ESPResSo 5.0-dev

README.md

@@ -1 +1,4 @@
-# dev.eessi.io-espresso
+# dev.eessi.io-espresso
+
+Repository for pre-release builds of [ESPResSo](https://github.com/espressomd/espresso).
+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

@@ -0,0 +1,142 @@
+easyblock = 'EB_ESPResSo'
+
+name = 'ESPResSo'
+version = '%(software_commit)s'
+
+homepage = 'https://espressomd.org/wordpress'
+description = """A software package for Molecular Dynamics and Monte Carlo
+simulations of bead-spring models, with electrostatics, magnetostatics,
+hydrodynamics and reaction-diffusion-advection solvers."""
+
+sources = [
+{
+    'source_urls': ['https://github.com/espressomd/espresso/archive/'],
+    'filename': 'espresso-%(software_commit)s.tar.gz',
+    'download_filename': '%(software_commit)s.tar.gz',
+},
+{
+    'source_urls': ['https://i10git.cs.fau.de/api/v4/projects/walberla%2Fwalberla/repository/archive?sha=59c9b8b1#'],
+    'filename': 'walberla-59c9b8b1.tar.gz',
+},
+{
+    'source_urls': ['https://github.com/icl-utk-edu/heffte/archive/'],
+    'filename': 'heffte-2.4.1.tar.gz',
+    'download_filename': 'v2.4.1.tar.gz',
+},
+{
+    'source_urls': ['https://github.com/kokkos/kokkos/archive/'],
+    'filename': 'kokkos-18b830e3360dff9f44a9a9c729ca9e74c037e354.tar.gz',
+    'download_filename': '18b830e3360dff9f44a9a9c729ca9e74c037e354.tar.gz',
+},
+{
+    'source_urls': ['https://github.com/ECP-copa/Cabana/archive/'],
+    'filename': 'Cabana-ebfaa51.tar.gz',
+    'download_filename': 'ebfaa51.tar.gz',
+},
+{
+    'source_urls': ['https://github.com/highfive-devs/highfive/archive/'],
+    'filename': 'highfive-0103467c3b609628fe3b892c6a85915610f2f3d2.tar.gz',
+    'download_filename': '0103467.tar.gz',
+},
+]
+checksums = [{
+  'espresso-%(software_commit)s.tar.gz': '73d71511eca932adcff4f33ac778c77279e97cec91ea1ac53987ba488fc1288d',
+  'walberla-59c9b8b1.tar.gz': 'a709d7299f2c06143946d9bb8033d4ddbb0cf8b9142e4bbaa15fecc78463038f',
+  'heffte-2.4.1.tar.gz': 'de2cf26df5d61baac7841525db3f393cb007f79612ac7534fd4757f154ba3e6c',
+  'kokkos-18b830e.tar.gz': 'dc0127134f47752f61e74c77237bd9ec560535c4283fef8c9643f947b3733063',
+  'Cabana-ebfaa51.tar.gz': 'fe5b1b1d419662b29a80cbd6703994b28c942ccbee3b201eca87e48a13836350',
+  'highfive-0103467.tar.gz': 'd0ce87abd07cdd676c6d6069d3b05f869138d115d8e22b935c9bd43c872c1f3d',
+}]
+patches = [
+  'espresso.patch',
+]
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Boost.MPI', '1.83.0'),
+    ('Mesa', '23.1.9'),
+    ('GSL', '2.7'),
+    ('IPython', '8.17.2'),
+    ('Pint', '0.24'),
+    ('HDF5', '1.14.3'),
+    #('VTK', '9.3.0'), # error: libpython3.10.so.1.0: file not found
+    #('PFFT', '20181230'), # not available in this toolchain
+    #('CUDA', '12.1.1', '', SYSTEM), # deferred for now
+]
+
+# default CUDA compute capabilities to use (override via --cuda-compute-capabilities)
+if any(x[0] == 'CUDA' for x in dependencies):
+    cuda_compute_capabilities = ['5.2', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0']
+
+configopts = f' -DCMAKE_SKIP_RPATH=OFF -DESPRESSO_BUILD_TESTS=ON'
+# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!)
+configopts += ' -D PYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python '
+configopts += ' -DCMAKE_INSTALL_LIBDIR:PATH=lib '
+# workaround for https://gitlab.kitware.com/cmake/cmake/-/issues/22678
+# (this only affects testsuite executable files in the build folder)
+_exe_linker_flags = ':'.join(f'%(builddir)s/easybuild_obj/_deps/{path}'
+                             for path in ['kokkos-build/containers/src',
+                                          'kokkos-build/core/src',
+                                          'kokkos-build/simd/src',
+                                          'heffte-build'])
+configopts += f' -DCMAKE_EXE_LINKER_FLAGS="-Wl,-rpath-link,{_exe_linker_flags}" '
+
+test_cmd = 'ninja'
+runtest = f'check_unit_tests && {test_cmd} check_python'
+
+modextrapaths = {'PYTHONPATH': ['lib64/python%(pyshortver)s/site-packages']}
+
+_binaries = ['ipypresso',  'pypresso']
+_libs = [
+    # ESPResSo
+    'espresso_core', 'espresso_shapes', 'espresso_walberla',
+    'espresso_script_interface', 'script_interface', 'utils', '_init',
+    # waLBerla
+    'libwalberla_core', 'libwalberla_executiontree', 'libwalberla_timeloop',
+    'libwalberla_field', 'libwalberla_blockforest', 'libwalberla_geometry',
+    'libwalberla_lbm', 'libwalberla_vtk', 'libwalberla_domain_decomposition',
+    'libwalberla_boundary', 'liblodepng',
+    # Kokkos
+    'libkokkoscontainers', 'libkokkoscore', 'libkokkossimd',
+    # heFFte
+    'libheffte',
+]
+_python_modules = [
+    '__init__.py', 'system.py', 'version.py', 'collision_detection.py', 'lb.py',
+    'accumulators.py', 'constraints.py', 'observables.py', 'particle_data.py',
+]
+if any(x[0] == 'PFFT' for x in dependencies):
+    _libs.append('libwalberla_fft')
+if any(x[0] == 'HDF5' for x in dependencies):
+    _libs.append('espresso_hdf5')
+    _python_modules.append('io/writer/h5md.py')
+if any(x[0] == 'CUDA' for x in dependencies):
+    _libs += [
+        'espresso_cuda', 'espresso_walberla_cuda', 'libwalberla_gpu',
+    ]
+    _python_modules.append('cuda_init.py')
+
+_lib_path = 'lib64/python%(pyshortver)s/site-packages/espressomd'
+sanity_check_paths = {
+    'files': [f'bin/{x}' for x in _binaries] +
+             [f'{_lib_path}/{x}.{SHLIB_EXT}' for x in _libs] +
+             [f'{_lib_path}/{x}' for x in _python_modules],
+    'dirs': ['bin', 'lib']
+}
+
+sanity_check_commands = [
+    'pypresso -h', 'ipypresso -h',
+    'pypresso -c "import espressomd.version;print(espressomd.version.friendly())"',
+    'python3 -c "import espressomd.version;print(espressomd.version.friendly())"',
+]
+
+moduleclass = 'chem'

easyconfigs/e/ESPResSo/espresso.patch

@@ -0,0 +1,15 @@
+# Cython 3.0.4 is supported, although it generates many warnings
+--- CMakeLists.txt
++++ CMakeLists.txt
+@@ -245,3 +245,3 @@
+   find_package(Python 3.11 REQUIRED COMPONENTS Interpreter Development NumPy)
+-  find_package(Cython 3.0.8...<3.1.0 REQUIRED)
++  find_package(Cython 3.0.4...<3.1.0 REQUIRED)
+   find_program(IPYTHON_EXECUTABLE NAMES jupyter ipython3 ipython)
+# skip fragile test which may crash hdf5 depending on how it was built
+--- testsuite/python/CMakeLists.txt
++++ testsuite/python/CMakeLists.txt
+@@ -386,3 +386,2 @@
+ python_test(FILE h5md.py MAX_NUM_PROC 2)
+-python_test(FILE h5md.py MAX_NUM_PROC 1 SUFFIX 1_core)
+ python_test(FILE p3m_fft.py MAX_NUM_PROC 6)

easyconfigs/e/ESPResSo/espresso.py

@@ -0,0 +1,154 @@
+#
+# Copyright 2025 Jean-Noël Grad
+#
+# This code is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#
+# This code is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+"""
+EasyBuild support for ESPResSo, implemented as an easyblock.
+
+@author: Jean-Noël Grad (University of Stuttgart)
+"""
+
+import os
+import re
+import shutil
+from easybuild.easyblocks.generic.cmakeninja import CMakeNinja
+from easybuild.tools.systemtools import get_cpu_architecture, get_cpu_features
+from easybuild.tools.systemtools import X86_64
+from easybuild.tools.utilities import trace_msg
+from easybuild.tools.build_log import print_error
+
+
+class EB_ESPResSo(CMakeNinja):
+    """Support for building and installing ESPResSo."""
+
+    def _get_extracted_tarball_paths(self):
+        """
+        Locate the source code of all dependencies.
+        """
+        extracted_paths = {}
+        for src in self.src:
+            name = src['name'].split('-', 1)[0]
+            # process main software
+            if name == 'espresso':
+                extracted_paths['espresso'] = src['finalpath']
+                continue
+            # process dependencies
+            tarball = src['name']
+            if not tarball.endswith('.tar.gz'):
+                raise ValueError(tarball + ' is not a tar.gz file')
+            prefix = tarball.rsplit('.', 2)[0]
+            matches = [x for x in os.listdir(src['finalpath']) if x.startswith(prefix)]
+            if len(matches) == 0:
+                raise RuntimeError(tarball + ' was not extracted')
+            if len(matches) > 1:
+                raise RuntimeError(tarball + ' matches multiple folders: ' + str(matches))
+            extracted_paths[name] = os.path.join(src['finalpath'], matches[0])
+        return extracted_paths
+
+    def _patch_fetchcontent(self):
+        """
+        Modify CMake ``FetchContent_Declare`` blocks to point to the folders
+        containing the already-downloaded dependencies rather than to URLs.
+        This avoids a download step during configuration.
+        """
+        extracted_paths = self._get_extracted_tarball_paths()
+        cmakelists_path = os.path.join(extracted_paths['espresso'], 'CMakeLists.txt')
+        with open(cmakelists_path, 'r') as f:
+            content = f.read()
+        for name, local_uri in extracted_paths.items():
+            if name == 'espresso':
+                continue
+            pattern = fr'FetchContent_Declare\(\s*{name}\s+GIT_REPOSITORY\s+\S+\s+GIT_TAG\s+\S+(?=\s|\))'
+            m = re.search(pattern, content, flags=re.IGNORECASE)
+            if m is None:
+                raise RuntimeError(f'{name} is not part of the ESPResSo FetchContent workflow')
+            content = re.sub(pattern, f'FetchContent_Declare({name} URL {local_uri}', content, flags=re.IGNORECASE)
+        with open(cmakelists_path, 'w') as f:
+            f.write(content)
+
+    def configure_step(self):
+        # patch FetchContent to avoid re-downloading dependencies
+        self._patch_fetchcontent()
+
+        configopts = self.cfg.get('configopts', '')
+        dependencies = self.cfg.get('dependencies', [])
+
+        cpu_features = get_cpu_features()
+        with_cuda = any(x.get('name', '') == 'CUDA' for x in dependencies)
+        with_pfft = any(x.get('name', '') == 'PFFT' for x in dependencies)
+        with_hdf5 = any(x.get('name', '') == 'HDF5' for x in dependencies)
+        with_gsl = any(x.get('name', '') == 'GSL' for x in dependencies)
+
+        if with_cuda:
+            configopts += ' -DESPRESSO_BUILD_WITH_CUDA=ON'
+        else:
+            configopts += ' -DESPRESSO_BUILD_WITH_CUDA=OFF'
+        if with_hdf5:
+            configopts += ' -DESPRESSO_BUILD_WITH_HDF5=ON'
+        else:
+            configopts += ' -DESPRESSO_BUILD_WITH_HDF5=OFF'
+        if with_gsl:
+            configopts += ' -DESPRESSO_BUILD_WITH_GSL=ON'
+        else:
+            configopts += ' -DESPRESSO_BUILD_WITH_GSL=OFF'
+
+        configopts += ' -DESPRESSO_BUILD_WITH_WALBERLA=ON'
+        if with_pfft:
+            configopts += ' -DESPRESSO_BUILD_WITH_WALBERLA_FFT=ON'
+        else:
+            configopts += ' -DESPRESSO_BUILD_WITH_WALBERLA_FFT=OFF'
+        if get_cpu_architecture() == X86_64 and 'avx2' in cpu_features:
+            configopts += ' -DESPRESSO_BUILD_WITH_WALBERLA_AVX=ON'
+
+        configopts += ' -DESPRESSO_BUILD_WITH_SHARED_MEMORY_PARALLELISM=ON'
+        configopts += ' -DESPRESSO_BUILD_WITH_FFTW=ON'
+
+        self.cfg['configopts'] = configopts
+
+        return super(EB_ESPResSo, self).configure_step()
+
+    def _cleanup_aux_files(self):
+        """
+        Remove files automatically installed by CMake outside the ESPResSo
+        main directory: header files, config files, duplicated shared objects.
+        """
+        def delete_dir(path):
+            if os.path.isdir(path):
+                trace_msg(f'removing directory \'%s\'' % path.replace(f'{self.installdir}/', ''))
+                shutil.rmtree(path)
+
+        def delete_file(path):
+            if os.path.isfile(path) or os.path.islink(path):
+                trace_msg(f'removing file \'%s\'' % path.replace(f'{self.installdir}/', ''))
+                os.remove(path)
+
+        lib_dir = f'{self.installdir}/lib'
+        if os.path.isdir(f'{self.installdir}/lib64'):
+            lib_dir = f'{self.installdir}/lib64'
+        delete_dir(f'{self.installdir}/include')
+        delete_dir(f'{self.installdir}/share')
+        delete_dir(f'{self.installdir}/walberla')
+        delete_dir(f'{lib_dir}/cmake')
+        for path in os.listdir(lib_dir):
+            if '.so' in path:
+                delete_file(f'{lib_dir}/{path}')
+
+    def post_processing_step(self):
+        try:
+            self._cleanup_aux_files()
+        except Exception as err:
+            print_error("Failed to remove some auxiliary files (easyblock: %s): %s" % (self.__class__.__name__, str(err)))
+        return super(EB_ESPResSo, self).post_processing_step()

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

@@ -0,0 +1,5 @@
+easyconfigs:
+  - ESPResSo-foss-2023b-software-commit.eb:
+      options:
+        software-commit: 8aa60cecd56cdd10ab62042c567552f347374f36 # waLBerla coupling and OpenMP support
+        include-easyblocks: easyconfigs/*/*/*.py