Sync

Author: SebastianAchilles

Custom_EasyBlocks/generic/bundle.py

@@ -40,6 +40,7 @@
 import easybuild.tools.environment as env
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM
+from easybuild.framework.easyconfig.default import DEFAULT_CONFIG
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
 from easybuild.tools.build_log import EasyBuildError, print_msg
 from easybuild.tools.modules import get_software_root, get_software_version
@@ -121,8 +122,21 @@ def __init__(self, *args, **kwargs):
             comp_cfg['name'] = comp_name
             comp_cfg['version'] = comp_version
 
+            # The copy above may include unexpected settings for common values.
+            # In particular for a Pythonbundle we have seen a component inheriting
+            #  runtest = True
+            # which is not a valid value for many easyblocks.
+            # Reset runtest to the original default, if people want the test step
+            # they can set it explicitly, in default_component_specs or by the component easyblock
+            if comp_cfg._config['runtest'] != DEFAULT_CONFIG["runtest"]:
+                self.log.warning(
+                    "Resetting runtest to default value for component easyblock "
+                    f"(from {comp_cfg._config['runtest']})."
+                    )
+                comp_cfg._config['runtest'] = DEFAULT_CONFIG["runtest"]
+
             # determine easyblock to use for this component
-            # - if an easyblock is specified explicitely, that will be used
+            # - if an easyblock is specified explicitly, that will be used
             # - if not, a software-specific easyblock will be considered by get_easyblock_class
             # - if no easyblock was found, default_easyblock is considered
             comp_easyblock = comp_specs.get('easyblock')
@@ -300,7 +314,7 @@ def install_step(self):
                 self.comp_cfgs_sanity_check.append(comp)
 
             # run relevant steps
-            for step_name in ['patch', 'configure', 'build', 'install']:
+            for step_name in ['patch', 'configure', 'build', 'test', 'install']:
                 if step_name in cfg['skipsteps']:
                     comp.log.info("Skipping '%s' step for component %s v%s", step_name, cfg['name'], cfg['version'])
                 else:

Golden_Repo/a/Ascent/Ascent-20250201-GCCcore-13.3.0-nompi.eb

@@ -9,7 +9,7 @@ local_commit = 'a5d12ce60eafc87cfbe0125c8a85fd0815ea651d'
 
 homepage = 'https://ascent.readthedocs.io'
 description = """
-Ascent is a many-core capable flyweight in situ visualization
+Ascent is a many-core capable flyweight in-situ visualization
 and analysis infrastructure for multi-physics HPC simulations.
 """
 

Golden_Repo/a/Ascent/Ascent-20250201-gompi-2024a.eb

@@ -26,6 +26,8 @@ builddependencies = [
 
 dependencies = [
     ('Python', '3.12.3'),
+    ('mpi4py', '4.0.1'),  # for mpi-support in Python
+    ('SciPy-bundle', '2024.05', '', ('gcccoreflexiblas', '13.3.0-3.4.4')),  # numpy needed for mpi-support in Python
     ('Conduit', '0.9.3'),
     ('camp', '2024.07.0'),
     ('RAJA', '2024.07.0'),

Golden_Repo/a/Ascent/Ascent-20250201-gpsmpi-2024a.eb

@@ -26,6 +26,8 @@ builddependencies = [
 
 dependencies = [
     ('Python', '3.12.3'),
+    ('mpi4py', '4.0.1'),  # for mpi-support in Python
+    ('SciPy-bundle', '2024.05', '', ('gcccoreflexiblas', '13.3.0-3.4.4')),  # numpy needed for mpi-support in Python
     ('Conduit', '0.9.3'),
     ('camp', '2024.07.0'),
     ('RAJA', '2024.07.0'),

Golden_Repo/b/Boost.Python/Boost.Python-1.86.0-GCCcore-13.3.0.eb

@@ -0,0 +1,26 @@
+# This file is part of JSC's public easybuild repository (https://github.com/easybuilders/jsc)
+easyblock = 'EB_Boost'
+
+name = 'Boost.Python'
+version = '1.86.0'
+
+homepage = 'https://boostorg.github.io/python'
+description = """Boost.Python is a C++ library which enables seamless interoperability between C++
+ and the Python programming language."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://archives.boost.io/release/%(version)s/source/']
+sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['2575e74ffc3ef1cd0babac2c1ee8bdb5782a0ee672b1912da40e5b4b591ca01f']
+
+dependencies = [
+    ('binutils', '2.42'),
+    ('Boost',  version),
+    ('Python', '3.12.3'),
+]
+
+only_python_bindings = True
+
+moduleclass = 'lib'

Golden_Repo/c/Code_Saturne/Code_Saturne-8.0.2-gompi-2024a.eb

@@ -0,0 +1,69 @@
+# This file is part of JSC's public easybuild repository (https://github.com/easybuilders/jsc)
+# easyconfig file for Code_Saturne
+name = 'Code_Saturne'
+version = '8.0.2'
+
+# extra option for the SLURM batch system
+# debug = False
+slurm = True
+
+homepage = 'https://www.code-saturne.org'
+description = """
+Code_saturne is the free, open-source software developed to analyze CFD applications.
+It solves the Navier-Stokes equations for 2D, 2D-axisymmetric and 3D flows, steady or
+unsteady, laminar or turbulent, incompressible or weakly dilatable, isothermal or not,
+with scalar transport.
+
+Code_Saturne %(version)s%(versionsuffix)s is installed in
+$EBROOTCODE_SATURNE
+"""
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+toolchainopts = {'optarch': True, 'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/code-saturne/code_saturne/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'code_saturne-8.0.2-integer.patch',
+]
+
+checksums = [
+    '911ec01e1bce3937ebb811622788a5671cd171b4411b5db2d66b02f00da6e90f',  # v8.0.2.tar.gz
+    '5c3bb622b3e0b54ab06f23b21b7fbec0bcd82a7b70d623128a8d8c4e0092236b',  # code_saturne-8.0.2-integer.patch
+]
+
+builddependencies = [
+    ('Autotools', '20231222'),
+    ('gettext', '0.22.5'),
+    ('Bison', '3.8.2'),
+    ('flex', '2.6.4'),
+    ('texlive', '20240312'),
+    ('Doxygen', '1.11.0'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('HDF5', '1.14.5'),
+    ('CGNS', '4.4.0'),
+    ('ParMETIS', '4.0.3'),
+    ('SCOTCH', '7.0.5'),
+    ('MED', '4.1.1'),
+]
+
+configopts = ' '
+configopts += '--disable-gui '
+configopts += '--with-med=$EBROOTMED --without-medcoupling '
+configopts += '--with-cgns=$EBROOTCGNS '
+configopts += '--with-metis=$EBROOTPARMETIS '
+configopts += '--with-scotch=$EBROOTSCOTCH '
+configopts += '--with-python_prefix=%(installdir)s --with-python_exec_prefix=%(installdir)s '
+
+modloadmsg = "=========================================================================\n"
+modloadmsg += "NOTE: To benefit from shell completion for %(name)s commands/options\n"
+modloadmsg += "you may also source a bash completion file by\n"
+modloadmsg += "> source $CS_BASH\n"
+modloadmsg += "Job submission needs a compute project activated by jutil\n"
+modloadmsg += "> jutil env activate -p <project> [-A <budget>]\n"
+modloadmsg += "=========================================================================\n"
+
+moduleclass = 'cae'

Golden_Repo/c/Code_Saturne/code_saturne-8.0.2-integer.patch

@@ -0,0 +1,18 @@
+diff -ruN code_saturne-8.0.2-orig/python/code_saturne/gui/case/BatchRunningDialogView.py code_saturne-8.0.2/python/code_saturne/gui/case/BatchRunningDialogView.py
+--- code_saturne-8.0.2-orig/python/code_saturne/gui/case/BatchRunningDialogView.py	2023-10-10 14:27:21.000000000 +0200
++++ code_saturne-8.0.2/python/code_saturne/gui/case/BatchRunningDialogView.py	2023-10-26 12:29:09.221361301 +0200
+@@ -970,10 +970,10 @@
+             seconds = job_walltime
+             minutes = seconds / 60
+             hours = minutes / 60
+-            days = hours / 24
+-            seconds = seconds % 60
+-            minutes = minutes % 60
+-            hours = hours % 24
++            days = int(hours / 24)
++            seconds = int(seconds % 60)
++            minutes = int(minutes % 60)
++            hours = int(hours % 24)
+             self.spinBoxDays.setValue(days)
+             self.spinBoxHours.setValue(hours)
+             self.spinBoxMinutes.setValue(minutes)

Golden_Repo/c/casacore/casacore-3.7.1-foss-2024a.eb

@@ -0,0 +1,62 @@
+# This file is part of JSC's public easybuild repository (https://github.com/easybuilders/jsc)
+easyblock = 'CMakeMake'
+
+name = 'casacore'
+version = '3.7.1'
+
+homepage = 'https://github.com/casacore/casacore'
+description = """A suite of C++ libraries for radio astronomy data processing."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+sources = [
+    {
+        'filename': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/%(name)s/%(name)s/archive'],
+    },
+    {
+        # Note: when updating this easyconfig, check the latest WSRT_Measures tarball on the FTP and update to that
+        'filename': 'WSRT_Measures_20250911-160001.ztar',
+        'source_urls': ['ftp://[email protected]/outgoing/Measures'],
+        'extract_cmd': 'tar xfvz %s --one-top-level=data',
+    }
+]
+checksums = [
+    {'v3.7.1.tar.gz': 'ad7ad865d5d8517524bdde71e0083a69442648b693850660dadb0ce6109d91c7'},
+    {'WSRT_Measures_20250911-160001.ztar': 'db03d79799e9e3dc67f0d17cf5dc3c2e97c6979d61ee167f88e820b732297f17'},
+]
+
+builddependencies = [
+    ('CMake', '3.30.3'),
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+    ('wget', '1.25.0'),
+]
+dependencies = [
+    ('CFITSIO', '4.4.1'),
+    ('WCSLIB', '8.4'),
+    ('HDF5', '1.14.5'),
+    ('GSL', '2.8'),
+    ('Boost.Python', '1.86.0'),
+    ('SciPy-bundle', '2024.05', '', ('gcccoreflexiblas', '13.3.0-3.4.4')),
+    ('ncurses', '6.5'),
+]
+
+configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" '
+configopts += '-DDATA_DIR=%(installdir)s/data -DUSE_OPENMP=ON -DUSE_HDF5=ON '
+configopts += '-DUSE_MPI=ON '
+
+postinstallcmds = ['cp -r %(builddir)s/data %(installdir)s']
+
+sanity_check_paths = {
+    'files': [
+        'lib/libcasa_casa.%s' % SHLIB_EXT,
+        'lib/libcasa_mirlib.%s' % SHLIB_EXT,
+        'lib/libcasa_ms.%s' % SHLIB_EXT,
+    ],
+    'dirs': ['bin', 'include/%(name)s', 'data/ephemerides', 'data/geodetic'],
+}
+
+sanity_check_commands = [('measuresdata', '')]
+
+moduleclass = 'lib'

Golden_Repo/e/ESMF/ESMF-8.7.0-foss-2024a.eb

@@ -27,6 +27,19 @@ dependencies = [
     ('libarchive', '3.7.4'),
 ]
 
+# ESMF ignores xxFLAGS
+preconfigopts = 'export ESMF_BOPT="O" && '
+preconfigopts += 'export ESMF_OPTLEVEL="2" && '
+preconfigopts += 'export ESMF_PNETCDF="standard && '
+preconfigopts += 'export ESMF_PNETCDF_INCLUDE=$EBROOTPNETCDF/include && '
+preconfigopts += 'export ESMF_PNETCDF_LIBPATH=$EBROOTPNETCDF/lib && '
+preconfigopts += 'export ESMF_PNETCDF_LIBS=-lpnetcdf && '
+
+preinstallopts = 'export ESMF_NETCDF_LIBS="$ESMF_NETCDF_LIBS -L${PNETCDF}/lib -lpnetcdf" &&'
+preinstallopts += 'export ESMF_PNETCDF_INCLUDE=$EBROOTPNETCDF/include && '
+preinstallopts += 'export ESMF_PNETCDF_LIBPATH=$EBROOTPNETCDF/lib && '
+preinstallopts += 'export ESMF_PNETCDF_LIBS=-lpnetcdf && '
+
 # disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour)
 prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"'
 

Golden_Repo/h/heat/heat-1.6.0-gompi-2024a.eb

@@ -0,0 +1,46 @@
+# This file is part of JSC's public easybuild repository (https://github.com/easybuilders/jsc)
+easyblock = 'PythonPackage'
+
+name = 'heat'
+version = '1.6.0'
+
+homepage = 'https://github.com/helmholtz-analytics/heat'
+description = """
+Heat builds on PyTorch and mpi4py to provide high-performance computing infrastructure for
+memory-intensive applications within the NumPy/SciPy ecosystem.
+"""
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+
+source_urls = ['https://pypi.python.org/packages/source/h/%(name)s']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['heat-1.6.0-license-fix.patch']
+checksums = [
+    {'%(name)s-%(version)s.tar.gz': 'cd011e67c284b7f94d0f1c6ff8bf5309535fa26a895b0db2df83290c47dae55b'},
+    {'heat-1.6.0-license-fix.patch': 'fd45ba7e5761209f6a7e0fbd28dabf5b82fb1e0db78e3fa1596de2f4df2bf016'},
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('PyTorch', '2.5.1', '', ('gcccoreflexiblas', '13.3.0-3.4.4')),
+    ('torchvision', '0.20.1', '', ('gcccoreflexiblas', '13.3.0-3.4.4')),
+    ('SciPy-bundle', '2024.05', '', ('gcccoreflexiblas', '13.3.0-3.4.4')),
+    ('Pillow-SIMD', '10.4.0'),
+    ('mpi4py', '4.0.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+download_dep_fail = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/heat']
+}
+
+# `import heat` requires a valid MPI environment and an accessible CUDA device.
+# Hence, a sanity_check will fail in most of our build environments
+skipsteps = ['sanitycheck']
+
+moduleclass = 'lib'