From 624b576b1e21ea476eaf7fdc3ee38a97194e45f7 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 2 Apr 2016 12:01:46 +0200 Subject: metis: fix compilation with Clang 7.3.0, add tests --- var/spack/repos/builtin/packages/metis/package.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py index 9301135f9f..d3bab554fe 100644 --- a/var/spack/repos/builtin/packages/metis/package.py +++ b/var/spack/repos/builtin/packages/metis/package.py @@ -79,10 +79,28 @@ class Metis(Package): if '+double' in spec: filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header) + # Make clang 7.3 happy. + # Prevents "ld: section __DATA/__thread_bss extends beyond end of file" + # See upstream LLVM issue https://llvm.org/bugs/show_bug.cgi?id=27059 + # Adopted from https://github.com/Homebrew/homebrew-science/blob/master/metis.rb + if spec.satisfies('%clang@7.3.0'): + filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24', join_path(source_directory, 'GKlib', 'error.c')) + with working_dir(build_directory, create=True): cmake(source_directory, *options) make() make("install") + # now run some tests: + for f in ["4elt", "copter2", "mdual"]: + graph = join_path(source_directory,'graphs','%s.graph' % f) + Executable(join_path(prefix.bin,'graphchk'))(graph) + Executable(join_path(prefix.bin,'gpmetis'))(graph,'2') + Executable(join_path(prefix.bin,'ndmetis'))(graph) + + graph = join_path(source_directory,'graphs','test.mgraph') + Executable(join_path(prefix.bin,'gpmetis'))(graph,'2') + graph = join_path(source_directory,'graphs','metis.mesh') + Executable(join_path(prefix.bin,'mpmetis'))(graph,'2') # install GKlib headers, which will be needed for ParMETIS GKlib_dist = join_path(prefix.include,'GKlib') -- cgit v1.2.3-70-g09d2 From a88c6da9acc234484d34acf6588c838bef09e8c4 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 2 Apr 2016 12:02:29 +0200 Subject: suite-sparse: fix a bug where interla metis was used; add TBB variant --- .../repos/builtin/packages/suite-sparse/package.py | 36 +++++++++++++++++----- 1 file changed, 29 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index c2196dcec4..f2e71f7479 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -10,10 +10,13 @@ class SuiteSparse(Package): version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') + variant('tbb', default=True, description='Build with Intel TBB') + depends_on('blas') depends_on('lapack') depends_on('metis@5.1.0', when='@4.5.1') + depends_on('tbb', when='+tbb') def install(self, spec, prefix): # The build system of SuiteSparse is quite old-fashioned @@ -21,16 +24,35 @@ class SuiteSparse(Package): # with a lot of convoluted logic in it. # Any kind of customization will need to go through filtering of that file - # FIXME : this actually uses the current workaround - # FIXME : (blas / lapack always provide libblas and liblapack as aliases) - make('install', 'INSTALL=%s' % prefix, + make_args = ['INSTALL=%s' % prefix] - # inject Spack compiler wrappers + # inject Spack compiler wrappers + make_args.extend([ 'AUTOCC=no', 'CC=cc', 'CXX=c++', 'F77=f77', + ]) + + # use Spack's metis in CHOLMOD/Partition module, + # otherwise internal Metis will be compiled + make_args.extend([ + 'MY_METIS_LIB=-L%s -lmetis' % spec['metis'].prefix.lib, + 'MY_METIS_INC=%s' % spec['metis'].prefix.include, + ]) + + # Intel TBB in SuiteSparseQR + if '+tbb' in spec: + make_args.extend([ + 'SPQR_CONFIG=-DHAVE_TBB', + 'TBB=-L%s -ltbb' % spec['tbb'].prefix.lib, + ]) + + # BLAS arguments require path to libraries + # FIXME : (blas / lapack always provide libblas and liblapack as aliases) + make_args.extend([ + 'BLAS=-lblas', + 'LAPACK=-llapack' + ]) - # BLAS arguments require path to libraries - 'BLAS=-lblas', - 'LAPACK=-llapack') + make('install', *make_args) -- cgit v1.2.3-70-g09d2 From adccd18015eec2589d69194fa30be45b04cb515e Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 2 Apr 2016 12:02:59 +0200 Subject: dealii: add extra test for Petsc+Metis --- var/spack/repos/builtin/packages/dealii/package.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 0b76db3827..d8a0df643d 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -174,6 +174,19 @@ class Dealii(Package): make('release') make('run',parallel=False) + # An example which uses Metis + PETSc + # FIXME: switch step-18 to MPI + with working_dir('examples/step-18'): + print('=====================================') + print('============= Step-18 ===============') + print('=====================================') + # list the number of cycles to speed up + filter_file(r'(end_time = 10;)', ('end_time = 3;'), 'step-18.cc') + if '^petsc' in spec and '^metis' in spec: + cmake('.') + make('release') + make('run',parallel=False) + # take step-40 which can use both PETSc and Trilinos # FIXME: switch step-40 to MPI run with working_dir('examples/step-40'): -- cgit v1.2.3-70-g09d2 From e0ff3f16cc142fb9ca55cc1c6000fb230627f8fe Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sun, 3 Apr 2016 19:41:20 +0200 Subject: dealii: blacklist boost --- var/spack/repos/builtin/packages/dealii/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index d8a0df643d..1f763ad358 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -23,8 +23,10 @@ class Dealii(Package): # required dependencies, light version depends_on ("blas") - depends_on ("boost", when='~mpi') - depends_on ("boost+mpi", when='+mpi') + # Boost 1.58 is blacklisted, see https://github.com/dealii/dealii/issues/1591 + # require at least 1.59 + depends_on ("boost@1.59.0:", when='~mpi') + depends_on ("boost@1.59.0:+mpi", when='+mpi') depends_on ("bzip2") depends_on ("cmake") depends_on ("lapack") -- cgit v1.2.3-70-g09d2 From 131d34f318a9955ff05c35eb8de0b399c31d5cc2 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 4 Apr 2016 09:05:27 +0200 Subject: suite-sparse: temporary disable TBB due to linking errors --- var/spack/repos/builtin/packages/suite-sparse/package.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index f2e71f7479..a4b3979a15 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -10,13 +10,18 @@ class SuiteSparse(Package): version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') - variant('tbb', default=True, description='Build with Intel TBB') + # FIXME: (see below) + # variant('tbb', default=True, description='Build with Intel TBB') depends_on('blas') depends_on('lapack') depends_on('metis@5.1.0', when='@4.5.1') - depends_on('tbb', when='+tbb') + # FIXME: + # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng flags + # does not seem to be used, which leads to linking errors on Linux. + # Try re-enabling in future versions. + # depends_on('tbb', when='+tbb') def install(self, spec, prefix): # The build system of SuiteSparse is quite old-fashioned -- cgit v1.2.3-70-g09d2