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Clusters

This page documents PyCOMPSs installation/setup and GROMACS installation on various clusters as a reference.

Leonardo Booster

Last update

2026/10/01

PyCOMPSs

See the main installation page.

GROMACS

Already provided as a module by the CINECA team. An example of manual installation is the following.

The main idea is to have GROMACS relying on installed libraries and softwares to exploit their optimization for the specific cluster.

By loading the cuda module, nvcc will be available to GROMACS. Moreover, cmake is able to find cuFFT from the LD_LIBRARY_PATH.

Procedure:

ml gcc/12.2
ml cuda/12.2
ml openmpi/4.1.6--gcc--12.2.0-cuda-12.2
ml fftw/3.3.10--openmpi--4.1.6--gcc--12.2.0-spack0.22
ml cmake/4.1.2
ml openblas/0.3.26--gcc--12.2.0
ml netlib-scalapack/2.2.0--openmpi--4.1.6--gcc--12.2.0-spack0.22
ml hdf5/1.14.3--openmpi--4.1.6--gcc--12.2.0-spack0.22

tar xfz gromacs-2026.3.tar.gz
cd gromacs-2026.3
mkdir build
cd build
cmake .. -DGMX_MPI=on -DGMX_GPU=CUDA -DCMAKE_INSTALL_PREFIX=$PUBLIC/gromacs/gromacs_2026_3 -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_CUDA_ARCHITECTURES=80 -DREGRESSIONTEST_DOWNLOAD=ON

# entering a Leonardo DCGP compute node
srun -A cin_staff -p dcgp_usr_prod -N1 -n16 -t 02:00:00 --pty /bin/bash
make -j 16
make check -j 16
make install

Then, one needs to prepare a module file in <pathToModules>/gromacs/2026.3, such as:

#%Module

module-whatis "GROMACS is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world."


proc ModulesHelp { } {
puts stderr "Loads GROMACS 2026.3"
}

set GROMACS_HOME "$PUBLIC/gromacs/gromacs_2026_3"
source-sh bash ${GROMACS_HOME}/bin/GMXRC

prereq gcc
prereq cuda/12.2
prereq openmpi/4.1.6--gcc--12.2.0-cuda-12.2
prereq fftw/3.3.10--openmpi--4.1.6--gcc--12.2.0-spack0.22
prereq openblas/0.3.26--gcc--12.2.0
prereq netlib-scalapack/2.2.0--openmpi--4.1.6--gcc--12.2.0-spack0.22
prereq hdf5/1.14.3--openmpi--4.1.6--gcc--12.2.0-spack0.22

Note that we need to make all the dynamically linked libraries available at runtime. Moreover, we just need to source with source-sh the bash script provided by GROMACS.

Dardel gpu

Last update

2026/09/01

PyCOMPSs

We use a custom Java 21 JRE installation because of dependencies mismatch with the OpenJDK available in Dardel. Hence, we use the Oracle JRE LTS 21:

cd # perform operation in the user home
wget https://download.oracle.com/java/21/latest/jdk-21_linux-x64_bin.tar.gz
tar -xvf jdk-21_linux-x64_bin.tar.gz
rm jdk-21_linux-x64_bin.tar.gz

The relative lua module saved in <pathToModules>/modules/java/21.lua is:

-- -*- lua -*-
-- Module: jdk
-- -- Sets up Java 21 (JDK 21.0.12.1)

help([[
This module sets up the Java Development Kit (JDK) 21.0.12.1.

It sets JAVA_HOME and adds $JAVA_HOME/bin to PATH.
]])

whatis("Name: JDK")
whatis("Version: 21.0.12.1")
whatis("Description: Java Development Kit")
whatis("Sets JAVA_HOME and prepends $JAVA_HOME/bin to PATH")

local HOME = "<userHomePathAbsolute>/jdk-21.0.12.1"

setenv("JAVA_HOME", HOME)
prepend_path("PATH", pathJoin(HOME, "bin"))

Then we can install COMPSs with:

# Load order might be important
ml PDCOLD/24.11
module use <pathToModules>/modules
ml java/21
ml boost/1.85.0-cpeGNU-24.11
ml all-spack-modules/0.23.1 # required for the following Python version
ml python/3.13.0-gcc-cgo
ml gcc/12.2.0
python -m ensurepip --upgrade
python -m pip install --user wheel setuptools --upgrade

wget https://compss.bsc.es/repo/sc/stable/COMPSs_3.4.tar.gz
tar -xvzf COMPSs_3.4.tar.gz
cd COMPSs
./install -T <proj>/installation/compss_3_4 dardel.cfg

And generated the following Lua module (for the Lmod system) in <pathToModules>/modules/compss/3.4.lua:

-- -*- lua -*-

local compss_home = "<pathToInstallation>/installation/compss_3_4/"

prepend_path("MODULEPATH", "<pathToModules>/modules")

depends_on("PDCOLD/24.11")
depends_on("all-spack-modules/0.23.1")
depends_on("boost/1.85.0-cpeGNU-24.11")
depends_on("python/3.13.0-gcc-cgo")
depends_on("java/21")

source_sh("bash", pathJoin(compss_home, "compssenv"))

setenv("COMPSS_HOME", compss_home)

GROMACS

The GROMACS version tested is gromacs/2026.1-cpeGNU-24.11, a module provided by the sysadmin.

Marenostrum5 ACC

Last update

2026/10/01

PyCOMPSs

Already provided as a module by the BSC team. The configuration file used is the one provided by default by COMPSs mn5_acc.cfg.

GROMACS

Already provided as a module by the BSC team. An example of manual installation is the following.

Within the ACC login: 

module load compenv-acc/gnu13.2.0-ompi # load compilation env
ml cmake/3.29 # required by recent GROMACS versions
module load cuda/12.8

cmake .. \
  -DGMX_FFT_LIBRARY=fftw3 -DGMX_BUILD_OWN_FFTW=OFF \
  -DREGRESSIONTEST_DOWNLOAD=OFF \
  -DGMX_GPU=CUDA \
  -DGMX_CUDA_TARGET_SM="90" -DGMX_CUDA_TARGET_COMPUTE="90" \
  -DCMAKE_INSTALL_PREFIX="/path/to/installations/gromacs/2026.4"
All downloading are set to OFF because MN5 nodes does not have internet access, otherwise the installation would hang.

LUMI-G

Last update

2026/10/01

PyCOMPSs

Within a compute node, in an interactive session: 

export JAVA_HOME=/users/salicari/jdk-27
ml PrgEnv-gnu/8.6.0
ml cray-python/3.11.7
export CFLAGS="-std=gnu17"
export BOOST_CPPFLAGS="-std=c++11 -pthread -O2 -s"
ml LUMI/25.03
ml Boost/1.88.0-cpeGNU-25.03

wget https://compss.bsc.es/repo/sc/stable/COMPSs_3.4.tar.gz
tar -xvzf COMPSs_3.4.tar.gz
cd COMPSs

# required because wheel and setuptools are not present by default
python -m pip install --upgrade pip setuptools wheel

./install -T /path/to/installation/compss/3.4 leonardo.cfg
leonardo.cfg is used as a placeholder. Lumi does not have a cfg file and therefore has to be created after installation. See our cfg directory in the repository.

GROMACS

It can be installed using the EasyBuild recipe provided: 

module load LUMI/25.03
module load partition/G
module load EasyBuild-user
eb GROMACS-2026.0-cpeAMD-25.03-HeFFTe-rocm-hip.eb -r
For more recipe, see eb -S gromacs.