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

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

15 files changed, 143 insertions, 55 deletions

diff --git a/etc/spack/modules.yaml b/etc/spack/modules.yaml
new file mode 100644
index 0000000000..aa2a2c3fe2
--- /dev/null
+++ b/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']
diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 6afd69b3ac..14e5aaf4fb 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -237,7 +237,29 @@ section_schemas = {
                                 '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)))
 
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 8ed98e5d38..d45fdde703 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -48,6 +48,7 @@ import textwrap
 
 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 @@ __all__ = ['EnvModule', 'Dotkit', 'TclModule']
 # 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 @@ class EnvModule(object):
 
         # Let the extendee modify their extensions before asking for
         # package-specific modifications
-        for extendee in self.pkg.extendees:
-            extendee_spec = self.spec[extendee]
-            extendee_spec.package.setup_dependent_package(
-                self.pkg.module, self.spec)
+        spack_env = EnvironmentModifications()
+        for item in self.pkg.extendees:
+            package = self.spec[item].package
+            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
diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py
index fc683363a7..b5504122b7 100644
--- a/var/spack/repos/builtin/packages/atlas/package.py
+++ b/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
-    ATLAS is an approach for the automatic generation and optimization of
-    numerical software. Currently ATLAS supplies optimized versions for the
-    complete set of linear algebra kernels known as the Basic Linear Algebra
-    Subroutines (BLAS), and a subset of the linear algebra routines in the
-    LAPACK library.
+    Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and
+    optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear
+    algebra kernels known as the Basic Linear Algebra 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
-    # TODO: to mark "beta" packages and require explicit invocation.
+    variant('shared', default=True, description='Builds shared library')
 
-    # 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 @@ class Atlas(Package):
         # 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):
-            configure = Executable('../configure')
-            configure('--prefix=%s' % prefix, '-C', 'ic', 'cc', '-C', 'if', 'f77', "--dylibs")
-            make()
-            make('check')
-            make('ptcheck')
-            make('time')
-            make("install")
 
+        options = []
+        if '+shared' in spec:
+            options.append('--shared')
 
-    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")
+        # 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, *options)
             make()
             make('check')
             make('ptcheck')
diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index cc93c7067c..1f93d39769 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -38,10 +38,12 @@ 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 +79,9 @@ class Cmake(Package):
             options.append('--sphinx-html')
             options.append('--sphinx-man')
 
-        options.append('--')
-        options.append('-DCMAKE_USE_OPENSSL=ON')
+        if '+openssl' in spec:
+            options.append('--')
+            options.append('-DCMAKE_USE_OPENSSL=ON')
 
         configure(*options)
         make()
diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index a2bf58f585..59f362ab46 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -32,6 +32,10 @@ class Espresso(Package):
         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)
 
diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py
index 9f16708af5..29bc21b65c 100644
--- a/var/spack/repos/builtin/packages/libelf/package.py
+++ b/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",
diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 5c120c37df..5a254dfd00 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -135,7 +135,8 @@ class Mumps(Package):
 
         self.write_makefile_inc()
 
-        make(*make_libs)
+        # Build fails in parallel, at least on OS-X
+        make(*make_libs, parallel=False)
 
         install_tree('lib', prefix.lib)
         install_tree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 781a1e2ec8..1d10f217c4 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/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'
diff --git a/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch b/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch
new file mode 100644
index 0000000000..faa809231e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch
@@ -0,0 +1,14 @@
+diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt
+index 9cfc8a7..dfc0125 100644
+--- a/libparmetis/CMakeLists.txt
++++ b/libparmetis/CMakeLists.txt
+@@ -5,7 +5,7 @@ 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 ${MPI_LIBRARIES} "-lm")
+ set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}")
+
+ install(TARGETS parmetis
+
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index c691cf4191..bc71fb7299 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -52,6 +52,8 @@ class Parmetis(Package):
     # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
     patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
 
+    patch('link-to-lm.patch')
+
     depends_on('gdb', when='+gdb')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index 0844ff5caa..a08e612df6 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -1,23 +1,43 @@
 from spack import *
 
 class PyNumpy(Package):
-    """array processing for numbers, strings, records, and objects."""
-    homepage = "https://pypi.python.org/pypi/numpy"
+    """NumPy is the fundamental package for scientific computing with Python.
+    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('1.9.2', '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('lapack+shared', when='+blas')
+    depends_on('blas',   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('library_dirs=%s/lib:%s/lib\n' % (spec['blas'].prefix, spec['lapack'].prefix))
+                f.write('libraries=%s\n'    % ','.join(libraries))
+                f.write('library_dirs=%s\n' % ':'.join(library_dirs))
+
         python('setup.py', 'install', '--prefix=%s' % prefix)
+
diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index 3a1124cc15..c2161c90c4 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -2,11 +2,12 @@ from spack import *
 
 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')
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 6d9030805b..f5237c3b57 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -105,7 +105,10 @@ class Python(Package):
 
         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 setup_dependent_package(self, module, ext_spec):
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index c4c76909b3..9a94de8ba5 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -54,6 +54,7 @@ class SuperluDist(Package):
         # need to install by hand
         headers_location = join_path(self.prefix.include,'superlu_dist')
         mkdirp(headers_location)
+        mkdirp(prefix.lib)
         # FIXME: fetch all headers in the folder automatically
         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)