Fixed Theano GPU support (#7325)

* Added a package for the MDAnalysis toolkit.

* Added a new package for pygpu, which is the python front end of the
libgpuarray.  Additionally changed the dependency for theano so that
it properly picks up the pygpu library.

* Added the libcheck package.  Fixed flake8 errors in py-pygpu recipe
and removed spurious dependency on cudnn for libgpuarray.

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

@@ -0,0 +1,36 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 Libcheck(CMakePackage):
+    """A unit testing framework for C."""
+
+    homepage = "https://libcheck.github.io/check/index.html"
+    url      = "https://github.com/libcheck/check/releases/download/0.12.0/check-0.12.0.tar.gz"
+
+    version('0.12.0', '31b17c6075820a434119592941186f70')
+    version('0.11.0', '9b90522b31f5628c2e0f55dda348e558')
+    version('0.10.0', '53c5e5c77d090e103a17f3ed7fd7d8b8')

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

@@ -33,11 +33,17 @@ class Libgpuarray(CMakePackage):
     homepage = "http://deeplearning.net/software/libgpuarray/"
     url      = "https://github.com/Theano/libgpuarray/archive/v0.6.1.tar.gz"
 
+    version('0.7.5', '2534011464555c3e99d14231db965c20')
+    version('0.7.4', '19f57cd381175162048c8154f5251546')
+    version('0.7.3', 'cb44aeb8482330974abdb36b0a477e5d')
+    version('0.7.2', '0f9d7748501bc5c71bf04aae2285ac4e')
+    version('0.7.1', '7eb5bb6689ddbc386a9d498f5c0027fb')
+    version('0.7.0', 'f71b066f21ef7666f3a851e96c26f52e')
+    version('0.6.9', '7f75c39f1436c920ed9c5ffde5631fc0')
     version('0.6.2', '7f163bd5f48f399cd6e608ee3d528ee4')
     version('0.6.1', 'cfcd1b54447f9d55b05514df62c70ae2')
     version('0.6.0', '98a4ec1b4c8f225f0b89c18b899a000b')
 
     depends_on('cuda')
     depends_on('cmake@3:', type='build')
-
+    depends_on('libcheck')
-    extends('python')

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

@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 PyPygpu(PythonPackage):
+    """Python packge for the libgpuarray C library."""
+
+    homepage = "http://deeplearning.net/software/libgpuarray/"
+    url      = "https://github.com/Theano/libgpuarray/archive/v0.6.1.tar.gz"
+
+    version('0.7.5', '2534011464555c3e99d14231db965c20')
+    version('0.7.4', '19f57cd381175162048c8154f5251546')
+    version('0.7.3', 'cb44aeb8482330974abdb36b0a477e5d')
+    version('0.7.2', '0f9d7748501bc5c71bf04aae2285ac4e')
+    version('0.7.1', '7eb5bb6689ddbc386a9d498f5c0027fb')
+    version('0.7.0', 'f71b066f21ef7666f3a851e96c26f52e')
+    version('0.6.9', '7f75c39f1436c920ed9c5ffde5631fc0')
+    version('0.6.2', '7f163bd5f48f399cd6e608ee3d528ee4')
+    version('0.6.1', 'cfcd1b54447f9d55b05514df62c70ae2')
+    version('0.6.0', '98a4ec1b4c8f225f0b89c18b899a000b')
+
+    depends_on('libgpuarray')
+    # not just build-time, requires pkg_resources
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-cython@0.25:', type=('build', 'run'))
+    depends_on('py-nose', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-mako', type=('build', 'run'))
+    depends_on('libcheck')

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

@@ -32,6 +32,7 @@ class PyTheano(PythonPackage):
     homepage = "http://deeplearning.net/software/theano/"
     url = "https://pypi.io/packages/source/T/Theano/Theano-0.8.2.tar.gz"
 
+    version('1.0.1', 'a38b36c0fdc3126c574163db0a253e69')
     version('0.8.2', 'f2d0dfe7df141115201077cd933b2c52')
     version('master', git='https://github.com/Theano/Theano.git', branch='master')
 
@@ -48,6 +49,8 @@ class PyTheano(PythonPackage):
     depends_on('blas')
 
     depends_on('cuda', when='+gpu')
+    depends_on('cudnn', when='+gpu')
+    depends_on('py-pygpu', when='+gpu', type=('build', 'run'))
     depends_on('libgpuarray', when='+gpu')
 
     # TODO: Add a 'test' deptype