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authorTodd Gamblin <tgamblin@llnl.gov>2016-06-20 10:48:12 -0700
committerGitHub <noreply@github.com>2016-06-20 10:48:12 -0700
commit9b299cb2bbe6e1e20df38c1900d6a05483c81a3f (patch)
treebc085a701e31109c81cdcc77af825e7f12f11d01
parentcec283f6087f08ec3991edb1ccc41fd30965296f (diff)
parent2d21693b9d98219db29eac4ceb9163f32aaf51e4 (diff)
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Merge pull request #1023 from epfl-scitas/packages/mumps
Corrected the shared libraries and tests in mumps package
-rw-r--r--var/spack/repos/builtin/packages/mumps/mumps-shared.patch119
-rw-r--r--var/spack/repos/builtin/packages/mumps/package.py168
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))