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Instructions for using VeloxChem software

VeloxChem is open-source software for quantum chemistry, written in Python and developed for calculating molecular properties and for various types of spectroscopy.

Licence

Open-source software - GNU Lesser General Public License version 2.1 (LGPLv2.1)

Installation

To install VeloxChem, use the modules available on CVMFS.

module load foss/2020b
module load Python/3.8.6-GCCcore-10.2.0
module load CMake/3.18.4-GCCcore-10.2.0
git clone https://gitlab.com/veloxchem/veloxchem.git
cd veloxchem/
python3 -m venv --system-site-packages venv
source venv/bin/activate
python3 -m pip install --upgrade pip setuptools
CC=gcc MPICC=mpicc python3 -m pip install mpi4py --no-binary=mpi4py
python3 -m pip install numpy pybind11 h5py pytest
export OPENBLASROOT=$EBROOTOPENBLAS
python3 setup.py install

Example of a SLURM task

The following example shows a task that will be run on 2 nodes and 12 cores. The job requires 2 GB RAM per core and will be carried out for 30 minutes on cpu partition.

#!/bin/bash

#SBATCH --job-name=veloxtest
#SBATCH --time=00:30:00
#SBATCH --partition=cpu
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=12

module load foss/2020b
module load Python/3.8.6-GCCcore-10.2.0
module load CMake/3.18.4-GCCcore-10.2.0

source $HOME/veloxchem/venv/bin/activate

export OMP_NUM_THREADS=12

mpirun veloxchem ~/example.inp example.out

Example of sending with ARC

Firstly you will need a .xrsl file in which you state which resources you need to start the job.

&
(count = 12)
(countpernode = 6)
(jobname = vlx-test)
(inputfiles = 
  ("vlx.sh" "")
)
(executable = vlx.sh)
(outputfiles = ("example.out" ""))
(stdout=example.log)
(join=yes)
(gmlog=log)
(memory=2000)
(walltime="30 minutes")

And the executable file:

module load foss/2020b
module load Python/3.8.6-GCCcore-10.2.0
module load CMake/3.18.4-GCCcore-10.2.0

git clone https://gitlab.com/veloxchem/veloxchem.git
cd veloxchem/
python3 -m venv --system-site-packages venv
source venv/bin/activate
python3 -m pip install --upgrade pip setuptools
CC=gcc MPICC=mpicc python3 -m pip install mpi4py --no-binary=mpi4py
python3 -m pip install numpy pybind11 h5py pytest
export OPENBLASROOT=$EBROOTOPENBLAS
python3 setup.py install

export OMP_NUM_THREADS=12

mpirun veloxchem ~/example.inp example.out

Note

The modules used are available on the clusters Maister, Arnes and Vega. If you are sending the task to another Sling cluster, the loading of modules must be adapted accordingly.

Citing VeloxChem in articles

The instructions for citing VeloxChem are available at https://veloxchem.org/citation

Documentation