Running on HPC - AtChem/AtChem2 Wiki

AtChem2 can be used on High Performance Computing (HPC) systems. Consult the system administrator and the local documentation for information on how to install and compile AtChem2 on an HPC system.

Usually, HPC systems allocate computing resources via a job scheduler, which requires a job submission script. The format and the syntax of the submission script depend on the specific software and setup of the HPC system.

Some examples of job submission scripts are shown below, for reference.

Portable Batch System (PBS)

#!/bin/bash
#PBS -o atchem2.log
#PBS -e atchem2_error.log
#PBS -N basemodel1
#PBS -m bea
#PBS -l walltime=15:00:00
#PBS -l vmem=10gb
#PBS -l nodes=1:ppn=1

cd ~/AtChem2/
MODELDIR="base_model_v1"
./atchem2 --model=$MODELDIR --shared_lib=$MODELDIR/configuration/mechanism.so

Slurm

#!/bin/bash
#SBATCH -o atchem2.log
#SBATCH -e atchem2_error.log
#SBATCH --job-name=basemodel1
#SBATCH --mail-type=ALL
#SBATCH --time=15:00:00
#SBATCH --mem=10gb
#SBATCH --nodes=1
#SBATCH --ntasks=1

cd ~/AtChem2/
MODELDIR="base_model_v1"
./atchem2 --model=$MODELDIR --shared_lib=$MODELDIR/configuration/mechanism.so