACK=ON'
+            ])
+        else:
+            options.extend([
+                '-DDEAL_II_WITH_ARPACK=OFF'
+            ])
+
+        # since Netcdf is spread among two, need to do it by hand:
+        if '+netcdf' in spec:
+            options.extend([
+                '-DNETCDF_FOUND=true',
+                '-DNETCDF_LIBRARIES=%s;%s' %
+                    (join_path(spec['netcdf-cxx'].prefix.lib,'libnetcdf_c++.%s' % dsuf),
+                    join_path(spec['netcdf'].prefix.lib,'libnetcdf.%s' % dsuf)),
+                '-DNETCDF_INCLUDE_DIRS=%s;%s' %
+                    (spec['netcdf-cxx'].prefix.include,
+                    spec['netcdf'].prefix.include),
+            ])
+        else:
+            options.extend([
+                '-DDEAL_II_WITH_NETCDF=OFF'
+            ])
+
+        # Open Cascade
+        if '+oce' in spec:
+            options.extend([
+                '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix,
+                '-DDEAL_II_WITH_OPENCASCADE=ON'
+            ])
+        else:
+            options.extend([
+                '-DDEAL_II_WITH_OPENCASCADE=OFF'
+            ])
+
+        cmake('.', *options)
+
+        make()
+        make("test")
+        make("install")
+
+        # run some MPI examples with different solvers from PETSc and Trilinos
+        env['DEAL_II_DIR'] = prefix
+        print('=====================================')
+        print('============ EXAMPLES ===============')
+        print('=====================================')
+        # take bare-bones step-3
+        print('=====================================')
+        print('============ Step-3 =================')
+        print('=====================================')
+        with working_dir('examples/step-3'):
+            cmake('.')
+            make('release')
+            make('run',parallel=False)
+
+        # An example which uses Metis + PETSc
+        # FIXME: switch step-18 to MPI
+        with working_dir('examples/step-18'):
+            print('=====================================')
+            print('============= Step-18 ===============')
+            print('=====================================')
+            # list the number of cycles to speed up
+            filter_file(r'(end_time = 10;)',  ('end_time = 3;'), 'step-18.cc')
+            if '^petsc' in spec and '^metis' in spec:
+                cmake('.')
+                make('release')
+                make('run',parallel=False)
+
+        # take step-40 which can use both PETSc and Trilinos
+        # FIXME: switch step-40 to MPI run
+        with working_dir('examples/step-40'):
+            print('=====================================')
+            print('========== Step-40 PETSc ============')
+            print('=====================================')
+            # list the number of cycles to speed up
+            filter_file(r'(const unsigned int n_cycles = 8;)',  ('const unsigned int n_cycles = 2;'), 'step-40.cc')
+            cmake('.')
+            if '^petsc' in spec:
+                make('release')
+                make('run',parallel=False)
+
+            print('=====================================')
+            print('========= Step-40 Trilinos ==========')
+            print('=====================================')
+            # change Linear Algebra to Trilinos
+            filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)',  ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc')
+            if '^trilinos+hypre' in spec:
+                make('release')
+                make('run',parallel=False)
+
+            print('=====================================')
+            print('=== Step-40 Trilinos SuperluDist ====')
+            print('=====================================')
+            # change to direct solvers
+            filter_file(r'(LA::SolverCG solver\(solver_control\);)',  ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc')
+            filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)',  (''), 'step-40.cc')
+            filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)',  (''), 'step-40.cc')
+            filter_file(r'(preconditioner.initialize\(system_matrix, data\);)',  (''), 'step-40.cc')
+            filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)',  ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc')
+            filter_file(r'(preconditioner\);)',  (''), 'step-40.cc')
+            if '^trilinos+superlu-dist' in spec:
+                make('release')
+                make('run',paralle=False)
+
+            print('=====================================')
+            print('====== Step-40 Trilinos MUMPS =======')
+            print('=====================================')
+            # switch to Mumps
+            filter_file(r'(Amesos_Superludist)',  ('Amesos_Mumps'), 'step-40.cc')
+            if '^trilinos+mumps' in spec:
+                make('release')
+                make('run',parallel=False)
+
+        print('=====================================')
+        print('============ Step-36 ================')
+        print('=====================================')
+        with working_dir('examples/step-36'):
+            if 'slepc' in spec:
+                cmake('.')
+                make('release')
+                make('run',parallel=False)
+
+        print('=====================================')
+        print('============ Step-54 ================')
+        print('=====================================')
+        with working_dir('examples/step-54'):
+            if 'oce' in spec:
+                cmake('.')
+                make('release')
+                make('run',parallel=False)

var/spack/repos/builtin/packages/dia/package.py

@@ -0,0 +1,34 @@
+from spack import *
+
+class Dia(Package):
+    """Dia is a program for drawing structured diagrams."""
+    homepage  = 'https://wiki.gnome.org/Apps/Dia'
+    url       = 'https://ftp.gnome.org/pub/gnome/sources/dia/0.97/dia-0.97.3.tar.xz'
+
+    version('0.97.3',    '0e744a0f6a6c4cb6a089e4d955392c3c')
+
+    depends_on('gtkplus@2.6.0:')
+    depends_on('cairo')
+    #depends_on('libart') # optional dependency, not yet supported by spack.
+    depends_on('libpng')
+    depends_on('libxslt')
+    depends_on('python')
+    depends_on('swig')
+    # depends_on('py-gtk') # optional dependency, not yet supported by spack.
+
+    def url_for_version(self, version):
+        """Handle Dia's version-based custom URLs."""
+        return 'https://ftp.gnome.org/pub/gnome/source/dia/%s/dia-%s.tar.xz' % (version.up_to(2), version)
+
+    def install(self, spec, prefix):
+
+        # configure, build, install:
+        options = ['--prefix=%s' % prefix,
+                   '--with-cairo',
+                   '--with-xslt-prefix=%s' % spec['libxslt'].prefix,
+                   '--with-python',
+                   '--with-swig']
+
+        configure(*options)
+        make()
+        make('install')

var/spack/repos/builtin/packages/doxygen/package.py

@@ -4,6 +4,7 @@
 #------------------------------------------------------------------------------
 
 from spack import *
+import sys
 
 class Doxygen(Package):
     """Doxygen is the de facto standard tool for generating documentation
@@ -17,6 +18,10 @@ class Doxygen(Package):
     version('1.8.10', '79767ccd986f12a0f949015efb5f058f')
 
     depends_on("cmake@2.8.12:")
+    # flex does not build on OSX, but it's provided there anyway
+    depends_on("flex", sys.platform != 'darwin')
+    depends_on("bison", sys.platform != 'darwin')
+
 
     def install(self, spec, prefix):
         cmake('.', *std_cmake_args)

var/spack/repos/builtin/packages/dyninst/package.py

@@ -31,6 +31,8 @@ class Dyninst(Package):
     url      = "http://www.dyninst.org/sites/default/files/downloads/dyninst/8.1.2/DyninstAPI-8.1.2.tgz"
     list_url = "http://www.dyninst.org/downloads/dyninst-8.x"
 
+    version('9.1.0', '5c64b77521457199db44bec82e4988ac',
+            url="http://www.paradyn.org/release9.1.0/DyninstAPI-9.1.0.tgz")
     version('8.2.1', 'abf60b7faabe7a2e4b54395757be39c7',
             url="http://www.paradyn.org/release8.2/DyninstAPI-8.2.1.tgz")
     version('8.1.2', 'bf03b33375afa66fe0efa46ce3f4b17a',

var/spack/repos/builtin/packages/eigen/package.py

@@ -45,7 +45,7 @@ class Eigen(Package):
 
     # TODO : dependency on googlehash, superlu, adolc missing
 
-    depends_on('metis', when='+metis')
+    depends_on('metis@5:', when='+metis')
     depends_on('scotch', when='+scotch')
     depends_on('fftw', when='+fftw')
     depends_on('suite-sparse', when='+suitesparse')

var/spack/repos/builtin/packages/elk/package.py

@@ -0,0 +1,122 @@
+from spack import *
+import spack
+
+class Elk(Package):
+    '''An all-electron full-potential linearised augmented-plane wave
+    (FP-LAPW) code with many advanced features.'''
+
+    homepage = 'http://elk.sourceforge.net/'
+    url      = 'https://sourceforge.net/projects/elk/files/elk-3.3.17.tgz'
+
+    version('3.3.17', 'f57f6230d14f3b3b558e5c71f62f0592')
+
+    # Elk provides these libraries, but allows you to specify your own
+    variant('blas',   default=True, description='Build with custom BLAS library')
+    variant('lapack', default=True, description='Build with custom LAPACK library')
+    variant('fft',    default=True, description='Build with custom FFT library')
+
+    # Elk does not provide these libraries, but allows you to use them
+    variant('mpi',    default=True, description='Enable MPI parallelism')
+    variant('openmp', default=True, description='Enable OpenMP support')
+    variant('libxc',  default=True, description='Link to Libxc functional library')
+
+    depends_on('blas',   when='+blas')
+    depends_on('lapack', when='+lapack')
+    depends_on('fftw',   when='+fft')
+    depends_on('mpi',    when='+mpi')
+    depends_on('libxc',  when='+libxc')
+
+    # Cannot be built in parallel
+    parallel = False
+
+
+    def configure(self, spec):
+        # Dictionary of configuration options
+        config = {
+            'MAKE':      'make',
+            'F90':       join_path(spack.build_env_path, 'f90'),
+            'F77':       join_path(spack.build_env_path, 'f77'),
+            'AR':        'ar',
+            'LIB_FFT':   'fftlib.a',
+            'SRC_MPI':   'mpi_stub.f90',
+            'SRC_OMP':   'omp_stub.f90',
+            'SRC_libxc': 'libxcifc_stub.f90',
+            'SRC_FFT':   'zfftifc.f90'
+        }
+
+        # Compiler-specific flags
+        flags = ''
+        if   self.compiler.name == 'intel':
+            flags = '-O3 -ip -unroll -no-prec-div -openmp'
+        elif self.compiler.name == 'gcc':
+            flags = '-O3 -ffast-math -funroll-loops -fopenmp'
+        elif self.compiler.name == 'pgi':
+            flags = '-O3 -mp -lpthread'
+        elif self.compiler.name == 'g95':
+            flags = '-O3 -fno-second-underscore'
+        elif self.compiler.name == 'nag':
+            flags = '-O4 -kind=byte -dusty -dcfuns'
+        elif self.compiler.name == 'xl':
+            flags = '-O3 -qsmp=omp'
+        config['F90_OPTS'] = flags
+        config['F77_OPTS'] = flags
+
+        # BLAS/LAPACK support
+        blas   = 'blas.a'
+        lapack = 'lapack.a'
+        if '+blas'   in spec:
+            blas   = join_path(spec['blas'].prefix.lib,   'libblas.so')
+        if '+lapack' in spec:
+            lapack = join_path(spec['lapack'].prefix.lib, 'liblapack.so')
+        config['LIB_LPK'] = ' '.join([lapack, blas]) # lapack must come before blas
+
+        # FFT support
+        if '+fft' in spec:
+            config['LIB_FFT'] = join_path(spec['fftw'].prefix.lib, 'libfftw3.so')
+            config['SRC_FFT'] = 'zfftifc_fftw.f90'
+
+        # MPI support
+        if '+mpi' in spec:
+            config.pop('SRC_MPI')
+            config['F90'] = join_path(spec['mpi'].prefix.bin, 'mpif90')
+            config['F77'] = join_path(spec['mpi'].prefix.bin, 'mpif77')
+
+        # OpenMP support
+        if '+openmp' in spec:
+            config.pop('SRC_OMP')
+
+        # Libxc support
+        if '+libxc' in spec:
+            config['LIB_libxc'] = ' '.join([
+                join_path(spec['libxc'].prefix.lib, 'libxcf90.so'),
+                join_path(spec['libxc'].prefix.lib, 'libxc.so')
+            ])
+            config['SRC_libxc'] = ' '.join([
+                'libxc_funcs.f90',
+                'libxc.f90',
+                'libxcifc.f90'
+            ])
+
+        # Write configuration options to include file
+        with open('make.inc', 'w') as inc:
+            for key in config:
+                inc.write('{0} = {1}\n'.format(key, config[key]))
+
+
+    def install(self, spec, prefix):
+        # Elk only provides an interactive setup script
+        self.configure(spec)
+
+        make()
+        make('test')
+
+        # The Elk Makefile does not provide an install target
+        mkdirp(prefix.bin)
+
+        install('src/elk',                   prefix.bin)
+        install('src/eos/eos',               prefix.bin)
+        install('src/spacegroup/spacegroup', prefix.bin)
+
+        install_tree('examples', join_path(prefix, 'examples'))
+        install_tree('species',  join_path(prefix, 'species'))
+

var/spack/repos/builtin/packages/environment-modules/package.py

@@ -0,0 +1,38 @@
+from spack import *
+
+
+class EnvironmentModules(Package):
+    """The Environment Modules package provides for the dynamic
+    modification of a user's environment via modulefiles."""
+
+    homepage = "https://sourceforge.net/p/modules/wiki/Home/"
+    url      = "http://prdownloads.sourceforge.net/modules/modules-3.2.10.tar.gz"
+
+    version('3.2.10', '8b097fdcb90c514d7540bb55a3cb90fb')
+
+    # Dependencies:
+    depends_on('tcl')
+
+    def install(self, spec, prefix):
+        tcl_spec = spec['tcl']
+
+        # See: https://sourceforge.net/p/modules/bugs/62/
+        CPPFLAGS = ['-DUSE_INTERP_ERRORLINE']
+        config_args = [
+            "--without-tclx",
+            "--with-tclx-ver=0.0",
+            "--prefix=%s" % prefix,
+            "--with-tcl=%s" % join_path(tcl_spec.prefix, 'lib'),    # It looks for tclConfig.sh
+            "--with-tcl-ver=%d.%d" % (tcl_spec.version.version[0], tcl_spec.version.version[1]),
+            '--disable-debug',
+            '--disable-dependency-tracking',
+            '--disable-silent-rules',
+            '--disable-versioning', 
+            '--datarootdir=%s' % prefix.share,
+            'CPPFLAGS=%s' % ' '.join(CPPFLAGS)
+        ]
+
+
+        configure(*config_args)
+        make()
+        make('install')

var/spack/repos/builtin/packages/espresso/package.py

@@ -33,9 +33,10 @@ def check_variants(self, spec):
             raise RuntimeError(error.format(variant='elpa'))
 
     def install(self, spec, prefix):
+        from glob import glob
         self.check_variants(spec)
 
-        options = ['-prefix=%s' % prefix]
+        options = ['-prefix=%s' % prefix.bin]
 
         if '+mpi' in spec:
             options.append('--enable-parallel')
@@ -61,5 +62,11 @@ def install(self, spec, prefix):
 
         configure(*options)
         make('all')
-        make('install')        
+
+        if spec.architecture.startswith('darwin'):
+            mkdirp(prefix.bin)
+            for filename in glob("bin/*.x"):
+                install(filename, prefix.bin)
+        else:
+            make('install')
 

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.])])
+ 

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
+

var/spack/repos/builtin/packages/gcc/package.py

@@ -26,6 +26,8 @@
 
 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++,
@@ -47,24 +49,33 @@ 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("isl", when='@5.0:')
-    depends_on("binutils~libiberty", when='~gold')
+    depends_on("binutils~libiberty", when='+binutils ~gold')
-    depends_on("binutils~libiberty+gold", when='+gold')
+    depends_on("binutils~libiberty+gold", when='+binutils +gold')
 
+    # 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.
-        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:"):
+
+        if spec.satisfies("@4.7.1:") and sys.platform != 'darwin':
             enabled_languages.add('go')
 
         # Generic options to compile GCC
@@ -72,32 +83,40 @@ def install(self, spec, prefix):
                    "--libdir=%s/lib64" % prefix,
                    "--disable-multilib",
                    "--enable-languages=" + ','.join(enabled_languages),
-                   "--with-mpc=%s"    % spec['mpc'].prefix,
+                   "--with-mpc=%s" % spec['mpc'].prefix,
-                   "--with-mpfr=%s"   % spec['mpfr'].prefix,
+                   "--with-mpfr=%s" % spec['mpfr'].prefix,
-                   "--with-gmp=%s"    % spec['gmp'].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"
+        if spec.satisfies('+binutils'):
-        binutils_options = ["--with-sysroot=/",
+            static_bootstrap_flags = "-static-libstdc++ -static-libgcc"
-                            "--with-stage1-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags),
+            binutils_options = ["--with-sysroot=/",
-                            "--with-boot-ldflags=%s %s"   % (self.rpath_args, static_bootstrap_flags),
+                                "--with-stage1-ldflags=%s %s" %
-                            "--with-ld=%s/bin/ld" % spec['binutils'].prefix,
+                                    (self.rpath_args, static_bootstrap_flags),
-                            "--with-as=%s/bin/as" % spec['binutils'].prefix]
+                                "--with-boot-ldflags=%s %s" %
-        options.extend(binutils_options)
+                                    (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 'isl' in spec:
             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()
@@ -114,7 +133,8 @@ 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'))
@@ -124,5 +144,6 @@ 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)

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")

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')
+#    # Python3 is not supported.
-    depends_on('swig')
+#    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,
+        args = ["--prefix=%s" % prefix]
-                  "--enable-python")
+#        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")

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")

var/spack/repos/builtin/packages/git/package.py

@@ -36,6 +36,8 @@ class Git(Package):
     depends_on("curl", when="+curl")
     depends_on("expat", when="+expat")
 
+    # Also depends_on gettext: apt-get install gettext (Ubuntu)
+
     # Use system perl for now.
     # depends_on("perl")
     # depends_on("pcre")

var/spack/repos/builtin/packages/global/package.py

@@ -11,6 +11,7 @@ class Global(Package):
     version('6.5', 'dfec818b4f53d91721e247cf7b218078')
 
     depends_on('exuberant-ctags')
+    depends_on('ncurses')
 
     def install(self, spec, prefix):
         config_args = ['--prefix={0}'.format(prefix)]

var/spack/repos/builtin/packages/googletest/package.py

@@ -0,0 +1,24 @@
+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)
+

var/spack/repos/builtin/packages/graphviz/package.py

@@ -7,6 +7,12 @@ class Graphviz(Package):
 
     version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae')
 
+    # By default disable optional Perl language support to prevent build issues
+    # related to missing Perl packages. If spack begins support for Perl in the
+    # future, this package can be updated to depend_on('perl') and the
+    # ncecessary devel packages.
+    variant('perl', default=False, description='Enable if you need the optional Perl language bindings.')
+
     parallel = False
 
     depends_on("swig")
@@ -14,8 +20,10 @@ class Graphviz(Package):
     depends_on("ghostscript")
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" %prefix)
+        options = ['--prefix=%s' % prefix]
+        if not '+perl' in spec:
+            options.append('--disable-perl')
 
+        configure(*options)
         make()
         make("install")
-

var/spack/repos/builtin/packages/hdf5/package.py

@@ -37,6 +37,7 @@ class Hdf5(Package):
     list_url = "http://www.hdfgroup.org/ftp/HDF5/releases"
     list_depth = 3
 
+    version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199')
     version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618')
     version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
     version('1.8.13', 'c03426e9e77d7766944654280b467289')
@@ -80,10 +81,16 @@ def install(self, spec, prefix):
         # sanity check in configure, so this doesn't merit a variant.
         extra_args.append("--enable-unsupported")
 
-        if '+debug' in spec:
+        if spec.satisfies('@1.10:'):
-            extra_args.append('--enable-debug=all')
+            if '+debug' in spec:
+                extra_args.append('--enable-build-mode=debug')
+            else:
+                extra_args.append('--enable-build-mode=production')
         else:
-            extra_args.append('--enable-production')
+            if '+debug' in spec:
+                extra_args.append('--enable-debug=all')
+            else:
+                extra_args.append('--enable-production')
 
         if '+shared' in spec:
             extra_args.append('--enable-shared')
@@ -94,10 +101,10 @@ def install(self, spec, prefix):
             extra_args.append('--enable-cxx')
 
         if '+fortran' in spec:
-            extra_args.extend([
+            extra_args.append('--enable-fortran')
-                '--enable-fortran',
+            # '--enable-fortran2003' no longer exists as of version 1.10.0
-                '--enable-fortran2003'
+            if spec.satisfies('@:1.8.16'):
-            ])
+                extra_args.append('--enable-fortran2003')
 
         if '+mpi' in spec:
             # The HDF5 configure script warns if cxx and mpi are enabled
@@ -139,5 +146,7 @@ def url_for_version(self, version):
             return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + v + ".tar.gz"
         elif version < Version("1.7"):
             return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + version.up_to(2) + "/hdf5-" + v + ".tar.gz"
-        else:
+        elif version < Version("1.10"):
             return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + v + "/src/hdf5-" + v + ".tar.gz"
+        else:
+            return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + version.up_to(2) + "/hdf5-" + v + "/src/hdf5-" + v + ".tar.gz"

var/spack/repos/builtin/packages/hoomd-blue/package.py

@@ -0,0 +1,73 @@
+from spack import *
+import os
+
+class HoomdBlue(Package):
+    """HOOMD-blue is a general-purpose particle simulation toolkit. It scales
+    from a single CPU core to thousands of GPUs.
+
+    You define particle initial conditions and interactions in a high-level
+    python script. Then tell HOOMD-blue how you want to execute the job and it
+    takes care of the rest. Python job scripts give you unlimited flexibility
+    to create custom initialization routines, control simulation parameters,
+    and perform in situ analysis."""
+
+    homepage = "https://codeblue.umich.edu/hoomd-blue/index.html"
+    url      = "https://bitbucket.org/glotzer/hoomd-blue/get/v1.3.3.tar.bz2"
+
+    version('1.3.3', '1469ef4531dc14b579c0acddbfe6a273')
+
+    variant('mpi',  default=True, description='Compile with MPI enabled')
+    variant('cuda', default=True, description='Compile with CUDA Toolkit')
+    variant('doc',  default=True, description='Generate documentation')
+
+    extends('python')
+    depends_on('py-numpy')
+    depends_on('boost+python')
+    depends_on('cmake')
+    depends_on('mpi', when='+mpi')
+    depends_on('cuda', when='+cuda')
+    depends_on('doxygen', when='+doc')
+
+    def install(self, spec, prefix):
+
+        cmake_args = [
+            '-DPYTHON_EXECUTABLE=%s/python' % spec['python'].prefix.bin,
+            '-DBOOST_ROOT=%s'               % spec['boost' ].prefix
+        ]
+
+        # MPI support
+        if '+mpi' in spec:
+            os.environ['MPI_HOME'] = spec['mpi'].prefix
+            cmake_args.append('-DENABLE_MPI=ON')
+        else:
+            cmake_args.append('-DENABLE_MPI=OFF')
+
+        # CUDA support
+        if '+cuda' in spec:
+            cmake_args.append('-DENABLE_CUDA=ON')
+        else:
+            cmake_args.append('-DENABLE_CUDA=OFF')
+
+        # CUDA-aware MPI library support
+        #if '+cuda' in spec and '+mpi' in spec:
+        #    cmake_args.append('-DENABLE_MPI_CUDA=ON')
+        #else:
+        #    cmake_args.append('-DENABLE_MPI_CUDA=OFF')
+
+        # There may be a bug in the MPI-CUDA code. See:
+        # https://groups.google.com/forum/#!msg/hoomd-users/2griTESmc5I/E69s_M5fDwAJ
+        # This prevented "make test" from passing for me.
+        cmake_args.append('-DENABLE_MPI_CUDA=OFF')
+
+        # Documentation
+        if '+doc' in spec:
+            cmake_args.append('-DENABLE_DOXYGEN=ON')
+        else:
+            cmake_args.append('-DENABLE_DOXYGEN=OFF')
+
+        cmake_args.extend(std_cmake_args)
+        cmake('.', *cmake_args)
+
+        make()
+        make("test")
+        make("install")

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 +12,10 @@ 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)")
+    # SuperluDist have conflicting headers with those in Hypre
+    variant('internal-superlu', default=True, description="Use internal Superlu routines")
 
     depends_on("mpi")
     depends_on("blas")
@@ -37,6 +40,12 @@ 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")
+            # 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.
         with working_dir("src"):

var/spack/repos/builtin/packages/ipopt/package.py

@@ -0,0 +1,51 @@
+from spack import *
+
+class Ipopt(Package):
+    """Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a
+       software package for large-scale nonlinear optimization."""
+    homepage = "https://projects.coin-or.org/Ipopt"
+    url      = "http://www.coin-or.org/download/source/Ipopt/Ipopt-3.12.4.tgz"
+
+    version('3.12.4', '12a8ecaff8dd90025ddea6c65b49cb03')
+    version('3.12.3', 'c560cbfa9cbf62acf8b485823c255a1b')
+    version('3.12.2', 'ec1e855257d7de09e122c446506fb00d')
+    version('3.12.1', 'ceaf895ce80c77778f2cab68ba9f17f3')
+    version('3.12.0', 'f7dfc3aa106a6711a85214de7595e827')
+
+    depends_on("blas")
+    depends_on("lapack")
+    depends_on("pkg-config")
+    depends_on("mumps+double~mpi") 
+    
+    def install(self, spec, prefix):
+        # Dependency directories
+        blas_dir = spec['blas'].prefix
+        lapack_dir = spec['lapack'].prefix
+        mumps_dir = spec['mumps'].prefix
+
+        # Add directory with fake MPI headers in sequential MUMPS
+        # install to header search path
+        mumps_flags = "-ldmumps -lmumps_common -lpord -lmpiseq"
+        mumps_libcmd = "-L%s " % mumps_dir.lib + mumps_flags
+
+        # By convention, spack links blas & lapack libs to libblas & liblapack
+        blas_lib = "-L%s" % blas_dir.lib + " -lblas"
+        lapack_lib = "-L%s" % lapack_dir.lib + " -llapack"
+        
+        configure_args = [
+            "--prefix=%s" % prefix,
+            "--with-mumps-incdir=%s" % mumps_dir.include,
+            "--with-mumps-lib=%s" % mumps_libcmd,
+            "--enable-shared",
+            "--with-blas-incdir=%s" % blas_dir.include,
+            "--with-blas-lib=%s" % blas_lib,
+            "--with-lapack-incdir=%s" % lapack_dir.include,
+            "--with-lapack-lib=%s" % lapack_lib
+            ]
+        
+        configure(*configure_args)
+
+        # IPOPT does not build correctly in parallel on OS X
+        make(parallel=False)
+        make("test", parallel=False)
+        make("install", parallel=False)

var/spack/repos/builtin/packages/julia/openblas.patch

@@ -0,0 +1,68 @@
+diff --git a/deps/Makefile b/deps/Makefile
+index 6cb73be..bcd8520 100644
+--- a/deps/Makefile
++++ b/deps/Makefile
+@@ -1049,7 +1049,7 @@ OPENBLAS_BUILD_OPTS += NO_AFFINITY=1
+ 
+ # Build for all architectures - required for distribution
+ ifeq ($(OPENBLAS_DYNAMIC_ARCH), 1)
+-OPENBLAS_BUILD_OPTS += DYNAMIC_ARCH=1
++OPENBLAS_BUILD_OPTS += DYNAMIC_ARCH=1 MAKE_NO_J=1
+ endif
+ 
+ # 64-bit BLAS interface
+@@ -1085,6 +1085,7 @@ OPENBLAS_BUILD_OPTS += NO_AVX2=1
+ endif
+ 
+ $(OPENBLAS_SRC_DIR)/config.status: $(OPENBLAS_SRC_DIR)/Makefile
++	cd $(dir $@) && patch -p1 < ../openblas-make.patch
+ ifeq ($(OS),WINNT)
+ 	cd $(dir $@) && patch -p1 < ../openblas-win64.patch
+ endif
+diff --git a/deps/openblas.version b/deps/openblas.version
+index 7c97e1b..58b9467 100644
+--- a/deps/openblas.version
++++ b/deps/openblas.version
+@@ -1,2 +1,2 @@
+-OPENBLAS_BRANCH=v0.2.15
+-OPENBLAS_SHA1=53e849f4fcae4363a64576de00e982722c7304f9
++OPENBLAS_BRANCH=v0.2.17
++OPENBLAS_SHA1=a71e8c82f6a9f73093b631e5deab1e8da716b61f
+--- a/deps/openblas-make.patch
++++ b/deps/openblas-make.patch
+@@ -0,0 +1,35 @@
++diff --git a/Makefile.system b/Makefile.system
++index b89f60e..2dbdad0 100644
++--- a/Makefile.system
+++++ b/Makefile.system
++@@ -139,6 +139,10 @@ NO_PARALLEL_MAKE=0
++ endif
++ GETARCH_FLAGS  += -DNO_PARALLEL_MAKE=$(NO_PARALLEL_MAKE)
++ 
+++ifdef MAKE_NO_J
+++GETARCH_FLAGS += -DMAKE_NO_J=$(MAKE_NO_J)
+++endif
+++
++ ifdef MAKE_NB_JOBS
++ GETARCH_FLAGS += -DMAKE_NB_JOBS=$(MAKE_NB_JOBS)
++ endif
++diff --git a/getarch.c b/getarch.c
++index f9c49e6..dffad70 100644
++--- a/getarch.c
+++++ b/getarch.c
++@@ -1012,6 +1012,7 @@ int main(int argc, char *argv[]){
++ #endif
++ #endif
++ 
+++#ifndef MAKE_NO_J
++ #ifdef MAKE_NB_JOBS
++     printf("MAKE += -j %d\n", MAKE_NB_JOBS);
++ #elif NO_PARALLEL_MAKE==1
++@@ -1021,6 +1022,7 @@ int main(int argc, char *argv[]){
++     printf("MAKE += -j %d\n", get_num_cores());
++ #endif
++ #endif
+++#endif
++ 
++     break;
++ 

var/spack/repos/builtin/packages/julia/package.py

@@ -4,43 +4,56 @@
 class Julia(Package):
     """The Julia Language: A fresh approach to technical computing"""
     homepage = "http://julialang.org"
-    url      = "http://github.com/JuliaLang/julia/releases/download/v0.4.2/julia-0.4.2.tar.gz"
+    url      = "https://github.com/JuliaLang/julia/releases/download/v0.4.3/julia-0.4.3-full.tar.gz"
 
-    version('0.4.3', '7b9f096798fca4bef262a64674bc2b52')
+    version('master',
-    version('0.4.2', 'ccfeb4f4090c8b31083f5e1ccb03eb06')
+            git='https://github.com/JuliaLang/julia.git', branch='master')
+    version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6')
+    version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac')
 
     patch('gc.patch')
+    patch('openblas.patch', when='@0.4:0.4.5')
 
-    # Build-time dependencies
+    # Build-time dependencies:
-    depends_on("cmake @2.8:")
     # depends_on("awk")
     # depends_on("m4")
     # depends_on("pkg-config")
-    depends_on("python @2.6:2.9")
 
-    # I think that Julia requires the dependencies above, but it builds find (on
+    # Combined build-time and run-time dependencies:
-    # my system) without these. We should enable them as necessary.
+    depends_on("binutils")
+    depends_on("cmake @2.8:")
+    depends_on("git")
+    depends_on("openssl")
+    depends_on("python @2.7:2.999")
 
-    # Run-time dependencies
+    # I think that Julia requires the dependencies above, but it
+    # builds fine (on my system) without these. We should enable them
+    # as necessary.
+
+    # Run-time dependencies:
     # depends_on("arpack")
     # depends_on("fftw +float")
     # depends_on("gmp")
+    # depends_on("libgit")
     # depends_on("mpfr")
+    # depends_on("openblas")
     # depends_on("pcre2")
 
-    # ARPACK: Requires BLAS and LAPACK; needs to use the same version as Julia.
+    # ARPACK: Requires BLAS and LAPACK; needs to use the same version
+    # as Julia.
 
-    # BLAS and LAPACK: Julia prefers 64-bit versions on 64-bit systems. OpenBLAS
+    # BLAS and LAPACK: Julia prefers 64-bit versions on 64-bit
-    # has an option for this; make it available as variant.
+    # systems. OpenBLAS has an option for this; make it available as
+    # variant.
 
-    # FFTW: Something doesn't work when using a pre-installed FFTW library; need
+    # FFTW: Something doesn't work when using a pre-installed FFTW
-    # to investigate.
+    # library; need to investigate.
 
-    # GMP, MPFR: Something doesn't work when using a pre-installed FFTW library;
+    # GMP, MPFR: Something doesn't work when using a pre-installed
-    # need to investigate.
+    # FFTW library; need to investigate.
 
-    # LLVM: Julia works only with specific versions, and might require patches.
+    # LLVM: Julia works only with specific versions, and might require
-    # Thus we let Julia install its own LLVM.
+    # patches. Thus we let Julia install its own LLVM.
 
     # Other possible dependencies:
     # USE_SYSTEM_OPENLIBM=0
@@ -50,11 +63,21 @@ class Julia(Package):
     # USE_SYSTEM_UTF8PROC=0
     # USE_SYSTEM_LIBGIT2=0
 
+    # Run-time dependencies for Julia packages:
+    depends_on("hdf5")
+    depends_on("mpi")
+
     def install(self, spec, prefix):
-        # Explicitly setting CC, CXX, or FC breaks building libuv, one of
+        if '@master' in spec:
-        # Julia's dependencies. This might be a Darwin-specific problem. Given
+            # Julia needs to know the offset from a specific commit
-        # how Spack sets up compilers, Julia should still use Spack's compilers,
+            git = which('git')
-        # even if we don't specify them explicitly.
+            git('fetch', '--unshallow')
+
+        # Explicitly setting CC, CXX, or FC breaks building libuv, one
+        # of Julia's dependencies. This might be a Darwin-specific
+        # problem. Given how Spack sets up compilers, Julia should
+        # still use Spack's compilers, even if we don't specify them
+        # explicitly.
         options = [#"CC=cc",
                    #"CXX=c++",
                    #"FC=fc",

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")

var/spack/repos/builtin/packages/libdrm/package.py

@@ -11,6 +11,8 @@ class Libdrm(Package):
     version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6')
     version('2.4.33', '86e4e3debe7087d5404461e0032231c8')
 
+    depends_on('libpciaccess')
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
 

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",

var/spack/repos/builtin/packages/libpng/package.py

@@ -8,6 +8,11 @@ class Libpng(Package):
     version('1.6.16', '1a4ad377919ab15b54f6cb6a3ae2622d')
     version('1.6.15', '829a256f3de9307731d4f52dc071916d')
     version('1.6.14', '2101b3de1d5f348925990f9aa8405660')
+    version('1.5.26', '3ca98347a5541a2dad55cd6d07ee60a9')
+    version('1.4.19', '89bcbc4fc8b31f4a403906cf4f662330')
+    version('1.2.56', '9508fc59d10a1ffadd9aae35116c19ee')
+
+    depends_on('zlib')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)

var/spack/repos/builtin/packages/libxc/package.py

@@ -0,0 +1,18 @@
+from spack import *
+
+class Libxc(Package):
+    """Libxc is a library of exchange-correlation functionals for
+    density-functional theory."""
+
+    homepage = "http://www.tddft.org/programs/octopus/wiki/index.php/Libxc"
+    url      = "http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.2.tar.gz"
+
+    version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec')
+
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix,
+                  '--enable-shared')
+
+        make()
+        make("install")

var/spack/repos/builtin/packages/libxcb/package.py

@@ -14,6 +14,9 @@ class Libxcb(Package):
     depends_on("python")
     depends_on("xcb-proto")
 
+    # depends_on('pthread')    # Ubuntu: apt-get install libpthread-stubs0-dev
+    # depends_on('xau')        # Ubuntu: apt-get install libxau-dev
+
     def patch(self):
         filter_file('typedef struct xcb_auth_info_t {', 'typedef struct {', 'src/xcb.h')
 

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()

var/spack/repos/builtin/packages/metis/package.py

@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-
+import glob, sys, os
 
 class Metis(Package):
     """
@@ -36,7 +36,10 @@ class Metis(Package):
     homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview'
     url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz"
 
-    version('5.1.0', '5465e67079419a69e0116de24fce58fe')
+    version('5.1.0', '5465e67079419a69e0116de24fce58fe',
+            url='http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz')
+    version('4.0.3', '5efa35de80703c1b2c4d0de080fafbcf4e0d363a21149a1ad2f96e0144841a55',
+            url='http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD/metis-4.0.3.tar.gz')
 
     variant('shared', default=True, description='Enables the build of shared libraries')
     variant('debug', default=False, description='Builds the library in debug mode')
@@ -45,10 +48,85 @@ class Metis(Package):
     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-time dependency
+    depends_on('cmake @2.8:', when='@5:')  # build-time dependency
-
     depends_on('gdb', when='+gdb')
 
+    patch('install_gklib_defs_rename.patch', when='@5:')
+
+
+    @when('@4:4.0.3')
+    def install(self, spec, prefix):
+
+        if '+gdb' in spec:
+            raise InstallError('gdb support not implemented in METIS 4!')
+        if '+idx64' in spec:
+            raise InstallError('idx64 option not implemented in METIS 4!')
+        if '+double' in spec:
+            raise InstallError('double option not implemented for METIS 4!')
+
+        options = ['COPTIONS=-fPIC']
+        if '+debug' in spec:
+            options.append('OPTFLAGS=-g -O0')
+        make(*options)
+
+        mkdir(prefix.bin)
+        for x in ('pmetis', 'kmetis', 'oemetis', 'onmetis', 'partnmesh',
+                  'partdmesh', 'mesh2nodal', 'mesh2dual', 'graphchk'):
+            install(x, prefix.bin)
+
+        mkdir(prefix.lib)
+        install('libmetis.a', prefix.lib)
+
+        mkdir(prefix.include)
+        for h in glob.glob(join_path('Lib', '*.h')):
+            install(h, prefix.include)
+
+        mkdir(prefix.share)
+        for f in (join_path(*p)
+                  for p in (('Programs', 'io.c'),
+                            ('Test','mtest.c'),
+                            ('Graphs','4elt.graph'),
+                            ('Graphs', 'metis.mesh'),
+                            ('Graphs', 'test.mgraph'))):
+            install(f, prefix.share)
+
+        if '+shared' in spec:
+            if sys.platform == 'darwin':
+                lib_dsuffix = 'dylib'
+                load_flag = '-Wl,-all_load'
+                no_load_flag = ''
+            else:
+                lib_dsuffix = 'so'
+                load_flag = '-Wl,-whole-archive'
+                no_load_flag = '-Wl,-no-whole-archive'
+
+            os.system(spack_cc + ' -fPIC -shared ' + load_flag +
+                      ' libmetis.a ' + no_load_flag + ' -o libmetis.' +
+                      lib_dsuffix)
+            install('libmetis.' + lib_dsuffix, prefix.lib)
+
+        # Set up and run tests on installation
+        symlink(join_path(prefix.share, 'io.c'), 'io.c')
+        symlink(join_path(prefix.share, 'mtest.c'), 'mtest.c')
+        os.system(spack_cc + ' -I%s' % prefix.include + ' -c io.c')
+        os.system(spack_cc + ' -I%s' % prefix.include +
+                  ' -L%s' % prefix.lib + ' -lmetis mtest.c io.o -o mtest')
+        _4eltgraph = join_path(prefix.share, '4elt.graph')
+        test_mgraph = join_path(prefix.share, 'test.mgraph')
+        metis_mesh = join_path(prefix.share, 'metis.mesh')
+        kmetis = join_path(prefix.bin, 'kmetis')
+        os.system('./mtest ' + _4eltgraph)
+        os.system(kmetis + ' ' + _4eltgraph + ' 40')
+        os.system(join_path(prefix.bin, 'onmetis') + ' ' + _4eltgraph)
+        os.system(join_path(prefix.bin, 'pmetis') + ' ' + test_mgraph + ' 2')
+        os.system(kmetis + ' ' + test_mgraph + ' 2')
+        os.system(kmetis + ' ' + test_mgraph + ' 5')
+        os.system(join_path(prefix.bin, 'partnmesh') + metis_mesh + ' 10')
+        os.system(join_path(prefix.bin, 'partdmesh') + metis_mesh + ' 10')
+        os.system(join_path(prefix.bin, 'mesh2dual') + metis_mesh)
+
+
+    @when('@5:')
     def install(self, spec, prefix):
 
         options = []
@@ -77,7 +155,36 @@ def install(self, spec, prefix):
         if '+double' in spec:
             filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
 
+        # Make clang 7.3 happy.
+        # Prevents "ld: section __DATA/__thread_bss extends beyond end of file"
+        # See upstream LLVM issue https://llvm.org/bugs/show_bug.cgi?id=27059
+        # Adopted from https://github.com/Homebrew/homebrew-science/blob/master/metis.rb
+        if spec.satisfies('%clang@7.3.0'):
+            filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24', join_path(source_directory, 'GKlib', 'error.c'))
+
         with working_dir(build_directory, create=True):
             cmake(source_directory, *options)
             make()
             make("install")
+            # now run some tests:
+            for f in ["4elt", "copter2", "mdual"]:
+                graph = join_path(source_directory,'graphs','%s.graph' % f)
+                Executable(join_path(prefix.bin,'graphchk'))(graph)
+                Executable(join_path(prefix.bin,'gpmetis'))(graph,'2')
+                Executable(join_path(prefix.bin,'ndmetis'))(graph)
+
+            graph = join_path(source_directory,'graphs','test.mgraph')
+            Executable(join_path(prefix.bin,'gpmetis'))(graph,'2')
+            graph = join_path(source_directory,'graphs','metis.mesh')
+            Executable(join_path(prefix.bin,'mpmetis'))(graph,'2')
+
+            # 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)
+
+            # 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)

var/spack/repos/builtin/packages/mpich/package.py

@@ -47,12 +47,12 @@ class Mpich(Package):
     provides('mpi@:3.0', when='@3:')
     provides('mpi@:1.3', when='@1:')
 
-    def setup_dependent_environment(self, env, dependent_spec):
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        env.set('MPICH_CC', spack_cc)
+        spack_env.set('MPICH_CC', spack_cc)
-        env.set('MPICH_CXX', spack_cxx)
+        spack_env.set('MPICH_CXX', spack_cxx)
-        env.set('MPICH_F77', spack_f77)
+        spack_env.set('MPICH_F77', spack_f77)
-        env.set('MPICH_F90', spack_f90)
+        spack_env.set('MPICH_F90', spack_fc)
-        env.set('MPICH_FC', spack_fc)
+        spack_env.set('MPICH_FC', spack_fc)
 
     def setup_dependent_package(self, module, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
@@ -78,6 +78,9 @@ def install(self, spec, prefix):
         if not self.compiler.fc:
             config_args.append("--disable-fc")
 
+        if not self.compiler.fc and not self.compiler.f77:
+            config_args.append("--disable-fortran")
+
         configure(*config_args)
         make()
         make("install")

var/spack/repos/builtin/packages/mrnet/krell-5.0.1.patch

@@ -0,0 +1,154 @@
+--- mrnet-3093918/include/mrnet/Types.h	2015-12-10 09:32:24.000000000 -0800
++++ mrnet_top_of_tree/include/mrnet/Types.h	2016-03-16 12:29:33.986132302 -0700
+@@ -23,7 +23,7 @@
+ #ifndef MRNET_VERSION_MAJOR
+ # define MRNET_VERSION_MAJOR 5
+ # define MRNET_VERSION_MINOR 0
+-# define MRNET_VERSION_REV   0
++# define MRNET_VERSION_REV   1
+ #endif
+ 
+ namespace MRN
+--- mrnet-3093918/include/mrnet_lightweight/Types.h	2015-12-10 09:32:24.000000000 -0800
++++ mrnet_top_of_tree/include/mrnet_lightweight/Types.h	2016-03-16 12:29:33.987132302 -0700
+@@ -30,7 +30,7 @@
+ #ifndef MRNET_VERSION_MAJOR
+ #define MRNET_VERSION_MAJOR 5
+ #define MRNET_VERSION_MINOR 0
+-#define MRNET_VERSION_REV   0
++#define MRNET_VERSION_REV   1
+ #endif
+ void get_Version(int* major,
+                  int* minor,
+--- mrnet-3093918/src/lightweight/SerialGraph.c	2015-12-10 09:32:24.000000000 -0800
++++ mrnet_top_of_tree/src/lightweight/SerialGraph.c	2016-03-16 12:29:33.995132302 -0700
+@@ -59,7 +59,7 @@
+ 
+     mrn_dbg_func_begin();
+ 
+-    sprintf(hoststr, "[%s:%hu:%u:", ihostname, iport, irank);
++    sprintf(hoststr, "[%s:%05hu:%u:", ihostname, iport, irank);
+     mrn_dbg(5, mrn_printf(FLF, stderr, "looking for SubTreeRoot: '%s'\n", hoststr));
+  
+     byte_array = sg->byte_array;
+@@ -110,7 +110,7 @@
+     
+     mrn_dbg_func_begin();
+ 
+-    len = (size_t) sprintf(hoststr, "[%s:%hu:%u:0]", ihostname, iport, irank);
++    len = (size_t) sprintf(hoststr, "[%s:%05hu:%u:0]", ihostname, iport, irank);
+     mrn_dbg(5, mrn_printf(FLF, stderr, "adding sub tree leaf: %s\n", hoststr));
+ 
+     len += strlen(sg->byte_array) + 1;
+@@ -139,7 +139,7 @@
+ 
+     mrn_dbg_func_begin();
+ 
+-    len = (size_t) sprintf(hoststr, "[%s:%hu:%u:1", ihostname, iport, irank);
++    len = (size_t) sprintf(hoststr, "[%s:%05hu:%u:1", ihostname, iport, irank);
+     mrn_dbg(5, mrn_printf(FLF, stderr, "adding sub tree root: %s\n", hoststr));
+ 
+     len += strlen(sg->byte_array) + 1;
+@@ -360,8 +360,8 @@
+     char old_hoststr[256];
+     char new_hoststr[256];
+ 
+-    sprintf(old_hoststr, "[%s:%hu:%u:", hostname, UnknownPort, irank);
+-    sprintf(new_hoststr, "[%s:%hu:%u:", hostname, port, irank);
++    sprintf(old_hoststr, "[%s:%05hu:%u:", hostname, UnknownPort, irank);
++    sprintf(new_hoststr, "[%s:%05hu:%u:", hostname, port, irank);
+     
+     old_byte_array = sg->byte_array;
+     new_byte_array = (char*) malloc( strlen(old_byte_array) + 10 );
+--- mrnet-3093918/xplat/src/lightweight/SocketUtils.c	2015-12-10 09:32:24.000000000 -0800
++++ mrnet_top_of_tree/xplat/src/lightweight/SocketUtils.c	2016-03-16 12:29:34.006132303 -0700
+@@ -15,7 +15,7 @@
+ #else
+ const XPlat_Socket InvalidSocket = INVALID_SOCKET;
+ #endif
+-const XPlat_Port InvalidPort = (XPlat_Port)-1;
++const XPlat_Port InvalidPort = (XPlat_Port)0;
+ 
+ static bool_t SetTcpNoDelay( XPlat_Socket sock )
+ {
+--- mrnet-3093918/conf/configure.in	2015-12-10 09:32:24.000000000 -0800
++++ mrnet_top_of_tree/conf/configure.in	2016-03-16 12:45:54.573196781 -0700
+@@ -107,6 +107,18 @@
+ AC_SUBST(PURIFY)
+ 
+ 
++AC_ARG_WITH(expat,
++            [AS_HELP_STRING([--with-expat=PATH],
++                            [Absolute path to installation of EXPAT libraries (note: specify the path to the directory containing "include" and "lib" sub-directories)])],
++            [EXPAT_DIR="${withval}"],
++            [EXPAT_DIR=""])
++
++if test "x$EXPAT_DIR" = "x" ; then
++   EXPAT_LIB=""
++else
++   EXPAT_LIB="-L$EXPAT_DIR/lib"
++fi
++
+ dnl === Checks for header files.
+ AC_CHECK_HEADERS([assert.h errno.h fcntl.h limits.h netdb.h signal.h stddef.h stdlib.h stdio.h string.h unistd.h arpa/inet.h netinet/in.h sys/ioctl.h sys/socket.h sys/sockio.h sys/time.h])
+ AC_HEADER_STDBOOL
+@@ -432,7 +444,7 @@
+         CRAYXT_ATH_LIBS_SO="$CRAYXT_ATH_LIBS -lalps"
+         CRAYXT_ATH_LIBS="$CRAYXT_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc -Wl,-Bdynamic"
+         CRAYXE_ATH_LIBS_SO="$CRAYXE_ATH_LIBS -lalps"
+-        CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi -lexpat -Wl,-Bdynamic"
++        CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi $EXPAT_LIB -lexpat -Wl,-Bdynamic"
+ 
+         AC_CHECK_LIB( [alps], [alps_launch_tool_helper],
+                       [HAVE_ATH_LIBS="yes"; EXTRA_LIBS="$CRAYXT_ATH_LIBS $EXTRA_LIBS"; EXTRA_LIBS_SO="$CRAYXT_ATH_LIBS_SO $EXTRA_LIBS_SO"],
+--- mrnet-3093918/configure	2015-12-10 09:32:24.000000000 -0800
++++ mrnet_top_of_tree/configure	2016-03-16 13:47:20.386439143 -0700
+@@ -742,6 +742,7 @@
+ enable_debug
+ enable_ltwt_threadsafe
+ with_purify
++with_expat
+ '
+       ac_precious_vars='build_alias
+ host_alias
+@@ -1399,6 +1400,9 @@
+                           containing "include" and "lib" sub-directories)
+   --with-launchmon=PATH   Absolute path to installation of LaunchMON
+   --with-purify           Use purify for memory debugging
++  --with-expat=PATH       Absolute path to installation of EXPAT libraries
++                          (note: specify the path to the directory containing
++                          "include" and "lib" sub-directories)
+ 
+ Some influential environment variables:
+   CC          C compiler command
+@@ -3541,6 +3545,21 @@
+ 
+ 
+ 
++# Check whether --with-expat was given.
++if test "${with_expat+set}" = set; then :
++  withval=$with_expat; EXPAT_DIR="${withval}"
++else
++  EXPAT_DIR=""
++fi
++
++
++if test "x$EXPAT_DIR" = "x" ; then
++   EXPAT_LIB=""
++else
++   EXPAT_LIB="-L$EXPAT_DIR/lib"
++fi
++
++
+ ac_ext=cpp
+ ac_cpp='$CXXCPP $CPPFLAGS'
+ ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+@@ -5473,7 +5492,7 @@
+         CRAYXT_ATH_LIBS_SO="$CRAYXT_ATH_LIBS -lalps"
+         CRAYXT_ATH_LIBS="$CRAYXT_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc -Wl,-Bdynamic"
+         CRAYXE_ATH_LIBS_SO="$CRAYXE_ATH_LIBS -lalps"
+-        CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi -lexpat -Wl,-Bdynamic"
++        CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi $EXPAT_LIB -lexpat -Wl,-Bdynamic"
+ 
+         { $as_echo "$as_me:${as_lineno-$LINENO}: checking for alps_launch_tool_helper in -lalps" >&5
+ $as_echo_n "checking for alps_launch_tool_helper in -lalps... " >&6; }

var/spack/repos/builtin/packages/mrnet/package.py

@@ -3,11 +3,17 @@
 class Mrnet(Package):
     """The MRNet Multi-Cast Reduction Network."""
     homepage = "http://paradyn.org/mrnet"
-    url      = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_4.0.0.tar.gz"
+    url      = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_5.0.1.tar.gz"
+    list_url = "http://ftp.cs.wisc.edu/paradyn/mrnet"
 
-    version('4.0.0', 'd00301c078cba57ef68613be32ceea2f')
-    version('4.1.0', '5a248298b395b329e2371bf25366115c')
     version('5.0.1', '17f65738cf1b9f9b95647ff85f69ecdd')
+    version('4.1.0', '5a248298b395b329e2371bf25366115c')
+    version('4.0.0', 'd00301c078cba57ef68613be32ceea2f')
+
+    # Add a patch that brings mrnet-5.0.1 up to date with the current development tree
+    # The development tree contains fixes needed for the krell based tools
+    variant('krellpatch', default=False, description="Build MRNet with krell openspeedshop based patch.")
+    patch('krell-5.0.1.patch', when='@5.0.1+krellpatch')
 
     variant('lwthreads', default=False, description="Also build the MRNet LW threadsafe libraries")
     parallel = False

var/spack/repos/builtin/packages/mumps/Makefile.inc

@@ -8,12 +8,9 @@ IORDERINGSF = $(ISCOTCH)
 IORDERINGSC = $(IMETIS) $(IPORD) $(ISCOTCH)
 
 PLAT    =
-LIBEXT  = .a
 OUTC    = -o
 OUTF    = -o
 RM = /bin/rm -f
-AR = ar vr 
-RANLIB = ranlib
 
 INCSEQ  = -I$(topdir)/libseq
 LIBSEQ  = -L$(topdir)/libseq -lmpiseq

var/spack/repos/builtin/packages/mumps/package.py

@@ -1,6 +1,5 @@
 from spack import *
-import os
+import os, sys, glob
-
 
 class Mumps(Package):
     """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@@ -19,11 +18,12 @@ 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')
     depends_on('scotch + esmumps + mpi', when='+ptscotch')
-    depends_on('metis', when='+metis')
+    depends_on('metis@5:', when='+metis')
     depends_on('parmetis', when="+parmetis")
     depends_on('blas')
     depends_on('lapack')
@@ -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',
+                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),
-                 'OPTL    = -O ',
+                 'OPTL    = %s -O ' % fpic,
-                 'OPTC    = -O -DINTSIZE64'])
+                 'OPTC    = %s -O -DINTSIZE64' % fpic])
         else:
             makefile_conf.extend(
-                ['OPTF    = -O  -DALLOW_NON_INIT',
+                ['OPTF    = %s -O  -DALLOW_NON_INIT' % fpic,
-                 'OPTL    = -O ',
+                 'OPTL    = %s -O ' % fpic,
-                 'OPTC    = -O '])
+                 'OPTC    = %s -O ' % fpic])
 
 
         if '+mpi' in self.spec:
@@ -105,6 +108,27 @@ 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 -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 -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,
+                    '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 +145,7 @@ 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')
@@ -135,9 +159,27 @@ def install(self, spec, prefix):
 
         self.write_makefile_inc()
 
-        make(*make_libs)
+        # 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)
+            for f in glob.glob(join_path('libseq','*.h')):
+                install(f, prefix.include)
+
+        # 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')

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(parallel=False)
+        make("install")

var/spack/repos/builtin/packages/mvapich2/package.py

@@ -140,6 +140,13 @@ def set_network_type(self, spec, configure_args):
 
         configure_args.extend(network_options)
 
+    def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+        spack_env.set('MPICH_CC', spack_cc)
+        spack_env.set('MPICH_CXX', spack_cxx)
+        spack_env.set('MPICH_F77', spack_f77)
+        spack_env.set('MPICH_F90', spack_fc)
+        spack_env.set('MPICH_FC', spack_fc)
+
     def install(self, spec, prefix):
         # we'll set different configure flags depending on our environment
         configure_args = [

var/spack/repos/builtin/packages/ncurses/package.py

@@ -8,11 +8,10 @@ class Ncurses(Package):
     """
 
     homepage = "http://invisible-island.net/ncurses/ncurses.html"
+    url      = "http://ftp.gnu.org/pub/gnu/ncurses/ncurses-6.0.tar.gz"
 
-    version('5.9', '8cb9c412e5f2d96bc6f459aa8c6282a1',
+    version('6.0', 'ee13d052e1ead260d7c28071f46eefb1')
-            url='http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz')
+    version('5.9', '8cb9c412e5f2d96bc6f459aa8c6282a1')
-    version('6.0', 'ee13d052e1ead260d7c28071f46eefb1',
-            url='http://ftp.gnu.org/pub/gnu/ncurses/ncurses-6.0.tar.gz')
 
     patch('patch_gcc_5.txt', when='%gcc@5.0:')
 

var/spack/repos/builtin/packages/netcdf-cxx/package.py

@@ -0,0 +1,19 @@
+from spack import *
+
+class NetcdfCxx(Package):
+    """Deprecated C++ compatibility bindings for NetCDF.
+    These do NOT read or write NetCDF-4 files, and are no longer
+    maintained by Unidata.  Developers should migrate to current
+    NetCDF C++ bindings, in Spack package netcdf-cxx4."""
+
+    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")

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')
 

var/spack/repos/builtin/packages/netlib-blas/package.py

@@ -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')

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
+    LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix
-    linear algebra operations including matrix inversions, least
+    inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value
-    squared solutions to linear sets of equations, eigenvector
+    decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the
-    analysis, singular value decomposition, etc. It is a very
+    scientific community.
-    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('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101')
     version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
@@ -19,41 +18,67 @@ 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('fpic', default=False, description="Build with -fpic compiler option")
+    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', when='~external-blas')
     provides('lapack')
 
-    # blas is a virtual dependency.
-    depends_on('blas')
     depends_on('cmake')
+    depends_on('blas', when='+external-blas')
 
-    # Doesn't always build correctly in parallel
-    parallel = False
 
-    @when('^netlib-blas')
+    def patch(self):
-    def get_blas_libs(self):
+        # Fix cblas CMakeLists.txt -- has wrong case for subdirectory name.
-        blas = self.spec['netlib-blas']
+        if self.spec.satisfies('@3.6.0:'):
-        return [join_path(blas.prefix.lib, 'blas.a')]
+            filter_file('${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/',
+                        '${CMAKE_CURRENT_SOURCE_DIR}/cmake/', 'CBLAS/CMakeLists.txt', string=True)
+
+    def install_one(self, spec, prefix, shared):
+        cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared 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 spec.satisfies('@3.6.0:'):
+            cmake_args.extend(['-DCBLAS=ON']) # always build CBLAS
+
+        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)
+
+        build_dir = 'spack-build' + ('-shared' if shared else '-static')
+        with working_dir(build_dir, create=True):
+            cmake('..', *cmake_args)
+            make()
+            make("install")
 
-    @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())
+        # Always build static libraries.
-        cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs]
+        self.install_one(spec, prefix, False)
 
+        # Build shared libraries if requested.
         if '+shared' in spec:
-            cmake_args.append('-DBUILD_SHARED_LIBS=ON')
+            self.install_one(spec, prefix, True)
-        if '+fpic' in spec:
-            cmake_args.append('-DCMAKE_POSITION_INDEPENDENT_CODE=ON')
 
-        cmake_args += std_cmake_args
 
-        cmake(*cmake_args)
+    def setup_dependent_package(self, module, dspec):
-        make()
+        # This is WIP for a prototype interface for virtual packages.
-        make("install")
+        # We can update this as more builds start depending on BLAS/LAPACK.
+        libdir = find_library_path('libblas.a', self.prefix.lib64, self.prefix.lib)
+
+        self.spec.blas_static_lib   = join_path(libdir, 'libblas.a')
+        self.spec.lapack_static_lib = join_path(libdir, 'liblapack.a')
+
+        if '+shared' in self.spec:
+            self.spec.blas_shared_lib   = join_path(libdir, 'libblas.%s' % dso_suffix)
+            self.spec.lapack_shared_lib = join_path(libdir, 'liblapack.%s' % dso_suffix)

var/spack/repos/builtin/packages/netlib-scalapack/package.py

@@ -18,6 +18,7 @@ class NetlibScalapack(Package):
 
     provides('scalapack')
 
+    depends_on('cmake')
     depends_on('mpi')
     depends_on('lapack')
 
@@ -41,6 +42,11 @@ 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'

var/spack/repos/builtin/packages/ninja/package.py

@@ -16,7 +16,7 @@ def install(self, spec, prefix):
 
         cp = which('cp')
 
-        bindir = os.path.join(prefix, 'bin')
+        bindir = os.path.join(prefix, 'bin/')
         mkdir(bindir)
-        cp('-a', '-t', bindir, 'ninja')
+        cp('-a', 'ninja', bindir)
-        cp('-ra', 'misc', prefix)
+        cp('-a', 'misc', prefix)

var/spack/repos/builtin/packages/numdiff/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 *
+import sys
+
+class Numdiff(Package):
+    """Numdiff is a little program that can be used to compare putatively
+    similar files line by line and field by field, ignoring small numeric
+    differences or/and different numeric formats."""
+
+    homepage  = 'https://www.nongnu.org/numdiff'
+    url       = 'http://nongnu.askapache.com/numdiff/numdiff-5.8.1.tar.gz'
+
+    version('5.8.1',    'a295eb391f6cb1578209fc6b4f9d994e')
+
+    depends_on('gettext', sys.platform=='darwin')
+
+    def install(self, spec, prefix):
+        options = ['--prefix=%s' % prefix]
+        configure(*options)
+        make()
+        make('install')

var/spack/repos/builtin/packages/oce/null.patch

@@ -0,0 +1,482 @@
+From 61cb965b9ffeca419005bc15e635e67589c421dd Mon Sep 17 00:00:00 2001
+From: Martin Siggel <martin.siggel@dlr.de>
+Date: Thu, 28 Jan 2016 19:05:00 +0100
+Subject: [PATCH] Workaround clang optimizations for null references
+
+OCCT/OCE includes some evil code that uses NULL references,
+which are normally not possible. Clang removes code in
+branches like if(&myNullRef==NULL) as it assumes this can
+never be true. This fix was inspired from the mantis issue
+http://tracker.dev.opencascade.org/view.php?id=26042. This
+code will be fixed in OCCT 7, but we might require the fix
+for earlier releases as well.
+
+Fixes issue #576
+---
+ inc/PLib.hxx                               |  2 +-
+ src/BSplCLib/BSplCLib.cxx                  | 16 ++++++-------
+ src/BSplCLib/BSplCLib_2.cxx                |  6 ++---
+ src/BSplCLib/BSplCLib_CurveComputation.gxx | 26 ++++++++++-----------
+ src/BSplSLib/BSplSLib.cxx                  | 36 +++++++++++++++---------------
+ src/BSplSLib/BSplSLib_BzSyntaxes.cxx       |  2 +-
+ src/PLib/PLib.cxx                          | 10 ++++-----
+ 7 files changed, 49 insertions(+), 49 deletions(-)
+
+diff --git a/inc/PLib.hxx b/inc/PLib.hxx
+index 7513234..52b1f84 100644
+--- a/inc/PLib.hxx
++++ b/inc/PLib.hxx
+@@ -343,6 +343,6 @@ friend class PLib_DoubleJacobiPolynomial;
+ 
+ 
+ 
+-
++#define IS_NULL_REF(ref) ((reinterpret_cast<size_t>(&ref) & 0xFFFFFF) == 0)
+ 
+ #endif // _PLib_HeaderFile
+diff --git a/src/BSplCLib/BSplCLib.cxx b/src/BSplCLib/BSplCLib.cxx
+index 683e4ab..2a2d9ea 100644
+--- a/src/BSplCLib/BSplCLib.cxx
++++ b/src/BSplCLib/BSplCLib.cxx
+@@ -298,7 +298,7 @@ void BSplCLib::LocateParameter
+  Standard_Real&                 NewU) 
+ {
+   Standard_Integer first,last;
+-  if (&Mults) {
++  if (!IS_NULL_REF(Mults)) {
+     if (Periodic) {
+       first = Knots.Lower();
+       last  = Knots.Upper();
+@@ -1434,7 +1434,7 @@ void BSplCLib::BuildKnots(const Standard_Integer         Degree,
+   const Standard_Real * pkn = &Knots(KLower);
+   pkn -= KLower;
+   Standard_Real *knot = &LK;
+-  if (&Mults == NULL) {
++  if (IS_NULL_REF(Mults)) {
+     switch (Degree) {
+     case 1 : {
+       Standard_Integer j = Index    ;
+@@ -1672,7 +1672,7 @@ Standard_Boolean  BSplCLib::PrepareInsertKnots
+  const Standard_Real            Tolerance,
+  const Standard_Boolean         Add)
+ {
+-  Standard_Boolean addflat = &AddMults == NULL;
++  Standard_Boolean addflat = IS_NULL_REF(AddMults);
+   
+   Standard_Integer first,last;
+   if (Periodic) {
+@@ -1856,7 +1856,7 @@ void BSplCLib::InsertKnots
+  const Standard_Real            Tolerance,
+  const Standard_Boolean         Add)
+ {
+-  Standard_Boolean addflat  = &AddMults == NULL;
++  Standard_Boolean addflat  = IS_NULL_REF(AddMults);
+   
+   Standard_Integer i,k,mult,firstmult;
+   Standard_Integer index,kn,curnk,curk;
+@@ -3902,7 +3902,7 @@ void BSplCLib::Resolution(      Standard_Real&        Poles,
+   num_poles = FlatKnots.Length() - Deg1;
+   switch (ArrayDimension) {
+   case 2 : {
+-    if (&Weights != NULL) {
++    if (!IS_NULL_REF(Weights)) {
+       const Standard_Real * WG = &Weights(Weights.Lower());
+       min_weights = WG[0];
+       
+@@ -3970,7 +3970,7 @@ void BSplCLib::Resolution(      Standard_Real&        Poles,
+     break;
+   }
+   case 3 : {
+-    if (&Weights != NULL) {
++    if (!IS_NULL_REF(Weights)) {
+       const Standard_Real * WG = &Weights(Weights.Lower());
+       min_weights = WG[0];
+       
+@@ -4047,7 +4047,7 @@ void BSplCLib::Resolution(      Standard_Real&        Poles,
+     break;
+   }
+   case 4 : {
+-    if (&Weights != NULL) {
++    if (!IS_NULL_REF(Weights)) {
+       const Standard_Real * WG = &Weights(Weights.Lower());
+       min_weights = WG[0];
+       
+@@ -4134,7 +4134,7 @@ void BSplCLib::Resolution(      Standard_Real&        Poles,
+   }
+     default : {
+       Standard_Integer kk;
+-      if (&Weights != NULL) {
++      if (!IS_NULL_REF(Weights)) {
+ 	const Standard_Real * WG = &Weights(Weights.Lower());
+ 	min_weights = WG[0];
+ 	
+diff --git a/src/BSplCLib/BSplCLib_2.cxx b/src/BSplCLib/BSplCLib_2.cxx
+index 35c4639..653b7cd 100644
+--- a/src/BSplCLib/BSplCLib_2.cxx
++++ b/src/BSplCLib/BSplCLib_2.cxx
+@@ -70,7 +70,7 @@ void  BSplCLib::BuildEval(const Standard_Integer         Degree,
+   Standard_Integer i;
+   Standard_Integer ip = PLower + Index - 1;
+   Standard_Real w, *pole = &LP;
+-  if (&Weights == NULL) {
++  if (IS_NULL_REF(Weights)) {
+     
+     for (i = 0; i <= Degree; i++) {
+       ip++;
+@@ -115,13 +115,13 @@ static void PrepareEval
+   
+   // make the knots
+   BSplCLib::BuildKnots(Degree,index,Periodic,Knots,Mults,*dc.knots);
+-  if (&Mults == NULL)
++  if (IS_NULL_REF(Mults))
+     index -= Knots.Lower() + Degree;
+   else
+     index = BSplCLib::PoleIndex(Degree,index,Periodic,Mults);
+   
+   // check truly rational
+-  rational = (&Weights != NULL);
++  rational = (!IS_NULL_REF(Weights));
+   if (rational) {
+     Standard_Integer WLower = Weights.Lower() + index;
+     rational = BSplCLib::IsRational(Weights, WLower, WLower + Degree);
+diff --git a/src/BSplCLib/BSplCLib_CurveComputation.gxx b/src/BSplCLib/BSplCLib_CurveComputation.gxx
+index e71b4e0..9d42643 100644
+--- a/src/BSplCLib/BSplCLib_CurveComputation.gxx
++++ b/src/BSplCLib/BSplCLib_CurveComputation.gxx
+@@ -92,7 +92,7 @@ Standard_Boolean BSplCLib::RemoveKnot
+  TColStd_Array1OfInteger&       NewMults,
+  const Standard_Real            Tolerance) 
+ {
+-  Standard_Boolean rational = &Weights  != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim;
+   dim = Dimension_gen;
+   if (rational) dim++;
+@@ -133,7 +133,7 @@ void BSplCLib::InsertKnots
+  const Standard_Real            Epsilon,
+  const Standard_Boolean         Add) 
+ {
+-  Standard_Boolean rational = &Weights  != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim;
+   dim = Dimension_gen;
+   if (rational) dim++;
+@@ -222,7 +222,7 @@ void BSplCLib::IncreaseDegree
+  TColStd_Array1OfReal&           NewKnots,
+  TColStd_Array1OfInteger&        NewMults) 
+ {
+-  Standard_Boolean rational = &Weights  != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim;
+   dim = Dimension_gen;
+   if (rational) dim++;
+@@ -256,7 +256,7 @@ void  BSplCLib::Unperiodize
+  Array1OfPoints&          NewPoles,
+  TColStd_Array1OfReal&    NewWeights)
+ {
+-  Standard_Boolean rational = &Weights  != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim;
+   dim = Dimension_gen;
+   if (rational) dim++;
+@@ -292,7 +292,7 @@ void BSplCLib::Trimming(const Standard_Integer         Degree,
+ 			Array1OfPoints&          NewPoles,
+ 			TColStd_Array1OfReal&    NewWeights)
+ {
+-  Standard_Boolean rational = &Weights  != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim;
+   dim = Dimension_gen;
+   if (rational) dim++;
+@@ -339,7 +339,7 @@ void  BSplCLib::BuildEval(const Standard_Integer         Degree,
+   Standard_Integer PUpper = Poles.Upper();
+   Standard_Integer i;
+   Standard_Integer ip = PLower + Index - 1;
+-  if (&Weights == NULL) {
++  if (IS_NULL_REF(Weights)) {
+     for (i = 0; i <= Degree; i++) {
+       ip++;
+       if (ip > PUpper) ip = PLower;
+@@ -384,13 +384,13 @@ static void PrepareEval
+ 
+   // make the knots
+   BSplCLib::BuildKnots(Degree,index,Periodic,Knots,Mults,*dc.knots);
+-  if (&Mults == NULL)
++  if (IS_NULL_REF(Mults))
+     index -= Knots.Lower() + Degree;
+   else
+     index = BSplCLib::PoleIndex(Degree,index,Periodic,Mults);
+   
+   // check truly rational
+-  rational = (&Weights != NULL);
++  rational = (!IS_NULL_REF(Weights));
+   if (rational) {
+     Standard_Integer WLower = Weights.Lower() + index;
+     rational = BSplCLib::IsRational(Weights, WLower, WLower + Degree);
+@@ -741,7 +741,7 @@ void  BSplCLib::CacheD0(const Standard_Real                  Parameter,
+ 		       Degree * Dimension_gen,
+ 		       PArray[0],
+ 		       myPoint[0]) ;
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     Standard_Real *
+       WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ;
+     PLib::NoDerivativeEvalPolynomial(NewParameter,
+@@ -798,7 +798,7 @@ void  BSplCLib::CacheD1(const Standard_Real                  Parameter,
+ 
+   ModifyCoords (LocalPDerivatives + Dimension_gen, /= SpanLenght);
+   
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     Standard_Real *
+       WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ;
+     PLib::EvalPolynomial(NewParameter,
+@@ -878,7 +878,7 @@ void  BSplCLib::CacheD2(const Standard_Real                  Parameter,
+     Index += Dimension_gen;
+   }
+ 
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     Standard_Real *
+       WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ;
+     
+@@ -971,7 +971,7 @@ void  BSplCLib::CacheD3(const Standard_Real                  Parameter,
+     Index  += Dimension_gen;
+   }
+   
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     Standard_Real *
+       WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ;
+     
+@@ -1081,7 +1081,7 @@ void BSplCLib::BuildCache
+       LocalValue *= SpanDomain / (Standard_Real) ii ;
+     }
+ 
+-    if (&Weights != NULL) { 
++    if (!IS_NULL_REF(Weights)) {
+       for (ii = 1 ; ii <= Degree + 1 ; ii++)
+ 	CacheWeights(ii) = 0.0e0 ;
+       CacheWeights(1) = 1.0e0 ;
+diff --git a/src/BSplSLib/BSplSLib.cxx b/src/BSplSLib/BSplSLib.cxx
+index 5ad633c..07040d5 100644
+--- a/src/BSplSLib/BSplSLib.cxx
++++ b/src/BSplSLib/BSplSLib.cxx
+@@ -309,12 +309,12 @@ static Standard_Boolean  PrepareEval (const Standard_Real            U,
+     BSplCLib::BuildKnots(UDegree,uindex,UPer,UKnots,UMults,*dc.knots1);
+     BSplCLib::BuildKnots(VDegree,vindex,VPer,VKnots,VMults,*dc.knots2);
+     
+-    if (&UMults == NULL)
++    if (IS_NULL_REF(UMults))
+       uindex -= UKLower + UDegree;
+     else
+       uindex  = BSplCLib::PoleIndex(UDegree,uindex,UPer,UMults);
+ 
+-    if (&VMults == NULL)
++    if (IS_NULL_REF(VMults))
+       vindex -= VKLower + VDegree;
+     else
+       vindex  = BSplCLib::PoleIndex(VDegree,vindex,VPer,VMults);
+@@ -460,12 +460,12 @@ static Standard_Boolean  PrepareEval (const Standard_Real            U,
+     BSplCLib::BuildKnots(UDegree,uindex,UPer,UKnots,UMults,*dc.knots2);
+     BSplCLib::BuildKnots(VDegree,vindex,VPer,VKnots,VMults,*dc.knots1);
+ 
+-    if (&UMults == NULL)
++    if (IS_NULL_REF(UMults))
+       uindex -= UKLower + UDegree;
+     else
+       uindex  = BSplCLib::PoleIndex(UDegree,uindex,UPer,UMults);
+ 
+-    if (&VMults == NULL)
++    if (IS_NULL_REF(VMults))
+       vindex -= VKLower + VDegree;
+     else
+       vindex  = BSplCLib::PoleIndex(VDegree,vindex,VPer,VMults);
+@@ -1299,7 +1299,7 @@ void  BSplSLib::Iso(const Standard_Real            Param,
+ {
+   Standard_Integer index = 0;
+   Standard_Real    u = Param;
+-  Standard_Boolean rational = &Weights != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim = rational ? 4 : 3;
+   
+   // compute local knots
+@@ -1307,7 +1307,7 @@ void  BSplSLib::Iso(const Standard_Real            Param,
+   NCollection_LocalArray<Standard_Real> locknots1 (2*Degree);  
+   BSplCLib::LocateParameter(Degree,Knots,Mults,u,Periodic,index,u);
+   BSplCLib::BuildKnots(Degree,index,Periodic,Knots,Mults,*locknots1);
+-  if (&Mults == NULL)
++  if (IS_NULL_REF(Mults))
+     index -= Knots.Lower() + Degree;
+   else
+     index = BSplCLib::PoleIndex(Degree,index,Periodic,Mults);
+@@ -1381,7 +1381,7 @@ void  BSplSLib::Iso(const Standard_Real            Param,
+   }
+   
+   // if the input is not rational but weights are wanted
+-  if (!rational && (&CWeights != NULL)) {
++  if (!rational && (!IS_NULL_REF(CWeights))) {
+ 
+     for (i = CWeights.Lower(); i <= CWeights.Upper(); i++)
+       CWeights(i) = 1.;
+@@ -1741,7 +1741,7 @@ void  BSplSLib::InsertKnots(const Standard_Boolean         UDirection,
+ 			    const Standard_Real            Epsilon, 
+ 			    const Standard_Boolean         Add )
+ {
+-  Standard_Boolean rational = &Weights != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim = 3;
+   if (rational) dim++;
+   
+@@ -1787,7 +1787,7 @@ Standard_Boolean  BSplSLib::RemoveKnot
+  TColStd_Array1OfInteger& NewMults,
+  const Standard_Real            Tolerance)
+ {
+-  Standard_Boolean rational = &Weights != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim = 3;
+   if (rational) dim++;
+   
+@@ -1834,7 +1834,7 @@ void  BSplSLib::IncreaseDegree
+  TColStd_Array1OfReal&    NewKnots, 
+  TColStd_Array1OfInteger& NewMults)
+ {
+-  Standard_Boolean rational = &Weights != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim = 3;
+   if (rational) dim++;
+   
+@@ -1876,7 +1876,7 @@ void  BSplSLib::Unperiodize
+  TColgp_Array2OfPnt&      NewPoles,
+  TColStd_Array2OfReal&    NewWeights)
+ {
+-  Standard_Boolean rational = &Weights != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim = 3;
+   if (rational) dim++;
+   
+@@ -1929,7 +1929,7 @@ void BSplSLib::BuildCache
+   Standard_Boolean rational,rational_u,rational_v,flag_u_or_v;                  
+   Standard_Integer kk,d1,d1p1,d2,d2p1,ii,jj,iii,jjj,Index;
+   Standard_Real u1,min_degree_domain,max_degree_domain,f,factor[2],u2;
+-  if (&Weights != NULL) 
++  if (!IS_NULL_REF(Weights))
+     rational_u = rational_v = Standard_True;
+   else
+     rational_u = rational_v = Standard_False;
+@@ -2025,7 +2025,7 @@ void BSplSLib::BuildCache
+       }
+       factor[0] *= max_degree_domain / (Standard_Real) (iii) ;
+     }
+-    if (&Weights != NULL) {
++    if (!IS_NULL_REF(Weights)) {
+       //
+       // means that PrepareEval did found out that the surface was 
+       // locally polynomial but since the surface is constructed
+@@ -2110,7 +2110,7 @@ void  BSplSLib::CacheD0(const Standard_Real                  UParameter,
+ 		       (min_degree << 1) + min_degree,
+ 		       locpoles[0],
+ 		       myPoint[0]) ;
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     dimension = min_degree + 1 ;
+     Standard_Real *
+       WArray = (Standard_Real *) 
+@@ -2190,7 +2190,7 @@ void  BSplSLib::CacheD1(const Standard_Real                  UParameter,
+   // the coefficients
+   //
+   //
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+ 
+     local_poles_array            [0][0][0] = 0.0e0 ;
+     local_poles_array            [0][0][1] = 0.0e0 ;
+@@ -2275,7 +2275,7 @@ void  BSplSLib::CacheD1(const Standard_Real                  UParameter,
+ 		       locpoles[dimension],
+ 		       local_poles_array[1][0][0]) ;
+   
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     dimension = min_degree + 1 ;
+     Standard_Real *
+       WArray = (Standard_Real *) 
+@@ -2435,7 +2435,7 @@ void  BSplSLib::CacheD2(const Standard_Real                  UParameter,
+   // the coefficients
+   //
+   //
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     
+     local_poles_and_weights_array[0][0][0] = 0.0e0 ;
+     local_poles_and_weights_array[0][0][1] = 0.0e0 ;
+@@ -2564,7 +2564,7 @@ void  BSplSLib::CacheD2(const Standard_Real                  UParameter,
+ 		       locpoles[dimension + dimension],
+ 		       local_poles_array[2][0][0]) ;
+   
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     dimension = min_degree + 1 ;
+     Standard_Real *
+       WArray = (Standard_Real *) 
+diff --git a/src/BSplSLib/BSplSLib_BzSyntaxes.cxx b/src/BSplSLib/BSplSLib_BzSyntaxes.cxx
+index 0faf6b6..f2c0f74 100644
+--- a/src/BSplSLib/BSplSLib_BzSyntaxes.cxx
++++ b/src/BSplSLib/BSplSLib_BzSyntaxes.cxx
+@@ -68,7 +68,7 @@ void BSplSLib::PolesCoefficients (const TColgp_Array2OfPnt& Poles,
+ 			 biduflatknots,bidvflatknots,
+ 			 Poles,Weights,
+ 			 CPoles,CWeights);
+-    if (&Weights == NULL) {
++    if (IS_NULL_REF(Weights)) {
+       
+       for (ii = 1; ii <= uclas; ii++) {
+ 	
+diff --git a/src/PLib/PLib.cxx b/src/PLib/PLib.cxx
+index 23fa302..7ee231f 100644
+--- a/src/PLib/PLib.cxx
++++ b/src/PLib/PLib.cxx
+@@ -2427,7 +2427,7 @@ void PLib::CoefficientsPoles (const Standard_Integer      dim,
+ 			      TColStd_Array1OfReal&       Poles, 
+ 			      TColStd_Array1OfReal&       Weights)
+ {
+-  Standard_Boolean rat = &WCoefs != NULL;
++  Standard_Boolean rat = !IS_NULL_REF(WCoefs);
+   Standard_Integer loc = Coefs.Lower();
+   Standard_Integer lop = Poles.Lower();
+   Standard_Integer lowc=0;
+@@ -2550,7 +2550,7 @@ void PLib::Trimming(const Standard_Real U1,
+   Standard_Integer indc, indw=0;
+   Standard_Integer upc = Coefs.Upper() - dim + 1, upw=0;
+   Standard_Integer len = Coefs.Length()/dim;
+-  Standard_Boolean rat = &WCoefs != NULL;
++  Standard_Boolean rat = !IS_NULL_REF(WCoefs);
+ 
+   if (rat) {
+     if(len != WCoefs.Length())
+@@ -2607,7 +2607,7 @@ void PLib::CoefficientsPoles (const TColgp_Array2OfPnt&   Coefs,
+ 			      TColgp_Array2OfPnt&         Poles,
+ 			      TColStd_Array2OfReal&       Weights) 
+ {
+-  Standard_Boolean rat = (&WCoefs != NULL);
++  Standard_Boolean rat = (!IS_NULL_REF(WCoefs));
+   Standard_Integer LowerRow  = Poles.LowerRow();
+   Standard_Integer UpperRow  = Poles.UpperRow();
+   Standard_Integer LowerCol  = Poles.LowerCol();
+@@ -2701,7 +2701,7 @@ void PLib::UTrimming(const Standard_Real U1,
+ 		     TColgp_Array2OfPnt& Coeffs, 
+ 		     TColStd_Array2OfReal& WCoeffs)
+ {
+-  Standard_Boolean rat = &WCoeffs != NULL;
++  Standard_Boolean rat = !IS_NULL_REF(WCoeffs);
+   Standard_Integer lr = Coeffs.LowerRow();
+   Standard_Integer ur = Coeffs.UpperRow();
+   Standard_Integer lc = Coeffs.LowerCol();
+@@ -2735,7 +2735,7 @@ void PLib::VTrimming(const Standard_Real V1,
+ 		     TColgp_Array2OfPnt& Coeffs, 
+ 		     TColStd_Array2OfReal& WCoeffs)
+ {
+-  Standard_Boolean rat = &WCoeffs != NULL;
++  Standard_Boolean rat = !IS_NULL_REF(WCoeffs);
+   Standard_Integer lr = Coeffs.LowerRow();
+   Standard_Integer ur = Coeffs.UpperRow();
+   Standard_Integer lc = Coeffs.LowerCol();

var/spack/repos/builtin/packages/oce/package.py

@@ -0,0 +1,67 @@
+from spack import *
+import platform, sys
+
+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')
+
+    variant('tbb', default=True, description='Build with Intel Threading Building Blocks')
+
+    depends_on('cmake@2.8:')
+    depends_on('tbb', when='+tbb')
+
+    # There is a bug in OCE which appears with Clang (version?) or GCC 6.0
+    # and has to do with compiler optimization, see
+    # https://github.com/tpaviot/oce/issues/576
+    # http://tracker.dev.opencascade.org/view.php?id=26042
+    # https://github.com/tpaviot/oce/issues/605
+    # https://github.com/tpaviot/oce/commit/61cb965b9ffeca419005bc15e635e67589c421dd.patch
+    patch('null.patch',when='@0.16:0.17.1')
+
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+        options.extend([
+            '-DOCE_INSTALL_PREFIX=%s' % prefix,
+            '-DOCE_BUILD_SHARED_LIB:BOOL=ON',
+            '-DCMAKE_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=%s' % ('TBB' if '+tbb' in spec else 'NONE'),
+            '-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")
+
+        # OCE tests build is brocken at least on Darwin.
+        # Unit tests are linked against libTKernel.10.dylib isntead of /full/path/libTKernel.10.dylib
+        # see https://github.com/tpaviot/oce/issues/612
+        # make("test")
+
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin'):
+            fix_darwin_install_name(prefix.lib)

var/spack/repos/builtin/packages/openblas/package.py

@@ -1,30 +1,78 @@
 from spack import *
 import sys
+import os
 
 class Openblas(Package):
     """OpenBLAS: An optimized BLAS library"""
     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')
 
+    variant('shared', default=True, description="Build shared libraries as well as static libs.")
+    variant('openmp', default=True, description="Enable OpenMP support.")
+
     # virtual dependency
     provides('blas')
     provides('lapack')
 
-    def install(self, spec, prefix):
-        make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77')
-        make('install', "PREFIX='%s'" % prefix)
 
-        lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so'
+    def install(self, spec, prefix):
+        # Openblas is picky about compilers. Configure fails with
+        # FC=/abs/path/to/f77, whereas FC=f77 works fine.
+        # To circumvent this, provide basename only:
+        make_defs = ['CC=%s' % os.path.basename(spack_cc),
+                     'FC=%s' % os.path.basename(spack_f77)]
+
+        make_targets = ['libs', 'netlib']
+
+        # Build shared if variant is set.
+        if '+shared' in spec:
+            make_targets += ['shared']
+        else:
+            make_defs += ['NO_SHARED=1']
+
+        # fix missing _dggsvd_ and _sggsvd_
+        if spec.satisfies('@0.2.16'):
+            make_defs += ['BUILD_LAPACK_DEPRECATED=1']
+
+        # Add support for OpenMP
+        # Note: Make sure your compiler supports OpenMP
+        if '+openmp' in spec:
+            make_defs += ['USE_OPENMP=1']
+
+        make_args = make_defs + make_targets
+        make(*make_args)
+
+        make("tests", *make_defs)
+
+        # no quotes around prefix (spack doesn't use a shell)
+        make('install', "PREFIX=%s" % prefix, *make_defs)
+
         # Blas virtual package should provide blas.a and libblas.a
         with working_dir(prefix.lib):
             symlink('libopenblas.a', 'blas.a')
             symlink('libopenblas.a', 'libblas.a')
-            symlink('libopenblas.%s' % lib_dsuffix, 'libblas.%s' % lib_dsuffix)
+            if '+shared' in spec:
+                symlink('libopenblas.%s' % dso_suffix, 'libblas.%s' % dso_suffix)
 
         # Lapack virtual package should provide liblapack.a
         with working_dir(prefix.lib):
             symlink('libopenblas.a', 'liblapack.a')
-            symlink('libopenblas.%s' % lib_dsuffix, 'liblapack.%s' % lib_dsuffix)
+            if '+shared' in spec:
+                symlink('libopenblas.%s' % dso_suffix, 'liblapack.%s' % dso_suffix)
+
+
+    def setup_dependent_package(self, module, dspec):
+        # This is WIP for a prototype interface for virtual packages.
+        # We can update this as more builds start depending on BLAS/LAPACK.
+        libdir = find_library_path('libopenblas.a', self.prefix.lib64, self.prefix.lib)
+
+        self.spec.blas_static_lib   = join_path(libdir, 'libopenblas.a')
+        self.spec.lapack_static_lib = self.spec.blas_static_lib
+
+        if '+shared' in self.spec:
+            self.spec.blas_shared_lib   = join_path(libdir, 'libopenblas.%s' % dso_suffix)
+            self.spec.lapack_shared_lib = self.spec.blas_shared_lib

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")

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")

var/spack/repos/builtin/packages/parallel-netcdf/package.py

@@ -8,6 +8,7 @@ class ParallelNetcdf(Package):
     homepage = "https://trac.mcs.anl.gov/projects/parallel-netcdf"
     url      = "http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/parallel-netcdf-1.6.1.tar.gz"
 
+    version('1.7.0', '267eab7b6f9dc78c4d0e6def2def3aea4bc7c9f0')
     version('1.6.1', '62a094eb952f9d1e15f07d56e535052604f1ac34')
 
     depends_on("m4")

var/spack/repos/builtin/packages/paraview/package.py

@@ -27,13 +27,14 @@ class Paraview(Package):
 
     depends_on('bzip2')
     depends_on('freetype')
-    depends_on('hdf5+mpi', when='+mpi')
+    #depends_on('hdf5+mpi', when='+mpi')
-    depends_on('hdf5~mpi', when='~mpi')
+    #depends_on('hdf5~mpi', when='~mpi')
     depends_on('jpeg')
     depends_on('libpng')
     depends_on('libtiff')
     depends_on('libxml2')
-    depends_on('netcdf')
+    #depends_on('netcdf')
+    #depends_on('netcdf-cxx')
     #depends_on('protobuf') # version mismatches?
     #depends_on('sqlite') # external version not supported
     depends_on('zlib')
@@ -75,13 +76,13 @@ def nfeature_to_bool(feature):
             cmake('..',
                 '-DCMAKE_INSTALL_PREFIX:PATH=%s' % prefix,
                 '-DBUILD_TESTING:BOOL=OFF',
-                '-DVTK_USER_SYSTEM_FREETYPE:BOOL=ON',
+                '-DVTK_USE_SYSTEM_FREETYPE:BOOL=ON',
-                '-DVTK_USER_SYSTEM_HDF5:BOOL=ON',
+                '-DVTK_USE_SYSTEM_HDF5:BOOL=OFF',
-                '-DVTK_USER_SYSTEM_JPEG:BOOL=ON',
+                '-DVTK_USE_SYSTEM_JPEG:BOOL=ON',
-                '-DVTK_USER_SYSTEM_LIBXML2:BOOL=ON',
+                '-DVTK_USE_SYSTEM_LIBXML2:BOOL=ON',
-                '-DVTK_USER_SYSTEM_NETCDF:BOOL=ON',
+                '-DVTK_USE_SYSTEM_NETCDF:BOOL=OFF',
-                '-DVTK_USER_SYSTEM_TIFF:BOOL=ON',
+                '-DVTK_USE_SYSTEM_TIFF:BOOL=ON',
-                '-DVTK_USER_SYSTEM_ZLIB:BOOL=ON',
+                '-DVTK_USE_SYSTEM_ZLIB:BOOL=ON',
                 *feature_args)
             make()
             make('install')

var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch

@@ -1,13 +1,71 @@
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index ca945dd..1bf94e9 100644
+index ca945dd..aff8b5f 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)
++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
++++ 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"

var/spack/repos/builtin/packages/parmetis/package.py

@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-
+import sys
 
 class Parmetis(Package):
     """
@@ -44,7 +44,7 @@ class Parmetis(Package):
     depends_on('mpi')
 
     patch('enable_external_metis.patch')
-    depends_on('metis')
+    depends_on('metis@5:')
 
     # bug fixes from PETSc developers
     # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/
@@ -64,7 +64,7 @@ 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'])
@@ -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)

var/spack/repos/builtin/packages/petsc/package.py

@@ -17,14 +17,18 @@ 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('shared',  default=True,  description='Enables the build of shared libraries')
-    variant('mpi', default=True, description='Activates MPI support')
+    variant('mpi',     default=True,  description='Activates MPI support')
-    variant('double', default=True, description='Switches between single and double precision')
+    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('metis',   default=True,  description='Activates support for metis and parmetis')
-    variant('hdf5', default=True, description='Activates support for HDF5 (only parallel)')
+    variant('hdf5',    default=True,  description='Activates support for HDF5 (only parallel)')
-    variant('boost', default=True, description='Activates support for Boost')
+    variant('boost',   default=True,  description='Activates support for Boost')
-    variant('hypre', default=True, description='Activates support for Hypre')
+    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')
@@ -36,11 +40,17 @@ class Petsc(Package):
 
     # Other dependencies
     depends_on('boost', when='+boost')
-    depends_on('metis', when='+metis')
+    depends_on('metis@5:', when='+metis')
 
     depends_on('hdf5+mpi', when='+hdf5+mpi')
     depends_on('parmetis', when='+metis+mpi')
-    depends_on('hypre',    when='+hypre+mpi')
+    # 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')
 
     def mpi_dependent_options(self):
         if '~mpi' in self.spec:
@@ -55,38 +65,30 @@ 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','superlu-dist')
                       if ('+'+x) in self.spec]
             if errors:
                 errors = ['incompatible variants given'] + errors
                 raise RuntimeError('\n'.join(errors))
         else:
-            if self.compiler.name == "clang":
+            compiler_opts = [
-                compiler_opts = [
+                '--with-mpi=1',
-                    '--with-mpi=1',
+                '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
-                    '--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 = ['--with-debugging=0',
+        options = ['--with-ssl=0']
-                   '--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'))
             )
@@ -94,9 +96,24 @@ 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)
 
         # 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)

var/spack/repos/builtin/packages/pkg-config/package.py

@@ -10,7 +10,12 @@ class PkgConfig(Package):
     parallel = False
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" %prefix, "--enable-shared")
+        configure("--prefix=%s" %prefix,
+                "--enable-shared",
+                "--with-internal-glib") # There's a bootstrapping problem here;
+                                        # glib uses pkg-config as well, so
+                                        # break the cycle by using the internal
+                                        # glib.
 
         make()
         make("install")