Merge branch 'develop' into eschnett/petsc-python-2

# Conflicts:
#	var/spack/packages/petsc/package.py

18 files changed, 336 insertions, 78 deletions

diff --git a/var/spack/packages/cgal/package.py b/var/spack/packages/cgal/package.py
new file mode 100644
index 0000000000..97356433be
--- /dev/null
+++ b/var/spack/packages/cgal/package.py
@@ -0,0 +1,73 @@
+##############################################################################
+# 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 Cgal(Package):
+    """
+    CGAL is a software project that provides easy access to efficient and reliable geometric algorithms in the form of
+    a C++ library. CGAL is used in various areas needing geometric computation, such as geographic information systems,
+    computer aided design, molecular biology, medical imaging, computer graphics, and robotics.
+    """
+    homepage = 'http://www.cgal.org/'
+    url = 'https://github.com/CGAL/cgal/archive/releases/CGAL-4.7.tar.gz'
+
+    version('4.7', '4826714810f3b4c65cac96b90fb03b67')
+    version('4.6.3', 'e8ee2ecc8d2b09b94a121c09257b576d')
+
+    # Installation instructions : http://doc.cgal.org/latest/Manual/installation.html
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('debug', default=False, description='Builds a debug version of the libraries')
+
+    depends_on('boost')
+    depends_on('mpfr')
+    depends_on('gmp')
+    depends_on('zlib')
+
+    # FIXME : Qt5 dependency missing (needs Qt5 and OpenGL)
+    # FIXME : Optional third party libraries missing
+
+    def install(self, spec, prefix):
+
+        options = []
+        options.extend(std_cmake_args)
+        # CGAL supports only Release and Debug build type. Any other build type will raise an error at configure time
+        if '+debug' in spec:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Debug')
+        else:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Release')
+
+        if '+shared' in spec:
+            options.append('-DBUILD_SHARED_LIBS:BOOL=ON')
+        else:
+            options.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
+
+        build_directory = join_path(self.stage.path, 'spack-build')
+        source_directory = self.stage.source_path
+        with working_dir(build_directory, create=True):
+            cmake(source_directory, *options)
+            make()
+            make("install")
diff --git a/var/spack/packages/cmake/package.py b/var/spack/packages/cmake/package.py
index cb54c92d69..173f72742c 100644
--- a/var/spack/packages/cmake/package.py
+++ b/var/spack/packages/cmake/package.py
@@ -38,8 +38,9 @@ class Cmake(Package):
     version('3.4.0', 'cd3034e0a44256a0917e254167217fc8',
             url = 'https://cmake.org/files/v3.4/cmake-3.4.0.tar.gz')
 
-#    version('3.0.1', 'e2e05d84cb44a42f1371d9995631dcf5')
-#    version('3.0.0', '21a1c85e1a3b803c4b48e7ff915a863e')
+    variant('ncurses', default=True, description='Enables the build of the ncurses gui')
+
+    depends_on('ncurses', when='+ncurses')
 
     def install(self, spec, prefix):
         configure('--prefix='   + prefix,
diff --git a/var/spack/packages/gdb/package.py b/var/spack/packages/gdb/package.py
index fd567f346b..85ed3215e2 100644
--- a/var/spack/packages/gdb/package.py
+++ b/var/spack/packages/gdb/package.py
@@ -32,13 +32,13 @@ class Gdb(Package):
     -- or what another program was doing at the moment it crashed.
     """
     homepage = "https://www.gnu.org/software/gdb"
-    url = "http://ftp.gnu.org/gnu/gdb/gdb-7.10.tar.xz"
+    url = "http://ftp.gnu.org/gnu/gdb/gdb-7.10.tar.gz"
 
-    version('7.10.1', '39e654460c9cdd80200a29ac020cfe11')
-    version('7.10', '2a35bac41fa8e10bf04f3a0dd7f7f363')
-    version('7.9.1', '35374c77a70884eb430c97061053a36e')
-    version('7.9', 'e6279f26559d839f0b4218a482bcb43e')
-    version('7.8.2', 'a80cf252ed2e775d4e4533341bbf2459')
+    version('7.10.1', 'b93a2721393e5fa226375b42d567d90b')
+    version('7.10', 'fa6827ad0fd2be1daa418abb11a54d86')
+    version('7.9.1', 'f3b97de919a9dba84490b2e076ec4cb0')
+    version('7.9', '8f8ced422fe462a00e0135a643544f17')
+    version('7.8.2', '8b0ea8b3559d3d90b3ff4952f0aeafbc')
 
     depends_on('texinfo')
 
diff --git a/var/spack/packages/git/package.py b/var/spack/packages/git/package.py
index 28c7aa8161..ddc5078c4d 100644
--- a/var/spack/packages/git/package.py
+++ b/var/spack/packages/git/package.py
@@ -5,14 +5,14 @@ class Git(Package):
        system designed to handle everything from small to very large
        projects with speed and efficiency."""
     homepage = "http://git-scm.com"
-    url      = "https://www.kernel.org/pub/software/scm/git/git-2.2.1.tar.xz"
-
-    version('2.6.3', '5a6375349c3f13c8dbbabfc327bae429')
-    version('2.6.2', '32ae5ad29763fc927bfcaeab55385fd9')
-    version('2.6.1', 'dd4a3a7fe96598c553edd39d40c9c290')
-    version('2.6.0', '6b7d43d615fb3f0dfecf4d131e23f438')
-    version('2.5.4', 'ec118fcd1cf984edc17eb6588b78e81b')
-    version('2.2.1', '43e01f9d96ba8c11611e0eef0d9f9f28')
+    url      = "https://www.kernel.org/pub/software/scm/git/git-2.2.1.tar.gz"
+
+    version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423')
+    version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8')
+    version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd')
+    version('2.6.0', 'eb76a07148d94802a1745d759716a57e')
+    version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b')
+    version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c')
 
 
     # Git compiles with curl support by default on but if your system
diff --git a/var/spack/packages/gperftools/package.py b/var/spack/packages/gperftools/package.py
index 0ba44c9329..22b2e6c424 100644
--- a/var/spack/packages/gperftools/package.py
+++ b/var/spack/packages/gperftools/package.py
@@ -30,8 +30,11 @@ class Gperftools(Package):
     homepage = "https://code.google.com/p/gperftools"
     url      = "https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz"
 
+    version('2.4', '2171cea3bbe053036fb5d5d25176a160', url="https://github.com/gperftools/gperftools/releases/download/gperftools-2.4/gperftools-2.4.tar.gz")
     version('2.3', 'f54dd119f0e46ac1f13264f8d97adf90', url="https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz")
 
+    depends_on("libunwind")
+
     def install(self, spec, prefix):
         configure("--prefix=" + prefix)
         make()
diff --git a/var/spack/packages/julia/gc.patch b/var/spack/packages/julia/gc.patch
new file mode 100644
index 0000000000..6db69c6c1b
--- /dev/null
+++ b/var/spack/packages/julia/gc.patch
@@ -0,0 +1,11 @@
+--- julia/src/gc.c
++++ julia/src/gc.c
+@@ -162,7 +162,7 @@
+ // A region is contiguous storage for up to REGION_PG_COUNT naturally aligned GC_PAGE_SZ pages
+ // It uses a very naive allocator (see malloc_page & free_page)
+ #if defined(_P64) && !defined(_COMPILER_MICROSOFT_)
+-#define REGION_PG_COUNT 16*8*4096 // 8G because virtual memory is cheap
++#define REGION_PG_COUNT 8*4096 // 512M
+ #else
+ #define REGION_PG_COUNT 8*4096 // 512M
+ #endif
diff --git a/var/spack/packages/julia/package.py b/var/spack/packages/julia/package.py
index 9fd946c905..d978842d9c 100644
--- a/var/spack/packages/julia/package.py
+++ b/var/spack/packages/julia/package.py
@@ -8,11 +8,14 @@ class Julia(Package):
 
     version('0.4.2', 'ccfeb4f4090c8b31083f5e1ccb03eb06')
 
+    patch('gc.patch')
+
     # Build-time dependencies
-    # depends_on("cmake")
+    depends_on("cmake @2.8:")
     # depends_on("awk")
     # depends_on("m4")
     # depends_on("pkg-config")
+    depends_on("python @2.6:2.9")
 
     # I think that Julia requires the dependencies above, but it builds find (on
     # my system) without these. We should enable them as necessary.
diff --git a/var/spack/packages/libpciaccess/package.py b/var/spack/packages/libpciaccess/package.py
index 403bafbbd2..0c0847d323 100644
--- a/var/spack/packages/libpciaccess/package.py
+++ b/var/spack/packages/libpciaccess/package.py
@@ -5,12 +5,10 @@ class Libpciaccess(Package):
     """Generic PCI access library."""
 
     homepage = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
-    url      = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
+    url      = "http://xorg.freedesktop.org/archive/individual/lib/libpciaccess-0.13.4.tar.bz2"
 
-    version('0.13.4', git='http://anongit.freedesktop.org/git/xorg/lib/libpciaccess.git',
-            tag='libpciaccess-0.13.4')
+    version('0.13.4', 'ace78aec799b1cf6dfaea55d3879ed9f')
 
-    depends_on('autoconf')
     depends_on('libtool')
 
     def install(self, spec, prefix):
@@ -20,9 +18,6 @@ class Libpciaccess(Package):
             mkdir(prefix.lib)
             return
 
-        from subprocess import call
-        call(["./autogen.sh"])
         configure("--prefix=%s" % prefix)
-
         make()
         make("install")
diff --git a/var/spack/packages/lua/package.py b/var/spack/packages/lua/package.py
index 6d8f7806d9..ca8cfc5365 100644
--- a/var/spack/packages/lua/package.py
+++ b/var/spack/packages/lua/package.py
@@ -6,6 +6,7 @@ class Lua(Package):
     homepage = "http://www.lua.org"
     url      = "http://www.lua.org/ftp/lua-5.1.5.tar.gz"
 
+    version('5.3.2', '33278c2ab5ee3c1a875be8d55c1ca2a1')
     version('5.3.1', '797adacada8d85761c079390ff1d9961')
     version('5.3.0', 'a1b0a7e92d0c85bbff7a8d27bf29f8af')
     version('5.2.4', '913fdb32207046b273fdb17aad70be13')
@@ -18,11 +19,16 @@ class Lua(Package):
     version('5.1.3', 'a70a8dfaa150e047866dc01a46272599')
 
     depends_on('ncurses')
+    depends_on('readline')
 
     def install(self, spec, prefix):
+        if spec.satisfies("=darwin-i686") or spec.satisfies("=darwin-x86_64"):
+            target = 'macosx'
+        else:
+            target = 'linux'
         make('INSTALL_TOP=%s' % prefix,
-             'MYLDFLAGS="-L%s/lib -Wl,-rpath,%s"' % (spec['ncurses'].prefix,spec['ncurses'].prefix),
-             'linux')
+             'MYLDFLAGS=-L%s -lncurses' % spec['ncurses'].prefix.lib,
+             target)
         make('INSTALL_TOP=%s' % prefix,
-             'MYLDFLAGS="-L%s/lib -Wl,-rpath,%s"' % (spec['ncurses'].prefix,spec['ncurses'].prefix),
+             'MYLDFLAGS=-L%s -lncurses' % spec['ncurses'].prefix.lib,
              'install')
diff --git a/var/spack/packages/metis/package.py b/var/spack/packages/metis/package.py
index 7ce5ae1925..bbfc4de7d1 100644
--- a/var/spack/packages/metis/package.py
+++ b/var/spack/packages/metis/package.py
@@ -1,27 +1,83 @@
+##############################################################################
+# 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 Metis(Package):
-    """METIS is a set of serial programs for partitioning graphs,
-       partitioning finite element meshes, and producing fill reducing
-       orderings for sparse matrices. The algorithms implemented in
-       METIS are based on the multilevel recursive-bisection,
-       multilevel k-way, and multi-constraint partitioning schemes."""
+    """
+    METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill
+    reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel
+    recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
+    """
 
-    homepage = "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview"
-    url      = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz"
+    homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview'
+    url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz"
 
     version('5.1.0', '5465e67079419a69e0116de24fce58fe')
 
-    depends_on('mpi')
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    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-time dependency
+
+    depends_on('gdb', when='+gdb')
 
     def install(self, spec, prefix):
-        cmake(".",
-              '-DGKLIB_PATH=%s/GKlib' % pwd(),
-              '-DSHARED=1',
-              '-DCMAKE_C_COMPILER=mpicc',
-              '-DCMAKE_CXX_COMPILER=mpicxx',
-              '-DSHARED=1',
-              *std_cmake_args)
-
-        make()
-        make("install")
+
+        options = []
+        options.extend(std_cmake_args)
+
+        build_directory = join_path(self.stage.path, 'spack-build')
+        source_directory = self.stage.source_path
+
+        options.append('-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=source_directory))
+
+        if '+shared' in spec:
+            options.append('-DSHARED:BOOL=ON')
+
+        if '+debug' in spec:
+            options.extend(['-DDEBUG:BOOL=ON',
+                            '-DCMAKE_BUILD_TYPE:STRING=Debug'])
+
+        if '+gdb' in spec:
+            options.append('-DGDB:BOOL=ON')
+
+        metis_header = join_path(source_directory, '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")
\ No newline at end of file
diff --git a/var/spack/packages/openssl/package.py b/var/spack/packages/openssl/package.py
index a24de20cc3..bbb169ec6b 100644
--- a/var/spack/packages/openssl/package.py
+++ b/var/spack/packages/openssl/package.py
@@ -17,6 +17,10 @@ class Openssl(Package):
     parallel = False
 
     def install(self, spec, prefix):
+        # OpenSSL uses a variable APPS in its Makefile. If it happens to be set
+        # in the environment, then this will override what is set in the
+        # Makefile, leading to build errors.
+        env.pop('APPS', None)
         if spec.satisfies("=darwin-x86_64") or spec.satisfies("=ppc64"):
             # This needs to be done for all 64-bit architectures (except Linux,
             # where it happens automatically?)
diff --git a/var/spack/packages/parmetis/package.py b/var/spack/packages/parmetis/package.py
index d8cd337304..c897dec7e4 100644
--- a/var/spack/packages/parmetis/package.py
+++ b/var/spack/packages/parmetis/package.py
@@ -1,26 +1,95 @@
+##############################################################################
+# 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 *
 
+# 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):
-    """ParMETIS is an MPI-based parallel library that implements a
-       variety of algorithms for partitioning unstructured graphs,
-       meshes, and for computing fill-reducing orderings of sparse
-       matrices."""
-    homepage = "http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview"
-    url      = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz"
+    """
+    ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured
+    graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
+    """
+    homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview'
+    url = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz'
 
     version('4.0.3', 'f69c479586bf6bb7aff6a9bc0c739628')
 
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    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
+
+    depends_on('gdb', when='+gdb')
+
     def install(self, spec, prefix):
-        cmake(".",
-              '-DGKLIB_PATH=%s/metis/GKlib' % pwd(),
-              '-DMETIS_PATH=%s/metis' % pwd(),
-              '-DSHARED=1',
-              '-DCMAKE_C_COMPILER=mpicc',
-              '-DCMAKE_CXX_COMPILER=mpicxx',
-              '-DSHARED=1',
-              *std_cmake_args)
-
-        make()
-        make("install")
+        options = []
+        options.extend(std_cmake_args)
+
+        build_directory = join_path(self.stage.path, 'spack-build')
+        source_directory = self.stage.source_path
+        metis_source = join_path(source_directory, 'metis')
+
+        # FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
+        # FIXME : they use a non-standard name
+        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source),
+                        '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=metis_source),
+                        '-DCMAKE_C_COMPILER:STRING=mpicc',
+                        '-DCMAKE_CXX_COMPILER:STRING=mpicxx'])
+
+        if '+shared' in spec:
+            options.append('-DSHARED:BOOL=ON')
+
+        if '+debug' in spec:
+            options.extend(['-DDEBUG:BOOL=ON',
+                            '-DCMAKE_BUILD_TYPE:STRING=Debug'])
+
+        if '+gdb' in spec:
+            options.append('-DGDB:BOOL=ON')
+
+        metis_header = join_path(metis_source, 'include', 'metis.h')
+
+        if '+idx64' in spec:
+            filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header)
+
+        if '+double' in spec:
+            filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
+
+        with working_dir(build_directory, create=True):
+            cmake(source_directory, *options)
+            make()
+            make("install")
+            # Parmetis build system doesn't allow for an external metis to be used, but doesn't copy the required
+            # metis header either
+            install(metis_header, self.prefix.include)
diff --git a/var/spack/packages/patchelf/package.py b/var/spack/packages/patchelf/package.py
new file mode 100644
index 0000000000..036dc6bd17
--- /dev/null
+++ b/var/spack/packages/patchelf/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class Patchelf(Package):
+    """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables."""
+
+    homepage = "https://nixos.org/patchelf.html"
+    url      = "http://nixos.org/releases/patchelf/patchelf-0.8/patchelf-0.8.tar.gz"
+    list_url = "http://nixos.org/releases/patchelf/"
+    list_depth = 2
+
+    version('0.8', '407b229e6a681ffb0e2cdd5915cb2d01')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make("install")
diff --git a/var/spack/packages/petsc/package.py b/var/spack/packages/petsc/package.py
index 1463f360c2..87f700629d 100644
--- a/var/spack/packages/petsc/package.py
+++ b/var/spack/packages/petsc/package.py
@@ -25,9 +25,6 @@ class Petsc(Package):
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix,
-                  "CC=cc",
-                  "CXX=c++",
-                  "FC=f90",
                   "--with-blas-lib=%s/libblas.a"     % spec['blas'].prefix.lib,
                   "--with-lapack-lib=%s/liblapack.a" % spec['lapack'].prefix.lib,
                   "--with-boost-dir=%s"              % spec['boost'].prefix,
@@ -35,6 +32,7 @@ class Petsc(Package):
                   "--with-parmetis-dir=%s"           % spec['parmetis'].prefix,
                   "--with-metis-dir=%s"              % spec['metis'].prefix,
                   "--with-hdf5-dir=%s"               % spec['hdf5'].prefix,
+                  "--with-mpi-dir=%s"                % spec['mpi'].prefix,
                   "--with-shared-libraries=0")
 
         # PETSc has its own way of doing parallel make.
diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index eae2566b57..a1ce06feb0 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -11,15 +11,16 @@ import spack
 class Python(Package):
     """The Python programming language."""
     homepage = "http://www.python.org"
-    url      = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tar.xz"
+    url      = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz"
 
     extendable = True
 
-    version('2.7.8', 'd235bdfa75b8396942e360a70487ee00')
-    version('2.7.10', 'c685ef0b8e9f27b5e3db5db12b268ac6')
-    version('2.7.11', '1dbcc848b4cd8399a8199d000f9f823c', preferred=True)
-    version('3.5.0', 'd149d2812f10cbe04c042232e7964171')
-    version('3.5.1', 'e9ea6f2623fffcdd871b7b19113fde80')
+    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')
 
     depends_on("openssl")
     depends_on("bzip2")
diff --git a/var/spack/packages/szip/package.py b/var/spack/packages/szip/package.py
new file mode 100644
index 0000000000..c48c5b431e
--- /dev/null
+++ b/var/spack/packages/szip/package.py
@@ -0,0 +1,21 @@
+from spack import *
+
+class Szip(Package):
+    """Szip is an implementation of the extended-Rice lossless compression algorithm.
+    It provides lossless compression of scientific data, and is provided with HDF
+    software products."""
+
+    homepage = "https://www.hdfgroup.org/doc_resource/SZIP/"
+    url      = "http://www.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz"
+
+    version('2.1', '902f831bcefb69c6b635374424acbead')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix,
+                  '--enable-production',
+                  '--enable-shared',
+                  '--enable-static',
+                  '--enable-encoding')
+
+        make()
+        make("install")
diff --git a/var/spack/packages/texinfo/package.py b/var/spack/packages/texinfo/package.py
index 460db65b3e..1b22c72e72 100644
--- a/var/spack/packages/texinfo/package.py
+++ b/var/spack/packages/texinfo/package.py
@@ -33,12 +33,12 @@ class Texinfo(Package):
     used by many non-GNU projects as well.FIXME: put a proper description of your package here.
     """
     homepage = "https://www.gnu.org/software/texinfo/"
-    url      = "http://ftp.gnu.org/gnu/texinfo/texinfo-6.0.tar.xz"
+    url      = "http://ftp.gnu.org/gnu/texinfo/texinfo-6.0.tar.gz"
 
-    version('6.0', '02818e62a5b8ae0213a7ff572991bb50')
-    version('5.2', 'cb489df8a7ee9d10a236197aefdb32c5')
-    version('5.1', '52ee905a3b705020d2a1b6ec36d53ca6')
-    version('5.0', 'ef2fad34c71ddc95b20c7d6a08c0d7a6')
+    version('6.0', 'e1a2ef5dce5018b53f0f6eed45b247a7')
+    version('5.2', '1b8f98b80a8e6c50422125e07522e8db')
+    version('5.1', '54e250014fe698fb4832016158747c03')
+    version('5.0', '918432285abe6fe96c98355594c5656a')
 
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix)
diff --git a/var/spack/packages/wget/package.py b/var/spack/packages/wget/package.py
index c8fd025122..55728b0515 100644
--- a/var/spack/packages/wget/package.py
+++ b/var/spack/packages/wget/package.py
@@ -8,9 +8,10 @@ class Wget(Package):
        etc."""
 
     homepage = "http://www.gnu.org/software/wget/"
-    url      = "http://ftp.gnu.org/gnu/wget/wget-1.16.tar.xz"
+    url      = "http://ftp.gnu.org/gnu/wget/wget-1.16.tar.gz"
 
-    version('1.16', 'fe102975ab3a6c049777883f1bb9ad07')
+    version('1.17', 'c4c4727766f24ac716936275014a0536')
+    version('1.16', '293a37977c41b5522f781d3a3a078426')
 
     depends_on("openssl")