Merge pull request #1059 from epfl-scitas/packages/mpi_wrappers_with_rpath

MPI : have wrappers set RPATH instead of RUNPATH

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

@@ -23,15 +23,14 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
 
 
 class Mpich(Package):
     """MPICH is a high performance and widely portable implementation of
        the Message Passing Interface (MPI) standard."""
     homepage = "http://www.mpich.org"
-    url      = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"
+    url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"
-    list_url   = "http://www.mpich.org/static/downloads/"
+    list_url = "http://www.mpich.org/static/downloads/"
     list_depth = 2
 
     version('3.2',   'f414cfa77099cd1fa1a5ae4e22db508a')
@@ -42,7 +41,8 @@ class Mpich(Package):
     version('3.1',   '5643dd176499bfb7d25079aaff25f2ec')
     version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0')
 
-    variant('verbs', default=False, description='Build support for OpenFabrics verbs.')
+    variant('verbs', default=False,
+            description='Build support for OpenFabrics verbs.')
     variant('pmi', default=True, description='Build with PMI support')
     variant('hydra', default=True, description='Build the hydra process manager')
 
@@ -57,9 +57,9 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         spack_env.set('MPICH_FC', spack_fc)
 
     def setup_dependent_package(self, module, dep_spec):
-        self.spec.mpicc  = join_path(self.prefix.bin, 'mpicc')
+        self.spec.mpicc = join_path(self.prefix.bin, 'mpicc')
         self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++')
-        self.spec.mpifc  = join_path(self.prefix.bin, 'mpif90')
+        self.spec.mpifc = join_path(self.prefix.bin, 'mpif90')
         self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
 
     def install(self, spec, prefix):
@@ -92,7 +92,6 @@ def install(self, spec, prefix):
 
         self.filter_compilers()
 
-
     def filter_compilers(self):
         """Run after install to make the MPI compilers use the
            compilers that Spack built the package with.
@@ -102,18 +101,20 @@ def filter_compilers(self):
            be bound to whatever compiler they were built with.
         """
         bin = self.prefix.bin
-        mpicc  = os.path.join(bin, 'mpicc')
+        mpicc = join_path(bin, 'mpicc')
-        mpicxx = os.path.join(bin, 'mpicxx')
+        mpicxx = join_path(bin, 'mpicxx')
-        mpif77 = os.path.join(bin, 'mpif77')
+        mpif77 = join_path(bin, 'mpif77')
-        mpif90 = os.path.join(bin, 'mpif90')
+        mpif90 = join_path(bin, 'mpif90')
 
-        spack_cc  = os.environ['CC']
+        # Substitute Spack compile wrappers for the real
-        spack_cxx = os.environ['CXX']
+        # underlying compiler
-        spack_f77 = os.environ['F77']
+        kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
-        spack_fc  = os.environ['FC']
+        filter_file(env['CC'], self.compiler.cc,  mpicc,  **kwargs)
+        filter_file(env['CXX'], self.compiler.cxx, mpicxx, **kwargs)
+        filter_file(env['F77'], self.compiler.f77, mpif77, **kwargs)
+        filter_file(env['FC'], self.compiler.fc,  mpif90, **kwargs)
 
-        kwargs = { 'ignore_absent' : True, 'backup' : False, 'string' : True }
+        # Remove this linking flag if present
-        filter_file('CC="%s"' % spack_cc , 'CC="%s"'  % self.compiler.cc,  mpicc,  **kwargs)
+        # (it turns RPATH into RUNPATH)
-        filter_file('CXX="%s"'% spack_cxx, 'CXX="%s"' % self.compiler.cxx, mpicxx, **kwargs)
+        for wrapper in (mpicc, mpicxx, mpif77, mpif90):
-        filter_file('F77="%s"'% spack_f77, 'F77="%s"' % self.compiler.f77, mpif77, **kwargs)
+            filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs)
-        filter_file('FC="%s"' % spack_fc , 'FC="%s"'  % self.compiler.fc,  mpif90, **kwargs)

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

@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
 
 
 class Mvapich2(Package):
@@ -245,27 +244,20 @@ def filter_compilers(self):
            be bound to whatever compiler they were built with.
         """
         bin = self.prefix.bin
-        mpicc  = os.path.join(bin, 'mpicc')
+        mpicc  = join_path(bin, 'mpicc')
-        mpicxx = os.path.join(bin, 'mpicxx')
+        mpicxx = join_path(bin, 'mpicxx')
-        mpif77 = os.path.join(bin, 'mpif77')
+        mpif77 = join_path(bin, 'mpif77')
-        mpif90 = os.path.join(bin, 'mpif90')
+        mpif90 = join_path(bin, 'mpif90')
 
-        spack_cc  = os.environ['CC']
+        # Substitute Spack compile wrappers for the real
-        spack_cxx = os.environ['CXX']
+        # underlying compiler
-        spack_f77 = os.environ['F77']
+        kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
-        spack_fc  = os.environ['FC']
+        filter_file(env['CC'], self.compiler.cc, mpicc, **kwargs)
+        filter_file(env['CXX'], self.compiler.cxx, mpicxx, **kwargs)
+        filter_file(env['F77'], self.compiler.f77, mpif77, **kwargs)
+        filter_file(env['FC'], self.compiler.fc, mpif90, **kwargs)
 
-        kwargs = {
+        # Remove this linking flag if present
-            'ignore_absent': True,
+        # (it turns RPATH into RUNPATH)
-            'backup': False,
+        for wrapper in (mpicc, mpicxx, mpif77, mpif90):
-            'string': True
+            filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs)
-        }
-
-        filter_file('CC="%s"' % spack_cc,
-                    'CC="%s"' % self.compiler.cc, mpicc, **kwargs)
-        filter_file('CXX="%s"' % spack_cxx,
-                    'CXX="%s"' % self.compiler.cxx, mpicxx, **kwargs)
-        filter_file('F77="%s"' % spack_f77,
-                    'F77="%s"' % self.compiler.f77, mpif77, **kwargs)
-        filter_file('FC="%s"' % spack_fc,
-                    'FC="%s"' % self.compiler.fc, mpif90, **kwargs)

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

@@ -73,20 +73,27 @@ class Openmpi(Package):
     patch('configure.patch', when="@1.10.0:1.10.1")
 
     variant('psm', default=False, description='Build support for the PSM library.')
-    variant('psm2', default=False, description='Build support for the Intel PSM2 library.')
+    variant('psm2', default=False,
-    variant('pmi', default=False, description='Build support for PMI-based launchers')
+            description='Build support for the Intel PSM2 library.')
-    variant('verbs', default=_verbs_dir() is not None, description='Build support for OpenFabrics verbs.')
+    variant('pmi', default=False,
+            description='Build support for PMI-based launchers')
+    variant('verbs', default=_verbs_dir() is not None,
+            description='Build support for OpenFabrics verbs.')
     variant('mxm', default=False, description='Build Mellanox Messaging support')
 
-    variant('thread_multiple', default=False, description='Enable MPI_THREAD_MULTIPLE support')
+    variant('thread_multiple', default=False,
+            description='Enable MPI_THREAD_MULTIPLE support')
 
     # TODO : variant support for alps, loadleveler  is missing
-    variant('tm', default=False, description='Build TM (Torque, PBSPro, and compatible) support')
+    variant('tm', default=False,
-    variant('slurm', default=False, description='Build SLURM scheduler component')
+            description='Build TM (Torque, PBSPro, and compatible) support')
+    variant('slurm', default=False,
+            description='Build SLURM scheduler component')
 
     variant('sqlite3', default=False, description='Build sqlite3 support')
 
-    variant('vt', default=True, description='Build support for contributed package vt')
+    variant('vt', default=True,
+            description='Build support for contributed package vt')
 
     # TODO : support for CUDA is missing
 
@@ -97,8 +104,7 @@ class Openmpi(Package):
     depends_on('sqlite', when='+sqlite3')
 
     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)
+        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('OMPI_CC', spack_cc)
@@ -107,14 +113,15 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         spack_env.set('OMPI_F77', spack_f77)
 
     def setup_dependent_package(self, module, dep_spec):
-        self.spec.mpicc  = join_path(self.prefix.bin, 'mpicc')
+        self.spec.mpicc = join_path(self.prefix.bin, 'mpicc')
         self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++')
-        self.spec.mpifc  = join_path(self.prefix.bin, 'mpif90')
+        self.spec.mpifc = join_path(self.prefix.bin, 'mpif90')
         self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
 
     @property
     def verbs(self):
-        # Up through version 1.6, this option was previously named --with-openib
+        # Up through version 1.6, this option was previously named
+        # --with-openib
         if self.spec.satisfies('@:1.6'):
             return 'openib'
         # In version 1.7, it was renamed to be --with-verbs
@@ -143,7 +150,7 @@ def install(self, spec, prefix):
             '--with-psm2' if '+psm2' in spec else '--without-psm2',
             '--with-mxm' if '+mxm' in spec else '--without-mxm',
             # Other options
-            '--enable-mpi-thread-multiple' if '+thread_multiple' in spec else '--disable-mpi-thread-multiple',
+            '--enable-mpi-thread-multiple' if '+thread_multiple' in spec else '--disable-mpi-thread-multiple',  # NOQA: ignore=E501
             '--with-pmi' if '+pmi' in spec else '--without-pmi',
             '--with-sqlite3' if '+sqlite3' in spec else '--without-sqlite3',
             '--enable-vt' if '+vt' in spec else '--disable-vt'
@@ -161,7 +168,7 @@ def install(self, spec, prefix):
         # use this for LANL builds, but for LLNL builds, we need:
         #     "--with-platform=contrib/platform/llnl/optimized"
         if self.version == ver("1.6.5") and '+lanl' in spec:
-            config_args.append("--with-platform=contrib/platform/lanl/tlcc2/optimized-nopanasas")
+            config_args.append("--with-platform=contrib/platform/lanl/tlcc2/optimized-nopanasas")  # NOQA: ignore=E501
 
         if not self.compiler.f77 and not self.compiler.fc:
             config_args.append("--enable-mpi-fortran=no")
@@ -181,40 +188,33 @@ def filter_compilers(self):
            be bound to whatever compiler they were built with.
         """
         kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
-        dir = os.path.join(self.prefix, 'share/openmpi/')
+        wrapper_basepath = join_path(self.prefix, 'share', 'openmpi')
 
-        cc_wrappers = ['mpicc-vt-wrapper-data.txt', 'mpicc-wrapper-data.txt',
+        wrappers = [
-                       'ortecc-wrapper-data.txt', 'shmemcc-wrapper-data.txt']
+            ('mpicc-vt-wrapper-data.txt', self.compiler.cc),
+            ('mpicc-wrapper-data.txt', self.compiler.cc),
+            ('ortecc-wrapper-data.txt', self.compiler.cc),
+            ('shmemcc-wrapper-data.txt', self.compiler.cc),
+            ('mpic++-vt-wrapper-data.txt', self.compiler.cxx),
+            ('mpic++-wrapper-data.txt', self.compiler.cxx),
+            ('ortec++-wrapper-data.txt', self.compiler.cxx),
+            ('mpifort-vt-wrapper-data.txt', self.compiler.fc),
+            ('mpifort-wrapper-data.txt', self.compiler.fc),
+            ('shmemfort-wrapper-data.txt', self.compiler.fc),
+            ('mpif90-vt-wrapper-data.txt', self.compiler.fc),
+            ('mpif90-wrapper-data.txt', self.compiler.fc),
+            ('mpif77-vt-wrapper-data.txt',  self.compiler.f77),
+            ('mpif77-wrapper-data.txt',  self.compiler.f77)
+        ]
 
-        cxx_wrappers = ['mpic++-vt-wrapper-data.txt', 'mpic++-wrapper-data.txt',
+        for wrapper_name, compiler in wrappers:
-                        'ortec++-wrapper-data.txt']
+            wrapper = join_path(wrapper_basepath, wrapper_name)
-
+            if not os.path.islink(wrapper):
-        fc_wrappers = ['mpifort-vt-wrapper-data.txt',
+                # Substitute Spack compile wrappers for the real
-                       'mpifort-wrapper-data.txt', 'shmemfort-wrapper-data.txt']
+                # underlying compiler
-
+                match = 'compiler=.*'
-        for wrapper in cc_wrappers:
+                substitute = 'compiler={compiler}'.format(compiler=compiler)
-            filter_file('compiler=.*', 'compiler=%s' % self.compiler.cc,
+                filter_file(match, substitute, wrapper, **kwargs)
-                        os.path.join(dir, wrapper), **kwargs)
+                # Remove this linking flag if present
-
+                # (it turns RPATH into RUNPATH)
-        for wrapper in cxx_wrappers:
+                filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs)
-            filter_file('compiler=.*', 'compiler=%s' % self.compiler.cxx,
-                        os.path.join(dir, wrapper), **kwargs)
-
-        for wrapper in fc_wrappers:
-            filter_file('compiler=.*', 'compiler=%s' % self.compiler.fc,
-                        os.path.join(dir, wrapper), **kwargs)
-
-        # These are symlinks in newer versions, so check that here
-        f77_wrappers = ['mpif77-vt-wrapper-data.txt', 'mpif77-wrapper-data.txt']
-        f90_wrappers = ['mpif90-vt-wrapper-data.txt', 'mpif90-wrapper-data.txt']
-
-        for wrapper in f77_wrappers:
-            path = os.path.join(dir, wrapper)
-            if not os.path.islink(path):
-                filter_file('compiler=.*', 'compiler=%s' % self.compiler.f77,
-                            path, **kwargs)
-        for wrapper in f90_wrappers:
-            path = os.path.join(dir, wrapper)
-            if not os.path.islink(path):
-                filter_file('compiler=.*', 'compiler=%s' % self.compiler.fc,
-                            path, **kwargs)