Add foss/2025a toolchain

README.md

@@ -3,15 +3,75 @@
 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.
 
+## Run workflow with the bot
+
+See [our wiki](https://github.com/multixscale/dev.eessi.io-espresso/wiki).
+
 ## Run workflow locally
 
 ```sh
-source /cvmfs/software.eessi.io/versions/2023.06/init/bash
-module load EasyBuild/5.1.1
-eb easyconfigs/ESPResSo-foss-2023b-software-commit.eb \
+source /cvmfs/software.eessi.io/versions/2025.06/init/bash
+module load EasyBuild/5.1.2
+eb easyconfigs/ESPResSo-foss-2025a-software-commit.eb \
    --include-easyblocks=easyconfigs/e/ESPResSo/espresso.py \
-   --software-commit=dc87ede --max-parallel $(nproc)
+   --software-commit=11393df --max-parallel $(nproc)
 module use ~/.local/easybuild/modules/all
 module spider ESPResSo
-module load ESPResSo/dc87ede-foss-2023b
+module load ESPResSo/11393df-foss-2025a
+```
+
+### Build missing dependencies locally
+
+```sh
+source /cvmfs/software.eessi.io/versions/2025.06/init/bash
+module load EasyBuild/5.1.2
+eb easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.88.0-gompi-2025a.eb \
+   --dump-test-report=Boost.MPI-1.88.0-gompi-2025a_$(date "+%Y%m%d").md \
+   --robot --max-parallel $(nproc)
+module use ~/.local/easybuild/modules/all
+module spider Boost.MPI
+eb easyconfigs/ESPResSo-foss-2025a-software-commit.eb \
+   --include-easyblocks=easyconfigs/e/ESPResSo/espresso.py \
+   --software-commit=11393df --max-parallel $(nproc)
+module load ESPResSo/11393df-foss-2025a
+python -c 'import numpy, espressomd;print(f"numpy {numpy.__version__}, ESPResSo {espressomd.__version__}")'
 ```
+
+### Contribute missing dependencies upstream
+
+- contribute the easyconfig with a test report
+  ([instructions](https://docs.easybuild.io/contributing/#contributing_easyconfigs),
+  example: [easybuilders/easybuild-easyconfigs#24421](https://github.com/easybuilders/easybuild-easyconfigs/pull/24421))
+- add easyconfig to the software layer
+  ([instructions](https://www.eessi.io/docs/adding_software/opening_pr/),
+  example: [EESSI/software-layer#1279](https://github.com/EESSI/software-layer/pull/1279))
+- deploy new software ([instructions](https://www.eessi.io/docs/adding_software/adding_development_software/))
+
+## Migrate to a newer toolchain
+
+- go to the top-level directory of your local `dev.eessi.io-espresso` fork
+- select new `foss` toolchain version, e.g. 2025a, and create the corresponding
+  easyconfig file using any available older easyconfig file from that toolchain,
+  e.g. `cp easyconfigs/ESPResSo-foss-2023b-software-commit.eb easyconfigs/ESPResSo-foss-2025a-software-commit.eb`
+- select the software layer version that ships the selected toolchain version
+  (see [EESSI versions](https://www.eessi.io/docs/repositories/versions/)),
+  and create the corresponding easystack file with the updated EasyBuild version, e.g.
+  `cp easystacks/software.eessi.io/2023.06/espresso-eb-5.1.0-dev.yml easystacks/software.eessi.io/2025.06/espresso-eb-5.1.2-dev.yml`
+- lookup GCC version for that toolchain version
+  ([toolchain list](https://docs.easybuild.io/common-toolchains/#common_toolchains_overview))
+- for each ESPResSo dependency, find the dependency version that matches
+  the GCC version or toolchain version
+   - use `module spider` followed by the dependency name,
+     or the online database of supported software (example:
+     [c/CMake](https://docs.easybuild.io/version-specific/supported-software/c/CMake/))
+   - toolchains `GCCcore`, `GCC`, `gfbf`, and `gompi` are subsets of `foss`
+     ([dependency tree](https://docs.easybuild.io/common-toolchains/#newest-generations-2022b-and-later)),
+     therefore package variants matched by a `module spider` search from any
+     of these base toolchains can be ingested by a `foss` easyconfig
+- source the chosen software layer version,
+  e.g. `source /cvmfs/software.eessi.io/versions/2025.06/init/bash`
+- load the chosen EasyBuild version,
+  e.g. `module load EasyBuild/5.1.2`
+- make sure that GCC and other modules are *not* loaded!
+- make sure you are *not* in a Python environment!
+- run `eb easyconfigs/ESPResSo-foss-2025a-software-commit.eb`

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

@@ -8,6 +8,29 @@ description = """A software package for Molecular Dynamics and Monte Carlo
 simulations of bead-spring models, with electrostatics, magnetostatics,
 hydrodynamics and reaction-diffusion-advection solvers."""
 
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('Ninja', '1.11.1'),
+    ('Cython', '3.0.10'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Boost.MPI', '1.83.0'),
+    ('HeFFTe', '2.4.1'),
+    ('Mesa', '23.1.9'),
+    ('GSL', '2.7'),
+    ('IPython', '8.17.2'),
+    ('Pint', '0.24'),
+    ('HDF5', '1.14.3'),
+    ('h5py', '3.11.0'),
+    ('VTK', '9.3.0'),
+]
+
 sources = [
 {
     'source_urls': ['https://github.com/espressomd/espresso/archive/'],
@@ -25,52 +48,38 @@ sources = [
 },
 {
     'source_urls': ['https://github.com/ECP-copa/Cabana/archive/'],
-    'filename': 'Cabana-ebfaa51.tar.gz',
-    'download_filename': 'ebfaa51.tar.gz',
+    'filename': 'Cabana-e76c1a1.tar.gz',
+    'download_filename': 'e76c1a1.tar.gz',
 },
 {
     'source_urls': ['https://github.com/highfive-devs/highfive/archive/'],
-    'filename': 'highfive-b8d21eb39d4c6c66a72646ddd338d4c552b1a645.tar.gz',
-    'download_filename': 'b8d21eb.tar.gz',
+    'filename': 'highfive-3.2.0.tar.gz',
+    'download_filename': 'v3.2.0.tar.gz',
 },
 ]
+if any(x[0] == 'HDF5' for x in dependencies):
+    sources += [
+        {
+            'source_urls': ['https://github.com/highfive-devs/highfive/archive/'],
+            'filename': 'highfive-3.2.0.tar.gz',
+            'download_filename': 'v3.2.0.tar.gz',
+        },
+    ]
 checksums = [{
-  'espresso-%(software_commit)s.tar.gz': '571ad31186d5304cef6799cb82024376e693947ca2d6f49dfbd72d92b66f16a1',
+  'espresso-%(software_commit)s.tar.gz': 'b0f816ba9ec7422beb716b624af205c8ae780642a5b8c8e3d0fbe3214860590d',
   'walberla-fc081850.tar.gz': '686c8f26e225971ae5beed6f25ada7536bfacb96db11f2ff9cce6f267fc7f8ea',
   'kokkos-18b830e.tar.gz': 'dc0127134f47752f61e74c77237bd9ec560535c4283fef8c9643f947b3733063',
-  'Cabana-ebfaa51.tar.gz': 'fe5b1b1d419662b29a80cbd6703994b28c942ccbee3b201eca87e48a13836350',
-  'highfive-b8d21eb.tar.gz': '4da57be993b3e2c344e01c21f488a30640ebf6457534e3bb81cfd756a50a455d',
+  'Cabana-e76c1a1.tar.gz': '20dbd352fe1da744a312e556730287f52a205d1e767ac45557a3998b7fc80ca7',
+  'highfive-3.2.0.tar.gz': '01ea2eed7dbce1cf5dfff59476cfa113a7822b641aecbd99c674592fe7a4e630',
 }]
 
-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'),
-    ('HeFFTe', '2.4.1'),
-    ('Mesa', '23.1.9'),
-    ('GSL', '2.7'),
-    ('IPython', '8.17.2'),
-    ('Pint', '0.24'),
-    ('HDF5', '1.14.3'),
-    ('h5py', '3.11.0'),
-    ('VTK', '9.3.0'),
-]
-
 # 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' -DESPRESSO_BUILD_TESTS=ON '
 # make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!)
-configopts += ' -D PYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python '
+configopts += ' -DPYTHON_EXECUTABLE=$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)
@@ -95,11 +104,6 @@ _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',
 ]
 _python_modules = [
     '__init__.py', 'system.py', 'version.py', 'collision_detection.py', 'lb.py',
@@ -109,9 +113,7 @@ 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',
-    ]
+    libs.append('espresso_cuda')
     _python_modules.append('cuda_init.py')
 
 _lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd'

easyconfigs/ESPResSo-foss-2025a-software-commit.eb

@@ -0,0 +1,128 @@
+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."""
+
+toolchain = {'name': 'foss', 'version': '2025a'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+builddependencies = [
+    ('CMake', '3.31.3'),
+    ('Ninja', '1.12.1'),
+    ('Cython', '3.1.1'),
+]
+
+dependencies = [
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('Boost.MPI', '1.88.0'),
+    ('HeFFTe', '2.4.1'),
+    ('Mesa', '25.1.3'),
+    ('GSL', '2.8'),
+    ('IPython', '9.3.0'),
+    ('Pint', '0.24.4'),
+    ('HDF5', '1.14.6'),
+    ('h5py', '3.14.0'),
+#    ('VTK', '9.5.0'),
+]
+
+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=fc081850#'],
+    'filename': 'walberla-fc081850.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-e76c1a1.tar.gz',
+    'download_filename': 'e76c1a1.tar.gz',
+},
+]
+if any(x[0] == 'HDF5' for x in dependencies):
+    sources += [
+        {
+            'source_urls': ['https://github.com/highfive-devs/highfive/archive/'],
+            'filename': 'highfive-3.2.0.tar.gz',
+            'download_filename': 'v3.2.0.tar.gz',
+        },
+    ]
+checksums = [{
+  'espresso-%(software_commit)s.tar.gz': 'b0f816ba9ec7422beb716b624af205c8ae780642a5b8c8e3d0fbe3214860590d',
+  'walberla-fc081850.tar.gz': '686c8f26e225971ae5beed6f25ada7536bfacb96db11f2ff9cce6f267fc7f8ea',
+  'kokkos-18b830e.tar.gz': 'dc0127134f47752f61e74c77237bd9ec560535c4283fef8c9643f947b3733063',
+  'Cabana-e76c1a1.tar.gz': '20dbd352fe1da744a312e556730287f52a205d1e767ac45557a3998b7fc80ca7',
+  'highfive-3.2.0.tar.gz': '01ea2eed7dbce1cf5dfff59476cfa113a7822b641aecbd99c674592fe7a4e630',
+}]
+
+# 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' -DESPRESSO_BUILD_TESTS=ON '
+# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!)
+configopts += ' -DPYTHON_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}" '
+
+# build_cmd_targets does not work with CMakeNinja, use buildopts instead
+buildopts = 'espresso_packaging_dependencies'
+
+test_cmd = 'ctest'
+runtest = '-L "unit_test|python_test"'
+testopts = '--output-on-failure --no-tests=error'
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+_binaries = ['ipypresso',  'pypresso']
+_libs = [
+    # ESPResSo
+    'espresso_core', 'espresso_shapes', 'espresso_walberla',
+    'espresso_script_interface', 'script_interface', 'utils', '_init',
+]
+_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] == '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.append('espresso_cuda')
+    _python_modules.append('cuda_init.py')
+
+_lib_path = 'lib/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.py

@@ -109,8 +109,11 @@ def configure_step(self):
         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=OFF'
+        configopts += ' -DESPRESSO_BUILD_WITH_SHARED_MEMORY_PARALLELISM=ON'
         configopts += ' -DESPRESSO_BUILD_WITH_FFTW=ON'
+        configopts += ' -DESPRESSO_BUILD_WITH_PYTHON=ON'
+        configopts += ' -DESPRESSO_BUILD_WITH_SCAFACOS=OFF'
+        configopts += ' -DESPRESSO_BUILD_WITH_STOKESIAN_DYNAMICS=OFF'
 
         self.cfg['configopts'] = configopts
 

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

@@ -1,5 +1,5 @@
 easyconfigs:
   - ESPResSo-foss-2023b-software-commit.eb:
       options:
-        software-commit: dc87ede3f6c218bb71624460752bc8c26a271c33
+        software-commit: 11393dfe1aaade7240395f37a24fc1f743f868b9
         include-easyblocks: easyconfigs/*/*/*.py

easystacks/software.eessi.io/2025.06/espresso-eb-5.1.2-dev.yml

@@ -0,0 +1,5 @@
+easyconfigs:
+  - ESPResSo-foss-2025a-software-commit.eb:
+      options:
+        software-commit: 11393dfe1aaade7240395f37a24fc1f743f868b9
+        include-easyblocks: easyconfigs/*/*/*.py