Merge pull request #1164 from epfl-scitas/revert-1023-packages/mumps

Revert "Corrected the shared libraries and tests in mumps package"

2 files changed, 73 insertions, 214 deletions

diff --git a/var/spack/repos/builtin/packages/mumps/mumps-shared.patch b/var/spack/repos/builtin/packages/mumps/mumps-shared.patch
deleted file mode 100644
index 592f48037c..0000000000
--- a/var/spack/repos/builtin/packages/mumps/mumps-shared.patch
+++ /dev/null
@@ -1,119 +0,0 @@
-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 8a90ef72d0..92c45c9b95 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -23,10 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
-import sys
-import subprocess
-
+import os, sys, glob
 
 class Mumps(Package):
     """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@@ -47,6 +44,7 @@ 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')
@@ -56,64 +54,49 @@ 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')  # NOQA: E501
+        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')
 
-        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:
-            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')
-            ])
+            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')])
 
             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:
@@ -121,7 +104,7 @@ 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'),  # NOQA: E501
+                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),
                  'OPTL    = %s -O ' % fpic,
                  'OPTC    = %s -O -DINTSIZE64' % fpic])
         else:
@@ -130,47 +113,49 @@ class Mumps(Package):
                  'OPTL    = %s -O ' % fpic,
                  'OPTC    = %s -O ' % fpic])
 
+
         if '+mpi' in self.spec:
             makefile_conf.extend(
-                ["CC = %s" % self.spec['mpi'].mpicc,
-                 "FC = %s" % self.spec['mpi'].mpifc,
+                ["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'),
                  "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.extend([
-            'CDEFS   = -DAdd_',
-            'FL = $(FC)',
-        ])
+        makefile_conf.append("CDEFS   = -DAdd_")
 
         if '+shared' in self.spec:
-            makefile_conf.append('SHLIBEXT = .%s' % dso_suffix)
             if sys.platform == 'darwin':
-                makefile_conf.append(
-                    'LDFLAGS = -dynamiclib -Wl,-install_name -Wl,{0}/$(notdir $@) {1}{0} -undefined dynamic_lookup'.format(prefix.lib, self.compiler.fc_rpath_arg)  # NOQA: E501
-                )
+                # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew)
+                makefile_conf.extend([
+                    'LIBEXT=.dylib',
+                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib),
+                    'RANLIB=echo'
+                ])
             else:
-                makefile_conf.append(
-                    'LDFLAGS = -shared {0}{1}'.format(
-                        self.compiler.fc_rpath_arg,
-                        prefix.lib)
-                )
-
-        makefile_conf.extend([
-            'LIBEXT  = .a',
-            'AR = ar vr ',
-            'RANLIB = ranlib'
-        ])
-
-        makefile_inc_template = \
-            join_path(os.path.dirname(self.module.__file__),
-                      'Makefile.inc')
+                makefile_conf.extend([
+                    'LIBEXT=.so',
+                    'AR=$(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')
         with open(makefile_inc_template, "r") as fh:
             makefile_conf.extend(fh.read().split('\n'))
 
@@ -179,53 +164,46 @@ 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('s')
+            make_libs.append('sexamples')
             if '+complex' in spec:
-                make_libs.append('c')
+                make_libs.append('cexamples')
 
         if '+double' in spec:
-            make_libs.append('d')
+            make_libs.append('dexamples')
             if '+complex' in spec:
-                make_libs.append('z')
+                make_libs.append('zexamples')
 
         self.write_makefile_inc()
 
-        make('mumps_lib', parallel=False)
-        make(*make_libs)
+        # Build fails in parallel
+        make(*make_libs, parallel=False)
 
         install_tree('lib', prefix.lib)
         install_tree('include', prefix.include)
 
-        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))
+        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')