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authorTodd Gamblin <tgamblin@llnl.gov>2016-07-04 10:02:33 -0700
committerGitHub <noreply@github.com>2016-07-04 10:02:33 -0700
commit9fb80303704a72ed295563a528f18d43f1170d08 (patch)
tree6b6f65325b22b7ed509bbff81e5e5d943d5a111e
parent890df7153aa528fdd98ee11b850498c6f81f0279 (diff)
parent85982017b605f2c21bbe01149a92e512b8be27f7 (diff)
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Merge pull request #1164 from epfl-scitas/revert-1023-packages/mumps
Revert "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, 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')