Merge remote-tracking branch 'upstream/develop' into pkg-numdiff

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/env/cc

@@ -65,7 +65,7 @@ function die {
 }
 
 for param in $parameters; do
-    if [ -z "${!param}" ]; then
+    if [[ -z ${!param} ]]; then
         die "Spack compiler must be run from spack!  Input $param was missing!"
     fi
 done
@@ -78,12 +78,17 @@ done
 # 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90]
 #
 # 'mode' is set to one of:
+#    cpp     preprocess
 #    cc      compile
+#    as      assemble
 #    ld      link
 #    ccld    compile & link
-#    cpp     preprocessor
 #    vcheck  version check
 #
+# Depending on the mode, we may or may not add extra rpaths.
+# This variable controls whether they are added.
+add_rpaths=true
+
 command=$(basename "$0")
 case "$command" in
     cc|c89|c99|gcc|clang|icc|pgcc|xlc)
@@ -107,13 +112,26 @@ case "$command" in
         ;;
     ld)
         mode=ld
+
+        # Darwin's linker has a -r argument that merges object files
+        # together. It doesn't work with -rpath.
+        if [[ $OSTYPE = darwin* ]]; then
+            for arg in "$@"; do
+                if [ "$arg" = -r ]; then
+                    add_rpaths=false
+                    break
+	            fi
+            done
+        fi
         ;;
     *)
         die "Unkown compiler: $command"
         ;;
 esac
 
-# If any of the arguments below is present then the mode is vcheck. In vcheck mode nothing is added in terms of extra search paths or libraries
+# If any of the arguments below is present then the mode is vcheck. In
+# vcheck mode nothing is added in terms of extra search paths or
+# libraries
 if [ -z "$mode" ]; then
     for arg in "$@"; do
         if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
@@ -124,13 +142,15 @@ if [ -z "$mode" ]; then
 fi
 
 # Finish setting up the mode.
-
 if [ -z "$mode" ]; then
     mode=ccld
     for arg in "$@"; do
         if [ "$arg" = -E ]; then
             mode=cpp
             break
+        elif [ "$arg" = -S ]; then
+            mode=as
+            break
         elif [ "$arg" = -c ]; then
             mode=cc
             break
@@ -146,168 +166,56 @@ fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [ -z "$command" ]; then
+if [[ -z $command ]]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
-# Save original command for debug logging
-input_command="$@"
-
 if [ "$mode" == vcheck ] ; then
     exec ${command} "$@"
 fi
 
-#
+# Save original command for debug logging
-# Now do real parsing of the command line args, trying hard to keep
+input_command="$@"
-# non-rpath linker arguments in the proper order w.r.t. other command
+args=("$@")
-# 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 +231,37 @@ unset DYLD_LIBRARY_PATH
 #
 IFS=':' read -ra env_path <<< "$PATH"
 IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH"
-spack_env_dirs+=(".")
+spack_env_dirs+=("" ".")
 PATH=""
 for dir in "${env_path[@]}"; do
     remove=""
     for rm_dir in "${spack_env_dirs[@]}"; do
-        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
+        if [[ $dir = $rm_dir ]]; then remove=True; fi
     done
-    if [ -z "$remove" ]; then
+    if [[ -z $remove ]]; then
-        if [ -z "$PATH" ]; then
+        PATH="${PATH:+$PATH:}$dir"
-            PATH="$dir"
-        else
-            PATH="$PATH:$dir"
-        fi
     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 +27,10 @@
            'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file',
            'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
            'set_executable', 'copy_mode', 'unset_executable_mode',
-           'remove_dead_links', 'remove_linked_tree']
+           'remove_dead_links', 'remove_linked_tree', 'fix_darwin_install_name']
 
 import os
+import glob
 import sys
 import re
 import shutil
@@ -38,6 +39,7 @@
 import getpass
 from contextlib import contextmanager, closing
 from tempfile import NamedTemporaryFile
+import subprocess
 
 import llnl.util.tty as tty
 from spack.util.compression import ALLOWED_ARCHIVE_TYPES
@@ -392,3 +394,29 @@ def remove_linked_tree(path):
             os.unlink(path)
         else:
             shutil.rmtree(path, True)
+
+def fix_darwin_install_name(path):
+    """
+    Fix install name of dynamic libraries on Darwin to have full path.
+    There are two parts of this task:
+    (i) use install_name('-id',...) to change install name of a single lib;
+    (ii) use install_name('-change',...) to change the cross linking between libs.
+    The function assumes that all libraries are in one folder and currently won't
+    follow subfolders.
+
+    Args:
+        path: directory in which .dylib files are alocated
+
+    """
+    libs = glob.glob(join_path(path,"*.dylib"))
+    for lib in libs:
+        # fix install name first:
+        subprocess.Popen(["install_name_tool", "-id",lib,lib], stdout=subprocess.PIPE).communicate()[0]
+        long_deps = subprocess.Popen(["otool", "-L",lib], stdout=subprocess.PIPE).communicate()[0].split('\n')
+        deps = [dep.partition(' ')[0][1::] for dep in long_deps[2:-1]]
+        # fix all dependencies:
+        for dep in deps:
+            for loc in libs:
+                if dep == os.path.basename(loc):
+                    subprocess.Popen(["install_name_tool", "-change",dep,loc,lib], stdout=subprocess.PIPE).communicate()[0]
+                    break

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/build_environment.py

@@ -225,7 +225,7 @@ def set_module_variables_for_package(pkg, module):
     m.spack_cc  = join_path(link_dir, pkg.compiler.link_paths['cc'])
     m.spack_cxx = join_path(link_dir, pkg.compiler.link_paths['cxx'])
     m.spack_f77 = join_path(link_dir, pkg.compiler.link_paths['f77'])
-    m.spack_f90 = join_path(link_dir, pkg.compiler.link_paths['fc'])
+    m.spack_fc  = join_path(link_dir, pkg.compiler.link_paths['fc'])
 
     # Emulate some shell commands for convenience
     m.pwd          = os.getcwd
@@ -270,32 +270,56 @@ def parent_class_modules(cls):
     return result
 
 
+def setup_module_variables_for_dag(pkg):
+    """Set module-scope variables for all packages in the DAG."""
+    for spec in pkg.spec.traverse(order='post'):
+        # If a user makes their own package repo, e.g.
+        # spack.repos.mystuff.libelf.Libelf, and they inherit from
+        # an existing class like spack.repos.original.libelf.Libelf,
+        # then set the module variables for both classes so the
+        # parent class can still use them if it gets called.
+        spkg = spec.package
+        modules = parent_class_modules(spkg.__class__)
+        for mod in modules:
+            set_module_variables_for_package(spkg, mod)
+        set_module_variables_for_package(spkg, spkg.module)
+
+
 def setup_package(pkg):
     """Execute all environment setup routines."""
     spack_env = EnvironmentModifications()
     run_env   = EnvironmentModifications()
 
+    # Before proceeding, ensure that specs and packages are consistent
+    #
+    # This is a confusing behavior due to how packages are
+    # constructed.  `setup_dependent_package` may set attributes on
+    # specs in the DAG for use by other packages' install
+    # method. However, spec.package will look up a package via
+    # spack.repo, which defensively copies specs into packages.  This
+    # code ensures that all packages in the DAG have pieces of the
+    # same spec object at build time.
+    #
+    # This is safe for the build process, b/c the build process is a
+    # throwaway environment, but it is kind of dirty.
+    #
+    # TODO: Think about how to avoid this fix and do something cleaner.
+    for s in pkg.spec.traverse(): s.package.spec = s
+
     set_compiler_environment_variables(pkg, spack_env)
     set_build_environment_variables(pkg, spack_env)
-
+    setup_module_variables_for_dag(pkg)
-    # If a user makes their own package repo, e.g.
-    # spack.repos.mystuff.libelf.Libelf, and they inherit from
-    # an existing class like spack.repos.original.libelf.Libelf,
-    # then set the module variables for both classes so the
-    # parent class can still use them if it gets called.
-    modules = parent_class_modules(pkg.__class__)
-    for mod in modules:
-        set_module_variables_for_package(pkg, mod)
 
     # Allow dependencies to modify the module
-    for dependency_spec in pkg.spec.traverse(root=False):
+    spec = pkg.spec
+    for dependency_spec in spec.traverse(root=False):
         dpkg = dependency_spec.package
-        dpkg.setup_dependent_python_module(pkg.module, pkg.spec)
+        dpkg.setup_dependent_package(pkg.module, spec)
 
     # Allow dependencies to set up environment as well
-    for dependency_spec in pkg.spec.traverse(root=False):
+    for dependency_spec in spec.traverse(root=False):
         dpkg = dependency_spec.package
-        dpkg.setup_dependent_environment(spack_env, run_env, pkg.spec)
+        dpkg.setup_dependent_environment(spack_env, run_env, spec)
 
     # Allow the package to apply some settings.
     pkg.setup_environment(spack_env, run_env)

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/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 +161,13 @@ 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(
+            package = self.spec[item].package
-                self.pkg.module, extendee_spec, self.spec)
+            package.setup_dependent_package(self.pkg.module, self.spec)
+            package.setup_dependent_environment(spack_env, env, self.spec)
 
         # Package-specific environment modifications
-        spack_env = EnvironmentModifications()
         self.spec.package.setup_environment(spack_env, env)
 
         # TODO : implement site-specific modifications and filters
@@ -275,6 +278,6 @@ def write_header(self, module_file):
         # Long description
         if self.long_description:
             module_file.write('proc ModulesHelp { } {\n')
-            doc = re.sub(r'"', '\"', self.long_description)
+            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

@@ -1075,7 +1075,7 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         self.setup_environment(spack_env, run_env)
 
 
-    def setup_dependent_python_module(self, module, dependent_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         """Set up Python module-scope variables for dependent packages.
 
         Called before the install() method of dependents.

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/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')

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

@@ -35,6 +35,10 @@ class ArpackNg(Package):
     variant('shared', default=True, description='Enables the build of shared libraries')
     variant('mpi', default=False, description='Activates MPI support')
 
+    # The function pdlamch10 does not set the return variable. This is fixed upstream
+    # see https://github.com/opencollab/arpack-ng/issues/34
+    patch('pdlamch10.patch', when='@3.3:')
+
     depends_on('blas')
     depends_on('lapack')
     depends_on('mpi', when='+mpi')
@@ -46,7 +50,10 @@ def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix]
 
         if '+mpi' in spec:
-            options.append('--enable-mpi')
+            options.extend([
+                '--enable-mpi',
+                'F77=mpif77' #FIXME: avoid hardcoding MPI wrapper names
+            ])
 
         if '~shared' in spec:
             options.append('--enable-shared=no')

var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch

@@ -0,0 +1,15 @@
+diff --git a/PARPACK/SRC/MPI/pdlamch10.f b/PARPACK/SRC/MPI/pdlamch10.f
+index 6571da9..2882c2e 100644
+--- a/PARPACK/SRC/MPI/pdlamch10.f
++++ b/PARPACK/SRC/MPI/pdlamch10.f
+@@ -86,8 +86,8 @@
+           TEMP = TEMP1
+       END IF
+ *
+-      PDLAMCH = TEMP
++      PDLAMCH10 = TEMP
+ *
+-*     End of PDLAMCH
++*     End of PDLAMCH10
+ *
+       END

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/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
@@ -45,34 +49,34 @@ class Boost(Package):
     version('1.34.1', '2d938467e8a448a2c9763e0a9f8ca7e5')
     version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0')
 
-    default_install_libs = set(['atomic', 
+    default_install_libs = set(['atomic',
-        'chrono', 
+        'chrono',
-        'date_time', 
+        'date_time',
-        'filesystem', 
+        'filesystem',
         'graph',
         'iostreams',
         'locale',
         'log',
-        'math', 
+        'math',
         'program_options',
-        'random', 
+        'random',
-        'regex', 
+        'regex',
-        'serialization', 
+        'serialization',
-        'signals', 
+        'signals',
-        'system', 
+        'system',
-        'test', 
+        'test',
-        'thread', 
+        'thread',
         'wave'])
 
-    # mpi/python are not installed by default because they pull in many 
+    # mpi/python are not installed by default because they pull in many
-    # dependencies and/or because there is a great deal of customization 
+    # dependencies and/or because there is a great deal of customization
     # possible (and it would be difficult to choose sensible defaults)
     default_noinstall_libs = set(['mpi', 'python'])
 
     all_libs = default_install_libs | default_noinstall_libs
 
     for lib in all_libs:
-        variant(lib, default=(lib not in default_noinstall_libs), 
+        variant(lib, default=(lib not in default_noinstall_libs),
             description="Compile with {0} library".format(lib))
 
     variant('debug', default=False, description='Switch to the debug version of Boost')
@@ -124,9 +128,9 @@ def determine_bootstrap_options(self, spec, withLibs, options):
 
         with open('user-config.jam', 'w') as f:
             compiler_wrapper = join_path(spack.build_env_path, 'c++')
-            f.write("using {0} : : {1} ;\n".format(boostToolsetId, 
+            f.write("using {0} : : {1} ;\n".format(boostToolsetId,
                 compiler_wrapper))
-            
+
             if '+mpi' in spec:
                 f.write('using mpi : %s ;\n' %
                     join_path(spec['mpi'].prefix.bin, 'mpicxx'))
@@ -155,7 +159,7 @@ def determine_b2_options(self, spec, options):
         linkTypes = ['static']
         if '+shared' in spec:
             linkTypes.append('shared')
-        
+
         threadingOpts = []
         if '+multithreaded' in spec:
             threadingOpts.append('multi')
@@ -163,28 +167,38 @@ def determine_b2_options(self, spec, options):
             threadingOpts.append('single')
         if not threadingOpts:
             raise RuntimeError("At least one of {singlethreaded, multithreaded} must be enabled")
-        
+
         options.extend([
             'toolset=%s' % self.determine_toolset(spec),
             'link=%s' % ','.join(linkTypes),
             '--layout=tagged'])
-        
+
         return threadingOpts
 
     def install(self, spec, prefix):
+        # 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:
                 withLibs.append(lib)
         if not withLibs:
-            # if no libraries are specified for compilation, then you dont have 
+            # if no libraries are specified for compilation, then you dont have
             # to configure/build anything, just copy over to the prefix directory.
             src = join_path(self.stage.source_path, 'boost')
             mkdirp(join_path(prefix, 'include'))
             dst = join_path(prefix, 'include', 'boost')
             install_tree(src, dst)
             return
-    
+
         # to make Boost find the user-config.jam
         env['BOOST_BUILD_PATH'] = './'
 
@@ -207,4 +221,7 @@ def install(self, spec, prefix):
         # Boost.MPI if the threading options are not separated.
         for threadingOpt in threadingOpts:
             b2('install', 'threading=%s' % threadingOpt, *b2_options)
-        
+
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin') and ('+shared' in spec):
+            fix_darwin_install_name(prefix.lib)

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/dbus/package.py

@@ -13,6 +13,7 @@ class Dbus(Package):
     homepage = "http://dbus.freedesktop.org/"
     url      = "http://dbus.freedesktop.org/releases/dbus/dbus-1.8.8.tar.gz"
 
+    version('1.11.2', '957a07f066f3730d2bb3ea0932f0081b')
     version('1.9.0', 'ec6895a4d5c0637b01f0d0e7689e2b36')
     version('1.8.8', 'b9f4a18ee3faa1e07c04aa1d83239c43')
     version('1.8.6', '6a08ba555d340e9dfe2d623b83c0eea8')

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

@@ -48,7 +48,7 @@ class Eigen(Package):
     depends_on('metis', when='+metis')
     depends_on('scotch', when='+scotch')
     depends_on('fftw', when='+fftw')
-    depends_on('SuiteSparse', when='+suitesparse')
+    depends_on('suite-sparse', when='+suitesparse')
     depends_on('mpfr@2.3.0:')  # Eigen 3.2.7 requires at least 2.3.0
     depends_on('gmp')
 

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

@@ -32,6 +32,10 @@ def check_variants(self, spec):
         if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec):
             raise RuntimeError(error.format(variant='elpa'))
 
+    def setup_environment(self, spack_env, run_env):
+        # Espresso copies every executable in prefix without creating sub-folders
+        run_env.prepend_path('PATH', self.prefix)
+
     def install(self, spec, prefix):
         self.check_variants(spec)
 

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/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/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/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/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/llvm/package.py

@@ -52,7 +52,7 @@ class Llvm(Package):
     depends_on('cmake @2.8.12.2:')
 
     # Universal dependency
-    depends_on('python@2.7:')
+    depends_on('python@2.7:2.8')  # Seems not to support python 3.X.Y
 
     # lldb dependencies
     depends_on('ncurses', when='+lldb')
@@ -132,6 +132,21 @@ class Llvm(Package):
                         'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk',
                         }
                   },
+                  {
+                    'version' : '3.8.0',
+                    'md5':'07a7a74f3c6bd65de4702bf941b511a0',
+                    'resources' : {
+                        'compiler-rt' : 'd6fcbe14352ffb708e4d1ac2e48bb025',
+                        'openmp' : '8fd7cc35d48051613cf1e750e9f22e40',
+                        'polly' : '1b3b20f52d34a4024e21a4ea7112caa7',
+                        'libcxx' : 'd6e0bdbbee39f7907ad74fd56d03b88a',
+                        'libcxxabi' : 'bbe6b4d72c7c5978550d370af529bcf7',
+                        'clang' : 'cc99e7019bb74e6459e80863606250c5',
+                        'clang-tools-extra' : 'c2344f50e0eea0b402f0092a80ddc036',
+                        'lldb' : 'a5da35ed9cc8c8817ee854e3dbfba00e',
+                        'llvm-libunwind' : '162ade468607f153cca12be90b5194fa',
+                        }
+                  },
                   {
                     'version' : '3.7.1',
                     'md5':'bf8b3a2c79e61212c5409041dfdbd319',

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
 
 class Metis(Package):
     """
@@ -49,6 +49,8 @@ class Metis(Package):
 
     depends_on('gdb', when='+gdb')
 
+    patch('install_gklib_defs_rename.patch')
+
     def install(self, spec, prefix):
 
         options = []
@@ -80,4 +82,15 @@ def install(self, spec, prefix):
         with working_dir(build_directory, create=True):
             cmake(source_directory, *options)
             make()
-            make("install")
+            make("install")
+
+            # install GKlib headers, which will be needed for ParMETIS
+            GKlib_dist = join_path(prefix.include,'GKlib')
+            mkdirp(GKlib_dist)
+            fs = glob.glob(join_path(source_directory,'GKlib',"*.h"))
+            for f in fs:
+                install(f, GKlib_dist)
+
+            # 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

@@ -54,7 +54,7 @@ def setup_dependent_environment(self, env, dependent_spec):
         env.set('MPICH_F90', spack_f90)
         env.set('MPICH_FC', spack_fc)
 
-    def setup_dependent_python_module(self, module, spec, dep_spec):
+    def setup_dependent_package(self, module, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
         # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers?
         module.mpicc = join_path(self.prefix.bin, 'mpicc')

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

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

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

@@ -1,6 +1,5 @@
 from spack import *
-import os
+import os, sys
-
 
 class Mumps(Package):
     """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@@ -19,11 +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='~parmetis+metis')
+    depends_on('metis', when='+metis')
     depends_on('parmetis', when="+parmetis")
     depends_on('blas')
     depends_on('lapack')
@@ -38,11 +38,11 @@ class Mumps(Package):
     def write_makefile_inc(self):
         if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec:
             raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')
-        
+
         makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib]
 
         orderings = ['-Dpord']
-        
+
         if '+ptscotch' in self.spec or '+scotch' in self.spec:
             join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '')
             makefile_conf.extend(
@@ -54,18 +54,25 @@ def write_makefile_inc(self):
             if '+ptscotch' in self.spec:
                 orderings.append('-Dptscotch')
 
-        if '+parmetis' in self.spec or '+metis' in self.spec:
+        if '+parmetis' in self.spec and '+metis' in self.spec:
             libname = 'parmetis' if '+parmetis' in self.spec else 'metis'
             makefile_conf.extend(
-                ["IMETIS = -I%s" % self.spec[libname].prefix.include,
+                ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
-                 "LMETIS = -L%s -l%s" % (self.spec[libname].prefix.lib, libname)])
+                 "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')])
+
+            orderings.append('-Dparmetis')
+        elif '+metis' in self.spec:
+            makefile_conf.extend(
+                ["IMETIS = -I%s" % self.spec['metis'].prefix.include,
+                 "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')])
 
             orderings.append('-Dmetis')
-            if '+parmetis' in self.spec:
-                orderings.append('-Dparmetis')
 
         makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
 
+        # 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:
@@ -73,14 +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:
@@ -101,12 +108,33 @@ 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')
         with open(makefile_inc_template, "r") as fh:
             makefile_conf.extend(fh.read().split('\n'))
-        
+
         with working_dir('.'):
             with open("Makefile.inc", "w") as fh:
                 makefile_inc = '\n'.join(makefile_conf)
@@ -117,7 +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')
@@ -130,10 +158,25 @@ def install(self, spec, prefix):
                 make_libs.append('zexamples')
 
         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)
+
+        # 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/netcdf-cxx/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+class NetcdfCxx(Package):
+    """C++ compatibility bindings for NetCDF"""
+    homepage = "http://www.unidata.ucar.edu/software/netcdf"
+    url      = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx-4.2.tar.gz"
+
+    version('4.2', 'd32b20c00f144ae6565d9e98d9f6204c')
+
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make("install")

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')
@@ -19,42 +18,34 @@ class NetlibLapack(Package):
     version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
     version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
 
-    variant('shared', default=False, description="Build shared library version")
+    variant('debug', default=False, description='Activates the Debug build type')
+    variant('shared', default=True, description="Build shared library version")
+    variant('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 get_blas_libs(self):
-        blas = self.spec['netlib-blas']
-        return [join_path(blas.prefix.lib, 'blas.a')]
-
-
-    @when('^atlas')
-    def get_blas_libs(self):
-        blas = self.spec['atlas']
-        return [join_path(blas.prefix.lib, l)
-                for l in ('libf77blas.a', 'libatlas.a')]
-
 
     def install(self, spec, prefix):
-        blas_libs = ";".join(self.get_blas_libs())
+        cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
-        cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs]
+                      '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
+                      '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
+        if '+external-blas' in spec:
+            # TODO : the mechanism to specify the library should be more general,
+            # TODO : but this allows to have an hook to an external blas
+            cmake_args.extend([
+                '-DUSE_OPTIMIZED_BLAS:BOOL=ON',
+                '-DBLAS_LIBRARIES:PATH=%s' % join_path(spec['blas'].prefix.lib, 'libblas.a')
+            ])
 
-        if '+shared' in spec:
+        cmake_args.extend(std_cmake_args)
-            cmake_args.append('-DBUILD_SHARED_LIBS=ON')
-
-        cmake_args += std_cmake_args
-
-        cmake(*cmake_args)
-        make()
-        make("install")
 
+        with working_dir('spack-build', create=True):
+            cmake('..', *cmake_args)
+            make()
+            make("install")

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

@@ -1,4 +1,5 @@
 from spack import *
+import sys
 
 class NetlibScalapack(Package):
     """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines"""
@@ -11,16 +12,16 @@ class NetlibScalapack(Package):
     version('2.0.0', '9e76ae7b291be27faaad47cfc256cbfe')
     # versions before 2.0.0 are not using cmake and requires blacs as
     # a separated package
-    
+
     variant('shared', default=True, description='Build the shared library version')
     variant('fpic', default=False, description="Build with -fpic compiler option")
-    
+
     provides('scalapack')
-    
+
     depends_on('mpi')
     depends_on('lapack')
-    
+
-    def install(self, spec, prefix):       
+    def install(self, spec, prefix):
         options = [
             "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'),
             "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else 'ON'),
@@ -40,10 +41,16 @@ def install(self, spec, prefix):
             make()
             make("install")
 
-    def setup_dependent_python_module(self, module, spec, dependent_spec):
+        # The shared libraries are not installed correctly on Darwin; correct this
-        lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
+        if (sys.platform == 'darwin') and ('+shared' in spec):
-        lib_suffix = lib_dsuffix if '+shared' in spec['scalapack'] else '.a'
+            fix_darwin_install_name(prefix.lib)
 
-        spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib
+
-        spec['scalapack'].cc_link = spec['scalapack'].fc_link
+    def setup_dependent_package(self, module, dependent_spec):
-        spec['scalapack'].libraries = [join_path(spec['scalapack'].prefix.lib, 'libscalapack%s' % lib_suffix)]
+        spec = self.spec
+        lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
+        lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
+
+        spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib
+        spec.cc_link = spec.fc_link
+        spec.libraries = [join_path(spec.prefix.lib, 'libscalapack%s' % lib_suffix)]

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

@@ -0,0 +1,51 @@
+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')
+    version('0.15'  , '7ec541a1c350ca8a684f74980e48801c')
+
+    depends_on('cmake@2.8:')
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+        options.extend([
+            '-DOCE_INSTALL_PREFIX=%s' % prefix,
+            '-DOCE_BUILD_SHARED_LIB:BOOL=ON',
+            '-DOCE_BUILD_TYPE:STRING=Release',
+            '-DOCE_DATAEXCHANGE:BOOL=ON',
+            '-DOCE_DISABLE_X11:BOOL=ON',
+            '-DOCE_DRAW:BOOL=OFF',
+            '-DOCE_MODEL:BOOL=ON',
+            '-DOCE_MULTITHREAD_LIBRARY:STRING=NONE', # FIXME: add tbb
+            '-DOCE_OCAF:BOOL=ON',
+            '-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF',
+            '-DOCE_VISUALISATION:BOOL=OFF',
+            '-DOCE_WITH_FREEIMAGE:BOOL=OFF',
+            '-DOCE_WITH_GL2PS:BOOL=OFF',
+            '-DOCE_WITH_OPENCL:BOOL=OFF'
+        ])
+
+        if platform.system() == 'Darwin':
+            options.extend([
+                '-DOCE_OSX_USE_COCOA:BOOL=ON',
+            ])
+
+        cmake('.', *options)
+
+        make("install/strip")
+
+        # 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/octave/package.py

@@ -62,7 +62,7 @@ class Octave(Package):
     depends_on('qrupdate',    when='+qrupdate')
     #depends_on('qscintilla',  when='+qscintilla) # TODO: add package
     depends_on('qt',          when='+qt')
-    depends_on('SuiteSparse', when='+suitesparse')
+    depends_on('suite-sparse',when='+suitesparse')
     depends_on('zlib',        when='+zlib')
 
 

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

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

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/parmetis/enable_external_metis.patch

@@ -0,0 +1,71 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+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)
++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

@@ -24,10 +24,7 @@
 ##############################################################################
 
 from spack import *
-
+import sys
-# FIXME : lot of code is duplicated from packages/metis/package.py . Inheriting from there may reduce
-# FIXME : the installation rules to just a few lines
-
 
 class Parmetis(Package):
     """
@@ -43,13 +40,17 @@ class Parmetis(Package):
     variant('debug', default=False, description='Builds the library in debug mode')
     variant('gdb', default=False, description='Enables gdb support')
 
-    variant('idx64', default=False, description='Use int64_t as default index type')
-    variant('double', default=False, description='Use double precision floating point types')
-
     depends_on('cmake @2.8:')  # build dependency
     depends_on('mpi')
 
-    # FIXME : this should conflict with metis as it builds its own version internally
+    patch('enable_external_metis.patch')
+    depends_on('metis')
+
+    # bug fixes from PETSc developers
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/
+    patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch')
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
+    patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
 
     depends_on('gdb', when='+gdb')
 
@@ -63,8 +64,8 @@ def install(self, spec, prefix):
 
         # FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
         # FIXME : they use a non-standard name
-        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source),
+        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=spec['metis'].prefix.include),
-                        '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=metis_source),
+                        '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix),
                         '-DCMAKE_C_COMPILER:STRING=mpicc',
                         '-DCMAKE_CXX_COMPILER:STRING=mpicxx'])
 
@@ -78,18 +79,11 @@ def install(self, spec, prefix):
         if '+gdb' in spec:
             options.append('-DGDB:BOOL=ON')
 
-        metis_header = join_path(metis_source, 'include', 'metis.h')
-
-        if '+idx64' in spec:
-            filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header)
-
-        if '+double' in spec:
-            filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
-
         with working_dir(build_directory, create=True):
             cmake(source_directory, *options)
             make()
             make("install")
-            # Parmetis build system doesn't allow for an external metis to be used, but doesn't copy the required
+
-            # metis header either
+            # The shared library is not installed correctly on Darwin; correct this
-            install(metis_header, self.prefix.include)
+            if (sys.platform == 'darwin') and ('+shared' in spec):
+                fix_darwin_install_name(prefix.lib)

var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch

@@ -0,0 +1,77 @@
+From 1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b Mon Sep 17 00:00:00 2001
+From: Jed Brown <jed@59A2.org>
+Date: Fri, 12 Oct 2012 15:45:10 -0500
+Subject: [PATCH] ParMetis bug fixes reported by John Fettig [petsc-maint
+ #133631]
+
+'''
+I have also reported to to Karypis but have received zero
+response and he hasn't released any updates to the original release
+either.  At least he approved my forum posting so that other people
+can see the bug and the fix.
+http://glaros.dtc.umn.edu/gkhome/node/837
+'''
+
+Hg-commit: 1c2b9fe39201d404b493885093b5992028b9b8d4
+---
+ libparmetis/xyzpart.c | 12 ++++++------
+ 1 file changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c
+index 3a2c289..63abfcb 100644
+--- a/libparmetis/xyzpart.c
++++ b/libparmetis/xyzpart.c
+@@ -104,7 +104,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+ 
+     for (i=0; i<nbins; i++)
+       emarkers[i] = gmin + (gmax-gmin)*i/nbins;
+-    emarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON);
++    emarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON);
+ 
+     /* get into a iterative backet boundary refinement */
+     for (l=0; l<5; l++) {
+@@ -152,7 +152,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+         }
+       }
+       nemarkers[0]     = gmin;
+-      nemarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON);
++      nemarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON);
+       rcopy(nbins+1, nemarkers, emarkers);
+     }
+ 
+@@ -218,7 +218,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+ 
+     emarkers[0] = gmin;
+     emarkers[1] = gsum/gnvtxs;
+-    emarkers[2] = gmax*(1.0+2.0*REAL_EPSILON);
++    emarkers[2] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON);
+     cnbins = 2;
+ 
+     /* get into a iterative backet boundary refinement */
+@@ -227,7 +227,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+       iset(cnbins, 0, lcounts);
+       rset(cnbins, 0, lsums);
+       for (j=0, i=0; i<nvtxs;) {
+-        if (cand[i].key < emarkers[j+1]) {
++        if (cand[i].key <= emarkers[j+1]) {
+           lcounts[j]++;
+           lsums[j] += cand[i].key;
+           i++;
+@@ -272,12 +272,12 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+       
+       rsorti(cnbins, nemarkers);
+       rcopy(cnbins, nemarkers, emarkers);
+-      emarkers[cnbins] = gmax*(1.0+2.0*REAL_EPSILON);
++      emarkers[cnbins] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON);
+     }
+ 
+     /* assign the coordinate to the appropriate bin */
+     for (j=0, i=0; i<nvtxs;) {
+-      if (cand[i].key < emarkers[j+1]) {
++      if (cand[i].key <= emarkers[j+1]) {
+         bxyz[cand[i].val*ndims+k] = j;
+         i++;
+       }
+-- 
+2.1.1.1.g1fb337f
+

var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch

@@ -0,0 +1,35 @@
+From 82409d68aa1d6cbc70740d0f35024aae17f7d5cb Mon Sep 17 00:00:00 2001
+From: Sean Farley <sean@mcs.anl.gov>
+Date: Tue, 20 Mar 2012 11:59:44 -0500
+Subject: [PATCH] parmetis: fix bug reported by jfettig; '<' to '<=' in xyzpart
+
+Hg-commit: 2dd2eae596acaabbc80e0ef875182616f868dbc2
+---
+ libparmetis/xyzpart.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c
+index 307aed9..3a2c289 100644
+--- a/libparmetis/xyzpart.c
++++ b/libparmetis/xyzpart.c
+@@ -111,7 +111,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+       /* determine bucket counts */
+       iset(nbins, 0, lcounts);
+       for (j=0, i=0; i<nvtxs;) {
+-        if (cand[i].key < emarkers[j+1]) {
++        if (cand[i].key <= emarkers[j+1]) {
+           lcounts[j]++;
+           i++;
+         }
+@@ -158,7 +158,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+ 
+     /* assign the coordinate to the appropriate bin */
+     for (j=0, i=0; i<nvtxs;) {
+-      if (cand[i].key < emarkers[j+1]) {
++      if (cand[i].key <= emarkers[j+1]) {
+         bxyz[cand[i].val*ndims+k] = j;
+         i++;
+       }
+-- 
+2.1.1.1.g1fb337f
+

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')
@@ -40,7 +44,13 @@ class Petsc(Package):
 
     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:
@@ -55,7 +65,7 @@ def mpi_dependent_options(self):
             # If mpi is disabled (~mpi), it's an error to have any of these enabled.
             # This generates a list of any such errors.
             errors = [error_message_fmt.format(library=x)
-                      for x in ('hdf5', 'hypre', 'parmetis')
+                      for x in ('hdf5', 'hypre', 'parmetis','mumps','superlu-dist')
                       if ('+'+x) in self.spec]
             if errors:
                 errors = ['incompatible variants given'] + errors
@@ -68,15 +78,17 @@ def mpi_dependent_options(self):
         return compiler_opts
 
     def install(self, spec, prefix):
-        options = []
+        options = ['--with-ssl=0']
         options.extend(self.mpi_dependent_options())
         options.extend([
             '--with-precision=%s' % ('double' if '+double' in spec else 'single'),
+            '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'),
             '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
+            '--with-debugging=%s' % ('1' if '+debug' in spec else '0'),
             '--with-blas-lapack-dir=%s' % spec['lapack'].prefix
         ])
         # Activates library support if needed
-        for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis'):
+        for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis','mumps','scalapack'):
             options.append(
                 '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))
             )
@@ -84,9 +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/py-bottleneck/package.py

@@ -0,0 +1,14 @@
+from spack import *
+
+class PyBottleneck(Package):
+    """Bottleneck is a collection of fast NumPy array functions written in Cython."""
+    homepage = "https://pypi.python.org/pypi/Bottleneck/1.0.0"
+    url      = "https://pypi.python.org/packages/source/B/Bottleneck/Bottleneck-1.0.0.tar.gz"
+
+    version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2')
+
+    extends('python', ignore=r'bin/f2py$')
+    depends_on('py-numpy')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/repos/builtin/packages/py-cython/package.py

@@ -3,10 +3,14 @@
 class PyCython(Package):
     """The Cython compiler for writing C extensions for the Python language."""
     homepage = "https://pypi.python.org/pypi/cython"
-    url      = "https://pypi.python.org/packages/source/C/Cython/cython-0.22.tar.gz"
+    url      = "https://pypi.python.org/packages/source/C/Cython/Cython-0.22.tar.gz"
 
-    version('0.21.2', 'd21adb870c75680dc857cd05d41046a4')
+    version('0.23.5', '66b62989a67c55af016c916da36e7514')
+    version('0.23.4', '157df1f69bcec6b56fd97e0f2e057f6e')
+
+    # These versions contain illegal Python3 code...
     version('0.22', '1ae25add4ef7b63ee9b4af697300d6b6')
+    version('0.21.2', 'd21adb870c75680dc857cd05d41046a4')
 
     extends('python')
 

var/spack/repos/builtin/packages/py-dateutil/package.py

@@ -7,6 +7,7 @@ class PyDateutil(Package):
 
     version('2.4.0', '75714163bb96bedd07685cdb2071b8bc')
     version('2.4.2', '4ef68e1c485b09e9f034e10473e5add2')
+    version('2.5.2', 'eafe168e8f404bf384514f5116eedbb6')
 
     extends('python')
     depends_on('py-setuptools')

var/spack/repos/builtin/packages/py-libxml2/package.py

@@ -1,15 +0,0 @@
-from spack import *
-
-class PyLibxml2(Package):
-    """A Python wrapper around libxml2."""
-    homepage = "https://xmlsoft.org/python.html"
-    url      = "ftp://xmlsoft.org/libxml2/python/libxml2-python-2.6.21.tar.gz"
-
-    version('2.6.21', '229dd2b3d110a77defeeaa73af83f7f3')
-
-    extends('python')
-    depends_on('libxml2')
-    depends_on('libxslt')
-
-    def install(self, spec, prefix):
-        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/repos/builtin/packages/py-matplotlib/package.py

@@ -12,7 +12,7 @@ class PyMatplotlib(Package):
     variant('gui', default=False, description='Enable GUI')
     variant('ipython', default=False, description='Enable ipython support')
 
-    extends('python', ignore=r'bin/nosetests.*$|bin/pbr$')
+    extends('python', ignore=r'bin/nosetests.*$|bin/pbr$|bin/f2py$')
 
     depends_on('py-pyside', when='+gui')
     depends_on('py-ipython', when='+ipython')

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

@@ -0,0 +1,16 @@
+from spack import *
+
+class PyNetcdf(Package):
+    """Python interface to the netCDF Library."""
+    homepage = "http://unidata.github.io/netcdf4-python"
+    url      = "https://github.com/Unidata/netcdf4-python/tarball/v1.2.3.1rel"
+
+    version('1.2.3.1', '4fc4320d4f2a77b894ebf8da1c9895af')
+
+    extends('python')
+    depends_on('py-numpy')
+    depends_on('py-cython')
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/repos/builtin/packages/py-nose/package.py

@@ -10,6 +10,7 @@ class PyNose(Package):
 
     version('1.3.4', '6ed7169887580ddc9a8e16048d38274d')
     version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16')
+    version('1.3.7', '4d3ad0ff07b61373d2cefc89c5d0b20b')
 
     extends('python', ignore=r'bin/nosetests.*$')
     depends_on('py-setuptools')

var/spack/repos/builtin/packages/py-numexpr/package.py

@@ -7,8 +7,9 @@ class PyNumexpr(Package):
     url      = "https://pypi.python.org/packages/source/n/numexpr/numexpr-2.4.6.tar.gz"
 
     version('2.4.6', '17ac6fafc9ea1ce3eb970b9abccb4fbd')
+    version('2.5', '84f66cced45ba3e30dcf77a937763aaa')
 
-    extends('python')
+    extends('python', ignore=r'bin/f2py$')
     depends_on('py-numpy')
 
     def install(self, spec, prefix):

var/spack/repos/builtin/packages/py-numpy/package.py

@@ -1,24 +1,44 @@
 from spack import *
 
 class PyNumpy(Package):
-    """array processing for numbers, strings, records, and objects."""
+    """NumPy is the fundamental package for scientific computing with Python.
-    homepage = "https://pypi.python.org/pypi/numpy"
+    It contains among other things: a powerful N-dimensional array object,
+    sophisticated (broadcasting) functions, tools for integrating C/C++ and
+    Fortran code, and useful linear algebra, Fourier transform, and random
+    number capabilities"""
+    homepage = "http://www.numpy.org/"
     url      = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz"
 
-    version('1.9.1', '78842b73560ec378142665e712ae4ad9')
+    version('1.11.0', 'bc56fb9fc2895aa4961802ffbdb31d0b')
-    version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645')
+    version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad')
+    version('1.9.2',  'a1ed53432dbcd256398898d35bc8e645')
+    version('1.9.1',  '78842b73560ec378142665e712ae4ad9')
 
-    variant('blas', default=True)
+
+    variant('blas',   default=True)
+    variant('lapack', default=True)
 
     extends('python')
     depends_on('py-nose')
-    depends_on('netlib-blas+fpic', when='+blas')
+    depends_on('blas',   when='+blas')
-    depends_on('netlib-lapack+shared', when='+blas')
+    depends_on('lapack', when='+lapack')
 
     def install(self, spec, prefix):
+        libraries    = []
+        library_dirs = []
+
         if '+blas' in spec:
+            libraries.append('blas')
+            library_dirs.append(spec['blas'].prefix.lib)
+        if '+lapack' in spec:
+            libraries.append('lapack')
+            library_dirs.append(spec['lapack'].prefix.lib)
+
+        if '+blas' in spec or '+lapack' in spec:
             with open('site.cfg', 'w') as f:
                 f.write('[DEFAULT]\n')
-                f.write('libraries=lapack,blas\n')
+                f.write('libraries=%s\n'    % ','.join(libraries))
-                f.write('library_dirs=%s/lib:%s/lib\n' % (spec['blas'].prefix, spec['lapack'].prefix))
+                f.write('library_dirs=%s\n' % ':'.join(library_dirs))
+
         python('setup.py', 'install', '--prefix=%s' % prefix)
+

var/spack/repos/builtin/packages/py-pandas/package.py

@@ -8,18 +8,15 @@ class PyPandas(Package):
 
     version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73')
     version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8')
+    version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6')
 
-    extends('python')
+    extends('python', ignore=r'bin/f2py$')
     depends_on('py-dateutil')
     depends_on('py-numpy')
-    depends_on('py-matplotlib')
-    depends_on('py-scipy')
     depends_on('py-setuptools')
     depends_on('py-pytz')
-    depends_on('libdrm')
+    depends_on('py-numexpr')
-    depends_on('libpciaccess')
+    depends_on('py-bottleneck')
-    depends_on('llvm')
-    depends_on('mesa')
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/repos/builtin/packages/py-pytz/package.py

@@ -7,6 +7,7 @@ class PyPytz(Package):
 
     version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7')
     version('2015.4', '417a47b1c432d90333e42084a605d3d8')
+    version('2016.3', 'abae92c3301b27bd8a9f56b14f52cb29')
 
     extends('python')
 

var/spack/repos/builtin/packages/py-scipy/package.py

@@ -2,11 +2,12 @@
 
 class PyScipy(Package):
     """Scientific Library for Python."""
-    homepage = "https://pypi.python.org/pypi/scipy"
+    homepage = "http://www.scipy.org/"
     url      = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
 
-    version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
+    version('0.17.0', '5ff2971e1ce90e762c59d2cd84837224')
     version('0.15.1', 'be56cd8e60591d6332aac792a5880110')
+    version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
 
     extends('python')
     depends_on('py-nose')

var/spack/repos/builtin/packages/py-setuptools/package.py

@@ -9,6 +9,7 @@ class PySetuptools(Package):
     version('16.0', '0ace0b96233516fc5f7c857d086aa3ad')
     version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06')
     version('19.2', '78353b1f80375ca5e088f4b4627ffe03')
+    version('20.5', 'fadc1e1123ddbe31006e5e43e927362b')
 
     extends('python')
 

var/spack/repos/builtin/packages/py-six/package.py

@@ -6,6 +6,7 @@ class PySix(Package):
     url      = "https://pypi.python.org/packages/source/s/six/six-1.9.0.tar.gz"
 
     version('1.9.0', '476881ef4012262dfc8adc645ee786c4')
+    version('1.10.0', '34eed507548117b2ab523ab14b2f8b55')
 
     extends('python')
     depends_on('py-setuptools')

var/spack/repos/builtin/packages/py-tuiview/package.py

@@ -0,0 +1,19 @@
+from spack import *
+
+class PyTuiview(Package):
+    """
+       TuiView is a lightweight raster GIS with powerful raster attribute
+       table manipulation abilities.
+    """
+    homepage = "https://bitbucket.org/chchrsc/tuiview"
+    url      = "https://bitbucket.org/chchrsc/tuiview/get/tuiview-1.1.7.tar.gz"
+
+    version('1.1.7', '4b3b38a820cc239c8ab4a181ac5d4c30')
+
+    extends("python")
+    depends_on("py-pyqt")
+    depends_on("py-numpy")
+    depends_on("gdal")
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/repos/builtin/packages/py-virtualenv/package.py

@@ -8,6 +8,7 @@ class PyVirtualenv(Package):
 
     version('1.11.6', 'f61cdd983d2c4e6aeabb70b1060d6f49')
     version('13.0.1', '1ffc011bde6667f0e37ecd976f4934db')
+    version('15.0.1', '28d76a0d9cbd5dc42046dd14e76a6ecc')
 
     extends('python')
     depends_on('py-setuptools')

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

@@ -105,10 +105,13 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
 
         pythonpath = ':'.join(python_paths)
         spack_env.set('PYTHONPATH', pythonpath)
-        run_env.set('PYTHONPATH', pythonpath)
+
+        # For run time environment set only the path for extension_spec and prepend it to PYTHONPATH
+        if extension_spec.package.extends(self.spec):
+            run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))
 
 
-    def modify_module(self, module, spec, ext_spec):
+    def setup_dependent_package(self, module, ext_spec):
         """
         Called before python modules' install() methods.
 
@@ -118,17 +121,18 @@ def modify_module(self, module, spec, ext_spec):
         """
         # Python extension builds can have a global python executable function
         if self.version >= Version("3.0.0") and self.version < Version("4.0.0"):
-            module.python = Executable(join_path(spec.prefix.bin, 'python3'))
+            module.python = Executable(join_path(self.spec.prefix.bin, 'python3'))
         else:
-            module.python = Executable(join_path(spec.prefix.bin, 'python'))
+            module.python = Executable(join_path(self.spec.prefix.bin, 'python'))
 
         # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
         module.python_lib_dir     = os.path.join(ext_spec.prefix, self.python_lib_dir)
         module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir)
         module.site_packages_dir  = os.path.join(ext_spec.prefix, self.site_packages_dir)
 
-        # Make the site packages directory if it does not exist already.
+        # Make the site packages directory for extensions, if it does not exist already.
-        mkdirp(module.site_packages_dir)
+        if ext_spec.package.is_extension:
+            mkdirp(module.site_packages_dir)
 
     # ========================================================================
     # Handle specifics of activating and deactivating python modules.

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

@@ -30,7 +30,7 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
         # The actual installation path for this gem
         spack_env.set('GEM_HOME', extension_spec.prefix)
 
-    def modify_module(self, module, spec, ext_spec):
+    def setup_dependent_package(self, module, ext_spec):
         """Called before ruby modules' install() methods.  Sets GEM_HOME
         and GEM_PATH to values appropriate for the package being built.
 
@@ -39,5 +39,5 @@ def modify_module(self, module, spec, ext_spec):
             gem('install', '<gem-name>.gem')
         """
         # Ruby extension builds have global ruby and gem functions
-        module.ruby = Executable(join_path(spec.prefix.bin, 'ruby'))
+        module.ruby = Executable(join_path(self.spec.prefix.bin, 'ruby'))
-        module.gem = Executable(join_path(spec.prefix.bin, 'gem'))
+        module.gem = Executable(join_path(self.spec.prefix.bin, 'gem'))

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

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

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

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

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

@@ -0,0 +1,77 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+#import os
+
+class Subversion(Package):
+    """Apache Subversion - an open source version control system."""
+    homepage  = 'https://subversion.apache.org/'
+    url       = 'http://archive.apache.org/dist/subversion/subversion-1.8.13.tar.gz'
+
+    version('1.8.13',    '8065b3698d799507fb72dd7926ed32b6')
+    version('1.9.3',     'a92bcfaec4e5038f82c74a7b5bbd2f46')
+
+    depends_on('apr')
+    depends_on('apr-util')
+    depends_on('zlib')
+    depends_on('sqlite')
+
+    # Optional: We need swig if we want the Perl, Python or Ruby
+    # bindings.
+    #depends_on('swig')
+    #depends_on('python')
+    #depends_on('perl')
+    #depends_on('ruby')
+
+    def install(self, spec, prefix):
+
+        # configure, build, install:
+        # Ref: http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html
+        options = ['--prefix=%s' % prefix]
+        options.append('--with-apr=%s' % spec['apr'].prefix)
+        options.append('--with-apr-util=%s' % spec['apr-util'].prefix)
+        options.append('--with-zlib=%s' % spec['zlib'].prefix)
+        options.append('--with-sqlite=%s' % spec['sqlite'].prefix)
+        #options.append('--with-swig=%s' % spec['swig'].prefix)
+
+        configure(*options)
+        make()
+        make('install')
+
+        # python bindings
+        #make('swig-py',
+        #     'swig-pydir=/usr/lib/python2.7/site-packages/libsvn',
+        #     'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn')
+        #make('install-swig-py',
+        #     'swig-pydir=/usr/lib/python2.7/site-packages/libsvn',
+        #     'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn')
+
+        # perl bindings
+        #make('swig-pl')
+        #make('install-swig-pl')
+
+        # ruby bindings
+        #make('swig-rb')
+        #make('isntall-swig-rb')

var/spack/repos/builtin/packages/suite-sparse/package.py

@@ -1,7 +1,7 @@
 from spack import *
 
 
-class Suitesparse(Package):
+class SuiteSparse(Package):
     """
     SuiteSparse is a suite of sparse matrix algorithms
     """
@@ -23,5 +23,14 @@ def install(self, spec, prefix):
 
         # FIXME : this actually uses the current workaround
         # FIXME : (blas / lapack always provide libblas and liblapack as aliases)
-        make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack')
+        make('install', 'INSTALL=%s' % prefix,
 
+             # inject Spack compiler wrappers
+             'AUTOCC=no',
+             'CC=cc',
+             'CXX=c++',
+             'F77=f77',
+
+             # BLAS arguments require path to libraries
+             'BLAS=-lblas',
+             'LAPACK=-llapack')

var/spack/repos/builtin/packages/superlu-dist/package.py

@@ -1,4 +1,5 @@
 from spack import *
+import glob
 
 class SuperluDist(Package):
     """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines."""
@@ -52,12 +53,13 @@ def install(self, spec, prefix):
         # system "make"
 
         # need to install by hand
-        headers_location = join_path(self.prefix.include,'superlu_dist')
+        headers_location = self.prefix.include
         mkdirp(headers_location)
-        # FIXME: fetch all headers in the folder automatically
+        mkdirp(prefix.lib)
-        for header in ['Cnames.h','cublas_utils.h','dcomplex.h','html_mainpage.h','machines.h','old_colamd.h','psymbfact.h','superlu_ddefs.h','superlu_defs.h','superlu_enum_consts.h','superlu_zdefs.h','supermatrix.h','util_dist.h']:
+
-            superludist_header = join_path(self.stage.source_path, 'SRC/',header)
+        headers = glob.glob(join_path(self.stage.source_path, 'SRC','*.h'))
-            install(superludist_header, headers_location)
+        for h in headers:
+            install(h,headers_location)
 
         superludist_lib = join_path(self.stage.source_path, 'lib/libsuperlu_dist.a')
         install(superludist_lib,self.prefix.lib)

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

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

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

@@ -1,15 +1,22 @@
 from spack import *
+import os, sys, glob
 
-
+# Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it:
+# https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111
+# https://github.com/koecher/candi/blob/master/deal.II-toolchain/packages/trilinos.package
+# https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh
+# https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb
+# and some relevant documentation/examples:
+# https://github.com/trilinos/Trilinos/issues/175
 class Trilinos(Package):
-    """
+    """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
-    The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
     software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.
     A unique design feature of Trilinos is its focus on packages.
     """
     homepage = "https://trilinos.org/"
     url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz"
 
+    version('12.6.1', 'adcf2d3aab74cdda98f88fee19cd1442604199b0515ee3da4d80cbe8f37d00e4')
     version('12.4.2', '7c830f7f0f68b8ad324690603baf404e')
     version('12.2.1', '6161926ea247863c690e927687f83be9')
     version('12.0.1', 'bd99741d047471e127b8296b2ec08017')
@@ -17,8 +24,16 @@ class Trilinos(Package):
     version('11.14.2', 'a43590cf896c677890d75bfe75bc6254')
     version('11.14.1', '40febc57f76668be8b6a77b7607bb67f')
 
-    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('metis',        default=True,  description='Compile with METIS and ParMETIS')
-    variant('debug', default=False, description='Builds a debug version of the libraries')
+    variant('mumps',        default=True,  description='Compile with support for MUMPS solvers')
+    variant('superlu-dist', default=True,  description='Compile with SuperluDist solvers')
+    variant('hypre',        default=True,  description='Compile with Hypre preconditioner')
+    variant('hdf5',         default=True,  description='Compile with HDF5')
+    variant('suite-sparse', default=True,  description='Compile with SuiteSparse solvers')
+    # not everyone has py-numpy activated, keep it disabled by default to avoid configure errors
+    variant('python',       default=False, description='Build python wrappers')
+    variant('shared',       default=True,  description='Enables the build of shared libraries')
+    variant('debug',        default=False, description='Builds a debug version of the libraries')
 
     # Everything should be compiled with -fpic
     depends_on('blas')
@@ -27,28 +42,205 @@ class Trilinos(Package):
     depends_on('matio')
     depends_on('glm')
     depends_on('swig')
+    depends_on('metis',when='+metis')
+    depends_on('suite-sparse',when='+suite-sparse')
 
     # MPI related dependencies
     depends_on('mpi')
     depends_on('netcdf+mpi')
+    depends_on('parmetis',when='+metis')
+    # Trilinos' Tribits config system is limited which makes it
+    # very tricky to link Amesos with static MUMPS, see
+    # https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html
+    # One could work it out by getting linking flags from mpif90 --showme:link (or alike)
+    # and adding results to -DTrilinos_EXTRA_LINK_FLAGS
+    # together with Blas and Lapack and ScaLAPACK and Blacs and -lgfortran and
+    # it may work at the end. But let's avoid all this by simply using shared libs
+    depends_on('mumps@5.0:+mpi+shared',when='+mumps')
+    depends_on('scalapack',when='+mumps')
+    depends_on('superlu-dist',when='+superlu-dist')
+    depends_on('hypre~internal-superlu',when='+hypre')
+    depends_on('hdf5+mpi',when='+hdf5')
 
-    depends_on('python') #  Needs py-numpy activated
+    depends_on('python',when='+python')
+
+    patch('umfpack_from_suitesparse.patch')
+
+    # check that the combination of variants makes sense
+    def variants_check(self):
+        if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'):
+            # For Trilinos v11 we need to force SuperLUDist=OFF,
+            # since only the deprecated SuperLUDist v3.3 together with an Amesos patch
+            # is working.
+            raise RuntimeError('The superlu-dist variant can only be used with Trilinos @12.0.1:')
 
     def install(self, spec, prefix):
+        self.variants_check()
+
+        cxx_flags = []
         options = []
         options.extend(std_cmake_args)
 
+        mpi_bin = spec['mpi'].prefix.bin
         options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
+                        '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
+                        '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF',
                         '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
                         '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
-                        '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
+                        '-DCMAKE_BUILD_TYPE:STRING=%s' % ('DEBUG' if '+debug' in spec else 'RELEASE'),
                         '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
-                        '-DTPL_ENABLE_MPI:STRING=ON',
+                        '-DTPL_ENABLE_MPI:BOOL=ON',
-                        '-DBLAS_LIBRARY_DIRS:PATH=%s' % spec['blas'].prefix,
+                        '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
-                        '-DLAPACK_LIBRARY_DIRS:PATH=%s' % spec['lapack'].prefix
+                        '-DTPL_ENABLE_BLAS=ON',
+                        '-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names
+                        '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
+                        '-DTPL_ENABLE_LAPACK=ON',
+                        '-DLAPACK_LIBRARY_NAMES=lapack',
+                        '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
+                        '-DTPL_ENABLE_Boost:BOOL=ON',
+                        '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include,
+                        '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib,
+                        '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
+                        '-DTrilinos_ENABLE_CXX11:BOOL=ON',
+                        '-DTPL_ENABLE_Netcdf:BOOL=ON',
+                        '-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'),
+                        '-DTPL_ENABLE_HDF5:BOOL=%s' % ('ON' if '+hdf5' in spec else 'OFF'),
                         ])
 
+        # Fortran lib
+        libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read())
+        options.extend([
+            '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
+            '-DTrilinos_ENABLE_Fortran=ON'
+        ])
+
+        # for build-debug only:
+        #options.extend([
+        #   '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
+        #])
+
+        # suite-sparse related
+        if '+suite-sparse' in spec:
+            options.extend([
+                '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file?
+                #'-DTPL_ENABLE_Cholmod:BOOL=ON',
+                #'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
+                #'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
+                '-DTPL_ENABLE_UMFPACK:BOOL=ON',
+                '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
+                '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
+                '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
+            ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_Cholmod:BOOL=OFF',
+                '-DTPL_ENABLE_UMFPACK:BOOL=OFF',
+            ])
+
+        # metis / parmetis
+        if '+metis' in spec:
+            options.extend([
+                '-DTPL_ENABLE_METIS:BOOL=ON',
+                '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib,
+                '-DMETIS_LIBRARY_NAMES=metis',
+                '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include,
+                '-DTPL_ENABLE_ParMETIS:BOOL=ON',
+                '-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib),
+                '-DParMETIS_LIBRARY_NAMES=parmetis;metis',
+                '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include
+            ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_METIS:BOOL=OFF',
+                '-DTPL_ENABLE_ParMETIS:BOOL=OFF',
+            ])
+
+        # mumps / scalapack
+        if '+mumps' in spec:
+            options.extend([
+                '-DTPL_ENABLE_MUMPS:BOOL=ON',
+                '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
+                '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord', # order is important!
+                '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
+                '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
+            ])
+            # see https://github.com/trilinos/Trilinos/blob/master/packages/amesos/README-MUMPS
+            cxx_flags.extend([
+                '-DMUMPS_5_0'
+            ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_MUMPS:BOOL=OFF',
+                '-DTPL_ENABLE_SCALAPACK:BOOL=OFF',
+            ])
+
+        # superlu-dist:
+        if '+superlu-dist' in spec:
+            # Amesos, conflicting types of double and complex SLU_D
+            # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
+            # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
+            options.extend([
+                '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
+                '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
+            ])
+            options.extend([
+                '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
+                '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib,
+                '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
+            ])
+            if spec.satisfies('^superlu-dist@4.0:'):
+                options.extend([
+                    '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
+                ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_SuperLUDist:BOOL=OFF',
+            ])
+
+
+        # python
+        if '+python' in spec:
+            options.extend([
+                '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON'
+            ])
+        else:
+            options.extend([
+                '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF'
+            ])
+
+        # collect CXX flags:
+        options.extend([
+            '-DCMAKE_CXX_FLAGS:STRING=%s' % (' '.join(cxx_flags)),
+        ])
+
+        # disable due to compiler / config errors:
+        options.extend([
+            '-DTrilinos_ENABLE_SEACAS=OFF',
+            '-DTrilinos_ENABLE_Pike=OFF',
+            '-DTrilinos_ENABLE_STK=OFF'
+        ])
+        if sys.platform == 'darwin':
+            options.extend([
+                '-DTrilinos_ENABLE_FEI=OFF'
+            ])
+
+
         with working_dir('spack-build', create=True):
             cmake('..', *options)
             make()
             make('install')
+
+            # When trilinos is built with Python, libpytrilinos is included through
+            # cmake configure files. Namely, Trilinos_LIBRARIES in TrilinosConfig.cmake
+            # contains pytrilinos. This leads to a run-time error:
+            # Symbol not found: _PyBool_Type
+            # and prevents Trilinos to be used in any C++ code, which links executable
+            # against the libraries listed in Trilinos_LIBRARIES.
+            # See https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509
+            # A workaround it to remove PyTrilinos from the COMPONENTS_LIST :
+            if '+python' in self.spec:
+                filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)',  (r'\1\3'),  '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib)
+
+            # The shared libraries are not installed correctly on Darwin; correct this
+            if (sys.platform == 'darwin') and ('+shared' in spec):
+                fix_darwin_install_name(prefix.lib)

var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch

@@ -0,0 +1,12 @@
+diff --git a/cmake/TPLs/FindTPLUMFPACK.cmake b/cmake/TPLs/FindTPLUMFPACK.cmake
+index 963eb71..998cd02 100644
+--- a/cmake/TPLs/FindTPLUMFPACK.cmake
++++ b/cmake/TPLs/FindTPLUMFPACK.cmake
+@@ -55,6 +55,6 @@
+
+
+ TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( UMFPACK
+-  REQUIRED_HEADERS umfpack.h amd.h UFconfig.h
++  REQUIRED_HEADERS umfpack.h amd.h SuiteSparse_config.h
+   REQUIRED_LIBS_NAMES umfpack amd
+   )