Merge branch 'develop' into eschnett/julia

19 files changed, 152 insertions, 35 deletions

diff --git a/var/spack/repos/builtin/packages/bash/package.py b/var/spack/repos/builtin/packages/bash/package.py
new file mode 100644
index 0000000000..9c9fbeedcf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bash/package.py
@@ -0,0 +1,20 @@
+from spack import *
+
+class Bash(Package):
+    """The GNU Project's Bourne Again SHell."""
+
+    homepage = "https://www.gnu.org/software/bash/"
+    url      = "ftp://ftp.gnu.org/gnu/bash/bash-4.3.tar.gz"
+
+    version('4.3', '81348932d5da294953e15d4814c74dd1')
+
+    depends_on('readline')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix,
+                  '--with-curses',
+                  '--with-installed-readline=%s' % spec['readline'].prefix)
+
+        make()
+        make("tests")
+        make("install")
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index f889da21f2..12bc9508c3 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -199,6 +199,18 @@ class Boost(Package):
             install_tree(src, dst)
             return
 
+        # Remove libraries that the release version does not support
+        if not spec.satisfies('@1.54.0:'):
+            withLibs.remove('log')
+        if not spec.satisfies('@1.53.0:'):
+            withLibs.remove('atomic')
+        if not spec.satisfies('@1.48.0:'):
+            withLibs.remove('locale')
+        if not spec.satisfies('@1.47.0:'):
+            withLibs.remove('chrono')
+        if not spec.satisfies('@1.43.0:'):
+            withLibs.remove('random')
+
         # to make Boost find the user-config.jam
         env['BOOST_BUILD_PATH'] = './'
 
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 1f763ad358..b251d50ca1 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -40,7 +40,7 @@ class Dealii(Package):
     depends_on ("arpack-ng+mpi", when='+arpack+mpi')
     depends_on ("doxygen", when='+doc')
     depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why?
-    depends_on ("metis", when='+metis')
+    depends_on ("metis@5:", when='+metis')
     depends_on ("netcdf+mpi", when="+netcdf+mpi")
     depends_on ("netcdf-cxx", when='+netcdf+mpi')
     depends_on ("oce", when='+oce')
diff --git a/var/spack/repos/builtin/packages/dyninst/package.py b/var/spack/repos/builtin/packages/dyninst/package.py
index 0111dcbe08..b28e897a0f 100644
--- a/var/spack/repos/builtin/packages/dyninst/package.py
+++ b/var/spack/repos/builtin/packages/dyninst/package.py
@@ -31,6 +31,8 @@ class Dyninst(Package):
     url      = "http://www.dyninst.org/sites/default/files/downloads/dyninst/8.1.2/DyninstAPI-8.1.2.tgz"
     list_url = "http://www.dyninst.org/downloads/dyninst-8.x"
 
+    version('9.1.0', '5c64b77521457199db44bec82e4988ac',
+            url="http://www.paradyn.org/release9.1.0/DyninstAPI-9.1.0.tgz")
     version('8.2.1', 'abf60b7faabe7a2e4b54395757be39c7',
             url="http://www.paradyn.org/release8.2/DyninstAPI-8.2.1.tgz")
     version('8.1.2', 'bf03b33375afa66fe0efa46ce3f4b17a',
diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py
index 8d6e672f86..1501989812 100644
--- a/var/spack/repos/builtin/packages/eigen/package.py
+++ b/var/spack/repos/builtin/packages/eigen/package.py
@@ -45,7 +45,7 @@ class Eigen(Package):
 
     # TODO : dependency on googlehash, superlu, adolc missing
 
-    depends_on('metis', when='+metis')
+    depends_on('metis@5:', when='+metis')
     depends_on('scotch', when='+scotch')
     depends_on('fftw', when='+fftw')
     depends_on('suite-sparse', when='+suitesparse')
diff --git a/var/spack/repos/builtin/packages/global/package.py b/var/spack/repos/builtin/packages/global/package.py
index e8f06516d9..aac1cede30 100644
--- a/var/spack/repos/builtin/packages/global/package.py
+++ b/var/spack/repos/builtin/packages/global/package.py
@@ -11,6 +11,7 @@ class Global(Package):
     version('6.5', 'dfec818b4f53d91721e247cf7b218078')
 
     depends_on('exuberant-ctags')
+    depends_on('ncurses')
 
     def install(self, spec, prefix):
         config_args = ['--prefix={0}'.format(prefix)]
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index d3bab554fe..41e3ebb429 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-import glob,sys
+import glob, sys, os
 
 class Metis(Package):
     """
@@ -36,7 +36,10 @@ class Metis(Package):
     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')
+    version('5.1.0', '5465e67079419a69e0116de24fce58fe',
+            url='http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz')
+    version('4.0.3', '5efa35de80703c1b2c4d0de080fafbcf4e0d363a21149a1ad2f96e0144841a55',
+            url='http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD/metis-4.0.3.tar.gz')
 
     variant('shared', default=True, description='Enables the build of shared libraries')
     variant('debug', default=False, description='Builds the library in debug mode')
@@ -45,12 +48,85 @@ class Metis(Package):
     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('cmake @2.8:', when='@5:')  # build-time dependency
     depends_on('gdb', when='+gdb')
 
-    patch('install_gklib_defs_rename.patch')
+    patch('install_gklib_defs_rename.patch', when='@5:')
+
+
+    @when('@4:4.0.3')
+    def install(self, spec, prefix):
 
+        if '+gdb' in spec:
+            raise InstallError('gdb support not implemented in METIS 4!')
+        if '+idx64' in spec:
+            raise InstallError('idx64 option not implemented in METIS 4!')
+        if '+double' in spec:
+            raise InstallError('double option not implemented for METIS 4!')
+
+        options = ['COPTIONS=-fPIC']
+        if '+debug' in spec:
+            options.append('OPTFLAGS=-g -O0')
+        make(*options)
+
+        mkdir(prefix.bin)
+        for x in ('pmetis', 'kmetis', 'oemetis', 'onmetis', 'partnmesh',
+                  'partdmesh', 'mesh2nodal', 'mesh2dual', 'graphchk'):
+            install(x, prefix.bin)
+
+        mkdir(prefix.lib)
+        install('libmetis.a', prefix.lib)
+
+        mkdir(prefix.include)
+        for h in glob.glob(join_path('Lib', '*.h')):
+            install(h, prefix.include)
+
+        mkdir(prefix.share)
+        for f in (join_path(*p)
+                  for p in (('Programs', 'io.c'),
+                            ('Test','mtest.c'),
+                            ('Graphs','4elt.graph'),
+                            ('Graphs', 'metis.mesh'),
+                            ('Graphs', 'test.mgraph'))):
+            install(f, prefix.share)
+
+        if '+shared' in spec:
+            if sys.platform == 'darwin':
+                lib_dsuffix = 'dylib'
+                load_flag = '-Wl,-all_load'
+                no_load_flag = ''
+            else:
+                lib_dsuffix = 'so'
+                load_flag = '-Wl,-whole-archive'
+                no_load_flag = '-Wl,-no-whole-archive'
+
+            os.system(spack_cc + ' -fPIC -shared ' + load_flag +
+                      ' libmetis.a ' + no_load_flag + ' -o libmetis.' +
+                      lib_dsuffix)
+            install('libmetis.' + lib_dsuffix, prefix.lib)
+
+        # Set up and run tests on installation
+        symlink(join_path(prefix.share, 'io.c'), 'io.c')
+        symlink(join_path(prefix.share, 'mtest.c'), 'mtest.c')
+        os.system(spack_cc + ' -I%s' % prefix.include + ' -c io.c')
+        os.system(spack_cc + ' -I%s' % prefix.include +
+                  ' -L%s' % prefix.lib + ' -lmetis mtest.c io.o -o mtest')
+        _4eltgraph = join_path(prefix.share, '4elt.graph')
+        test_mgraph = join_path(prefix.share, 'test.mgraph')
+        metis_mesh = join_path(prefix.share, 'metis.mesh')
+        kmetis = join_path(prefix.bin, 'kmetis')
+        os.system('./mtest ' + _4eltgraph)
+        os.system(kmetis + ' ' + _4eltgraph + ' 40')
+        os.system(join_path(prefix.bin, 'onmetis') + ' ' + _4eltgraph)
+        os.system(join_path(prefix.bin, 'pmetis') + ' ' + test_mgraph + ' 2')
+        os.system(kmetis + ' ' + test_mgraph + ' 2')
+        os.system(kmetis + ' ' + test_mgraph + ' 5')
+        os.system(join_path(prefix.bin, 'partnmesh') + metis_mesh + ' 10')
+        os.system(join_path(prefix.bin, 'partdmesh') + metis_mesh + ' 10')
+        os.system(join_path(prefix.bin, 'mesh2dual') + metis_mesh)
+
+
+    @when('@5:')
     def install(self, spec, prefix):
 
         options = []
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 2d7955e08d..b317ec6651 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -47,12 +47,12 @@ class Mpich(Package):
     provides('mpi@:3.0', when='@3:')
     provides('mpi@:1.3', when='@1:')
 
-    def setup_dependent_environment(self, env, dependent_spec):
-        env.set('MPICH_CC', spack_cc)
-        env.set('MPICH_CXX', spack_cxx)
-        env.set('MPICH_F77', spack_f77)
-        env.set('MPICH_F90', spack_f90)
-        env.set('MPICH_FC', spack_fc)
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('MPICH_CC', spack_cc)
+        spack_env.set('MPICH_CXX', spack_cxx)
+        spack_env.set('MPICH_F77', spack_f77)
+        spack_env.set('MPICH_F90', spack_fc)
+        spack_env.set('MPICH_FC', spack_fc)
 
     def setup_dependent_package(self, module, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 025d86ebdc..58f790ec32 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -23,7 +23,7 @@ class Mumps(Package):
 
     depends_on('scotch + esmumps', when='~ptscotch+scotch')
     depends_on('scotch + esmumps + mpi', when='+ptscotch')
-    depends_on('metis', when='+metis')
+    depends_on('metis@5:', when='+metis')
     depends_on('parmetis', when="+parmetis")
     depends_on('blas')
     depends_on('lapack')
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index e4e95f92af..3e60b517db 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -140,6 +140,13 @@ class Mvapich2(Package):
 
         configure_args.extend(network_options)
 
+    def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+        spack_env.set('MPICH_CC', spack_cc)
+        spack_env.set('MPICH_CXX', spack_cxx)
+        spack_env.set('MPICH_F77', spack_f77)
+        spack_env.set('MPICH_F90', spack_fc)
+        spack_env.set('MPICH_FC', spack_fc)
+
     def install(self, spec, prefix):
         # we'll set different configure flags depending on our environment
         configure_args = [
diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py
index 8dc808caac..219fbce226 100644
--- a/var/spack/repos/builtin/packages/ncurses/package.py
+++ b/var/spack/repos/builtin/packages/ncurses/package.py
@@ -8,11 +8,10 @@ class Ncurses(Package):
     """
 
     homepage = "http://invisible-island.net/ncurses/ncurses.html"
+    url      = "http://ftp.gnu.org/pub/gnu/ncurses/ncurses-6.0.tar.gz"
 
-    version('5.9', '8cb9c412e5f2d96bc6f459aa8c6282a1',
-            url='http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz')
-    version('6.0', 'ee13d052e1ead260d7c28071f46eefb1',
-            url='http://ftp.gnu.org/pub/gnu/ncurses/ncurses-6.0.tar.gz')
+    version('6.0', 'ee13d052e1ead260d7c28071f46eefb1')
+    version('5.9', '8cb9c412e5f2d96bc6f459aa8c6282a1')
 
     patch('patch_gcc_5.txt', when='%gcc@5.0:')
 
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index 05436332ac..f70e634347 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -34,15 +34,17 @@ class NetlibLapack(Package):
 
     def patch(self):
         # Fix cblas CMakeLists.txt -- has wrong case for subdirectory name.
-        filter_file('${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/',
-                    '${CMAKE_CURRENT_SOURCE_DIR}/cmake/', 'CBLAS/CMakeLists.txt', string=True)
-
+        if self.spec.satisfies('@3.6.0:'):
+            filter_file('${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/',
+                        '${CMAKE_CURRENT_SOURCE_DIR}/cmake/', 'CBLAS/CMakeLists.txt', string=True)
 
     def install_one(self, spec, prefix, shared):
         cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'),
-                      '-DCBLAS=ON', # always build CBLAS
                       '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
                       '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
+        if spec.satisfies('@3.6.0:'):
+            cmake_args.extend(['-DCBLAS=ON']) # always build CBLAS
+
         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
@@ -80,6 +82,3 @@ class NetlibLapack(Package):
         if '+shared' in self.spec:
             self.spec.blas_shared_lib   = join_path(libdir, 'libblas.%s' % dso_suffix)
             self.spec.lapack_shared_lib = join_path(libdir, 'liblapack.%s' % dso_suffix)
-
-
-
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 4ec829a85b..9f13d0690b 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -19,8 +19,11 @@ class Openblas(Package):
 
 
     def install(self, spec, prefix):
-        make_defs = ['CC=%s' % spack_cc,
-                     'FC=%s' % spack_fc]
+        # Openblas is picky about compilers. Configure fails with
+        # FC=/abs/path/to/f77, whereas FC=f77 works fine.
+        # To circumvent this, provide basename only:
+        make_defs = ['CC=%s' % os.path.basename(spack_cc),
+                     'FC=%s' % os.path.basename(spack_f77)]
 
         make_targets = ['libs', 'netlib']
 
@@ -67,4 +70,3 @@ class Openblas(Package):
         if '+shared' in self.spec:
             self.spec.blas_shared_lib   = join_path(libdir, 'libopenblas.%s' % dso_suffix)
             self.spec.lapack_shared_lib = self.spec.blas_shared_lib
-
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index ff4370aa4b..b49f8dae00 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -44,7 +44,7 @@ class Parmetis(Package):
     depends_on('mpi')
 
     patch('enable_external_metis.patch')
-    depends_on('metis')
+    depends_on('metis@5:')
 
     # bug fixes from PETSc developers
     # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 5c1fc6cc92..1161dd7d67 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -40,7 +40,7 @@ class Petsc(Package):
 
     # Other dependencies
     depends_on('boost', when='+boost')
-    depends_on('metis', when='+metis')
+    depends_on('metis@5:', when='+metis')
 
     depends_on('hdf5+mpi', when='+hdf5+mpi')
     depends_on('parmetis', when='+metis+mpi')
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index ab09469042..8cb88e6c85 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -4,7 +4,6 @@ import os
 class Qt(Package):
     """Qt is a comprehensive cross-platform C++ application framework."""
     homepage = 'http://qt.io'
-    url      = 'http://download.qt.io/archive/qt/5.5/5.5.1/single/qt-everywhere-opensource-src-5.5.1.tar.gz'
 
     version('5.5.1',  '59f0216819152b77536cf660b015d784')
     version('5.4.2',  'fa1c4d819b401b267eb246a543a63ea5')
diff --git a/var/spack/repos/builtin/packages/readline/package.py b/var/spack/repos/builtin/packages/readline/package.py
index 1b870e0e7f..0c429ea756 100644
--- a/var/spack/repos/builtin/packages/readline/package.py
+++ b/var/spack/repos/builtin/packages/readline/package.py
@@ -2,12 +2,12 @@ from spack import *
 
 class Readline(Package):
     """The GNU Readline library provides a set of functions for use by
-       applications that allow users to edit command li nes as they
+       applications that allow users to edit command lines as they
        are typed in. Both Emacs and vi editing modes are
        available. The Readline library includes additional functions
        to maintain a list of previously-entered command lines, to
        recall and perhaps reedit those lines, and perform csh-like
-       history expansion on previous commands. """
+       history expansion on previous commands."""
     homepage = "http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html"
     url      = "ftp://ftp.cwru.edu/pub/bash/readline-6.3.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index ddcb7f9225..5cf5e129b4 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -15,7 +15,7 @@ class SuperluDist(Package):
     depends_on ('blas')
     depends_on ('lapack')
     depends_on ('parmetis')
-    depends_on ('metis')
+    depends_on ('metis@5:')
 
     def install(self, spec, prefix):
         makefile_inc = []
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 6223848c68..0f72055fa7 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -42,7 +42,7 @@ class Trilinos(Package):
     depends_on('matio')
     depends_on('glm')
     depends_on('swig')
-    depends_on('metis',when='+metis')
+    depends_on('metis@5:',when='+metis')
     depends_on('suite-sparse',when='+suite-sparse')
 
     # MPI related dependencies