Merge pull request #1023 from epfl-scitas/packages/mumps
Corrected the shared libraries and tests in mumps package
This commit is contained in:
Todd Gamblin
GitHub
commit
9b299cb2bb
2 changed files with 211 additions and 70 deletions
119
var/spack/repos/builtin/packages/mumps/mumps-shared.patch
Normal file
119
var/spack/repos/builtin/packages/mumps/mumps-shared.patch
Normal file
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@ -0,0 +1,119 @@
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diff -Naur MUMPS_5.0.1/libseq/Makefile MUMPS_5.0.1.new/libseq/Makefile
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--- MUMPS_5.0.1/libseq/Makefile 2015-07-23 19:08:32.000000000 +0200
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+++ MUMPS_5.0.1.new/libseq/Makefile 2016-06-07 10:41:16.585179151 +0200
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@@ -8,11 +8,15 @@
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include ../Makefile.inc
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-libmpiseq: libmpiseq$(PLAT)$(LIBEXT)
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+libmpiseq: libmpiseq$(PLAT)$(LIBEXT) libmpiseq$(PLAT)$(SHLIBEXT)
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libmpiseq$(PLAT)$(LIBEXT): mpi.o mpic.o elapse.o
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$(AR)$@ mpi.o mpic.o elapse.o
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$(RANLIB) $@
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+
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+libmpiseq$(PLAT)$(SHLIBEXT): mpi.o mpic.o elapse.o
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+ $(FC) $(LDFLAGS) $^ -o libmpiseq$(PLAT)$(SHLIBEXT)
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+
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.f.o:
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$(FC) $(OPTF) -c $*.f $(OUTF)$*.o
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.c.o:
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diff -Naur MUMPS_5.0.1/Makefile MUMPS_5.0.1.new/Makefile
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--- MUMPS_5.0.1/Makefile 2015-07-23 19:08:29.000000000 +0200
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+++ MUMPS_5.0.1.new/Makefile 2016-06-07 10:50:21.863281217 +0200
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@@ -51,7 +51,7 @@
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dexamples: d
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(cd examples ; $(MAKE) d)
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-requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT)
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+requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT)$(SHLIBEXT)
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# dummy MPI library (sequential version)
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@@ -62,16 +62,25 @@
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$(libdir)/libpord$(PLAT)$(LIBEXT):
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if [ "$(LPORDDIR)" != "" ] ; then \
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cd $(LPORDDIR); \
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- $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \
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+ $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT); \
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fi;
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if [ "$(LPORDDIR)" != "" ] ; then \
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cp $(LPORDDIR)/libpord$(LIBEXT) $@; \
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fi;
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+$(libdir)/libpord$(PLAT)$(SHLIBEXT):
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+ if [ "$(LPORDDIR)" != "" ] ; then \
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+ cd $(LPORDDIR); \
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+ $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT) libpord$(PLAT)$(SHLIBEXT); \
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+ fi;
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+ if [ "$(LPORDDIR)" != "" ] ; then \
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+ cp $(LPORDDIR)/libpord$(PLAT)$(SHLIBEXT) $@; \
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+ fi;
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+
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clean:
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(cd src; $(MAKE) clean)
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(cd examples; $(MAKE) clean)
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- (cd $(libdir); $(RM) *$(PLAT)$(LIBEXT))
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+ (cd $(libdir); $(RM) *$(PLAT)$(LIBEXT) *$(PLAT)$(SHLIBEXT))
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(cd libseq; $(MAKE) clean)
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if [ "$(LPORDDIR)" != "" ] ; then \
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cd $(LPORDDIR); $(MAKE) realclean; \
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diff -Naur MUMPS_5.0.1/PORD/lib/Makefile MUMPS_5.0.1.new/PORD/lib/Makefile
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--- MUMPS_5.0.1/PORD/lib/Makefile 2015-07-23 19:08:29.000000000 +0200
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+++ MUMPS_5.0.1.new/PORD/lib/Makefile 2016-06-07 10:49:48.889000958 +0200
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@@ -13,7 +13,7 @@
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OBJS = graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o \
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multisector.o gelim.o bucket.o tree.o \
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- symbfac.o interface.o sort.o minpriority.o
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+ symbfac.o interface.o sort.o minpriority.o
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# Note: numfac.c read.c mapping.c triangular.c matrix.c kernel.c
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# were not direcly used by MUMPS and have been removed from the
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@@ -24,12 +24,15 @@
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.c.o:
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$(CC) $(COPTIONS) -c $*.c $(OUTC)$*.o
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-libpord$(LIBEXT):$(OBJS)
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+libpord$(PLAT)$(LIBEXT):$(OBJS)
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$(AR)$@ $(OBJS)
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$(RANLIB) $@
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+libpord$(PLAT)$(SHLIBEXT): $(OBJS)
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+ $(CC) $(LDFLAGS) $(OBJS) -o libpord$(PLAT)$(SHLIBEXT)
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+
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clean:
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rm -f *.o
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realclean:
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- rm -f *.o libpord.a
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+ rm -f *.o libpord$(PLAT)$(SHLIBEXT) libpord$(PLAT)$(LIBEXT)
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diff -Naur MUMPS_5.0.1/src/Makefile MUMPS_5.0.1.new/src/Makefile
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--- MUMPS_5.0.1/src/Makefile 2015-07-23 19:08:29.000000000 +0200
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+++ MUMPS_5.0.1.new/src/Makefile 2016-06-07 10:40:52.534703722 +0200
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@@ -24,7 +24,10 @@
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include $(topdir)/Makefile.inc
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mumps_lib: $(libdir)/libmumps_common$(PLAT)$(LIBEXT) \
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- $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT)
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+ $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT) \
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+ $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT) \
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+ $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT)
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+
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OBJS_COMMON_MOD = \
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ana_omp_m.o\
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@@ -162,6 +165,13 @@
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$(AR)$@ $?
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$(RANLIB) $@
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+$(libdir)/libmumps_common$(PLAT)$(SHLIBEXT): $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER)
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+ $(FC) $(LDFLAGS) $^ -L$(libdir) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT)
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+
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+
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+$(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT): $(OBJS_MOD) $(OBJS_OTHER)
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+ $(FC) $(LDFLAGS) $^ -L$(libdir) -lmumps_common$(PLAT) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT)
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+
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# Dependencies between modules:
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$(ARITH)mumps_load.o: $(ARITH)mumps_comm_buffer.o \
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$(ARITH)mumps_struc_def.o \
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@ -23,7 +23,10 @@
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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##############################################################################
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from spack import *
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from spack import *
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import os, sys, glob
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import os
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import sys
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import subprocess
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class Mumps(Package):
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class Mumps(Package):
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"""MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
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"""MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
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@ -44,7 +47,6 @@ class Mumps(Package):
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variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
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variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
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variant('shared', default=True, description='Build shared libraries')
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variant('shared', default=True, description='Build shared libraries')
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depends_on('scotch + esmumps', when='~ptscotch+scotch')
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depends_on('scotch + esmumps', when='~ptscotch+scotch')
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depends_on('scotch + esmumps + mpi', when='+ptscotch')
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depends_on('scotch + esmumps + mpi', when='+ptscotch')
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depends_on('metis@5:', when='+metis')
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depends_on('metis@5:', when='+metis')
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@ -54,49 +56,64 @@ class Mumps(Package):
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depends_on('scalapack', when='+mpi')
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depends_on('scalapack', when='+mpi')
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depends_on('mpi', when='+mpi')
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depends_on('mpi', when='+mpi')
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patch('mumps-shared.patch', when='+shared')
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# this function is not a patch function because in case scalapack
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# this function is not a patch function because in case scalapack
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# is needed it uses self.spec['scalapack'].fc_link set by the
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# is needed it uses self.spec['scalapack'].fc_link set by the
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# setup_dependent_environment in scalapck. This happen after patch
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# setup_dependent_environment in scalapck. This happen after patch
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# end before install
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# end before install
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# def patch(self):
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# def patch(self):
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def write_makefile_inc(self):
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def write_makefile_inc(self):
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if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec:
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if (('+parmetis' in self.spec or
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raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')
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'+ptscotch' in self.spec)) and '+mpi' not in self.spec:
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raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') # NOQA: E501
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makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib]
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makefile_conf = [
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"LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib
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]
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orderings = ['-Dpord']
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orderings = ['-Dpord']
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if '+ptscotch' in self.spec or '+scotch' in self.spec:
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if '+ptscotch' in self.spec or '+scotch' in self.spec:
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join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '')
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join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '')
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makefile_conf.extend(
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makefile_conf.extend([
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["ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
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"ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
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"LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib,
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"LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib,
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join_lib,
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join_lib,
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join_lib.join(['esmumps', 'scotch', 'scotcherr']))])
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join_lib.join(['esmumps',
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'scotch',
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'scotcherr']))
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])
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orderings.append('-Dscotch')
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orderings.append('-Dscotch')
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if '+ptscotch' in self.spec:
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if '+ptscotch' in self.spec:
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orderings.append('-Dptscotch')
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orderings.append('-Dptscotch')
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if '+parmetis' in self.spec and '+metis' in self.spec:
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if '+parmetis' in self.spec and '+metis' in self.spec:
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libname = 'parmetis' if '+parmetis' in self.spec else 'metis'
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makefile_conf.extend([
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makefile_conf.extend(
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"IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
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["IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
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"LMETIS = -L%s -l%s -L%s -l%s" % (
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"LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')])
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self.spec['parmetis'].prefix.lib, 'parmetis',
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self.spec['metis'].prefix.lib, 'metis')
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])
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orderings.append('-Dparmetis')
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orderings.append('-Dparmetis')
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elif '+metis' in self.spec:
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elif '+metis' in self.spec:
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makefile_conf.extend(
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makefile_conf.extend([
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["IMETIS = -I%s" % self.spec['metis'].prefix.include,
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"IMETIS = -I%s" % self.spec['metis'].prefix.include,
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"LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')])
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"LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib,
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'metis')
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])
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orderings.append('-Dmetis')
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orderings.append('-Dmetis')
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makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
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makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
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# when building shared libs need -fPIC, otherwise
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# when building shared libs need -fPIC, otherwise /usr/bin/ld:
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# /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
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# graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can
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# not be used when making a shared object; recompile with
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# -fPIC
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fpic = '-fPIC' if '+shared' in self.spec else ''
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fpic = '-fPIC' if '+shared' in self.spec else ''
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# TODO: test this part, it needs a full blas, scalapack and
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# TODO: test this part, it needs a full blas, scalapack and
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# partitionning environment with 64bit integers
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# partitionning environment with 64bit integers
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if '+idx64' in self.spec:
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if '+idx64' in self.spec:
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@ -104,7 +121,7 @@ def write_makefile_inc(self):
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# the fortran compilation flags most probably are
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# the fortran compilation flags most probably are
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# working only for intel and gnu compilers this is
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# working only for intel and gnu compilers this is
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# perhaps something the compiler should provide
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# perhaps something the compiler should provide
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['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),
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['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), # NOQA: E501
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'OPTL = %s -O ' % fpic,
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'OPTL = %s -O ' % fpic,
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'OPTC = %s -O -DINTSIZE64' % fpic])
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'OPTC = %s -O -DINTSIZE64' % fpic])
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else:
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else:
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@ -113,48 +130,46 @@ def write_makefile_inc(self):
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'OPTL = %s -O ' % fpic,
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'OPTL = %s -O ' % fpic,
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'OPTC = %s -O ' % fpic])
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'OPTC = %s -O ' % fpic])
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if '+mpi' in self.spec:
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if '+mpi' in self.spec:
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makefile_conf.extend(
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makefile_conf.extend(
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["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'),
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["CC = %s" % self.spec['mpi'].mpicc,
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"FC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
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"FC = %s" % self.spec['mpi'].mpifc,
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"FL = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
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"SCALAP = %s" % self.spec['scalapack'].fc_link,
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"SCALAP = %s" % self.spec['scalapack'].fc_link,
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"MUMPS_TYPE = par"])
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"MUMPS_TYPE = par"])
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else:
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else:
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makefile_conf.extend(
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makefile_conf.extend(
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["CC = cc",
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["CC = cc",
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"FC = fc",
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"FC = fc",
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"FL = fc",
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"MUMPS_TYPE = seq"])
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"MUMPS_TYPE = seq"])
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# TODO: change the value to the correct one according to the
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# TODO: change the value to the correct one according to the
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# compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER
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# compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER
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makefile_conf.append("CDEFS = -DAdd_")
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makefile_conf.extend([
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'CDEFS = -DAdd_',
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'FL = $(FC)',
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])
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if '+shared' in self.spec:
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if '+shared' in self.spec:
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makefile_conf.append('SHLIBEXT = .%s' % dso_suffix)
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if sys.platform == 'darwin':
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if sys.platform == 'darwin':
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# Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew)
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makefile_conf.append(
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makefile_conf.extend([
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'LDFLAGS = -dynamiclib -Wl,-install_name -Wl,{0}/$(notdir $@) {1}{0} -undefined dynamic_lookup'.format(prefix.lib, self.compiler.fc_rpath_arg) # NOQA: E501
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'LIBEXT=.dylib',
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)
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'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib),
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|
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'RANLIB=echo'
|
|
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])
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|
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else:
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|
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makefile_conf.extend([
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|
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'LIBEXT=.so',
|
|
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'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,
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|
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'RANLIB=echo'
|
|
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])
|
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else:
|
else:
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makefile_conf.append(
|
||||||
|
'LDFLAGS = -shared {0}{1}'.format(
|
||||||
|
self.compiler.fc_rpath_arg,
|
||||||
|
prefix.lib)
|
||||||
|
)
|
||||||
|
|
||||||
makefile_conf.extend([
|
makefile_conf.extend([
|
||||||
'LIBEXT = .a',
|
'LIBEXT = .a',
|
||||||
'AR = ar vr',
|
'AR = ar vr ',
|
||||||
'RANLIB = ranlib'
|
'RANLIB = ranlib'
|
||||||
])
|
])
|
||||||
|
|
||||||
|
makefile_inc_template = \
|
||||||
makefile_inc_template = join_path(os.path.dirname(self.module.__file__),
|
join_path(os.path.dirname(self.module.__file__),
|
||||||
'Makefile.inc')
|
'Makefile.inc')
|
||||||
with open(makefile_inc_template, "r") as fh:
|
with open(makefile_inc_template, "r") as fh:
|
||||||
makefile_conf.extend(fh.read().split('\n'))
|
makefile_conf.extend(fh.read().split('\n'))
|
||||||
|
|
@ -164,46 +179,53 @@ def write_makefile_inc(self):
|
||||||
makefile_inc = '\n'.join(makefile_conf)
|
makefile_inc = '\n'.join(makefile_conf)
|
||||||
fh.write(makefile_inc)
|
fh.write(makefile_inc)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def install(self, spec, prefix):
|
def install(self, spec, prefix):
|
||||||
make_libs = []
|
make_libs = []
|
||||||
|
|
||||||
# the choice to compile ?examples is to have kind of a sanity
|
# the choice to compile ?examples is to have kind of a sanity
|
||||||
# check on the libraries generated.
|
# check on the libraries generated.
|
||||||
if '+float' in spec:
|
if '+float' in spec:
|
||||||
make_libs.append('sexamples')
|
make_libs.append('s')
|
||||||
if '+complex' in spec:
|
if '+complex' in spec:
|
||||||
make_libs.append('cexamples')
|
make_libs.append('c')
|
||||||
|
|
||||||
if '+double' in spec:
|
if '+double' in spec:
|
||||||
make_libs.append('dexamples')
|
make_libs.append('d')
|
||||||
if '+complex' in spec:
|
if '+complex' in spec:
|
||||||
make_libs.append('zexamples')
|
make_libs.append('z')
|
||||||
|
|
||||||
self.write_makefile_inc()
|
self.write_makefile_inc()
|
||||||
|
|
||||||
# Build fails in parallel
|
make('mumps_lib', parallel=False)
|
||||||
make(*make_libs, parallel=False)
|
make(*make_libs)
|
||||||
|
|
||||||
install_tree('lib', prefix.lib)
|
install_tree('lib', prefix.lib)
|
||||||
install_tree('include', prefix.include)
|
install_tree('include', prefix.include)
|
||||||
|
|
||||||
if '~mpi' in spec:
|
if '~mpi' in spec:
|
||||||
lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
|
install('libseq/libmpiseq.a', prefix.lib)
|
||||||
lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
|
if '+shared' in spec:
|
||||||
install('libseq/libmpiseq%s' % lib_suffix, prefix.lib)
|
install('libseq/libmpiseq.{0}'.format(dso_suffix), prefix.lib)
|
||||||
for f in glob.glob(join_path('libseq','*.h')):
|
install('libseq/mpi.h', prefix.include)
|
||||||
install(f, 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))
|
||||||
|
|
||||||
# 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'):
|
with working_dir('examples'):
|
||||||
if '+float' in spec:
|
for t in make_libs:
|
||||||
os.system('./ssimpletest < input_simpletest_real')
|
input_file = 'input_simpletest_{0}'.format(
|
||||||
if '+complex' in spec:
|
'real' if t in ['s', 'd'] else 'cmplx')
|
||||||
os.system('./csimpletest < input_simpletest_real')
|
with open(input_file) as input:
|
||||||
if '+double' in spec:
|
test = './{0}simpletest'.format(t)
|
||||||
os.system('./dsimpletest < input_simpletest_real')
|
ret = subprocess.call(test,
|
||||||
if '+complex' in spec:
|
stdin=input)
|
||||||
os.system('./zsimpletest < input_simpletest_cmplx')
|
if ret is not 0:
|
||||||
|
raise RuntimeError(
|
||||||
|
'The test {0} did not pass'.format(test))
|
||||||
|
|
|
||||||
Loading…
Reference in a new issue