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Commit 2ad78ac3 authored by Damian Alvarez's avatar Damian Alvarez
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Added a few packages left behind

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Golden_Repo/2019a/README.md
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The table below shows the details of the toolchains in the 2019a stage:
| Toolchain name | Toolchain version | Underlying GCC | Compiler | MPI | CUDA | Math libraries | Includes software from | Notes |
|----------------|---------------------------|----------------|------------------|------------------------|----------|----------------|---------------------------|----------------------------------------------------------|
| GCCcore | 8.3.0 | 8.3.0 | | | | | | Used for boostrapping other compilers and basic software |
| GCC | 8.3.0 | 8.3.0 | GCC 8.3.0 | | | | GCCcore | Compiler toolchain |
| iccifort | 2019.3.199-GCC-8.3.0 | 8.3.0 | Intel 2019.3.199 | | | | GCCcore | Compiler toolchain |
| iccifort | 2019.5.281-GCC-8.3.0 | 8.3.0 | Intel 2019.5.281 | | | | GCCcore | Compiler toolchain |
| PGI | 19.3-GCC-8.3.0 | 8.3.0 | PGI 19.3 | | | | GCCcore | Compiler toolchain |
| gpsmpi | 2019a | 8.3.0 | GCC 8.3.0 | ParaStationMPI 5.2.2-1 | | | GCCcore, GCC | Compiler+MPI toolchain |
| gpsmpi | 2019a | 8.3.0 | GCC 8.3.0 | ParaStationMPI 5.4.3-1 | | | GCCcore, GCC | Compiler+MPI toolchain |
| iimpi | 2019a | 8.3.0 | Intel 2019.3.199 | IntelMPI 2019.3.199 | | | GCCcore, iccifort | Compiler+MPI toolchain |
| iimpi | 2019a.1 | 8.3.0 | Intel 2019.3.199 | IntelMPI 2018.5.288 | | | GCCcore, iccifort | Compiler+MPI toolchain |
| ipsmpi | 2019a | 8.3.0 | Intel 2019.3.199 | ParaStationMPI 5.2.2-1 | | | GCCcore, iccifort | Compiler+MPI toolchain |
| ipsmpi | 2019a.1 | 8.3.0 | Intel 2019.5.281 | ParaStationMPI 5.4.3-1 | | | GCCcore, iccifort | Compiler+MPI toolchain |
| gmvapich2c | 2019a | 8.3.0 | GCC 8.3.0 | MVAPICH2 2.3.3-GDR | 10.1.105 | | GCCcore, GCC | Compiler+MPI+CUDA toolchain |
| pmvapich2c | 2019a | 8.3.0 | PGI 19.3 | MVAPICH2 2.3.3-GDR | 10.1.105 | | GCCcore, PGI | Compiler+MPI+CUDA toolchain |
| gpsmkl | 2019a | 8.3.0 | GCC 8.3.0 | ParaStationMPI 5.2.2-1 | | MKL 2019.3.199 | GCCcore, GCC, gpsmpi | Compiler+MPI+Math toolchain |
| gpsmkl | 2019a.1 | 8.3.0 | GCC 8.3.0 | ParaStationMPI 5.4.3-1 | | MKL 2019.3.199 | GCCcore, GCC, gpsmpi | Compiler+MPI+Math toolchain |
| intel-para | 2019a | 8.3.0 | Intel 2019.3.199 | ParaStationMPI 5.2.2-1 | | MKL 2019.3.199 | GCCcore, iccifort, ipsmpi | Compiler+MPI+Math toolchain |
| intel-para | 2019a.1 | 8.3.0 | Intel 2019.5.281 | ParaStationMPI 5.4.3-1 | | MKL 2019.3.199 | GCCcore, iccifort, ipsmpi | Compiler+MPI+Math toolchain |
| intel | 2019a | 8.3.0 | Intel 2019.3.199 | IntelMPI 2019.3.199 | | MKL 2019.3.199 | GCCcore, iccifort, iimpi | Compiler+MPI+Math toolchain |
| intel | 2019a.1 | 8.3.0 | Intel 2019.3.199 | IntelMPI 2018.5.288 | | MKL 2019.3.199 | GCCcore, iccifort, iimpi | Compiler+MPI+Math toolchain |
| gmvmklc | 2019a | 8.3.0 | GCC 8.3.0 | MVAPICH2 2.3.3-GDR | 10.1.105 | MKL 2019.3.199 | GCCcore, GCC, gmvapich2c | Compiler+MPI+CUDA+Math toolchain |
| pmvmklc | 2019a | 8.3.0 | PGI 19.3 | MVAPICH2 2.3.3-GDR | 10.1.105 | MKL 2019.3.199 | GCCcore, PGI, pmvapich2c | Compiler+MPI+CUDA+Math toolchain |
|----------------|---------------------------|----------------|------------------|------------------------|----------|----------------|---------------------------|
| Toolchain name | Toolchain version | Underlying GCC | Compiler | MPI | CUDA | Math libraries | Includes software from |
|----------------|---------------------------|----------------|------------------|------------------------|----------|----------------|---------------------------|
| Base |
|----------------|---------------------------|----------------|------------------|------------------------|----------|----------------|---------------------------|
| GCCcore | 8.3.0 | 8.3.0 | | | | | |
|----------------|---------------------------|----------------|------------------|------------------------|----------|----------------|---------------------------|
| Compilers |
|----------------|---------------------------|----------------|------------------|------------------------|----------|----------------|---------------------------|
| GCC | 8.3.0 | 8.3.0 | GCC 8.3.0 | | | | GCCcore |
| iccifort | 2019.3.199-GCC-8.3.0 | 8.3.0 | Intel 2019.3.199 | | | | GCCcore |
| iccifort | 2019.5.281-GCC-8.3.0 | 8.3.0 | Intel 2019.5.281 | | | | GCCcore |
| PGI | 19.3-GCC-8.3.0 | 8.3.0 | PGI 19.3 | | | | GCCcore |
|----------------|---------------------------|----------------|------------------|------------------------|----------|----------------|---------------------------|
| Compilers+MPI |
|----------------|---------------------------|----------------|------------------|------------------------|----------|----------------|---------------------------|
| gpsmpi | 2019a | 8.3.0 | GCC 8.3.0 | ParaStationMPI 5.2.2-1 | | | GCCcore, GCC |
| gpsmpi | 2019a | 8.3.0 | GCC 8.3.0 | ParaStationMPI 5.4.3-1 | | | GCCcore, GCC |
| gmvapich2c | 2019a | 8.3.0 | GCC 8.3.0 | MVAPICH2 2.3.3-GDR | 10.1.105 | | GCCcore, GCC |
| gompi | 2019a | 8.3.0 | GCC 8.3.0 | OpenMPI 4.0.2 | | | GCCcore, GCC |
| iimpi | 2019a | 8.3.0 | Intel 2019.3.199 | IntelMPI 2019.3.199 | | | GCCcore, iccifort |
| iimpi | 2019a.1 | 8.3.0 | Intel 2019.3.199 | IntelMPI 2018.5.288 | | | GCCcore, iccifort |
| ipsmpi | 2019a | 8.3.0 | Intel 2019.3.199 | ParaStationMPI 5.2.2-1 | | | GCCcore, iccifort |
| ipsmpi | 2019a.1 | 8.3.0 | Intel 2019.5.281 | ParaStationMPI 5.4.3-1 | | | GCCcore, iccifort |
| iompi | 2019a | 8.3.0 | Intel 2019.5.281 | OpenMPI 4.0.2 | | | GCCcore, iccifort |
| pmvapich2c | 2019a | 8.3.0 | PGI 19.3 | MVAPICH2 2.3.3-GDR | 10.1.105 | | GCCcore, PGI |
|----------------|---------------------------|----------------|------------------|------------------------|----------|----------------|---------------------------|
| Compilers+MPI+Math |
|----------------|---------------------------|----------------|------------------|------------------------|----------|----------------|---------------------------|
| gpsmkl | 2019a | 8.3.0 | GCC 8.3.0 | ParaStationMPI 5.2.2-1 | | MKL 2019.3.199 | GCCcore, GCC, gpsmpi |
| gpsmkl | 2019a.1 | 8.3.0 | GCC 8.3.0 | ParaStationMPI 5.4.3-1 | | MKL 2019.3.199 | GCCcore, GCC, gpsmpi |
| gmvmklc | 2019a | 8.3.0 | GCC 8.3.0 | MVAPICH2 2.3.3-GDR | 10.1.105 | MKL 2019.3.199 | GCCcore, GCC, gmvapich2c |
| gomkl | 2019a | 8.3.0 | GCC 8.3.0 | OpenMPI 4.0.2 | | MKL 2019.3.199 | GCCcore, GCC, gompi |
| intel-para | 2019a | 8.3.0 | Intel 2019.3.199 | ParaStationMPI 5.2.2-1 | | MKL 2019.3.199 | GCCcore, iccifort, ipsmpi |
| intel | 2019a | 8.3.0 | Intel 2019.3.199 | IntelMPI 2019.3.199 | | MKL 2019.3.199 | GCCcore, iccifort, iimpi |
| intel | 2019a.1 | 8.3.0 | Intel 2019.3.199 | IntelMPI 2018.5.288 | | MKL 2019.3.199 | GCCcore, iccifort, iimpi |
| intel-para | 2019a.1 | 8.3.0 | Intel 2019.5.281 | ParaStationMPI 5.4.3-1 | | MKL 2019.3.199 | GCCcore, iccifort, ipsmpi |
| iomkl | 2019a | 8.3.0 | Intel 2019.5.281 | OpenMPI 4.0.2 | | MKL 2019.3.199 | GCCcore, iccifort, iompi |
| pmvmklc | 2019a | 8.3.0 | PGI 19.3 | MVAPICH2 2.3.3-GDR | 10.1.105 | MKL 2019.3.199 | GCCcore, PGI, pmvapich2c |
|----------------|---------------------------|----------------|------------------|------------------------|----------|----------------|---------------------------|
Golden_Repo/2019a/h/hwloc/hwloc-2.1.0-GCCcore-8.3.0.eb 0 → 100644
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easyblock = 'ConfigureMake'
name = 'hwloc'
version = '2.1.0'
homepage = 'http://www.open-mpi.org/projects/hwloc/'
description = """
The Portable Hardware Locality (hwloc) software package provides a portable
abstraction (across OS, versions, architectures, ...) of the hierarchical
topology of modern architectures, including NUMA memory nodes, sockets, shared
caches, cores and simultaneous multithreading. It also gathers various system
attributes such as cache and memory information as well as the locality of I/O
devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily
aims at helping applications with gathering information about modern computing
hardware so as to exploit it accordingly and efficiently.
"""
site_contacts = 'sc@fz-juelich.de'
toolchain = {'name': 'GCCcore', 'version': '8.3.0'}
# need to build with -fno-tree-vectorize to avoid segfaulting lstopo on Intel Skylake
# cfr. https://github.com/open-mpi/hwloc/issues/315
toolchainopts = {'vectorize': False}
source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/']
sources = [SOURCE_TAR_GZ]
builddependencies = [
('binutils', '2.32'),
]
dependencies = [
('numactl', '2.0.12', '', True),
('libxml2', '2.9.9'),
('X11', '20190311'), # For libpciaccess
]
configopts = "--enable-libnuma=$EBROOTNUMACTL "
configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev "
sanity_check_paths = {
'files': ['bin/lstopo', 'include/hwloc/linux.h',
'lib/libhwloc.%s' % SHLIB_EXT],
'dirs': ['share/man/man3'],
}
sanity_check_commands = ['lstopo']
moduleclass = 'system'
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easyblock = "Toolchain"
name = 'gmvmklc'
version = '2019a-GDR'
homepage = '(none)'
description = """ GCC based compiler toolchain,
including CUDA and MVAPICH2 for CUDA-aware MPI support, and MKL
"""
site_contacts = 'sc@fz-juelich.de'
toolchain = {'name': 'dummy', 'version': 'dummy'}
comp_name = 'GCC'
comp_version = '8.3.0'
comp = (comp_name, comp_version)
# toolchain used to build dependencies
comp_mpi_tc_name = 'gmvapich2c'
comp_mpi_tc_ver = version
comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver)
# compiler toolchain dependencies
dependencies = [
comp,
('CUDA', '10.1.105', '', True),
('MVAPICH2', '2.3.1', '-GDR', comp),
('imkl', '2019.3.199', '', comp_mpi_tc),
]
moduleclass = 'toolchain'
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easyblock = "Toolchain"
name = 'pmvmklc'
version = '2019a-GDR'
homepage = '(none)'
description = """ PGI based compiler toolchain,
including CUDA and MVAPICH2 for CUDA-aware MPI support, and MKL
"""
site_contacts = 'sc@fz-juelich.de'
toolchain = {'name': 'dummy', 'version': 'dummy'}
comp_name = 'PGI'
comp_version = '19.3-GCC-8.3.0'
comp = (comp_name, comp_version)
# toolchain used to build dependencies
comp_mpi_tc_name = 'pmvapich2c'
comp_mpi_tc_ver = version
comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver)
# compiler toolchain dependencies
dependencies = [
comp,
('CUDA', '10.1.105', '', True),
('MVAPICH2', '2.3.1', '-GDR', comp),
('imkl', '2019.3.199', '', comp_mpi_tc),
]
moduleclass = 'toolchain'
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easyblock = 'ConfigureMake'
name = 'libfabric'
version = '1.9.0'
homepage = 'https://github.com/ofiwg/libfabric/'
description = """libfabric"""
site_contacts = 'sc@fz-juelich.de'
toolchain = {'name': 'dummy', 'version': 'dummy'}
source_urls = ['https://github.com/ofiwg/libfabric/releases/download/v%(version)s/']
sources = [SOURCELOWER_TAR_BZ2]
builddependencies = [
('binutils', '2.32'),
('Autotools', '20180311'),
]
configopts = '--enable-psm2=yes --enable-psm=no '
configopts += '--enable-rxd=no --enable-mlx=no '
configopts += '--enable-mrail=no --enable-rxm=no '
moduleclass = 'lib'
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easyblock = 'ConfigureMake'
name = 'OpenMPI'
version = '4.0.2'
homepage = 'http://www.open-mpi.org/'
description = """The Open MPI Project is an open source MPI-3 implementation."""
site_contacts = 'sc@fz-juelich.de'
toolchain = {'name': 'GCC', 'version': '8.3.0'}
source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads']
sources = [SOURCELOWER_TAR_GZ]
patches = ['openmpi_4.0.2_ucx_1.7.0.patch']
osdependencies = [
# needed for --with-verbs
('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel'),
# needed for --with-pmix
('pmix-devel'),
]
builddependencies = [
('Autotools', '20180311'),
# Automake 1.15 is needed, since the configuration relies on aclocal-1.15 explicitely
('Automake', '1.15.1'),
]
dependencies = [
('zlib', '1.2.11'),
('hwloc', '2.1.0'),
('libfabric', '1.9.0', '', True),
('libevent', '2.1.8'),
]
# Without this we might run into this https://github.com/open-mpi/ompi/issues/6058 for some reason. Observed with
# 4.0.2, but not with 4.0.1
preconfigopts = "./autogen.pl --force && "
configopts = '--enable-shared '
#configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path
configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support
configopts += '--with-ofi=$EBROOTLIBFABRIC '
configopts += '--with-libevent=$EBROOTLIBEVENT '
configopts += '--with-psm2 '
configopts += '--without-orte '
configopts += '--without-verbs '
configopts += '--disable-oshmem '
# to enable SLURM integration (site-specific)
configopts += '--with-slurm --with-pmix=external --with-libevent=external --with-ompi-pmix-rte'
libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"]
sanity_check_paths = {
'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper"]] +
["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] +
["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]],
'dirs': [],
}
modextravars = {
'SLURM_MPI_TYPE': 'pspmix'
}
# Configure OpenMPI
postinstallcmds = [
'echo "mca_base_component_show_load_errors = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "mpi_param_check = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "mpi_show_handle_leaks = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "mpi_warn_on_fork = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "btl = self,vader,openib" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "btl_openib_allow_ib = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "btl_openib_if_include = mlx5_0:1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "bml_r2_show_unreach_errors = 0" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "coll = ^ml" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "coll_hcoll_enable = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "coll_hcoll_np = 0" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "pml = ucx" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "osc = ^rdma" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "opal_abort_print_stack = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "opal_set_max_sys_limits = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "opal_event_include = epoll" >> %(installdir)s/etc/openmpi-mca-params.conf',
]
# Add a family for our naming scheme
modluafooter = '''
family("mpi")
add_property("arch","gpu")
'''
moduleclass = 'mpi'
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easyblock = 'ConfigureMake'
name = 'OpenMPI'
version = '4.0.2'
homepage = 'http://www.open-mpi.org/'
description = """The Open MPI Project is an open source MPI-3 implementation."""
site_contacts = 'sc@fz-juelich.de'
toolchain = {'name': 'iccifort', 'version': '2019.5.281-GCC-8.3.0'}
source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads']
sources = [SOURCELOWER_TAR_GZ]
patches = ['openmpi_4.0.2_ucx_1.7.0.patch']
osdependencies = [
# needed for --with-verbs
('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel'),
# needed for --with-pmix
('pmix-devel'),
]
builddependencies = [
('Autotools', '20180311'),
# Automake 1.15 is needed, since the configuration relies on aclocal-1.15 explicitely
('Automake', '1.15.1'),
]
dependencies = [
('zlib', '1.2.11'),
('hwloc', '2.1.0'),
('libfabric', '1.9.0', '', True),
('libevent', '2.1.8'),
]
# Without this we might run into this https://github.com/open-mpi/ompi/issues/6058 for some reason. Observed with
# 4.0.2, but not with 4.0.1
preconfigopts = "./autogen.pl --force && "
configopts = '--enable-shared '
#configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path
configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support
configopts += '--with-ofi=$EBROOTLIBFABRIC '
configopts += '--with-libevent=$EBROOTLIBEVENT '
configopts += '--with-psm2 '
configopts += '--without-orte '
configopts += '--without-verbs '
configopts += '--disable-oshmem '
# to enable SLURM integration (site-specific)
configopts += '--with-slurm --with-pmix=external --with-libevent=external --with-ompi-pmix-rte'
libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"]
sanity_check_paths = {
'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper"]] +
["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] +
["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]],
'dirs': [],
}
modextravars = {
'SLURM_MPI_TYPE': 'pspmix'
}
# Configure OpenMPI
postinstallcmds = [
'echo "mca_base_component_show_load_errors = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "mpi_param_check = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "mpi_show_handle_leaks = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "mpi_warn_on_fork = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "btl = self,vader,openib" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "btl_openib_allow_ib = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "btl_openib_if_include = mlx5_0:1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "bml_r2_show_unreach_errors = 0" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "coll = ^ml" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "coll_hcoll_enable = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "coll_hcoll_np = 0" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "pml = ucx" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "osc = ^rdma" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "opal_abort_print_stack = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "opal_set_max_sys_limits = 1" >> %(installdir)s/etc/openmpi-mca-params.conf',
'echo "opal_event_include = epoll" >> %(installdir)s/etc/openmpi-mca-params.conf',
]
# Add a family for our naming scheme
modluafooter = '''
family("mpi")
add_property("arch","gpu")
'''
moduleclass = 'mpi'
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