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[WIP] CEED 2.0 (#10903)

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* Initial commit for v2.0 of the CEED software suite.

* Update Nek packages and gslib

* Help spack concretize the hypre version for ceed-2.0.

* Fix nekcem install error

* Add support for gfortran v8 in nek5000 and nekcem.

* Split Nek5000 into Nek5000 and Nektools

* Get Nektools to build fine in Theta

* Fix travis failure: remove unused 'import numbers' from nek5000.

* Check for gfortran if it is wrapped

* Tweak the detection of gfortran in nek5000.

* Fix Nek packages to add -std=legacy when FC=gcc

* spack install ceed~petsc works fine on Theta

* Fix flake8 errors

* Fix more flake8 tests

* Fix an import issue

* Tweak the suite-sparse package to avoid interaction with existing system
installations of suite-sparse.

* petsc: update superlu-dist dependency

* Updates in the packages: occa, libceed, and ceed.

* In the libceed package, explicitly tell nvcc which host compiler to use.

* Fix python formatting.

* Simplify the test for gfortran in nek* packages.

* ceed: 2.0 uses petsc@3.11.0

* hpgmg-0.4; use from ceed@2.0.0

* Update the hypre dependency for ceed 2.0.

* Disable the superlu-dist dependency (through hypre) when using a
+quickbuild of ceed 2.0.

* petsc-3.11.0: add xlf fix

* nekcem: has a build dependency on Python 2.7+

* hpgmg: better setting of compiler options and use python for configure

* libceed: use v0.4 tag

* libceed: fix 0.4 release oops (pkgconfig version)

* Add a patch for magma-2.5.0 that brings it up the current 'master'.

* In the mfem package, install the examples, miniapps, and data under
$prefix/share/mfem.

* In the magma package, apply a patch to v2.5.0 that disables
magma_sparse - for testing purposes.

* In the magma package, link the 'magma' library with the
'nvToolsExt' library.

* In the magma package, update the 'magma-2.5.0.patch' with the latest
commits from the magma source repository. Also, remove the library
'nvToolsExt' from the 'magma-2.5.0-cmake.patch' - now it is not
needed.

* In the magma package, disable OpenMP when using v2.5.0 with the
IBM XL compiler.

 Please enter the commit message for your changes. Lines starting

* In the mfem package, add version for the 'laghos-v2.0' tag; also,
prefix the versions `laghos-v*` with their respective development
version numbers -- this way they are properly ordered within spack
relative to the official numbered versions.

* petsc: add version 3.11.1 (#11179)


(cherry picked from commit 1eab6e3c86)

* ceed-2.0: use petsc-3.11.1

* this-is-so-dumb.f -> empty.f
This commit is contained in:
Veselin Dobrev 2019-04-17 17:37:41 -07:00 committed by Tzanio Kolev
parent a26aec520b
commit 49334f006d
18 changed files with 926 additions and 144 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

57
var/spack/repos/builtin/packages/ceed/package.py
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@ -20,6 +20,7 @@ class Ceed(Package):
url = 'file://' + os.path.dirname(__file__) + '/README.md'
sha1 = 'b2eefd95c09ba573f663a761b84811a2d7e39788'
version('2.0.0', sha1, expand=False)
version('1.0.0', sha1, expand=False)
variant('cuda', default=False,
@ -38,22 +39,53 @@ class Ceed(Package):
# TODO: Add 'int64' variant?
# LibCEED
# ceed-2.0
depends_on('libceed@0.4~cuda', when='@2.0.0~cuda')
depends_on('libceed@0.4+cuda', when='@2.0.0+cuda')
depends_on('libceed@0.4+occa', when='@2.0.0+occa')
depends_on('libceed@0.4~occa', when='@2.0.0~occa')
# ceed-1.0
depends_on('libceed@0.2~cuda', when='@1.0.0~cuda')
depends_on('libceed@0.2+cuda', when='@1.0.0+cuda')
depends_on('libceed@0.2+occa', when='@1.0.0+occa')
depends_on('libceed@0.2~occa', when='@1.0.0~occa')
# OCCA
depends_on('occa@v1.0.0-alpha.5~cuda', when='@1.0.0+occa~cuda')
depends_on('occa@v1.0.0-alpha.5+cuda', when='@1.0.0+occa+cuda')
# ceed-2.0
depends_on('occa@1.0.8~cuda', when='@2.0.0+occa~cuda')
depends_on('occa@1.0.8+cuda', when='@2.0.0+occa+cuda')
# ceed-1.0
depends_on('occa@1.0.0-alpha.5~cuda', when='@1.0.0+occa~cuda')
depends_on('occa@1.0.0-alpha.5+cuda', when='@1.0.0+occa+cuda')
# Nek5000, GSLIB, Nekbone, and NekCEM
# ceed-2.0
depends_on('nek5000@17.0', when='@2.0.0+nek')
depends_on('nektools@17.0%gcc', when='@2.0.0+nek')
depends_on('gslib@1.0.2', when='@2.0.0+nek')
depends_on('nekbone@17.0', when='@2.0.0+nek')
depends_on('nekcem@7332619', when='@2.0.0+nek')
# ceed-1.0
depends_on('nek5000@17.0', when='@1.0.0+nek')
depends_on('nektools@17.0%gcc', when='@1.0.0+nek')
depends_on('gslib@1.0.2', when='@1.0.0+nek')
depends_on('nekbone@17.0', when='@1.0.0+nek')
depends_on('nekcem@0b8bedd', when='@1.0.0+nek')
# PETSc, HPGMG
# ceed-2.0
# For a +quickbuild we disable hdf5, and superlu-dist in PETSc.
# Ideally, these can be turned into recommendations to Spack for
# concretizing the PETSc spec, if Spack ever supports recommendations.
depends_on('petsc@3.11.1~hdf5~superlu-dist',
when='@2.0.0+petsc+quickbuild')
depends_on('petsc@3.11.1+mpi+double~int64', when='@2.0.0+petsc~mfem')
# The mfem petsc examples need the petsc variants +hypre, +suite-sparse,
# and +mumps:
depends_on('petsc@3.11.1+mpi+hypre+suite-sparse+mumps+double~int64',
when='@2.0.0+petsc+mfem')
depends_on('hpgmg@0.4+fe', when='@2.0.0+petsc')
# ceed-1.0
# For a +quickbuild we disable hdf5, and superlu-dist in PETSc.
# Ideally, these can be turned into recommendations to Spack for
# concretizing the PETSc spec, if Spack ever supports recommendations.
@ -67,12 +99,33 @@ class Ceed(Package):
depends_on('hpgmg@a0a5510df23b+fe', when='@1.0.0+petsc')
# MAGMA
# ceed-2.0
depends_on('magma@2.5.0', when='@2.0.0+cuda')
# ceed-1.0
depends_on('magma@2.3.0', when='@1.0.0+cuda')
# PUMI
# ceed-2.0
depends_on('pumi@2.2.0', when='@2.0.0+pumi')
# ceed-1.0
depends_on('pumi@2.1.0', when='@1.0.0+pumi')
# MFEM, Laghos
# ceed-2.0
depends_on('mfem@3.4.0+mpi+examples+miniapps', when='@2.0.0+mfem~petsc')
depends_on('mfem@3.4.0+mpi+petsc+examples+miniapps',
when='@2.0.0+mfem+petsc')
depends_on('mfem@3.4.0+pumi', when='@2.0.0+mfem+pumi')
depends_on('laghos@2.0', when='@2.0.0+mfem')
# Help the spack concretizer find a suitable version of hypre:
depends_on('hypre~internal-superlu', when='@2.0.0+mfem')
depends_on('hypre~internal-superlu~superlu-dist',
when='@2.0.0+mfem+quickbuild')
# If using gcc version <= 4.8 build suite-sparse version <= 5.1.0
depends_on('suite-sparse@:5.1.0', when='@2.0.0%gcc@:4.8+mfem+petsc')
# ceed-1.0
depends_on('mfem@3.3.2+mpi+examples+miniapps', when='@1.0.0+mfem~petsc')
depends_on('mfem@3.3.2+mpi+petsc+examples+miniapps',
when='@1.0.0+mfem+petsc')

1
var/spack/repos/builtin/packages/gslib/package.py
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@ -12,6 +12,7 @@ class Gslib(Package):
homepage = "https://github.com/gslib/gslib"
git = "https://github.com/gslib/gslib.git"
version('1.0.3', tag='v1.0.3')
version('1.0.2', tag='v1.0.2')
version('1.0.1', tag='v1.0.1')
version('1.0.0', tag='v1.0.0')

12
var/spack/repos/builtin/packages/hpgmg/package.py
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@ -23,6 +23,7 @@ class Hpgmg(Package):
tags = ['proxy-app']
version('develop', branch='master')
version('0.4', 'abdabfe09453487299500b5bd8da4e6dc3d88477199bcfa38ac41d0b3c780f6f')
version('a0a5510df23b', 'b9c50f25e541428d4735fb07344d1d0ed9fc821bdde918d8e0defa78c0d9b4f9')
version('0.3', '12a65da216fec91daea78594ae4b5a069c8f1a700f1ba21eed9f45a79a68c793')
@ -64,7 +65,14 @@ def configure_args(self):
if '+debug' in self.spec:
cflags.append('-g')
elif any(map(self.spec.satisfies, ['%gcc', '%clang', '%intel'])):
cflags += ['-O3', '-march=native']
cflags.append('-O3')
if self.compiler.target in ['x86_64']:
cflags.append('-march=native')
else:
cflags.append('-mcpu=native')
cflags.append('-mtune=native')
else:
cflags.append('-O3')
args.append('--CFLAGS=' + ' '.join(cflags))
@ -75,7 +83,7 @@ def configure_args(self):
return args
def configure(self, spec, prefix):
configure(*self.configure_args())
python('configure', *self.configure_args())
def build(self, spec, prefix):
make('-C', 'build')

10
var/spack/repos/builtin/packages/laghos/package.py
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@ -28,11 +28,13 @@ class Laghos(MakefilePackage):
depends_on('mfem@develop+mpi+metis', when='@develop+metis')
depends_on('mfem@develop+mpi~metis', when='@develop~metis')
depends_on('mfem@laghos-v2.0,3.4.0:+mpi+metis', when='@2.0:+metis')
depends_on('mfem@laghos-v2.0,3.4.0:+mpi~metis', when='@2.0:~metis')
# Recommended mfem version for laghos v2.0 is: ^mfem@3.4.1-laghos-v2.0
depends_on('mfem@3.4.0:+mpi+metis', when='@2.0+metis')
depends_on('mfem@3.4.0:+mpi~metis', when='@2.0~metis')
depends_on('mfem@laghos-v1.0,3.3.2:+mpi+metis', when='@1.0:+metis')
depends_on('mfem@laghos-v1.0,3.3.2:+mpi~metis', when='@1.0:~metis')
# Recommended mfem version for laghos v1.x is: ^mfem@3.3.1-laghos-v1.0
depends_on('mfem@3.3.1-laghos-v1.0:+mpi+metis', when='@1.0,1.1+metis')
depends_on('mfem@3.3.1-laghos-v1.0:+mpi~metis', when='@1.0,1.1~metis')
@property
def build_targets(self):

72
var/spack/repos/builtin/packages/libceed/package.py
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@ -13,18 +13,29 @@ class Libceed(Package):
git = "https://github.com/CEED/libCEED.git"
version('develop', branch='master')
version('0.4', tag='v0.4')
version('0.2', tag='v0.2')
version('0.1', tag='v0.1')
variant('occa', default=True, description='Enable OCCA backends')
variant('cuda', default=False, description='Enable CUDA support')
variant('debug', default=False, description='Enable debug build')
variant('libxsmm', default=False, description='Enable LIBXSMM backend')
conflicts('+libxsmm', when='@:0.2')
depends_on('cuda', when='+cuda')
depends_on('occa@v1.0.0-alpha.5,develop', when='+occa')
depends_on('occa@develop', when='@develop+occa')
depends_on('occa@1.0.8:', when='@0.4+occa')
depends_on('occa@1.0.0-alpha.5,develop', when='@:0.2+occa')
depends_on('occa+cuda', when='+occa+cuda')
depends_on('occa~cuda', when='+occa~cuda')
depends_on('libxsmm', when='+libxsmm')
patch('pkgconfig-version-0.4.diff', when='@0.4')
# occa: do not occaFree kernels
# Repeated creation and freeing of kernels appears to expose a caching
# bug in Occa.
@ -32,18 +43,71 @@ class Libceed(Package):
phases = ['build', 'install']
def build(self, spec, prefix):
@property
def common_make_opts(self):
spec = self.spec
compiler = self.compiler
# Note: The occa package exports OCCA_DIR in the environment
# Use verbose building output
makeopts = ['V=1']
makeopts += ['NDEBUG=%s' % ('' if '+debug' in spec else '1')]
if '@:0.2' in spec:
makeopts += ['NDEBUG=%s' % ('' if '+debug' in spec else '1')]
elif '@0.4:' in spec:
# Determine options based on the compiler:
if '+debug' in spec:
opt = '-g'
elif compiler.name == 'gcc':
opt = '-O -g -ffp-contract=fast'
if compiler.target in ['x86_64']:
opt += ' -march=native'
elif compiler.target in ['ppc64le']:
opt += ' -mcpu=native -mtune=native'
if compiler.version >= ver(4.9):
opt += ' -fopenmp-simd'
elif compiler.name == 'clang':
opt = '-O -g -march=native -ffp-contract=fast'
if compiler.version.string.endswith('-apple'):
if compiler.version >= ver(10):
opt += ' -fopenmp-simd'
else: # not apple clang
if compiler.version >= ver(6):
opt += ' -fopenmp-simd'
elif compiler.name in ['xl', 'xl_r']:
opt = '-O -g -qsimd=auto'
else:
opt = '-O -g'
makeopts += ['OPT=%s' % opt]
if '+cuda' in spec:
makeopts += ['CUDA_DIR=%s' % spec['cuda'].prefix]
nvccflags = ['-ccbin %s -Xcompiler "%s" -Xcompiler %s' %
(compiler.cxx, opt, compiler.pic_flag)]
nvccflags = ' '.join(nvccflags)
makeopts += ['NVCCFLAGS=%s' % nvccflags]
else:
# Disable CUDA auto-detection:
makeopts += ['CUDA_DIR=/disable-cuda']
if '+libxsmm' in spec:
makeopts += ['XSMM_DIR=%s' % spec['libxsmm'].prefix]
return makeopts
def build(self, spec, prefix):
makeopts = self.common_make_opts
make('info', *makeopts)
make(*makeopts)
if self.run_tests:
make('prove', *makeopts, parallel=False)
def install(self, spec, prefix):
make('install', 'prefix=%s' % prefix, parallel=False)
installopts = ['prefix=%s' % prefix]
installopts += self.common_make_opts
make('install', *installopts, parallel=False)
@when('@0.1')
def install(self, spec, prefix):

12
var/spack/repos/builtin/packages/libceed/pkgconfig-version-0.4.diff Normal file
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@ -0,0 +1,12 @@
diff --git c/ceed.pc.template w/ceed.pc.template
index 3216f08..5ada754 100644
--- c/ceed.pc.template
+++ w/ceed.pc.template
@@ -4,6 +4,6 @@ libdir=${prefix}/lib
Name: CEED
Description: Code for Efficient Extensible Discretization
-Version: 0.2.1
+Version: 0.4
Cflags: -I${includedir}
Libs: -L${libdir} -lceed

77
var/spack/repos/builtin/packages/magma/magma-2.5.0-cmake.patch Normal file
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@ -0,0 +1,77 @@
diff -ru magma-2.5.0-orig/CMakeLists.txt magma-2.5.0/CMakeLists.txt
--- magma-2.5.0-orig/CMakeLists.txt 2019-01-02 11:18:39.000000000 -0800
+++ magma-2.5.0/CMakeLists.txt 2019-04-03 15:58:01.871234891 -0700
@@ -440,18 +440,20 @@
# compile MAGMA sparse library
# sparse doesn't have Fortran at the moment, so no need for above shenanigans
-include_directories( sparse/include )
-include_directories( sparse/control )
-include_directories( testing )
-cuda_add_library( magma_sparse ${libsparse_all} )
-target_link_libraries( magma_sparse
- magma
+if (MAGMA_SPARSE)
+ include_directories( sparse/include )
+ include_directories( sparse/control )
+ include_directories( testing )
+ cuda_add_library( magma_sparse ${libsparse_all} )
+ target_link_libraries( magma_sparse
+ magma
${LAPACK_LIBRARIES}
${CUDA_CUDART_LIBRARY}
${CUDA_CUBLAS_LIBRARIES}
${CUDA_cusparse_LIBRARY}
-)
-set( LIBS_SPARSE ${LIBS} magma_sparse )
+ )
+ set( LIBS_SPARSE ${LIBS} magma_sparse )
+endif()
# ----------------------------------------
@@ -480,23 +482,31 @@
# ----------------------------------------
# compile each sparse tester
-set( CMAKE_RUNTIME_OUTPUT_DIRECTORY sparse/testing )
-foreach( TEST ${sparse_testing_all} )
+if (MAGMA_SPARSE)
+ set( CMAKE_RUNTIME_OUTPUT_DIRECTORY sparse/testing )
+ foreach( TEST ${sparse_testing_all} )
string( REGEX REPLACE "\\.(cpp|f90|F90)" "" EXE ${TEST} )
string( REGEX REPLACE "sparse/testing/" "" EXE ${EXE} )
#message( "${TEST} --> ${EXE}" )
add_executable( ${EXE} ${TEST} )
target_link_libraries( ${EXE} ${LIBS_SPARSE} )
-endforeach()
+ endforeach()
+endif()
# ----------------------------------------
# what to install
-install( TARGETS magma magma_sparse ${blas_fix}
+set(MAGMA_TARGETS magma)
+set(MAGMA_HEADERS_PATTERNS include/*.h)
+if (MAGMA_SPARSE)
+ set(MAGMA_TARGETS ${MAGMA_TARGETS} magma_sparse)
+ set(MAGMA_HEADERS_PATTERNS ${MAGMA_HEADERS_PATTERNS} sparse/include/*.h)
+endif()
+install( TARGETS ${MAGMA_TARGETS} ${blas_fix}
RUNTIME DESTINATION bin
LIBRARY DESTINATION lib
ARCHIVE DESTINATION lib )
-file( GLOB headers include/*.h sparse/include/*.h )
+file( GLOB headers ${MAGMA_HEADERS_PATTERNS} )
install( FILES ${headers}
DESTINATION include )
@@ -509,4 +519,6 @@
message( STATUS " NFLAGS ${CUDA_NVCC_FLAGS}" )
message( STATUS " FFLAGS ${CMAKE_Fortran_FLAGS}" )
message( STATUS " LIBS ${LIBS}" )
-message( STATUS " LIBS_SPARSE ${LIBS_SPARSE}" )
+if (MAGMA_SPARSE)
+ message( STATUS " LIBS_SPARSE ${LIBS_SPARSE}" )
+endif()

428
var/spack/repos/builtin/packages/magma/magma-2.5.0.patch Normal file
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@ -0,0 +1,428 @@
diff -r 89706c0efbdb .hgtags
--- a/.hgtags Wed Jan 02 14:17:26 2019 -0500
+++ b/.hgtags Wed Apr 03 15:50:54 2019 -0700
@@ -1,3 +1,4 @@
9c7e7cffa7d0e2decd23cde36a4830dfb55bea13 v2.2.0
b2b2e21c22a59a79eefbf1e5cff8e7d539a52c0c v2.3.0
04d08aaa27dc8a551513d268c68fc299e81b6780 v2.4.0
+89706c0efbdbfd48bf8a2c20cc0d73e53c3f387e v2.5.0
diff -r 89706c0efbdb include/magma_types.h
--- a/include/magma_types.h Wed Jan 02 14:17:26 2019 -0500
+++ b/include/magma_types.h Wed Apr 03 15:50:54 2019 -0700
@@ -77,7 +77,7 @@
typedef magma_int_t magma_device_t;
// Half precision in CUDA
- #if defined(__cplusplus) && CUDA_VERSION > 7500
+ #if defined(__cplusplus) && CUDA_VERSION >= 7500
#include <cuda_fp16.h>
typedef __half magmaHalf;
#else
diff -r 89706c0efbdb sparse/blas/magma_zsampleselect.cu
--- a/sparse/blas/magma_zsampleselect.cu Wed Jan 02 14:17:26 2019 -0500
+++ b/sparse/blas/magma_zsampleselect.cu Wed Apr 03 15:50:54 2019 -0700
@@ -15,9 +15,12 @@
#define PRECISION_z
+
namespace magma_sampleselect {
-__global__ void compute_abs(const magmaDoubleComplex* __restrict__ in, double* __restrict__ out, int32_t size) {
+__global__ void compute_abs(const magmaDoubleComplex* __restrict__ in, double* __restrict__ out, int32_t size)
+{
+#if (__CUDA_ARCH__ >= 350)
auto idx = threadIdx.x + blockDim.x * blockIdx.x;
if (idx >= size) {
return;
@@ -25,6 +28,7 @@
auto v = in[idx];
out[idx] = real(v) * real(v) + imag(v) * imag(v);
+#endif
}
} // namespace magma_sampleselect
@@ -164,36 +168,43 @@
magma_queue_t queue )
{
magma_int_t info = 0;
+ magma_int_t arch = magma_getdevice_arch();
- auto num_blocks = magma_ceildiv(total_size, block_size);
- auto local_work = (total_size + num_threads - 1) / num_threads;
- auto required_size = sizeof(double) * (total_size + searchtree_size)
+ if( arch >= 350 ) {
+ auto num_blocks = magma_ceildiv(total_size, block_size);
+ auto local_work = (total_size + num_threads - 1) / num_threads;
+ auto required_size = sizeof(double) * (total_size + searchtree_size)
+ sizeof(int32_t) * (searchtree_width * (num_grouped_blocks + 1) + 1);
- auto realloc_result = realloc_if_necessary(tmp_ptr, tmp_size, required_size);
+ auto realloc_result = realloc_if_necessary(tmp_ptr, tmp_size, required_size);
- double* gputmp = (double*)*tmp_ptr;
- double* gputree = gputmp + total_size;
- uint32_t* gpubucketidx = (uint32_t*)(gputree + searchtree_size);
- int32_t* gpurankout = (int32_t*)(gpubucketidx + 1);
- int32_t* gpucounts = gpurankout + 1;
- int32_t* gpulocalcounts = gpucounts + searchtree_width;
- uint32_t bucketidx{};
+ double* gputmp = (double*)*tmp_ptr;
+ double* gputree = gputmp + total_size;
+ uint32_t* gpubucketidx = (uint32_t*)(gputree + searchtree_size);
+ int32_t* gpurankout = (int32_t*)(gpubucketidx + 1);
+ int32_t* gpucounts = gpurankout + 1;
+ int32_t* gpulocalcounts = gpucounts + searchtree_width;
+ uint32_t bucketidx{};
- CHECK(realloc_result);
+ CHECK(realloc_result);
- compute_abs<<<num_blocks, block_size, 0, queue->cuda_stream()>>>
- (val, gputmp, total_size);
- build_searchtree<<<1, sample_size, 0, queue->cuda_stream()>>>
- (gputmp, gputree, total_size);
- count_buckets<<<num_grouped_blocks, block_size, 0, queue->cuda_stream()>>>
- (gputmp, gputree, gpulocalcounts, total_size, local_work);
- reduce_counts<<<searchtree_width, num_grouped_blocks, 0, queue->cuda_stream()>>>
- (gpulocalcounts, gpucounts, num_grouped_blocks);
- sampleselect_findbucket<<<1, searchtree_width / 2, 0, queue->cuda_stream()>>>
- (gpucounts, subset_size, gpubucketidx, gpurankout);
- magma_getvector(1, sizeof(uint32_t), gpubucketidx, 1, &bucketidx, 1, queue);
- magma_dgetvector(1, gputree + searchtree_width - 1 + bucketidx, 1, thrs, 1, queue);
- *thrs = std::sqrt(*thrs);
+ compute_abs<<<num_blocks, block_size, 0, queue->cuda_stream()>>>
+ (val, gputmp, total_size);
+ build_searchtree<<<1, sample_size, 0, queue->cuda_stream()>>>
+ (gputmp, gputree, total_size);
+ count_buckets<<<num_grouped_blocks, block_size, 0, queue->cuda_stream()>>>
+ (gputmp, gputree, gpulocalcounts, total_size, local_work);
+ reduce_counts<<<searchtree_width, num_grouped_blocks, 0, queue->cuda_stream()>>>
+ (gpulocalcounts, gpucounts, num_grouped_blocks);
+ sampleselect_findbucket<<<1, searchtree_width / 2, 0, queue->cuda_stream()>>>
+ (gpucounts, subset_size, gpubucketidx, gpurankout);
+ magma_getvector(1, sizeof(uint32_t), gpubucketidx, 1, &bucketidx, 1, queue);
+ magma_dgetvector(1, gputree + searchtree_width - 1 + bucketidx, 1, thrs, 1, queue);
+ *thrs = std::sqrt(*thrs);
+ }
+ else {
+ printf("error: this functionality needs CUDA architecture >= 3.5\n");
+ info = MAGMA_ERR_NOT_SUPPORTED;
+ }
cleanup:
return info;
diff -r 89706c0efbdb src/xhsgetrf_gpu.cpp
--- a/src/xhsgetrf_gpu.cpp Wed Jan 02 14:17:26 2019 -0500
+++ b/src/xhsgetrf_gpu.cpp Wed Apr 03 15:50:54 2019 -0700
@@ -16,6 +16,131 @@
#include <cuda_fp16.h>
#endif
+#if CUDA_VERSION < 9020
+// conversion float to half are not defined for host in CUDA version <9.2
+// thus uses the conversion below when CUDA VERSION is < 9.2.
+#include <string.h>
+//
+// Copyright (c) 1993-2016, NVIDIA CORPORATION. All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions
+// are met:
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+// * Neither the name of NVIDIA CORPORATION nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+// OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+// This code modified from the public domain code here:
+// https://gist.github.com/rygorous/2156668
+// The URL above includes more robust conversion routines
+// that handle Inf and NaN correctly.
+//
+// It is recommended to use the more robust versions in production code.
+
+typedef unsigned uint;
+
+union FP32
+{
+ uint u;
+ float f;
+ struct
+ {
+ uint Mantissa : 23;
+ uint Exponent : 8;
+ uint Sign : 1;
+ };
+};
+
+union FP16
+{
+ unsigned short u;
+ struct
+ {
+ uint Mantissa : 10;
+ uint Exponent : 5;
+ uint Sign : 1;
+ };
+};
+
+// Approximate solution. This is faster but converts some sNaNs to
+// infinity and doesn't round correctly. Handle with care.
+// Approximate solution. This is faster but converts some sNaNs to
+// infinity and doesn't round correctly. Handle with care.
+static half approx_float_to_half(float fl)
+{
+ FP32 f32infty = { 255 << 23 };
+ FP32 f16max = { (127 + 16) << 23 };
+ FP32 magic = { 15 << 23 };
+ FP32 expinf = { (255 ^ 31) << 23 };
+ uint sign_mask = 0x80000000u;
+ FP16 o = { 0 };
+
+ FP32 f = *((FP32*)&fl);
+
+ uint sign = f.u & sign_mask;
+ f.u ^= sign;
+
+ if (!(f.f < f32infty.u)) // Inf or NaN
+ o.u = f.u ^ expinf.u;
+ else
+ {
+ if (f.f > f16max.f) f.f = f16max.f;
+ f.f *= magic.f;
+ }
+
+ o.u = f.u >> 13; // Take the mantissa bits
+ o.u |= sign >> 16;
+ half tmp;
+ memcpy(&tmp, &o, sizeof(half));
+ //return *((half*)&o);
+ return tmp;
+}
+
+// from half->float code - just for verification.
+static float half_to_float(half hf)
+{
+ FP16 h;
+ memcpy(&h, &hf, sizeof(half));
+
+ static const FP32 magic = { 113 << 23 };
+ static const uint shifted_exp = 0x7c00 << 13; // exponent mask after shift
+ FP32 o;
+
+ o.u = (h.u & 0x7fff) << 13; // exponent/mantissa bits
+ uint exp = shifted_exp & o.u; // just the exponent
+ o.u += (127 - 15) << 23; // exponent adjust
+
+ // handle exponent special cases
+ if (exp == shifted_exp) // Inf/NaN?
+ o.u += (128 - 16) << 23; // extra exp adjust
+ else if (exp == 0) // Zero/Denormal?
+ {
+ o.u += 1 << 23; // extra exp adjust
+ o.f -= magic.f; // renormalize
+ }
+
+ o.u |= (h.u & 0x8000) << 16; // sign bit
+ return o.f;
+}
+#endif
+
#include "magma_internal.h"
//#include "nvToolsExt.h"
@@ -106,10 +231,13 @@
float c_one = MAGMA_S_ONE;
float c_neg_one = MAGMA_S_NEG_ONE;
#if 1
+ #if CUDA_VERSION >= 9020
const magmaHalf h_one = (magmaHalf) 1.0;
const magmaHalf h_neg_one = (magmaHalf)-1.0;
- //const magmaHalf h_one = approx_float_to_half(1.0);
- //const magmaHalf h_neg_one = approx_float_to_half(-1.0);
+ #else
+ const magmaHalf h_one = approx_float_to_half(1.0);
+ const magmaHalf h_neg_one = approx_float_to_half(-1.0);
+ #endif
#else
FP32 float_one = *((FP32*)&c_one);
FP16 half_one = float_to_half_full(float_one);
diff -r 89706c0efbdb src/xshgetrf_gpu.cpp
--- a/src/xshgetrf_gpu.cpp Wed Jan 02 14:17:26 2019 -0500
+++ b/src/xshgetrf_gpu.cpp Wed Apr 03 15:50:54 2019 -0700
@@ -92,7 +92,7 @@
magma_mp_type_t enable_tc,
magma_mp_type_t mp_algo_type )
{
-#if CUDA_VERSION >= 7500
+#if CUDA_VERSION >= 9000
#ifdef HAVE_clBLAS
#define dA(i_, j_) dA, (dA_offset + (i_) + (j_)*ldda)
#define dAT(i_, j_) dAT, (dAT_offset + (i_)*lddat + (j_))
diff -r 89706c0efbdb testing/testing_hgemm.cpp
--- a/testing/testing_hgemm.cpp Wed Jan 02 14:17:26 2019 -0500
+++ b/testing/testing_hgemm.cpp Wed Apr 03 15:50:54 2019 -0700
@@ -22,6 +22,131 @@
#include "magma_operators.h"
#include "testings.h"
+#if CUDA_VERSION < 9020
+// conversion float to half are not defined for host in CUDA version <9.2
+// thus uses the conversion below when CUDA VERSION is < 9.2.
+#include <string.h>
+//
+// Copyright (c) 1993-2016, NVIDIA CORPORATION. All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions
+// are met:
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+// * Neither the name of NVIDIA CORPORATION nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+// OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+// This code modified from the public domain code here:
+// https://gist.github.com/rygorous/2156668
+// The URL above includes more robust conversion routines
+// that handle Inf and NaN correctly.
+//
+// It is recommended to use the more robust versions in production code.
+
+typedef unsigned uint;
+
+union FP32
+{
+ uint u;
+ float f;
+ struct
+ {
+ uint Mantissa : 23;
+ uint Exponent : 8;
+ uint Sign : 1;
+ };
+};
+
+union FP16
+{
+ unsigned short u;
+ struct
+ {
+ uint Mantissa : 10;
+ uint Exponent : 5;
+ uint Sign : 1;
+ };
+};
+
+// Approximate solution. This is faster but converts some sNaNs to
+// infinity and doesn't round correctly. Handle with care.
+// Approximate solution. This is faster but converts some sNaNs to
+// infinity and doesn't round correctly. Handle with care.
+static half approx_float_to_half(float fl)
+{
+ FP32 f32infty = { 255 << 23 };
+ FP32 f16max = { (127 + 16) << 23 };
+ FP32 magic = { 15 << 23 };
+ FP32 expinf = { (255 ^ 31) << 23 };
+ uint sign_mask = 0x80000000u;
+ FP16 o = { 0 };
+
+ FP32 f = *((FP32*)&fl);
+
+ uint sign = f.u & sign_mask;
+ f.u ^= sign;
+
+ if (!(f.f < f32infty.u)) // Inf or NaN
+ o.u = f.u ^ expinf.u;
+ else
+ {
+ if (f.f > f16max.f) f.f = f16max.f;
+ f.f *= magic.f;
+ }
+
+ o.u = f.u >> 13; // Take the mantissa bits
+ o.u |= sign >> 16;
+ half tmp;
+ memcpy(&tmp, &o, sizeof(half));
+ //return *((half*)&o);
+ return tmp;
+}
+
+// from half->float code - just for verification.
+static float half_to_float(half hf)
+{
+ FP16 h;
+ memcpy(&h, &hf, sizeof(half));
+
+ static const FP32 magic = { 113 << 23 };
+ static const uint shifted_exp = 0x7c00 << 13; // exponent mask after shift
+ FP32 o;
+
+ o.u = (h.u & 0x7fff) << 13; // exponent/mantissa bits
+ uint exp = shifted_exp & o.u; // just the exponent
+ o.u += (127 - 15) << 23; // exponent adjust
+
+ // handle exponent special cases
+ if (exp == shifted_exp) // Inf/NaN?
+ o.u += (128 - 16) << 23; // extra exp adjust
+ else if (exp == 0) // Zero/Denormal?
+ {
+ o.u += 1 << 23; // extra exp adjust
+ o.f -= magic.f; // renormalize
+ }
+
+ o.u |= (h.u & 0x8000) << 16; // sign bit
+ return o.f;
+}
+#endif
+
/* ////////////////////////////////////////////////////////////////////////////
-- Testing sgemm
*/
@@ -47,8 +172,13 @@
float c_neg_one = MAGMA_S_NEG_ONE;
float alpha = MAGMA_S_MAKE( 0.29, -0.86 );
float beta = MAGMA_S_MAKE( -0.48, 0.38 );
- magmaHalf h_alpha = (magmaHalf)alpha;
- magmaHalf h_beta = (magmaHalf)beta;
+ #if CUDA_VERSION >= 9020
+ const magmaHalf h_alpha = (magmaHalf) alpha;
+ const magmaHalf h_beta = (magmaHalf) beta;
+ #else
+ const magmaHalf h_alpha = approx_float_to_half(alpha);
+ const magmaHalf h_beta = approx_float_to_half(beta);
+ #endif
magma_opts opts;
opts.parse_opts( argc, argv );

7
var/spack/repos/builtin/packages/magma/package.py
View file

@ -36,6 +36,8 @@ class Magma(CMakePackage):
patch('ibm-xl.patch', when='@2.2:%xl')
patch('ibm-xl.patch', when='@2.2:%xl_r')
patch('magma-2.3.0-gcc-4.8.patch', when='@2.3.0%gcc@:4.8')
patch('magma-2.5.0.patch', when='@2.5.0')
patch('magma-2.5.0-cmake.patch', when='@2.5.0')
def cmake_args(self):
spec = self.spec
@ -70,6 +72,11 @@ def cmake_args(self):
else:
options.extend(['-DGPU_TARGET=sm_30'])
if '@2.5.0' in spec:
options.extend(['-DMAGMA_SPARSE=OFF'])
if spec.compiler.name in ['xl', 'xl_r']:
options.extend(['-DCMAKE_DISABLE_FIND_PACKAGE_OpenMP=TRUE'])
return options
@run_after('install')

14
var/spack/repos/builtin/packages/mfem/package.py
View file

@ -45,6 +45,9 @@ class Mfem(Package):
# other version.
version('develop', branch='master')
# Tagged development version used by the laghos package:
version('3.4.1-laghos-v2.0', tag='laghos-v2.0')
version('3.4.0',
'4e73e4fe0482636de3c5dc983cd395839a83cb16f6f509bd88b053e8b3858e05',
url='https://bit.ly/mfem-3-4', extension='.tar.gz',
@ -54,7 +57,8 @@ class Mfem(Package):
'b70fa3c5080b9ec514fc05f4a04ff74322b99ac4ecd6d99c229f0ed5188fc0ce',
url='https://goo.gl/Kd7Jk8', extension='.tar.gz')
version('laghos-v1.0', tag='laghos-v1.0')
# Tagged development version used by the laghos package:
version('3.3.1-laghos-v1.0', tag='laghos-v1.0')
version('3.3',
'b17bd452593aada93dc0fee748fcfbbf4f04ce3e7d77fdd0341cc9103bcacd0b',
@ -424,16 +428,18 @@ def install(self, spec, prefix):
copy(str(self.config_mk), 'config.mk')
shutil.copystat('config.mk.orig', 'config.mk')
prefix_share = join_path(prefix, 'share', 'mfem')
if '+examples' in spec:
make('examples')
install_tree('examples', join_path(prefix, 'examples'))
install_tree('examples', join_path(prefix_share, 'examples'))
if '+miniapps' in spec:
make('miniapps')
install_tree('miniapps', join_path(prefix, 'miniapps'))
install_tree('miniapps', join_path(prefix_share, 'miniapps'))
if install_em:
install_tree('data', join_path(prefix, 'data'))
install_tree('data', join_path(prefix_share, 'data'))
@property
def suitesparse_components(self):

133
var/spack/repos/builtin/packages/nek5000/package.py
View file

@ -5,19 +5,9 @@
from spack import *
import numbers
import os
def is_integral(x):
"""Any integer value"""
try:
return isinstance(int(x), numbers.Integral) and \
not isinstance(x, bool) and int(x) > 0
except ValueError:
return False
class Nek5000(Package):
"""A fast and scalable high-order solver for computational fluid
dynamics"""
@ -40,33 +30,8 @@ class Nek5000(Package):
# TODO: add a variant 'blas' or 'external-blas' to enable the usage of
# Spack installed/configured blas.
# Variant for MAXNEL, we need to read this from user
variant(
'MAXNEL',
default=150000,
description='Maximum number of elements for Nek5000 tools.',
values=is_integral
)
# Variants for Nek tools
variant('genbox', default=True, description='Build genbox tool.')
variant('int_tp', default=True, description='Build int_tp tool.')
variant('n2to3', default=True, description='Build n2to3 tool.')
variant('postnek', default=True, description='Build postnek tool.')
variant('reatore2', default=True, description='Build reatore2 tool.')
variant('genmap', default=True, description='Build genmap tool.')
variant('nekmerge', default=True, description='Build nekmerge tool.')
variant('prenek', default=True, description='Build prenek tool.')
# Dependencies
depends_on('mpi', when="+mpi")
depends_on('libx11', when="+prenek")
depends_on('libx11', when="+postnek")
# libxt is needed for X11/Intrinsic.h but not for linking
depends_on('libxt', when="+prenek")
depends_on('xproto', when="+prenek")
depends_on('libxt', when="+postnek")
depends_on('visit', when="+visit")
@run_before('install')
def fortran_check(self):
@ -83,7 +48,6 @@ def test_install(self):
raise RuntimeError(msg)
def install(self, spec, prefix):
tools_dir = 'tools'
bin_dir = 'bin'
# Do not use the Spack compiler wrappers.
@ -93,102 +57,23 @@ def install(self, spec, prefix):
fflags = spec.compiler_flags['fflags']
cflags = spec.compiler_flags['cflags']
if ('+prenek' in spec) or ('+postnek' in spec):
libx11_h = find_headers('Xlib', spec['libx11'].prefix.include,
recursive=True)
if not libx11_h:
raise RuntimeError('Xlib.h not found in %s' %
spec['libx11'].prefix.include)
cflags += ['-I%s' % os.path.dirname(libx11_h.directories[0])]
xproto_h = find_headers('X', spec['xproto'].prefix.include,
recursive=True)
if not xproto_h:
raise RuntimeError('X.h not found in %s' %
spec['xproto'].prefix.include)
cflags += ['-I%s' % os.path.dirname(xproto_h.directories[0])]
libxt_h = find_headers('Intrinsic', spec['libxt'].prefix.include,
recursive=True)
if not libxt_h:
raise RuntimeError('X11/Intrinsic.h not found in %s' %
spec['libxt'].prefix.include)
cflags += ['-I%s' % os.path.dirname(libxt_h.directories[0])]
if self.compiler.name in ['xl', 'xl_r']:
# Use '-qextname' to add underscores.
# Use '-WF,-qnotrigraph' to fix an error about a string: '... ??'
fflags += ['-qextname', '-WF,-qnotrigraph']
error = Executable(fc)('empty.f', output=str, error=str,
fail_on_error=False)
if 'gfortran' in error or 'GNU' in error or 'gfortran' in fc:
# Use '-std=legacy' to suppress an error that used to be a
# warning in previous versions of gfortran.
fflags += ['-std=legacy']
fflags = ' '.join(fflags)
cflags = ' '.join(cflags)
# Build the tools, maketools copy them to Nek5000/bin by default.
# We will then install Nek5000/bin under prefix after that.
with working_dir(tools_dir):
# Update the maketools script to use correct compilers
filter_file(r'^#FC\s*=.*', 'FC="{0}"'.format(fc), 'maketools')
filter_file(r'^#CC\s*=.*', 'CC="{0}"'.format(cc), 'maketools')
if fflags:
filter_file(r'^#FFLAGS=.*', 'FFLAGS="{0}"'.format(fflags),
'maketools')
if cflags:
filter_file(r'^#CFLAGS=.*', 'CFLAGS="{0}"'.format(cflags),
'maketools')
if self.compiler.name in ['xl', 'xl_r']:
# Patch 'maketools' to use '-qextname' when checking for
# underscore becasue 'xl'/'xl_r' use this option to enable the
# addition of the underscore.
filter_file(r'^\$FC -c ', '$FC -qextname -c ', 'maketools')
libx11_lib = find_libraries('libX11', spec['libx11'].prefix.lib,
shared=True, recursive=True)
if not libx11_lib:
libx11_lib = \
find_libraries('libX11', spec['libx11'].prefix.lib64,
shared=True, recursive=True)
if not libx11_lib:
raise RuntimeError('libX11 not found in %s/{lib,lib64}' %
spec['libx11'].prefix)
# There is no other way to set the X11 library path except brute
# force:
filter_file(r'-L\$\(X\)', libx11_lib.search_flags,
join_path('prenek', 'makefile'))
filter_file(r'-L\$\(X\)', libx11_lib.search_flags,
join_path('postnek', 'makefile'))
if self.compiler.name in ['xl', 'xl_r']:
# Use '-qextname' when compiling mxm.f
filter_file(r'\$\(OLAGS\)', '-qextname $(OLAGS)',
join_path('postnek', 'makefile'))
# Define 'rename_' function that calls 'rename'
with open(join_path('postnek', 'xdriver.c'), 'a') as xdriver:
xdriver.write('\nvoid rename_(char *from, char *to)\n{\n'
' rename(from, to);\n}\n')
maxnel = self.spec.variants['MAXNEL'].value
filter_file(r'^#MAXNEL\s*=.*', 'MAXNEL=' + maxnel, 'maketools')
maketools = Executable('./maketools')
# Build the tools
if '+genbox' in spec:
maketools('genbox')
# "ERROR: int_tp does not exist!"
# if '+int_tp' in spec:
# maketools('int_tp')
if '+n2to3' in spec:
maketools('n2to3')
if '+postnek' in spec:
maketools('postnek')
if '+reatore2' in spec:
maketools('reatore2')
if '+genmap' in spec:
maketools('genmap')
if '+nekmerge' in spec:
maketools('nekmerge')
if '+prenek' in spec:
maketools('prenek')
with working_dir(bin_dir):
if '+mpi' in spec:
fc = spec['mpi'].mpif77

12
var/spack/repos/builtin/packages/nekbone/package.py
View file

@ -52,11 +52,21 @@ def install(self, spec, prefix):
install(makenek, prefix.bin)
install(nekpmpi, prefix.bin)
error = Executable(fc)('empty.f', output=str, error=str,
fail_on_error=False)
fflags = ''
if 'gfortran' in error or 'GNU' in error or 'gfortran' in fc:
# Use '-std=legacy' to suppress an error that used to be a
# warning in previous versions of gfortran.
fflags = ' -std=legacy'
with working_dir(prefix.bin):
filter_file(r'^SOURCE_ROOT\s*=.*', 'SOURCE_ROOT=\"' +
prefix.bin.Nekbone + '/src\"', 'makenek')
filter_file(r'^CC\s*=.*', 'CC=\"' + cc + '\"', 'makenek')
filter_file(r'^F77\s*=.*', 'F77=\"' + fc + '\"', 'makenek')
filter_file(r'^F77\s*=.*', 'F77=\"' + fc + fflags + '\"',
'makenek')
if '+mpi' not in spec:
filter_file(r'^#IFMPI=\"false\"', 'IFMPI=\"false\"', 'makenek')

10
var/spack/repos/builtin/packages/nekcem/package.py
View file

@ -22,11 +22,13 @@ class Nekcem(Package):
# We only have a development version
version('develop')
version('0b8bedd', commit='0b8beddfdcca646bfcc866dfda1c5f893338399b')
version('7332619', commit='7332619b73d03868a256614b61794dce2d95b360')
# dependencies
depends_on('mpi', when='+mpi')
depends_on('blas')
depends_on('lapack')
depends_on('python@2.7:', type='build')
@run_before('install')
def fortran_check(self):
@ -81,6 +83,14 @@ def install(self, spec, prefix):
fflags += ['-r8']
cflags += ['-DUNDERSCORE']
error = Executable(fc)('empty.f', output=str, error=str,
fail_on_error=False)
if 'gfortran' in error or 'GNU' in error or 'gfortran' in fc:
# Use '-std=legacy' to suppress an error that used to be a
# warning in previous versions of gfortran.
fflags += ['-std=legacy']
if '+mpi' in spec:
fflags += ['-DMPI', '-DMPIIO']
cflags += ['-DMPI', '-DMPIIO']

177
var/spack/repos/builtin/packages/nektools/package.py Normal file
View file

@ -0,0 +1,177 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import numbers
import os
def is_integral(x):
"""Any integer value"""
try:
return isinstance(int(x), numbers.Integral) and \
not isinstance(x, bool) and int(x) > 0
except ValueError:
return False
class Nektools(Package):
"""Tools reuqired by Nek5000"""
homepage = "https://nek5000.mcs.anl.gov/"
url = "https://github.com/Nek5000/Nek5000/releases/download/v17.0/Nek5000-v17.0.tar.gz"
git = "https://github.com/Nek5000/Nek5000.git"
tags = ['cfd', 'flow', 'hpc', 'solver', 'navier-stokes',
'spectral-elements', 'fluid', 'ecp', 'ecp-apps']
version('develop', branch='master')
version('17.0', '6a13bfad2ce023897010dd88f54a0a87')
# Variant for MAXNEL, we need to read this from user
variant(
'MAXNEL',
default=150000,
description='Maximum number of elements for Nek5000 tools.',
values=is_integral
)
# Variants for Nek tools
variant('genbox', default=True, description='Build genbox tool.')
variant('n2to3', default=True, description='Build n2to3 tool.')
variant('postnek', default=True, description='Build postnek tool.')
variant('reatore2', default=True, description='Build reatore2 tool.')
variant('genmap', default=True, description='Build genmap tool.')
variant('nekmerge', default=True, description='Build nekmerge tool.')
variant('prenek', default=True, description='Build prenek tool.')
depends_on('libx11', when="+prenek")
depends_on('libx11', when="+postnek")
# libxt is needed for X11/Intrinsic.h but not for linking
depends_on('libxt', when="+prenek")
depends_on('xproto', when="+prenek")
depends_on('libxt', when="+postnek")
depends_on('visit', when="+visit")
@run_before('install')
def fortran_check(self):
if not self.compiler.f77:
msg = 'Cannot build Nek5000 without a Fortran 77 compiler.'
raise RuntimeError(msg)
def install(self, spec, prefix):
tools_dir = 'tools'
bin_dir = 'bin'
fc = env['FC']
cc = env['CC']
fflags = spec.compiler_flags['fflags']
cflags = spec.compiler_flags['cflags']
if ('+prenek' in spec) or ('+postnek' in spec):
libx11_h = find_headers('Xlib', spec['libx11'].prefix.include,
recursive=True)
if not libx11_h:
raise RuntimeError('Xlib.h not found in %s' %
spec['libx11'].prefix.include)
cflags += ['-I%s' % os.path.dirname(libx11_h.directories[0])]
xproto_h = find_headers('X', spec['xproto'].prefix.include,
recursive=True)
if not xproto_h:
raise RuntimeError('X.h not found in %s' %
spec['xproto'].prefix.include)
cflags += ['-I%s' % os.path.dirname(xproto_h.directories[0])]
libxt_h = find_headers('Intrinsic', spec['libxt'].prefix.include,
recursive=True)
if not libxt_h:
raise RuntimeError('X11/Intrinsic.h not found in %s' %
spec['libxt'].prefix.include)
cflags += ['-I%s' % os.path.dirname(libxt_h.directories[0])]
if self.compiler.name in ['xl', 'xl_r']:
# Use '-qextname' to add underscores.
# Use '-WF,-qnotrigraph' to fix an error about a string: '... ??'
fflags += ['-qextname', '-WF,-qnotrigraph']
error = Executable(fc)('empty.f', output=str, error=str,
fail_on_error=False)
if 'gfortran' in error or 'GNU' in error or 'gfortran' in fc:
# Use '-std=legacy' to suppress an error that used to be a
# warning in previous versions of gfortran.
fflags += ['-std=legacy']
fflags = ' '.join(fflags)
cflags = ' '.join(cflags)
# Build the tools, maketools copy them to Nek5000/bin by default.
# We will then install Nek5000/bin under prefix after that.
with working_dir(tools_dir):
# Update the maketools script to use correct compilers
filter_file(r'^#FC\s*=.*', 'FC="{0}"'.format(fc), 'maketools')
filter_file(r'^#CC\s*=.*', 'CC="{0}"'.format(cc), 'maketools')
if fflags:
filter_file(r'^#FFLAGS=.*', 'FFLAGS="{0}"'.format(fflags),
'maketools')
if cflags:
filter_file(r'^#CFLAGS=.*', 'CFLAGS="{0}"'.format(cflags),
'maketools')
if self.compiler.name in ['xl', 'xl_r']:
# Patch 'maketools' to use '-qextname' when checking for
# underscore becasue 'xl'/'xl_r' use this option to enable the
# addition of the underscore.
filter_file(r'^\$FC -c ', '$FC -qextname -c ', 'maketools')
libx11_lib = find_libraries('libX11', spec['libx11'].prefix.lib,
shared=True, recursive=True)
if not libx11_lib:
libx11_lib = \
find_libraries('libX11', spec['libx11'].prefix.lib64,
shared=True, recursive=True)
if not libx11_lib:
raise RuntimeError('libX11 not found in %s/{lib,lib64}' %
spec['libx11'].prefix)
# There is no other way to set the X11 library path except brute
# force:
filter_file(r'-L\$\(X\)', libx11_lib.search_flags,
join_path('prenek', 'makefile'))
filter_file(r'-L\$\(X\)', libx11_lib.search_flags,
join_path('postnek', 'makefile'))
if self.compiler.name in ['xl', 'xl_r']:
# Use '-qextname' when compiling mxm.f
filter_file(r'\$\(OLAGS\)', '-qextname $(OLAGS)',
join_path('postnek', 'makefile'))
# Define 'rename_' function that calls 'rename'
with open(join_path('postnek', 'xdriver.c'), 'a') as xdriver:
xdriver.write('\nvoid rename_(char *from, char *to)\n{\n'
' rename(from, to);\n}\n')
maxnel = self.spec.variants['MAXNEL'].value
filter_file(r'^#MAXNEL\s*=.*', 'MAXNEL=' + maxnel, 'maketools')
maketools = Executable('./maketools')
# Build the tools
if '+genbox' in spec:
maketools('genbox')
if '+n2to3' in spec:
maketools('n2to3')
if '+postnek' in spec:
maketools('postnek')
if '+reatore2' in spec:
maketools('reatore2')
if '+genmap' in spec:
maketools('genmap')
if '+nekmerge' in spec:
maketools('nekmerge')
if '+prenek' in spec:
maketools('prenek')
# Install Nek5000/bin in prefix/bin
install_tree(bin_dir, prefix.bin)

7
var/spack/repos/builtin/packages/occa/package.py
View file

@ -20,9 +20,10 @@ class Occa(Package):
git = 'https://github.com/libocca/occa.git'
version('develop')
version('v1.0.0-alpha.5', tag='v1.0.0-alpha.5')
version('v0.2.0', tag='v0.2.0')
version('v0.1.0', tag='v0.1.0')
version('1.0.8', tag='v1.0.8')
version('1.0.0-alpha.5', tag='v1.0.0-alpha.5')
version('0.2.0', tag='v0.2.0')
version('0.1.0', tag='v0.1.0')
variant('cuda',
default=True,

2
var/spack/repos/builtin/packages/petsc/package.py
View file

@ -108,6 +108,8 @@ class Petsc(Package):
patch('xcode_stub_out_of_sync.patch', when='@:3.10.4')
patch('xlf_fix-dup-petscfecreate.patch', when='@3.11.0')
# Virtual dependencies
# Git repository needs sowing to build Fortran interface
depends_on('sowing', when='@develop')

31
var/spack/repos/builtin/packages/petsc/xlf_fix-dup-petscfecreate.patch Normal file
View file

@ -0,0 +1,31 @@
commit 5849cfbb8c629127894f722457da7b2cbb7f6a0b
Author: Satish Balay <balay@mcs.anl.gov>
Date: Sun Mar 31 21:43:12 2019 -0500
dm: remove duplicate PetscFECreate() definition from f90 modules. This fixes IBM xlf build.
"/tmp/dobrev1/spack-stage/spack-stage-Vp2QRG/petsc-3.11.0/src/tao/f90-mod/petsctaomod.F", line 38.13: 1514-264 (S) Procedure petscfecreate has more than one interface accessible by use association. The interfaces are assumed to be the same.
1501-511 Compilation failed for file petsctaomod.F.
Reported-by: "Dobrev, Veselin A." <dobrev1@llnl.gov>
diff --git a/src/dm/f90-mod/petscdt.h90 b/src/dm/f90-mod/petscdt.h90
index 339f7fd41e..766f0e37dc 100644
--- a/src/dm/f90-mod/petscdt.h90
+++ b/src/dm/f90-mod/petscdt.h90
@@ -49,15 +49,6 @@
End Subroutine
End Interface
- Interface
- Subroutine PetscFECreate(c,f,ierr)
- use petscdmdef
- MPI_Comm, intent(in) :: c
- PetscFE, intent(out) :: f
- PetscErrorCode, intent(out) :: ierr
- End Subroutine
- End Interface
-
Interface
Subroutine PetscFECreateDefault(c,d,n,i,str,o,f,ierr)
use petscdmdef

8
var/spack/repos/builtin/packages/suite-sparse/package.py
View file

@ -114,6 +114,14 @@ def install(self, spec, prefix):
'TBB=-L%s -ltbb' % spec['tbb'].prefix.lib,
]
if '@5.3:' in spec:
# Without CMAKE_LIBRARY_PATH defined, the CMake file in the
# Mongoose directory finds libsuitesparseconfig.so in system
# directories like /usr/lib.
make_args += [
'CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX=%s' % prefix +
' -DCMAKE_LIBRARY_PATH=%s' % prefix.lib]
make('install', *make_args)
@property