Merge pull request #1023 from epfl-scitas/packages/mumps

Corrected the shared libraries and tests in mumps package

2 files changed, 214 insertions, 73 deletions

diff --git a/var/spack/repos/builtin/packages/mumps/mumps-shared.patch b/var/spack/repos/builtin/packages/mumps/mumps-shared.patch
new file mode 100644
index 0000000000..592f48037c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mumps/mumps-shared.patch
@@ -0,0 +1,119 @@
+diff -Naur MUMPS_5.0.1/libseq/Makefile MUMPS_5.0.1.new/libseq/Makefile
+--- MUMPS_5.0.1/libseq/Makefile	2015-07-23 19:08:32.000000000 +0200
++++ MUMPS_5.0.1.new/libseq/Makefile	2016-06-07 10:41:16.585179151 +0200
+@@ -8,11 +8,15 @@
+ 
+ include ../Makefile.inc
+ 
+-libmpiseq: libmpiseq$(PLAT)$(LIBEXT)
++libmpiseq: libmpiseq$(PLAT)$(LIBEXT) libmpiseq$(PLAT)$(SHLIBEXT)
+ 
+ libmpiseq$(PLAT)$(LIBEXT): mpi.o mpic.o elapse.o
+ 	$(AR)$@ mpi.o mpic.o elapse.o
+ 	$(RANLIB) $@
++
++libmpiseq$(PLAT)$(SHLIBEXT): mpi.o mpic.o elapse.o
++	$(FC) $(LDFLAGS) $^ -o libmpiseq$(PLAT)$(SHLIBEXT)
++
+ .f.o:
+ 	$(FC) $(OPTF)              -c $*.f $(OUTF)$*.o
+ .c.o:
+diff -Naur MUMPS_5.0.1/Makefile MUMPS_5.0.1.new/Makefile
+--- MUMPS_5.0.1/Makefile	2015-07-23 19:08:29.000000000 +0200
++++ MUMPS_5.0.1.new/Makefile	2016-06-07 10:50:21.863281217 +0200
+@@ -51,7 +51,7 @@
+ dexamples:	d
+ 	(cd examples ; $(MAKE) d)
+ 
+-requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT)
++requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT)$(SHLIBEXT)
+ 
+ # dummy MPI library (sequential version)
+ 
+@@ -62,16 +62,25 @@
+ $(libdir)/libpord$(PLAT)$(LIBEXT):
+ 	if [ "$(LPORDDIR)" != "" ] ; then \
+ 	  cd $(LPORDDIR); \
+-	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \
++	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT); \
+ 	fi;
+ 	if [ "$(LPORDDIR)" != "" ] ; then \
+ 	  cp $(LPORDDIR)/libpord$(LIBEXT) $@; \
+ 	fi;
+ 
++$(libdir)/libpord$(PLAT)$(SHLIBEXT):
++	if [ "$(LPORDDIR)" != "" ] ; then \
++	  cd $(LPORDDIR); \
++	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT) libpord$(PLAT)$(SHLIBEXT); \
++	fi;
++	if [ "$(LPORDDIR)" != "" ] ; then \
++	  cp $(LPORDDIR)/libpord$(PLAT)$(SHLIBEXT) $@; \
++	fi;
++
+ clean:
+ 	(cd src; $(MAKE) clean)
+ 	(cd examples; $(MAKE) clean)
+-	(cd $(libdir); $(RM) *$(PLAT)$(LIBEXT))
++	(cd $(libdir); $(RM) *$(PLAT)$(LIBEXT) *$(PLAT)$(SHLIBEXT))
+ 	(cd libseq; $(MAKE) clean)
+ 	if [ "$(LPORDDIR)" != "" ] ; then \
+ 	  cd $(LPORDDIR); $(MAKE) realclean; \
+diff -Naur MUMPS_5.0.1/PORD/lib/Makefile MUMPS_5.0.1.new/PORD/lib/Makefile
+--- MUMPS_5.0.1/PORD/lib/Makefile	2015-07-23 19:08:29.000000000 +0200
++++ MUMPS_5.0.1.new/PORD/lib/Makefile	2016-06-07 10:49:48.889000958 +0200
+@@ -13,7 +13,7 @@
+ 
+ OBJS = graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o \
+        multisector.o gelim.o bucket.o tree.o \
+-       symbfac.o interface.o sort.o minpriority.o 
++       symbfac.o interface.o sort.o minpriority.o
+ 
+ # Note: numfac.c read.c mapping.c triangular.c matrix.c kernel.c
+ # were not direcly used by MUMPS and have been removed from the
+@@ -24,12 +24,15 @@
+ .c.o:
+ 	$(CC) $(COPTIONS) -c $*.c $(OUTC)$*.o
+ 
+-libpord$(LIBEXT):$(OBJS)
++libpord$(PLAT)$(LIBEXT):$(OBJS)
+ 	$(AR)$@ $(OBJS)
+ 	$(RANLIB) $@
+ 
++libpord$(PLAT)$(SHLIBEXT): $(OBJS)
++	$(CC) $(LDFLAGS) $(OBJS) -o libpord$(PLAT)$(SHLIBEXT)
++
+ clean:
+ 	rm -f *.o
+ 
+ realclean:
+-	rm -f *.o libpord.a
++	rm -f *.o libpord$(PLAT)$(SHLIBEXT) libpord$(PLAT)$(LIBEXT)
+diff -Naur MUMPS_5.0.1/src/Makefile MUMPS_5.0.1.new/src/Makefile
+--- MUMPS_5.0.1/src/Makefile	2015-07-23 19:08:29.000000000 +0200
++++ MUMPS_5.0.1.new/src/Makefile	2016-06-07 10:40:52.534703722 +0200
+@@ -24,7 +24,10 @@
+ include $(topdir)/Makefile.inc
+ 
+ mumps_lib:    $(libdir)/libmumps_common$(PLAT)$(LIBEXT) \
+-              $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT)
++              $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT) \
++              $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT) \
++              $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT)
++
+ 
+ OBJS_COMMON_MOD = \
+         ana_omp_m.o\
+@@ -162,6 +165,13 @@
+ 	$(AR)$@ $?
+ 	$(RANLIB) $@
+ 
++$(libdir)/libmumps_common$(PLAT)$(SHLIBEXT):	$(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER)
++	$(FC) $(LDFLAGS) $^ -L$(libdir) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT)
++
++
++$(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT):    $(OBJS_MOD) $(OBJS_OTHER)
++	$(FC) $(LDFLAGS) $^ -L$(libdir) -lmumps_common$(PLAT) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT)
++
+ # Dependencies between modules:
+ $(ARITH)mumps_load.o:		$(ARITH)mumps_comm_buffer.o \
+ 				$(ARITH)mumps_struc_def.o \
diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 92c45c9b95..8a90ef72d0 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -23,7 +23,10 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os, sys, glob
+import os
+import sys
+import subprocess
+
 
 class Mumps(Package):
     """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@@ -44,7 +47,6 @@ class Mumps(Package):
     variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
     variant('shared', default=True, description='Build shared libraries')
 
-
     depends_on('scotch + esmumps', when='~ptscotch+scotch')
     depends_on('scotch + esmumps + mpi', when='+ptscotch')
     depends_on('metis@5:', when='+metis')
@@ -54,49 +56,64 @@ class Mumps(Package):
     depends_on('scalapack', when='+mpi')
     depends_on('mpi', when='+mpi')
 
+    patch('mumps-shared.patch', when='+shared')
+
     # this function is not a patch function because in case scalapack
     # is needed it uses self.spec['scalapack'].fc_link set by the
     # setup_dependent_environment in scalapck. This happen after patch
     # end before install
     # def patch(self):
     def write_makefile_inc(self):
-        if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec:
-            raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')
+        if (('+parmetis' in self.spec or
+             '+ptscotch' in self.spec)) and '+mpi' not in self.spec:
+            raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')  # NOQA: E501
 
-        makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib]
+        makefile_conf = [
+            "LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib
+        ]
 
         orderings = ['-Dpord']
 
         if '+ptscotch' in self.spec or '+scotch' in self.spec:
             join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '')
-            makefile_conf.extend(
-                ["ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
-                 "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib,
-                                          join_lib,
-                                          join_lib.join(['esmumps', 'scotch', 'scotcherr']))])
+            makefile_conf.extend([
+                "ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
+                "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib,
+                                         join_lib,
+                                         join_lib.join(['esmumps',
+                                                        'scotch',
+                                                        'scotcherr']))
+            ])
             orderings.append('-Dscotch')
             if '+ptscotch' in self.spec:
                 orderings.append('-Dptscotch')
 
         if '+parmetis' in self.spec and '+metis' in self.spec:
-            libname = 'parmetis' if '+parmetis' in self.spec else 'metis'
-            makefile_conf.extend(
-                ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
-                 "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')])
+            makefile_conf.extend([
+                "IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
+                "LMETIS = -L%s -l%s -L%s -l%s" % (
+                    self.spec['parmetis'].prefix.lib, 'parmetis',
+                    self.spec['metis'].prefix.lib, 'metis')
+            ])
 
             orderings.append('-Dparmetis')
         elif '+metis' in self.spec:
-            makefile_conf.extend(
-                ["IMETIS = -I%s" % self.spec['metis'].prefix.include,
-                 "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')])
+            makefile_conf.extend([
+                "IMETIS = -I%s" % self.spec['metis'].prefix.include,
+                "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib,
+                                        'metis')
+            ])
 
             orderings.append('-Dmetis')
 
         makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
 
-        # when building shared libs need -fPIC, otherwise
-        # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
+        # when building shared libs need -fPIC, otherwise /usr/bin/ld:
+        # graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can
+        # not be used when making a shared object; recompile with
+        # -fPIC
         fpic = '-fPIC' if '+shared' in self.spec else ''
+
         # TODO: test this part, it needs a full blas, scalapack and
         # partitionning environment with 64bit integers
         if '+idx64' in self.spec:
@@ -104,7 +121,7 @@ class Mumps(Package):
                 # the fortran compilation flags most probably are
                 # working only for intel and gnu compilers this is
                 # perhaps something the compiler should provide
-                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),
+                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),  # NOQA: E501
                  'OPTL    = %s -O ' % fpic,
                  'OPTC    = %s -O -DINTSIZE64' % fpic])
         else:
@@ -113,49 +130,47 @@ class Mumps(Package):
                  'OPTL    = %s -O ' % fpic,
                  'OPTC    = %s -O ' % fpic])
 
-
         if '+mpi' in self.spec:
             makefile_conf.extend(
-                ["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'),
-                 "FC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
-                 "FL = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
+                ["CC = %s" % self.spec['mpi'].mpicc,
+                 "FC = %s" % self.spec['mpi'].mpifc,
                  "SCALAP = %s" % self.spec['scalapack'].fc_link,
                  "MUMPS_TYPE = par"])
         else:
             makefile_conf.extend(
                 ["CC = cc",
                  "FC = fc",
-                 "FL = fc",
                  "MUMPS_TYPE = seq"])
 
         # TODO: change the value to the correct one according to the
         # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER
-        makefile_conf.append("CDEFS   = -DAdd_")
+        makefile_conf.extend([
+            'CDEFS   = -DAdd_',
+            'FL = $(FC)',
+        ])
 
         if '+shared' in self.spec:
+            makefile_conf.append('SHLIBEXT = .%s' % dso_suffix)
             if sys.platform == 'darwin':
-                # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew)
-                makefile_conf.extend([
-                    'LIBEXT=.dylib',
-                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib),
-                    'RANLIB=echo'
-                ])
+                makefile_conf.append(
+                    'LDFLAGS = -dynamiclib -Wl,-install_name -Wl,{0}/$(notdir $@) {1}{0} -undefined dynamic_lookup'.format(prefix.lib, self.compiler.fc_rpath_arg)  # NOQA: E501
+                )
             else:
-                makefile_conf.extend([
-                    'LIBEXT=.so',
-                    'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,
-                    'RANLIB=echo'
-                ])
-        else:
-            makefile_conf.extend([
-                'LIBEXT  = .a',
-                'AR = ar vr',
-                'RANLIB = ranlib'
-            ])
-
-
-        makefile_inc_template = join_path(os.path.dirname(self.module.__file__),
-                                          'Makefile.inc')
+                makefile_conf.append(
+                    'LDFLAGS = -shared {0}{1}'.format(
+                        self.compiler.fc_rpath_arg,
+                        prefix.lib)
+                )
+
+        makefile_conf.extend([
+            'LIBEXT  = .a',
+            'AR = ar vr ',
+            'RANLIB = ranlib'
+        ])
+
+        makefile_inc_template = \
+            join_path(os.path.dirname(self.module.__file__),
+                      'Makefile.inc')
         with open(makefile_inc_template, "r") as fh:
             makefile_conf.extend(fh.read().split('\n'))
 
@@ -164,46 +179,53 @@ class Mumps(Package):
                 makefile_inc = '\n'.join(makefile_conf)
                 fh.write(makefile_inc)
 
-
-
     def install(self, spec, prefix):
         make_libs = []
 
         # the choice to compile ?examples is to have kind of a sanity
         # check on the libraries generated.
         if '+float' in spec:
-            make_libs.append('sexamples')
+            make_libs.append('s')
             if '+complex' in spec:
-                make_libs.append('cexamples')
+                make_libs.append('c')
 
         if '+double' in spec:
-            make_libs.append('dexamples')
+            make_libs.append('d')
             if '+complex' in spec:
-                make_libs.append('zexamples')
+                make_libs.append('z')
 
         self.write_makefile_inc()
 
-        # Build fails in parallel
-        make(*make_libs, parallel=False)
+        make('mumps_lib', parallel=False)
+        make(*make_libs)
 
         install_tree('lib', prefix.lib)
         install_tree('include', prefix.include)
 
-        if '~mpi' in spec:            
-            lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
-            lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
-            install('libseq/libmpiseq%s' % lib_suffix, prefix.lib)
-            for f in glob.glob(join_path('libseq','*.h')):
-                install(f, prefix.include)
-
-        # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI
-        # FIXME: use something like numdiff to compare blessed output with the current
-        with working_dir('examples'):
-            if '+float' in spec:
-                os.system('./ssimpletest < input_simpletest_real')
-                if '+complex' in spec:
-                    os.system('./csimpletest < input_simpletest_real')
-            if '+double' in spec:
-                os.system('./dsimpletest < input_simpletest_real')
-                if '+complex' in spec:
-                    os.system('./zsimpletest < input_simpletest_cmplx')
+        if '~mpi' in spec:
+            install('libseq/libmpiseq.a', prefix.lib)
+            if '+shared' in spec:
+                install('libseq/libmpiseq.{0}'.format(dso_suffix), prefix.lib)
+            install('libseq/mpi.h', prefix.include)
+            install('libseq/mpif.h', prefix.include)
+
+        # FIXME: extend the tests to mpirun -np 2 (or alike) when
+        # build with MPI
+        # FIXME: use something like numdiff to compare blessed output
+        # with the current
+        # TODO: test the installed mumps and not the one in stage
+        if '~mpi' in spec:
+            for t in make_libs:
+                make('{0}examples'.format(t))
+
+            with working_dir('examples'):
+                for t in make_libs:
+                    input_file = 'input_simpletest_{0}'.format(
+                        'real' if t in ['s', 'd'] else 'cmplx')
+                    with open(input_file) as input:
+                        test = './{0}simpletest'.format(t)
+                        ret = subprocess.call(test,
+                                              stdin=input)
+                        if ret is not 0:
+                            raise RuntimeError(
+                                'The test {0} did not pass'.format(test))