diff --git a/var/spack/repos/builtin/packages/ceed/package.py b/var/spack/repos/builtin/packages/ceed/package.py
index 4ed5925da10e5a5c62287d6e909004cc31a6f1f4..b066da4446a86cb6ef4f5b9e57c25b98af27903c 100644
--- a/var/spack/repos/builtin/packages/ceed/package.py
+++ b/var/spack/repos/builtin/packages/ceed/package.py
@@ -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')
diff --git a/var/spack/repos/builtin/packages/gslib/package.py b/var/spack/repos/builtin/packages/gslib/package.py
index 611f745895fc9debed40c2fc9f2e026b3bf36099..59a077b6288045e0edc4eedc5cdd98a16dc7da17 100644
--- a/var/spack/repos/builtin/packages/gslib/package.py
+++ b/var/spack/repos/builtin/packages/gslib/package.py
@@ -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')
diff --git a/var/spack/repos/builtin/packages/hpgmg/package.py b/var/spack/repos/builtin/packages/hpgmg/package.py
index 5a649e2289ae18039e944f89fb56d227a31584cb..b9c33c118aea3f102b063b7e1b2f7183221f4654 100644
--- a/var/spack/repos/builtin/packages/hpgmg/package.py
+++ b/var/spack/repos/builtin/packages/hpgmg/package.py
@@ -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')
diff --git a/var/spack/repos/builtin/packages/laghos/package.py b/var/spack/repos/builtin/packages/laghos/package.py
index 6e2a0f60f0819926f359cb16a07ed49ebc73d41d..953886c0dae40538533702852fd5937893dc3f0f 100644
--- a/var/spack/repos/builtin/packages/laghos/package.py
+++ b/var/spack/repos/builtin/packages/laghos/package.py
@@ -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):
diff --git a/var/spack/repos/builtin/packages/libceed/package.py b/var/spack/repos/builtin/packages/libceed/package.py
index 578da421812a1df7d2df8183ac486f848c82207d..ecce991e8fc6cc2bc46816bd6b43869165da4dbd 100644
--- a/var/spack/repos/builtin/packages/libceed/package.py
+++ b/var/spack/repos/builtin/packages/libceed/package.py
@@ -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):
diff --git a/var/spack/repos/builtin/packages/libceed/pkgconfig-version-0.4.diff b/var/spack/repos/builtin/packages/libceed/pkgconfig-version-0.4.diff
new file mode 100644
index 0000000000000000000000000000000000000000..5f08d9d454c84517e4b9bbcbb634bff8f5b866e3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libceed/pkgconfig-version-0.4.diff
@@ -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
diff --git a/var/spack/repos/builtin/packages/magma/magma-2.5.0-cmake.patch b/var/spack/repos/builtin/packages/magma/magma-2.5.0-cmake.patch
new file mode 100644
index 0000000000000000000000000000000000000000..56b58d85e7f7542e38a832fc4599ce62880a40e0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/magma/magma-2.5.0-cmake.patch
@@ -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()
diff --git a/var/spack/repos/builtin/packages/magma/magma-2.5.0.patch b/var/spack/repos/builtin/packages/magma/magma-2.5.0.patch
new file mode 100644
index 0000000000000000000000000000000000000000..1ac800c5f838e4533b139f778387557f5a64e6e5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/magma/magma-2.5.0.patch
@@ -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 );
+
diff --git a/var/spack/repos/builtin/packages/magma/package.py b/var/spack/repos/builtin/packages/magma/package.py
index a4ca3e0e40ba4c9fccdb5cde6ad47068ae206710..192bab856a81efbec4dff11e0d62fb3b3fad7a69 100644
--- a/var/spack/repos/builtin/packages/magma/package.py
+++ b/var/spack/repos/builtin/packages/magma/package.py
@@ -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')
diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py
index f471b37de0b10d952afc2bdc760b3b68a865ee64..16a977d48caa4a511843f19589f149ae41d6c089 100644
--- a/var/spack/repos/builtin/packages/mfem/package.py
+++ b/var/spack/repos/builtin/packages/mfem/package.py
@@ -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):
diff --git a/var/spack/repos/builtin/packages/nek5000/package.py b/var/spack/repos/builtin/packages/nek5000/package.py
index a522af8cf0f7d3594c89ccbb181b302ba51195e4..9e2af1d5fe55b6086a6c8fb97b7eb650c3313983 100644
--- a/var/spack/repos/builtin/packages/nek5000/package.py
+++ b/var/spack/repos/builtin/packages/nek5000/package.py
@@ -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.
@@ -93,101 +57,22 @@ 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']
- 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')
+ error = Executable(fc)('empty.f', output=str, error=str,
+ fail_on_error=False)
- 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 '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 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')
+ fflags = ' '.join(fflags)
+ cflags = ' '.join(cflags)
with working_dir(bin_dir):
if '+mpi' in spec:
diff --git a/var/spack/repos/builtin/packages/nekbone/package.py b/var/spack/repos/builtin/packages/nekbone/package.py
index 2666e77bf3631c80574ae7083d6aab0c4146f03a..9d46ee8623bf8dc12cf900d470f98e7a15755a0c 100644
--- a/var/spack/repos/builtin/packages/nekbone/package.py
+++ b/var/spack/repos/builtin/packages/nekbone/package.py
@@ -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')
diff --git a/var/spack/repos/builtin/packages/nekcem/package.py b/var/spack/repos/builtin/packages/nekcem/package.py
index 4dea04fb0898118882bc5572df703fbf56025913..710c465b073dfe7fce39dec641df579d617db15a 100644
--- a/var/spack/repos/builtin/packages/nekcem/package.py
+++ b/var/spack/repos/builtin/packages/nekcem/package.py
@@ -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']
diff --git a/var/spack/repos/builtin/packages/nektools/package.py b/var/spack/repos/builtin/packages/nektools/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..43dd014b0a20910d19b4a16a5e2de5165b43e6cd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nektools/package.py
@@ -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)
diff --git a/var/spack/repos/builtin/packages/occa/package.py b/var/spack/repos/builtin/packages/occa/package.py
index cb60d80d29ba6fda32a73046ddbdb1cf08c43fd8..c6528f296086712631864a8a63148d72429dc031 100644
--- a/var/spack/repos/builtin/packages/occa/package.py
+++ b/var/spack/repos/builtin/packages/occa/package.py
@@ -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,
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 3d9686eb2109f02270d199bc011d8743c5535e38..8cc961d3617fc0dffa330e7e0cd677c128072e29 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -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')
diff --git a/var/spack/repos/builtin/packages/petsc/xlf_fix-dup-petscfecreate.patch b/var/spack/repos/builtin/packages/petsc/xlf_fix-dup-petscfecreate.patch
new file mode 100644
index 0000000000000000000000000000000000000000..cce573c97ea7da171fc559abdba5eed277fc2cf0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/petsc/xlf_fix-dup-petscfecreate.patch
@@ -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
diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index ad3b984cc2e99c1fc8619a4cd165c2cbf312f54b..fc53051825cd8e6a95716d871946c4c25c9a36f3 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -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