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add patch to h5py 2.9.0 easyconfigs to avoid MPI_Init on 'import h5py' #11118

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Merged
verdurin merged 3 commits into from
Aug 24, 2020
Merged

add patch to h5py 2.9.0 easyconfigs to avoid MPI_Init on 'import h5py' #11118

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9ee3933
add patch to h5py 2.9.0 easyconfigs to avoid MPI_Init on 'import h5py'
boegel Aug 14, 2020
5e46333
use https in homepage for h5py 2.9.0
boegel Aug 14, 2020
84e21f3
switch to installing h5py 2.9.0 with pip
boegel Aug 21, 2020
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15 changes: 10 additions & 5 deletions easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ easyblock = 'PythonPackage'
name = 'h5py'
version = '2.9.0'

homepage = 'http://www.h5py.org/'
homepage = 'https://www.h5py.org/'
description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library,
version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous
amounts of data."""
Expand All @@ -13,7 +13,11 @@ toolchainopts = {'usempi': True}

source_urls = [PYPI_SOURCE]
sources = [SOURCE_TAR_GZ]
checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002']
patches = ['h5py-2.10.0_avoid-mpi-init.patch']
checksums = [
'9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002', # h5py-2.9.0.tar.gz
'6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch
]

multi_deps = {'Python': ['3.7.2', '2.7.15']}

Expand All @@ -24,10 +28,11 @@ dependencies = [
('HDF5', '1.10.5'),
]

use_pip = False
download_dep_fail = True
use_pip = True

preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" '

# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip
prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && '
sanity_pip_check = True

moduleclass = 'data'
15 changes: 10 additions & 5 deletions easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ easyblock = 'PythonPackage'
name = 'h5py'
version = '2.9.0'

homepage = 'http://www.h5py.org/'
homepage = 'https://www.h5py.org/'
description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library,
version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous
amounts of data."""
Expand All @@ -13,7 +13,11 @@ toolchainopts = {'usempi': True}

source_urls = [PYPI_SOURCE]
sources = [SOURCE_TAR_GZ]
checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002']
patches = ['h5py-2.10.0_avoid-mpi-init.patch']
checksums = [
'9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002', # h5py-2.9.0.tar.gz
'6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch
]

multi_deps = {'Python': ['3.7.2', '2.7.15']}

Expand All @@ -24,10 +28,11 @@ dependencies = [
('HDF5', '1.10.5'),
]

use_pip = False
download_dep_fail = True
use_pip = True

preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" '

# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip
prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && '
sanity_pip_check = True

moduleclass = 'data'
16 changes: 9 additions & 7 deletions easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ easyblock = 'PythonPackage'
name = 'h5py'
version = '2.9.0'

homepage = 'http://www.h5py.org/'
homepage = 'https://www.h5py.org/'
description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library,
version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous
amounts of data."""
Expand All @@ -13,7 +13,11 @@ toolchainopts = {'usempi': True}

source_urls = [PYPI_SOURCE]
sources = [SOURCE_TAR_GZ]
checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002']
patches = ['h5py-2.10.0_avoid-mpi-init.patch']
checksums = [
'9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002', # h5py-2.9.0.tar.gz
'6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch
]

multi_deps = {'Python': ['3.7.2', '2.7.15']}

Expand All @@ -24,13 +28,11 @@ dependencies = [
('HDF5', '1.10.5'),
]

use_pip = False
download_dep_fail = True
use_pip = True

# required because we're building Python packages using Intel compilers on top of Python built with GCC
check_ldshared = True
preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" '

# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip
prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && '
sanity_pip_check = True

moduleclass = 'data'
16 changes: 9 additions & 7 deletions easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ easyblock = 'PythonPackage'
name = 'h5py'
version = '2.9.0'

homepage = 'http://www.h5py.org/'
homepage = 'https://www.h5py.org/'
description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library,
version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous
amounts of data."""
Expand All @@ -13,7 +13,11 @@ toolchainopts = {'usempi': True}

source_urls = [PYPI_SOURCE]
sources = [SOURCE_TAR_GZ]
checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002']
patches = ['h5py-2.10.0_avoid-mpi-init.patch']
checksums = [
'9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002', # h5py-2.9.0.tar.gz
'6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch
]

multi_deps = {'Python': ['3.7.2', '2.7.15']}

Expand All @@ -24,13 +28,11 @@ dependencies = [
('HDF5', '1.10.5'),
]

use_pip = False
download_dep_fail = True
use_pip = True

# required because we're building Python packages using Intel compilers on top of Python built with GCC
check_ldshared = True
preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" '

# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip
prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && '
sanity_pip_check = True

moduleclass = 'data'