Merge branch 'develop' of https://github.com/LLNL/spack into packages/swift_durham

bin/spack

@@ -77,7 +77,7 @@ import llnl.util.tty as tty
 from llnl.util.tty.color import *
 import spack
 from spack.error import SpackError
-from external import argparse
+import argparse
 
 # Command parsing
 parser = argparse.ArgumentParser(

lib/spack/docs/configuration.rst

@@ -140,7 +140,6 @@ Here's an example packages.yaml file that sets preferred packages:
     packages:
       dyninst:
         compiler: [gcc@4.9]
-        variants: +debug
       gperftools:
         version: [2.2, 2.4, 2.3]
       all:
@@ -150,8 +149,8 @@ Here's an example packages.yaml file that sets preferred packages:
 
 
 At a high level, this example is specifying how packages should be
-concretized.  The dyninst package should prefer using gcc 4.9 and
+concretized.  The dyninst package should prefer using gcc 4.9.
-be built with debug options.  The gperftools package should prefer version
+The gperftools package should prefer version
 2.2 over 2.4.  Every package on the system should prefer mvapich for
 its MPI and gcc 4.4.7 (except for Dyninst, which overrides this by preferring gcc 4.9).
 These options are used to fill in implicit defaults.  Any of them can be overwritten
@@ -160,7 +159,7 @@ on the command line if explicitly requested.
 Each packages.yaml file begins with the string ``packages:`` and
 package names are specified on the next level. The special string ``all``
 applies settings to each package. Underneath each package name is
-one or more components: ``compiler``, ``variants``, ``version``,
+one or more components: ``compiler``, ``version``,
 or ``providers``.  Each component has an ordered list of spec
 ``constraints``, with earlier entries in the list being preferred over
 later entries.

lib/spack/llnl/util/filesystem.py

@@ -48,7 +48,7 @@
 def filter_file(regex, repl, *filenames, **kwargs):
     """Like sed, but uses python regular expressions.
 
-       Filters every line of file through regex and replaces the file
+       Filters every line of each file through regex and replaces the file
        with a filtered version.  Preserves mode of filtered files.
 
        As with re.sub, ``repl`` can be either a string or a callable.
@@ -59,7 +59,7 @@ def filter_file(regex, repl, *filenames, **kwargs):
 
        Keyword Options:
          string[=False]         If True, treat regex as a plain string.
-         backup[=True]          Make a backup files suffixed with ~
+         backup[=True]          Make backup file(s) suffixed with ~
          ignore_absent[=False]  Ignore any files that don't exist.
     """
     string = kwargs.get('string', False)
@@ -80,26 +80,26 @@ def groupid_to_group(x):
         regex = re.escape(regex)
 
     for filename in filenames:
-        backup = filename + "~"
+        backup_filename = filename + "~"
 
         if ignore_absent and not os.path.exists(filename):
             continue
 
-        shutil.copy(filename, backup)
+        shutil.copy(filename, backup_filename)
         try:
-            with closing(open(backup)) as infile:
+            with closing(open(backup_filename)) as infile:
                 with closing(open(filename, 'w')) as outfile:
                     for line in infile:
                         foo = re.sub(regex, repl, line)
                         outfile.write(foo)
         except:
             # clean up the original file on failure.
-            shutil.move(backup, filename)
+            shutil.move(backup_filename, filename)
             raise
 
         finally:
             if not backup:
-                shutil.rmtree(backup, ignore_errors=True)
+                os.remove(backup_filename)
 
 
 class FileFilter(object):
@@ -114,7 +114,7 @@ def filter(self, regex, repl, **kwargs):
 def change_sed_delimiter(old_delim, new_delim, *filenames):
     """Find all sed search/replace commands and change the delimiter.
        e.g., if the file contains seds that look like 's///', you can
-       call change_sed_delimeter('/', '@', file) to change the
+       call change_sed_delimiter('/', '@', file) to change the
        delimiter to '@'.
 
        NOTE that this routine will fail if the delimiter is ' or ".
@@ -179,7 +179,7 @@ def install(src, dest):
     """Manually install a file to a particular location."""
     tty.debug("Installing %s to %s" % (src, dest))
 
-    # Expand dsst to its eventual full path if it is a directory.
+    # Expand dest to its eventual full path if it is a directory.
     if os.path.isdir(dest):
         dest = join_path(dest, os.path.basename(src))
 
@@ -219,7 +219,7 @@ def mkdirp(*paths):
         if not os.path.exists(path):
             os.makedirs(path)
         elif not os.path.isdir(path):
-            raise OSError(errno.EEXIST, "File alredy exists", path)
+            raise OSError(errno.EEXIST, "File already exists", path)
 
 
 def force_remove(*paths):
@@ -309,7 +309,7 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
 
     Optional args:
 
-    order=[pre|post] -- Whether to do pre- or post-order traveral.
+    order=[pre|post] -- Whether to do pre- or post-order traversal.
 
     ignore=<predicate> -- Predicate indicating which files to ignore.
 
@@ -414,7 +414,7 @@ def fix_darwin_install_name(path):
     currently won't follow subfolders.
 
     Args:
-        path: directory in which .dylib files are alocated
+        path: directory in which .dylib files are located
 
     """
     libs = glob.glob(join_path(path, "*.dylib"))
@@ -438,7 +438,7 @@ def to_link_flags(library):
       A string of linking flags.
     """
     dir  = os.path.dirname(library)
-    # Asume   libXYZ.suffix
+    # Assume libXYZ.suffix
     name = os.path.basename(library)[3:].split(".")[0]
     res = '-L%s -l%s' % (dir, name)
     return res

lib/spack/spack/cmd/repo.py

@@ -26,7 +26,7 @@
 import re
 import shutil
 
-from external import argparse
+import argparse
 import llnl.util.tty as tty
 from llnl.util.filesystem import join_path, mkdirp
 

lib/spack/spack/config.py

@@ -307,6 +307,8 @@
                     'autoload': {'$ref': '#/definitions/dependency_selection'},
                     'prerequisites': {'$ref': '#/definitions/dependency_selection'},
                     'conflict': {'$ref': '#/definitions/array_of_strings'},
+                    'load': {'$ref': '#/definitions/array_of_strings'},
+                    'suffixes': {'$ref': '#/definitions/dictionary_of_strings'},
                     'environment': {
                         'type': 'object',
                         'default': {},

lib/spack/spack/database.py

@@ -631,11 +631,13 @@ def _exit(self):
 class CorruptDatabaseError(SpackError):
     def __init__(self, path, msg=''):
         super(CorruptDatabaseError, self).__init__(
-            "Spack database is corrupt: %s.  %s" % (path, msg))
+            "Spack database is corrupt: %s.  %s." + \
+            "Try running `spack reindex` to fix." % (path, msg))
 
 
 class InvalidDatabaseVersionError(SpackError):
     def __init__(self, expected, found):
         super(InvalidDatabaseVersionError, self).__init__(
-            "Expected database version %s but found version %s" %
+            "Expected database version %s but found version %s." + \
+            "Try running `spack reindex` to fix." %
             (expected, found))

lib/spack/spack/modules.py

@@ -285,11 +285,18 @@ def use_name(self):
         naming_tokens = self.tokens
         naming_scheme = self.naming_scheme
         name = naming_scheme.format(**naming_tokens)
-        name += '-' + self.spec.dag_hash(
-        )  # Always append the hash to make the module file unique
         # Not everybody is working on linux...
         parts = name.split('/')
         name = join_path(*parts)
+        # Add optional suffixes based on constraints
+        configuration, _ = parse_config_options(self)
+        suffixes = [name]
+        for constraint, suffix in configuration.get('suffixes', {}).items():
+            if constraint in self.spec:
+                suffixes.append(suffix)
+        # Always append the hash to make the module file unique
+        suffixes.append(self.spec.dag_hash())
+        name = '-'.join(suffixes)
         return name
 
     @property
@@ -381,6 +388,8 @@ def write(self):
         for x in filter_blacklisted(
                 module_configuration.pop('autoload', []), self.name):
             module_file_content += self.autoload(x)
+        for x in module_configuration.pop('load', []):
+            module_file_content += self.autoload(x)
         for x in filter_blacklisted(
                 module_configuration.pop('prerequisites', []), self.name):
             module_file_content += self.prerequisite(x)
@@ -402,8 +411,12 @@ def module_specific_content(self, configuration):
         return tuple()
 
     def autoload(self, spec):
-        m = type(self)(spec)
+        if not isinstance(spec, str):
-        return self.autoload_format.format(module_file=m.use_name)
+            m = type(self)(spec)
+            module_file = m.use_name
+        else:
+            module_file = spec
+        return self.autoload_format.format(module_file=module_file)
 
     def prerequisite(self, spec):
         m = type(self)(spec)

lib/spack/spack/repository.py

@@ -30,7 +30,7 @@
 import re
 import traceback
 from bisect import bisect_left
-from external import yaml
+import yaml
 
 import llnl.util.tty as tty
 from llnl.util.filesystem import *

lib/spack/spack/test/modules.py

@@ -27,6 +27,7 @@
 
 import StringIO
 import spack.modules
+import unittest
 from spack.test.mock_packages_test import MockPackagesTest
 
 FILE_REGISTRY = collections.defaultdict(StringIO.StringIO)
@@ -67,6 +68,24 @@ def mock_open(filename, mode):
     }
 }
 
+configuration_prerequisites_direct = {
+    'enable': ['tcl'],
+    'tcl': {
+        'all': {
+            'prerequisites': 'direct'
+        }
+    }
+}
+
+configuration_prerequisites_all = {
+    'enable': ['tcl'],
+    'tcl': {
+        'all': {
+            'prerequisites': 'all'
+        }
+    }
+}
+
 configuration_alter_environment = {
     'enable': ['tcl'],
     'tcl': {
@@ -74,8 +93,13 @@ def mock_open(filename, mode):
             'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']}
         },
         'platform=test target=x86_64': {
-            'environment': {'set': {'FOO': 'foo'},
+            'environment': {
-                            'unset': ['BAR']}
+                'set': {'FOO': 'foo'},
+                'unset': ['BAR']
+            }
+        },
+        'platform=test target=x86_32': {
+            'load': ['foo/bar']
         }
     }
 }
@@ -83,7 +107,8 @@ def mock_open(filename, mode):
 configuration_blacklist = {
     'enable': ['tcl'],
     'tcl': {
-        'blacklist': ['callpath'],
+        'whitelist': ['zmpi'],
+        'blacklist': ['callpath', 'mpi'],
         'all': {
             'autoload': 'direct'
         }
@@ -100,8 +125,68 @@ def mock_open(filename, mode):
     }
 }
 
+configuration_wrong_conflicts = {
+    'enable': ['tcl'],
+    'tcl': {
+        'naming_scheme': '{name}/{version}-{compiler.name}',
+        'all': {
+            'conflict': ['{name}/{compiler.name}']
+        }
+    }
+}
+
+configuration_suffix = {
+    'enable': ['tcl'],
+    'tcl': {
+        'mpileaks': {
+            'suffixes': {
+                '+debug': 'foo',
+                '~debug': 'bar'
+            }
+        }
+    }
+}
+
+
+class HelperFunctionsTests(unittest.TestCase):
+
+    def test_update_dictionary_extending_list(self):
+        target = {
+            'foo': {
+                'a': 1,
+                'b': 2,
+                'd': 4
+            },
+            'bar': [1, 2, 4],
+            'baz': 'foobar'
+        }
+        update = {
+            'foo': {
+                'c': 3,
+            },
+            'bar': [3],
+            'baz': 'foobaz',
+            'newkey': {
+                'd': 4
+            }
+        }
+        spack.modules.update_dictionary_extending_lists(target, update)
+        self.assertTrue(len(target) == 4)
+        self.assertTrue(len(target['foo']) == 4)
+        self.assertTrue(len(target['bar']) == 4)
+        self.assertEqual(target['baz'], 'foobaz')
+
+    def test_inspect_path(self):
+        env = spack.modules.inspect_path('/usr')
+        names = [item.name for item in env]
+        self.assertTrue('PATH' in names)
+        self.assertTrue('LIBRARY_PATH' in names)
+        self.assertTrue('LD_LIBRARY_PATH' in names)
+        self.assertTrue('CPATH' in names)
+
 
 class TclTests(MockPackagesTest):
+
     def setUp(self):
         super(TclTests, self).setUp()
         self.configuration_obj = spack.modules.CONFIGURATION
@@ -116,7 +201,6 @@ def tearDown(self):
 
     def get_modulefile_content(self, spec):
         spec.concretize()
-        print spec, '&&&&&'
         generator = spack.modules.TclModule(spec)
         generator.write()
         content = FILE_REGISTRY[generator.file_name].split('\n')
@@ -127,6 +211,8 @@ def test_simple_case(self):
         spec = spack.spec.Spec('mpich@3.0.4')
         content = self.get_modulefile_content(spec)
         self.assertTrue('module-whatis "mpich @3.0.4"' in content)
+        self.assertRaises(TypeError, spack.modules.dependencies,
+                          spec, 'non-existing-tag')
 
     def test_autoload(self):
         spack.modules.CONFIGURATION = configuration_autoload_direct
@@ -141,11 +227,21 @@ def test_autoload(self):
         self.assertEqual(len([x for x in content if 'is-loaded' in x]), 5)
         self.assertEqual(len([x for x in content if 'module load ' in x]), 5)
 
+    def test_prerequisites(self):
+        spack.modules.CONFIGURATION = configuration_prerequisites_direct
+        spec = spack.spec.Spec('mpileaks arch=x86-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(len([x for x in content if 'prereq' in x]), 2)
+
+        spack.modules.CONFIGURATION = configuration_prerequisites_all
+        spec = spack.spec.Spec('mpileaks arch=x86-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(len([x for x in content if 'prereq' in x]), 5)
+
     def test_alter_environment(self):
         spack.modules.CONFIGURATION = configuration_alter_environment
         spec = spack.spec.Spec('mpileaks platform=test target=x86_64')
         content = self.get_modulefile_content(spec)
-        print content
         self.assertEqual(
             len([x
                  for x in content
@@ -156,7 +252,6 @@ def test_alter_environment(self):
 
         spec = spack.spec.Spec('libdwarf %clang platform=test target=x86_32')
         content = self.get_modulefile_content(spec)
-        print content
         self.assertEqual(
             len([x
                  for x in content
@@ -164,6 +259,10 @@ def test_alter_environment(self):
         self.assertEqual(
             len([x for x in content if 'setenv FOO "foo"' in x]), 0)
         self.assertEqual(len([x for x in content if 'unsetenv BAR' in x]), 0)
+        self.assertEqual(
+            len([x for x in content if 'is-loaded foo/bar' in x]), 1)
+        self.assertEqual(
+            len([x for x in content if 'module load foo/bar' in x]), 1)
 
     def test_blacklist(self):
         spack.modules.CONFIGURATION = configuration_blacklist
@@ -171,6 +270,13 @@ def test_blacklist(self):
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'is-loaded' in x]), 1)
         self.assertEqual(len([x for x in content if 'module load ' in x]), 1)
+        spec = spack.spec.Spec('callpath arch=x86-linux')
+        # Returns a StringIO instead of a string as no module file was written
+        self.assertRaises(AttributeError, self.get_modulefile_content, spec)
+        spec = spack.spec.Spec('zmpi arch=x86-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(len([x for x in content if 'is-loaded' in x]), 1)
+        self.assertEqual(len([x for x in content if 'module load ' in x]), 1)
 
     def test_conflicts(self):
         spack.modules.CONFIGURATION = configuration_conflicts
@@ -182,3 +288,57 @@ def test_conflicts(self):
             len([x for x in content if x == 'conflict mpileaks']), 1)
         self.assertEqual(
             len([x for x in content if x == 'conflict intel/14.0.1']), 1)
+
+        spack.modules.CONFIGURATION = configuration_wrong_conflicts
+        self.assertRaises(SystemExit, self.get_modulefile_content, spec)
+
+    def test_suffixes(self):
+        spack.modules.CONFIGURATION = configuration_suffix
+        spec = spack.spec.Spec('mpileaks+debug arch=x86-linux')
+        spec.concretize()
+        generator = spack.modules.TclModule(spec)
+        self.assertTrue('foo' in generator.use_name)
+
+        spec = spack.spec.Spec('mpileaks~debug arch=x86-linux')
+        spec.concretize()
+        generator = spack.modules.TclModule(spec)
+        self.assertTrue('bar' in generator.use_name)
+
+
+configuration_dotkit = {
+    'enable': ['dotkit'],
+    'dotkit': {
+        'all': {
+            'prerequisites': 'direct'
+        }
+    }
+}
+
+
+class DotkitTests(MockPackagesTest):
+
+    def setUp(self):
+        super(DotkitTests, self).setUp()
+        self.configuration_obj = spack.modules.CONFIGURATION
+        spack.modules.open = mock_open
+        # Make sure that a non-mocked configuration will trigger an error
+        spack.modules.CONFIGURATION = None
+
+    def tearDown(self):
+        del spack.modules.open
+        spack.modules.CONFIGURATION = self.configuration_obj
+        super(DotkitTests, self).tearDown()
+
+    def get_modulefile_content(self, spec):
+        spec.concretize()
+        generator = spack.modules.Dotkit(spec)
+        generator.write()
+        content = FILE_REGISTRY[generator.file_name].split('\n')
+        return content
+
+    def test_dotkit(self):
+        spack.modules.CONFIGURATION = configuration_dotkit
+        spec = spack.spec.Spec('mpileaks arch=x86-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertTrue('#c spack' in content)
+        self.assertTrue('#d mpileaks @2.3' in content)

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

@@ -1,15 +1,18 @@
 import os
 
 from spack import *
+
+
 class Adios(Package):
-    """The Adaptable IO System (ADIOS) provides a simple, 
+    """
-        flexible way for scientists to describe the 
+    The Adaptable IO System (ADIOS) provides a simple,
-        data in their code that may need to be written, 
+    flexible way for scientists to describe the
-        read, or processed outside of the running simulation
+    data in their code that may need to be written,
+    read, or processed outside of the running simulation
     """
 
     homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
-    url      = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz"
+    url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz"
 
     version('1.9.0', 'dbf5cb10e32add2f04c9b4052b7ffa76')
 
@@ -27,7 +30,7 @@ def install(self, spec, prefix):
                           "--with-hdf5=%s" % spec['hdf5'].prefix,
                           "--with-netcdf=%s" % os.environ["NETCDF_DIR"],
                           "--with-infiniband=no",
-                          "MPICC=cc","MPICXX=CC","MPIFC=ftn",
+                          "MPICC=cc", "MPICXX=CC", "MPIFC=ftn",
                           "CPPFLAGS=-DMPICH_IGNORE_CXX_SEEK"]
 
         if spec.satisfies('%gcc'):

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

@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Curl(Package):
     """cURL is an open source command line tool and library for
     transferring data with URL syntax"""
@@ -31,6 +32,7 @@ class Curl(Package):
     homepage = "http://curl.haxx.se"
     url      = "http://curl.haxx.se/download/curl-7.46.0.tar.bz2"
 
+    version('7.49.1', '6bb1f7af5b58b30e4e6414b8c1abccab')
     version('7.47.1', '9ea3123449439bbd960cd25cf98796fb')
     version('7.46.0', '9979f989a2a9930d10f1b3deeabc2148')
     version('7.45.0', '62c1a352b28558f25ba6209214beadc8')

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

@@ -23,23 +23,44 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+import llnl.util.tty as tty
+
 
 class Emacs(Package):
     """The Emacs programmable text editor."""
+
     homepage = "https://www.gnu.org/software/emacs"
     url      = "http://ftp.gnu.org/gnu/emacs/emacs-24.5.tar.gz"
 
     version('24.5', 'd74b597503a68105e61b5b9f6d065b44')
 
+    variant('X', default=True, description="Enable a X toolkit (GTK+)")
+    variant('gtkplus', default=False, description="Enable a GTK+ as X toolkit (this variant is ignored if ~X)")
+
     depends_on('ncurses')
-    # Emacs also depends on:
+    depends_on('libtiff', when='+X')
-    #     GTK or other widget library
+    depends_on('libpng', when='+X')
-    #     libtiff, png, etc.
+    depends_on('libxpm', when='+X')
-    # For now, we assume the system provides all that stuff.
+    depends_on('giflib', when='+X')
-    # For Ubuntu 14.04 LTS:
+    depends_on('gtkplus', when='+X+gtkplus')
-    #     sudo apt-get install libgtk-3-dev libxpm-dev libtiff5-dev libjpeg8-dev libgif-dev libpng12-dev
 
     def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
+        args = []
+        if '+X' in spec:
+            if '+gtkplus' in spec:
+                toolkit = 'gtk{0}'.format(spec['gtkplus'].version.up_to(1))
+            else:
+                toolkit = 'no'
+            args = [
+                '--with-x',
+                '--with-x-toolkit={0}'.format(toolkit)
+            ]
+        else:
+            args = ['--without-x']
+            if '+gtkplus' in spec:
+                tty.warn('The variant +gtkplus is ignored if ~X is selected.')
+
+        configure('--prefix={0}'.format(prefix), *args)
+
         make()
         make("install")

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

@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 Giflib(Package):
+    """The GIFLIB project maintains the giflib service library, which has
+    been pulling images out of GIFs since 1989."""
+
+    homepage = "http://giflib.sourceforge.net/"
+    url      = "https://downloads.sourceforge.net/project/giflib/giflib-5.1.4.tar.bz2"
+
+    version('5.1.4', '2c171ced93c0e83bb09e6ccad8e3ba2b')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")

var/spack/repos/builtin/packages/glib/g_date_strftime.patch

@@ -0,0 +1,34 @@
+From 00148329967adb196138372771052a3f606a6ea3 Mon Sep 17 00:00:00 2001
+From: coypu <coypu@sdf.org>
+Date: Wed, 2 Mar 2016 19:43:10 +0200
+Subject: [PATCH 2/2] gdate: Suppress string format literal warning
+
+Newer versions of GCC emit an error here, but we know it's safe.
+https://bugzilla.gnome.org/761550
+---
+ glib/gdate.c | 5 +++++
+ 1 file changed, 5 insertions(+)
+
+diff --git a/glib/gdate.c b/glib/gdate.c
+index 4aece02..92c34d2 100644
+--- a/glib/gdate.c
++++ b/glib/gdate.c
+@@ -2439,6 +2439,9 @@ win32_strftime_helper (const GDate     *d,
+  *
+  * Returns: number of characters written to the buffer, or 0 the buffer was too small
+  */
++#pragma GCC diagnostic push
++#pragma GCC diagnostic ignored "-Wformat-nonliteral"
++
+ gsize     
+ g_date_strftime (gchar       *s, 
+                  gsize        slen, 
+@@ -2549,3 +2552,5 @@ g_date_strftime (gchar       *s,
+   return retval;
+ #endif
+ }
++
++#pragma GCC diagnostic pop
+-- 
+2.7.1
+

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

@@ -25,20 +25,24 @@
 from spack import *
 import sys
 
+
 class Glib(Package):
     """The GLib package contains a low-level libraries useful for
        providing data structure handling for C, portability wrappers
        and interfaces for such runtime functionality as an event loop,
        threads, dynamic loading and an object system."""
     homepage = "https://developer.gnome.org/glib/"
-    url      = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz"
+    url = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz"
 
     version('2.42.1', '89c4119e50e767d3532158605ee9121a')
 
     depends_on("libffi")
     depends_on("zlib")
     depends_on("pkg-config")
-    depends_on('gettext', sys.platform=='darwin')
+    depends_on('gettext', sys.platform == 'darwin')
+
+    # The following patch is needed for gcc-6.1
+    patch('g_date_strftime.patch')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)

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

@@ -22,8 +22,9 @@
 # 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 Julia(Package):
     """The Julia Language: A fresh approach to technical computing"""
@@ -32,10 +33,14 @@ class Julia(Package):
 
     version('master',
             git='https://github.com/JuliaLang/julia.git', branch='master')
+    version('release-0.4',
+            git='https://github.com/JuliaLang/julia.git', branch='release-0.4')
+    version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d', preferred=True)
     version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6')
     version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac')
 
-    patch('gc.patch')
+    patch('gc.patch', when='@0.4:0.4.5')
+    patch('gc.patch', when='@release-0.4')
     patch('openblas.patch', when='@0.4:0.4.5')
 
     # Build-time dependencies:
@@ -92,25 +97,21 @@ class Julia(Package):
     depends_on("mpi")
 
     def install(self, spec, prefix):
-        if '@master' in spec:
-            # Julia needs to know the offset from a specific commit
-            git = which('git')
-            git('fetch', '--unshallow')
-
         # Explicitly setting CC, CXX, or FC breaks building libuv, one
         # of Julia's dependencies. This might be a Darwin-specific
         # problem. Given how Spack sets up compilers, Julia should
         # still use Spack's compilers, even if we don't specify them
         # explicitly.
-        options = [#"CC=cc",
+        options = [
-                   #"CXX=c++",
+            # "CC=cc",
-                   #"FC=fc",
+            # "CXX=c++",
-                   #"USE_SYSTEM_ARPACK=1",
+            # "FC=fc",
-                   #"USE_SYSTEM_FFTW=1",
+            # "USE_SYSTEM_ARPACK=1",
-                   #"USE_SYSTEM_GMP=1",
+            # "USE_SYSTEM_FFTW=1",
-                   #"USE_SYSTEM_MPFR=1",
+            # "USE_SYSTEM_GMP=1",
-                   #TODO "USE_SYSTEM_PCRE=1",
+            # "USE_SYSTEM_MPFR=1",
-                   "prefix=%s" % prefix]
+            # "USE_SYSTEM_PCRE=1",
+            "prefix=%s" % prefix]
         with open('Make.user', 'w') as f:
             f.write('\n'.join(options) + '\n')
         make()

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

@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 Libxpm(Package):
+    """Xpm file format library"""
+
+    homepage = "https://www.x.org/"
+    url      = "https://www.x.org/archive//individual/lib/libXpm-3.5.11.tar.gz"
+
+    version('3.5.11', '7c67c878ee048206b070bc0b24154f04')
+    version('3.5.10', 'a70507638d74541bf30a771f1e5938bb')
+    version('3.5.9', 'd6d4b0f76248a6b346eb42dfcdaa72a6')
+    version('3.5.8', '2d81d6633e67ac5562e2fbee126b2897')
+    version('3.5.7', '7bbc8f112f7143ed6961a58ce4e14558')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")

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

@@ -50,6 +50,11 @@ class Mpich(Package):
     provides('mpi@:1.3', when='@1:')
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
+        spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
+        spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
+        spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
+
         spack_env.set('MPICH_CC', spack_cc)
         spack_env.set('MPICH_CXX', spack_cxx)
         spack_env.set('MPICH_F77', spack_f77)

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

@@ -191,6 +191,11 @@ def setup_environment(self, spack_env, run_env):
             run_env.set('SLURM_MPI_TYPE', 'pmi2')
 
     def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+        spack_env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
+        spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpicxx'))
+        spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
+        spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
+
         spack_env.set('MPICH_CC', spack_cc)
         spack_env.set('MPICH_CXX', spack_cxx)
         spack_env.set('MPICH_F77', spack_f77)

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

@@ -1,14 +1,15 @@
-import os
 from spack import *
 
+
 class Mxml(Package):
-    """Mini-XML is a small XML library that you can use to read and write XML 
+    """
-       and XML-like data files in your application without requiring large 
+    Mini-XML is a small XML library that you can use to read and write XML
-       non-standard libraries
+    and XML-like data files in your application without requiring large
+    non-standard libraries
     """
 
     homepage = "http://www.msweet.org"
-    url      = "http://www.msweet.org/files/project3/mxml-2.9.tar.gz"
+    url = "http://www.msweet.org/files/project3/mxml-2.9.tar.gz"
 
     version('2.9', 'e21cad0f7aacd18f942aa0568a8dee19')
     version('2.8', 'd85ee6d30de053581242c4a86e79a5d2')
@@ -16,11 +17,11 @@ class Mxml(Package):
     version('2.6', '68977789ae64985dddbd1a1a1652642e')
     version('2.5', 'f706377fba630b39fa02fd63642b17e5')
 
-    # module swap PrgEnv-intel PrgEnv-$COMP (Can use whatever compiler you want to use) 
+    # module swap PrgEnv-intel PrgEnv-$COMP
+    # (Can use whatever compiler you want to use)
     # Case statement to change CC and CXX flags
 
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix, "--disable-shared", 'CFLAGS=-static')
         make()
         make("install")
-

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

@@ -24,12 +24,14 @@
 ##############################################################################
 from spack import *
 
+
 class NetcdfFortran(Package):
     """Fortran interface for NetCDF4"""
 
     homepage = "http://www.unidata.ucar.edu/software/netcdf"
     url      = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.3.tar.gz"
 
+    version('4.4.4', 'e855c789cd72e1b8bc1354366bf6ac72')
     version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e')
 
     depends_on('netcdf')

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

@@ -109,6 +109,11 @@ def url_for_version(self, version):
         return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version)  # NOQA: ignore=E501
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
+        spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
+        spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
+        spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
+
         spack_env.set('OMPI_CC', spack_cc)
         spack_env.set('OMPI_CXX', spack_cxx)
         spack_env.set('OMPI_FC', spack_fc)

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

@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 PyProtobuf(Package):
+    """Protocol buffers are Google's language-neutral, platform-neutral,
+    extensible mechanism for serializing structured data - think XML, but
+    smaller, faster, and simpler. You define how you want your data to be
+    structured once, then you can use special generated source code to easily
+    write and read your structured data to and from a variety of data streams
+    and using a variety of languages."""
+
+    homepage = 'https://developers.google.com/protocol-buffers/'
+    url      = 'https://pypi.python.org/packages/source/p/protobuf/protobuf-3.0.0b2.tar.gz'
+
+    version('3.0.0b2', 'f0d3bd2394345a9af4a277cd0302ae83')
+    version('2.6.1', '6bf843912193f70073db7f22e2ea55e2')
+    version('2.5.0', '338813f3629d59e9579fed9035ecd457')
+    version('2.4.1', '72f5141d20ab1bcae6b1e00acfb1068a')
+    version('2.3.0', 'bb020c962f252fe81bfda8fb433bafdd')
+
+    extends('python')
+
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix={0}'.format(prefix))