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Merge pull request #1 from jngrad/easyblock
ESPResSo 5.0-dev
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‎README.md‎

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# dev.eessi.io-espresso
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# dev.eessi.io-espresso
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Repository for pre-release builds of [ESPResSo](https://github.com/espressomd/espresso).
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Builds are deployed to the [`dev.eessi.io`](https://www.eessi.io/docs/repositories/dev.eessi.io/) repository.

‎easyconfigs/ESPResSo-foss-2023b-software-commit.eb‎

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easyblock = 'EB_ESPResSo'
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name = 'ESPResSo'
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version = '%(software_commit)s'
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homepage = 'https://espressomd.org/wordpress'
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description = """A software package for Molecular Dynamics and Monte Carlo
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simulations of bead-spring models, with electrostatics, magnetostatics,
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hydrodynamics and reaction-diffusion-advection solvers."""
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sources = [
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{
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'source_urls': ['https://github.com/espressomd/espresso/archive/'],
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'filename': 'espresso-%(software_commit)s.tar.gz',
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'download_filename': '%(software_commit)s.tar.gz',
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},
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{
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'source_urls': ['https://i10git.cs.fau.de/api/v4/projects/walberla%2Fwalberla/repository/archive?sha=59c9b8b1#'],
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'filename': 'walberla-59c9b8b1.tar.gz',
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},
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{
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'source_urls': ['https://github.com/icl-utk-edu/heffte/archive/'],
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'filename': 'heffte-2.4.1.tar.gz',
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'download_filename': 'v2.4.1.tar.gz',
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},
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{
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'source_urls': ['https://github.com/kokkos/kokkos/archive/'],
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'filename': 'kokkos-18b830e3360dff9f44a9a9c729ca9e74c037e354.tar.gz',
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'download_filename': '18b830e3360dff9f44a9a9c729ca9e74c037e354.tar.gz',
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},
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{
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'source_urls': ['https://github.com/ECP-copa/Cabana/archive/'],
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'filename': 'Cabana-ebfaa51.tar.gz',
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'download_filename': 'ebfaa51.tar.gz',
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},
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{
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'source_urls': ['https://github.com/highfive-devs/highfive/archive/'],
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'filename': 'highfive-0103467c3b609628fe3b892c6a85915610f2f3d2.tar.gz',
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'download_filename': '0103467.tar.gz',
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},
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]
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checksums = [{
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'espresso-%(software_commit)s.tar.gz': '73d71511eca932adcff4f33ac778c77279e97cec91ea1ac53987ba488fc1288d',
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'walberla-59c9b8b1.tar.gz': 'a709d7299f2c06143946d9bb8033d4ddbb0cf8b9142e4bbaa15fecc78463038f',
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'heffte-2.4.1.tar.gz': 'de2cf26df5d61baac7841525db3f393cb007f79612ac7534fd4757f154ba3e6c',
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'kokkos-18b830e.tar.gz': 'dc0127134f47752f61e74c77237bd9ec560535c4283fef8c9643f947b3733063',
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'Cabana-ebfaa51.tar.gz': 'fe5b1b1d419662b29a80cbd6703994b28c942ccbee3b201eca87e48a13836350',
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'highfive-0103467.tar.gz': 'd0ce87abd07cdd676c6d6069d3b05f869138d115d8e22b935c9bd43c872c1f3d',
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}]
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patches = [
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'espresso.patch',
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]
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toolchain = {'name': 'foss', 'version': '2023b'}
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toolchainopts = {'usempi': True, 'pic': True}
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builddependencies = [
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('CMake', '3.27.6'),
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('Ninja', '1.11.1'),
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]
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dependencies = [
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('Python', '3.11.5'),
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('SciPy-bundle', '2023.11'),
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('Boost.MPI', '1.83.0'),
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('Mesa', '23.1.9'),
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('GSL', '2.7'),
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('IPython', '8.17.2'),
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('Pint', '0.24'),
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('HDF5', '1.14.3'),
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#('VTK', '9.3.0'), # error: libpython3.10.so.1.0: file not found
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#('PFFT', '20181230'), # not available in this toolchain
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#('CUDA', '12.1.1', '', SYSTEM), # deferred for now
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]
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# default CUDA compute capabilities to use (override via --cuda-compute-capabilities)
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if any(x[0] == 'CUDA' for x in dependencies):
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cuda_compute_capabilities = ['5.2', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0']
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configopts = f' -DESPRESSO_BUILD_TESTS=ON '
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# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!)
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configopts += ' -D PYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python '
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configopts += ' -DCMAKE_INSTALL_LIBDIR:PATH=lib '
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# workaround for https://gitlab.kitware.com/cmake/cmake/-/issues/22678
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# (this only affects testsuite executable files in the build folder)
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_exe_linker_flags = ':'.join(f'%(builddir)s/easybuild_obj/_deps/{path}'
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for path in ['kokkos-build/containers/src',
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'kokkos-build/core/src',
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'kokkos-build/simd/src',
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'heffte-build'])
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configopts += f' -DCMAKE_EXE_LINKER_FLAGS="-Wl,-rpath-link,{_exe_linker_flags}" '
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test_cmd = 'ninja'
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runtest = f'check_unit_tests && {test_cmd} check_python'
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modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
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_binaries = ['ipypresso', 'pypresso']
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_libs = [
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# ESPResSo
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'espresso_core', 'espresso_shapes', 'espresso_walberla',
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'espresso_script_interface', 'script_interface', 'utils', '_init',
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# waLBerla
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'libwalberla_core', 'libwalberla_executiontree', 'libwalberla_timeloop',
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'libwalberla_field', 'libwalberla_blockforest', 'libwalberla_geometry',
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'libwalberla_lbm', 'libwalberla_vtk', 'libwalberla_domain_decomposition',
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'libwalberla_boundary', 'liblodepng',
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# Kokkos
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'libkokkoscontainers', 'libkokkoscore', 'libkokkossimd',
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# heFFte
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'libheffte',
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]
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_python_modules = [
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'__init__.py', 'system.py', 'version.py', 'collision_detection.py', 'lb.py',
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'accumulators.py', 'constraints.py', 'observables.py', 'particle_data.py',
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]
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if any(x[0] == 'PFFT' for x in dependencies):
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_libs.append('libwalberla_fft')
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if any(x[0] == 'HDF5' for x in dependencies):
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_libs.append('espresso_hdf5')
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_python_modules.append('io/writer/h5md.py')
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if any(x[0] == 'CUDA' for x in dependencies):
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_libs += [
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'espresso_cuda', 'espresso_walberla_cuda', 'libwalberla_gpu',
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]
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_python_modules.append('cuda_init.py')
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_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd'
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sanity_check_paths = {
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'files': [f'bin/{x}' for x in _binaries] +
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[f'{_lib_path}/{x}.{SHLIB_EXT}' for x in _libs] +
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[f'{_lib_path}/{x}' for x in _python_modules],
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'dirs': ['bin', 'lib']
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}
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sanity_check_commands = [
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'pypresso -h', 'ipypresso -h',
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'pypresso -c "import espressomd.version;print(espressomd.version.friendly())"',
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'python3 -c "import espressomd.version;print(espressomd.version.friendly())"',
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]
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moduleclass = 'chem'

‎easyconfigs/e/ESPResSo/espresso.patch‎

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# Cython 3.0.4 is supported, although it generates many warnings
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--- CMakeLists.txt
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+++ CMakeLists.txt
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@@ -245,3 +245,3 @@
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find_package(Python 3.11 REQUIRED COMPONENTS Interpreter Development NumPy)
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- find_package(Cython 3.0.8...<3.1.0 REQUIRED)
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+ find_package(Cython 3.0.4...<3.1.0 REQUIRED)
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find_program(IPYTHON_EXECUTABLE NAMES jupyter ipython3 ipython)
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# skip fragile test which may crash hdf5 depending on how it was built
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--- testsuite/python/CMakeLists.txt
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+++ testsuite/python/CMakeLists.txt
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@@ -386,3 +386,2 @@
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python_test(FILE h5md.py MAX_NUM_PROC 2)
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-python_test(FILE h5md.py MAX_NUM_PROC 1 SUFFIX 1_core)
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python_test(FILE p3m_fft.py MAX_NUM_PROC 6)

‎easyconfigs/e/ESPResSo/espresso.py‎

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#
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# Copyright 2025 Jean-Noël Grad
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#
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# This code is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 2 of the License, or
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# (at your option) any later version.
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#
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# This code is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with this program. If not, see <http://www.gnu.org/licenses/>.
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#
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"""
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EasyBuild support for ESPResSo, implemented as an easyblock.
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@author: Jean-Noël Grad (University of Stuttgart)
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"""
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import os
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import re
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import shutil
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from easybuild.easyblocks.generic.cmakeninja import CMakeNinja
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from easybuild.tools.systemtools import get_cpu_architecture, get_cpu_features
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from easybuild.tools.systemtools import X86_64
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from easybuild.tools.utilities import trace_msg
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from easybuild.tools.build_log import print_error
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class EB_ESPResSo(CMakeNinja):
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"""Support for building and installing ESPResSo."""
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def _get_extracted_tarball_paths(self):
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"""
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Locate the source code of all dependencies.
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"""
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extracted_paths = {}
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for src in self.src:
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name = src['name'].split('-', 1)[0]
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# process main software
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if name == 'espresso':
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extracted_paths['espresso'] = src['finalpath']
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continue
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# process dependencies
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tarball = src['name']
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if not tarball.endswith('.tar.gz'):
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raise ValueError(tarball + ' is not a tar.gz file')
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prefix = tarball.rsplit('.', 2)[0]
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matches = [x for x in os.listdir(src['finalpath']) if x.startswith(prefix)]
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if len(matches) == 0:
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raise RuntimeError(tarball + ' was not extracted')
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if len(matches) > 1:
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raise RuntimeError(tarball + ' matches multiple folders: ' + str(matches))
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extracted_paths[name] = os.path.join(src['finalpath'], matches[0])
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return extracted_paths
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def _patch_fetchcontent(self):
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"""
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Modify CMake ``FetchContent_Declare`` blocks to point to the folders
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containing the already-downloaded dependencies rather than to URLs.
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This avoids a download step during configuration.
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"""
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extracted_paths = self._get_extracted_tarball_paths()
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cmakelists_path = os.path.join(extracted_paths['espresso'], 'CMakeLists.txt')
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with open(cmakelists_path, 'r') as f:
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content = f.read()
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for name, local_uri in extracted_paths.items():
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if name == 'espresso':
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continue
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pattern = fr'FetchContent_Declare\(\s*{name}\s+GIT_REPOSITORY\s+\S+\s+GIT_TAG\s+\S+(?=\s|\))'
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m = re.search(pattern, content, flags=re.IGNORECASE)
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if m is None:
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raise RuntimeError(f'{name} is not part of the ESPResSo FetchContent workflow')
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content = re.sub(pattern, f'FetchContent_Declare({name} URL {local_uri}', content, flags=re.IGNORECASE)
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with open(cmakelists_path, 'w') as f:
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f.write(content)
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def configure_step(self):
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# patch FetchContent to avoid re-downloading dependencies
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self._patch_fetchcontent()
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configopts = self.cfg.get('configopts', '')
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dependencies = self.cfg.get('dependencies', [])
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cpu_features = get_cpu_features()
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with_cuda = any(x.get('name', '') == 'CUDA' for x in dependencies)
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with_pfft = any(x.get('name', '') == 'PFFT' for x in dependencies)
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with_hdf5 = any(x.get('name', '') == 'HDF5' for x in dependencies)
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with_gsl = any(x.get('name', '') == 'GSL' for x in dependencies)
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if with_cuda:
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configopts += ' -DESPRESSO_BUILD_WITH_CUDA=ON'
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else:
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configopts += ' -DESPRESSO_BUILD_WITH_CUDA=OFF'
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if with_hdf5:
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configopts += ' -DESPRESSO_BUILD_WITH_HDF5=ON'
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else:
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configopts += ' -DESPRESSO_BUILD_WITH_HDF5=OFF'
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if with_gsl:
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configopts += ' -DESPRESSO_BUILD_WITH_GSL=ON'
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else:
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configopts += ' -DESPRESSO_BUILD_WITH_GSL=OFF'
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configopts += ' -DESPRESSO_BUILD_WITH_WALBERLA=ON'
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if with_pfft:
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configopts += ' -DESPRESSO_BUILD_WITH_WALBERLA_FFT=ON'
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else:
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configopts += ' -DESPRESSO_BUILD_WITH_WALBERLA_FFT=OFF'
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if get_cpu_architecture() == X86_64 and 'avx2' in cpu_features:
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configopts += ' -DESPRESSO_BUILD_WITH_WALBERLA_AVX=ON'
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configopts += ' -DESPRESSO_BUILD_WITH_SHARED_MEMORY_PARALLELISM=ON'
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configopts += ' -DESPRESSO_BUILD_WITH_FFTW=ON'
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self.cfg['configopts'] = configopts
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return super(EB_ESPResSo, self).configure_step()
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def _cleanup_aux_files(self):
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"""
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Remove files automatically installed by CMake outside the ESPResSo
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main directory: header files, config files, duplicated shared objects.
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"""
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def delete_dir(path):
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if os.path.isdir(path):
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trace_msg(f'removing directory \'%s\'' % path.replace(f'{self.installdir}/', ''))
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shutil.rmtree(path)
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def delete_file(path):
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if os.path.isfile(path) or os.path.islink(path):
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trace_msg(f'removing file \'%s\'' % path.replace(f'{self.installdir}/', ''))
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os.remove(path)
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lib_dir = f'{self.installdir}/lib'
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if os.path.isdir(f'{self.installdir}/lib64'):
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lib_dir = f'{self.installdir}/lib64'
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delete_dir(f'{self.installdir}/include')
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delete_dir(f'{self.installdir}/share')
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delete_dir(f'{self.installdir}/walberla')
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delete_dir(f'{lib_dir}/cmake')
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for path in os.listdir(lib_dir):
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if '.so' in path:
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delete_file(f'{lib_dir}/{path}')
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def post_processing_step(self):
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try:
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self._cleanup_aux_files()
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except Exception as err:
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print_error("Failed to remove some auxiliary files (easyblock: %s): %s" % (self.__class__.__name__, str(err)))
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return super(EB_ESPResSo, self).post_processing_step()

‎easystacks/software.eessi.io/2023.06/espresso-eb-5.1.0-dev.yml‎

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easyconfigs:
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- ESPResSo-foss-2023b-software-commit.eb:
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options:
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software-commit: 8aa60cecd56cdd10ab62042c567552f347374f36 # waLBerla coupling and OpenMP support
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include-easyblocks: easyconfigs/*/*/*.py

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