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Merge pull request #585 from davydden/mumps_w_parmetis

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fix mumps: when installed with parmetis has to be linked with metis
This commit is contained in:
Todd Gamblin 2016-03-22 02:44:04 -07:00
commit e32eb7e990
5 changed files with 151 additions and 32 deletions
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28
var/spack/repos/builtin/packages/mumps/package.py
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@ -20,10 +20,10 @@ class Mumps(Package):
variant('complex', default=True, description='Activate the compilation of cmumps and/or zmumps')
variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
depends_on('scotch + esmumps', when='~ptscotch+scotch')
depends_on('scotch + esmumps + mpi', when='+ptscotch')
depends_on('metis', when='~parmetis+metis')
depends_on('metis', when='+metis')
depends_on('parmetis', when="+parmetis")
depends_on('blas')
depends_on('lapack')
@ -38,11 +38,11 @@ class Mumps(Package):
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')
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(
@ -54,15 +54,19 @@ def write_makefile_inc(self):
if '+ptscotch' in self.spec:
orderings.append('-Dptscotch')
if '+parmetis' in self.spec or '+metis' in self.spec:
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[libname].prefix.include,
"LMETIS = -L%s -l%s" % (self.spec[libname].prefix.lib, libname)])
["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')])
orderings.append('-Dmetis')
if '+parmetis' in self.spec:
orderings.append('-Dparmetis')
makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
@ -101,12 +105,12 @@ def write_makefile_inc(self):
# compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER
makefile_conf.append("CDEFS = -DAdd_")
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'))
with working_dir('.'):
with open("Makefile.inc", "w") as fh:
makefile_inc = '\n'.join(makefile_conf)
@ -130,7 +134,7 @@ def install(self, spec, prefix):
make_libs.append('zexamples')
self.write_makefile_inc()
make(*make_libs)
install_tree('lib', prefix.lib)

13
var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch Normal file
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@ -0,0 +1,13 @@
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ca945dd..1bf94e9 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -33,7 +33,7 @@ include_directories(${GKLIB_PATH})
include_directories(${METIS_PATH}/include)
# List of directories that cmake will look for CMakeLists.txt
-add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
+#add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
add_subdirectory(include)
add_subdirectory(libparmetis)
add_subdirectory(programs)

30
var/spack/repos/builtin/packages/parmetis/package.py
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@ -25,9 +25,6 @@
from spack import *
# FIXME : lot of code is duplicated from packages/metis/package.py . Inheriting from there may reduce
# FIXME : the installation rules to just a few lines
class Parmetis(Package):
"""
@ -43,13 +40,17 @@ class Parmetis(Package):
variant('debug', default=False, description='Builds the library in debug mode')
variant('gdb', default=False, description='Enables gdb support')
variant('idx64', default=False, description='Use int64_t as default index type')
variant('double', default=False, description='Use double precision floating point types')
depends_on('cmake @2.8:') # build dependency
depends_on('mpi')
# FIXME : this should conflict with metis as it builds its own version internally
patch('enable_external_metis.patch')
depends_on('metis')
# bug fixes from PETSc developers
# https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/
patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch')
# https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
depends_on('gdb', when='+gdb')
@ -63,8 +64,8 @@ def install(self, spec, prefix):
# FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
# FIXME : they use a non-standard name
options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source),
'-DMETIS_PATH:PATH={metis_source}'.format(metis_source=metis_source),
options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), # still need headers from METIS source, and they are not installed with METIS. shame...
'-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix),
'-DCMAKE_C_COMPILER:STRING=mpicc',
'-DCMAKE_CXX_COMPILER:STRING=mpicxx'])
@ -78,18 +79,7 @@ def install(self, spec, prefix):
if '+gdb' in spec:
options.append('-DGDB:BOOL=ON')
metis_header = join_path(metis_source, 'include', 'metis.h')
if '+idx64' in spec:
filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header)
if '+double' in spec:
filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
with working_dir(build_directory, create=True):
cmake(source_directory, *options)
make()
make("install")
# Parmetis build system doesn't allow for an external metis to be used, but doesn't copy the required
# metis header either
install(metis_header, self.prefix.include)

77
var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch Normal file
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@ -0,0 +1,77 @@
From 1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b Mon Sep 17 00:00:00 2001
From: Jed Brown <jed@59A2.org>
Date: Fri, 12 Oct 2012 15:45:10 -0500
Subject: [PATCH] ParMetis bug fixes reported by John Fettig [petsc-maint
#133631]
'''
I have also reported to to Karypis but have received zero
response and he hasn't released any updates to the original release
either. At least he approved my forum posting so that other people
can see the bug and the fix.
http://glaros.dtc.umn.edu/gkhome/node/837
'''
Hg-commit: 1c2b9fe39201d404b493885093b5992028b9b8d4
---
libparmetis/xyzpart.c | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c
index 3a2c289..63abfcb 100644
--- a/libparmetis/xyzpart.c
+++ b/libparmetis/xyzpart.c
@@ -104,7 +104,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
for (i=0; i<nbins; i++)
emarkers[i] = gmin + (gmax-gmin)*i/nbins;
- emarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON);
+ emarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON);
/* get into a iterative backet boundary refinement */
for (l=0; l<5; l++) {
@@ -152,7 +152,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
}
}
nemarkers[0] = gmin;
- nemarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON);
+ nemarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON);
rcopy(nbins+1, nemarkers, emarkers);
}
@@ -218,7 +218,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
emarkers[0] = gmin;
emarkers[1] = gsum/gnvtxs;
- emarkers[2] = gmax*(1.0+2.0*REAL_EPSILON);
+ emarkers[2] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON);
cnbins = 2;
/* get into a iterative backet boundary refinement */
@@ -227,7 +227,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
iset(cnbins, 0, lcounts);
rset(cnbins, 0, lsums);
for (j=0, i=0; i<nvtxs;) {
- if (cand[i].key < emarkers[j+1]) {
+ if (cand[i].key <= emarkers[j+1]) {
lcounts[j]++;
lsums[j] += cand[i].key;
i++;
@@ -272,12 +272,12 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
rsorti(cnbins, nemarkers);
rcopy(cnbins, nemarkers, emarkers);
- emarkers[cnbins] = gmax*(1.0+2.0*REAL_EPSILON);
+ emarkers[cnbins] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON);
}
/* assign the coordinate to the appropriate bin */
for (j=0, i=0; i<nvtxs;) {
- if (cand[i].key < emarkers[j+1]) {
+ if (cand[i].key <= emarkers[j+1]) {
bxyz[cand[i].val*ndims+k] = j;
i++;
}
--
2.1.1.1.g1fb337f

35
var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch Normal file
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@ -0,0 +1,35 @@
From 82409d68aa1d6cbc70740d0f35024aae17f7d5cb Mon Sep 17 00:00:00 2001
From: Sean Farley <sean@mcs.anl.gov>
Date: Tue, 20 Mar 2012 11:59:44 -0500
Subject: [PATCH] parmetis: fix bug reported by jfettig; '<' to '<=' in xyzpart
Hg-commit: 2dd2eae596acaabbc80e0ef875182616f868dbc2
---
libparmetis/xyzpart.c | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c
index 307aed9..3a2c289 100644
--- a/libparmetis/xyzpart.c
+++ b/libparmetis/xyzpart.c
@@ -111,7 +111,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
/* determine bucket counts */
iset(nbins, 0, lcounts);
for (j=0, i=0; i<nvtxs;) {
- if (cand[i].key < emarkers[j+1]) {
+ if (cand[i].key <= emarkers[j+1]) {
lcounts[j]++;
i++;
}
@@ -158,7 +158,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
/* assign the coordinate to the appropriate bin */
for (j=0, i=0; i<nvtxs;) {
- if (cand[i].key < emarkers[j+1]) {
+ if (cand[i].key <= emarkers[j+1]) {
bxyz[cand[i].val*ndims+k] = j;
i++;
}
--
2.1.1.1.g1fb337f