From bb15e088dfc38cfdb5fc13181833badb33c5dccd Mon Sep 17 00:00:00 2001 From: Jan Siwiec <jan.siwiec@vsb.cz> Date: Mon, 7 Oct 2024 08:37:40 +0200 Subject: [PATCH] Update gaussian.md --- docs.it4i/software/chemistry/gaussian.md | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/docs.it4i/software/chemistry/gaussian.md b/docs.it4i/software/chemistry/gaussian.md index 638a60cea..63cf0a696 100644 --- a/docs.it4i/software/chemistry/gaussian.md +++ b/docs.it4i/software/chemistry/gaussian.md @@ -1,6 +1,3 @@ -!!!warning - This page has not been updated yet. The page does not reflect the transition from PBS to Slurm. - # Gaussian ## Introduction @@ -90,7 +87,7 @@ Include the `%UseSSH` keyword, as well. This enables Linda to spawn parallel wor ``` The number and placement of Linda workers may be controlled by %LindaWorkers keyword or by -GAUSS_WDEF environment variable. When running multi-node job via the PBS batch queue, loading +GAUSS_WDEF environment variable. When running multi-node job via the batch queue, loading the Linda-enabled module **automatically sets the `GAUSS_WDEF` variable** to the correct node-list, using one worker per node. In combination with the %CPU keyword, this enables a full-scale multi-node execution. @@ -211,12 +208,13 @@ up automatically by the module load. ```bash #!/bin/bash -#PBS -A OPEN-0-0 -#PBS -q qprod -N MyJobName -#PBS -l select=4 +#SBATCH --account=PROJECT_ID +#SBATCH --partition=qcpu +#SBATCH --job-name=MY_JOB +#SBATCH --nodes=4 # change to workdir -cd $PBS_O_WORKDIR +cd $$SLURM_SUBMIT_DIR # load Gaussian Linda enabled module and set up Linda ml Gaussian/16_rev_c0-binary-Linda @@ -225,7 +223,7 @@ ml Gaussian/16_rev_c0-binary-Linda GAUSS_SCRDIR=/scratch/work/project/open-0-0/GaussianJob mkdir -p $GAUSS_SCRDIR cd $GAUSS_SCRDIR || exit -cp $PBS_O_WORKDIR/* . +cp $SLURM_SUBMIT_DIR/* . # run Gaussian calculation # g16 < input.inp > output.out @@ -252,7 +250,7 @@ A 109.471221 EOF # copy output files to home - cp * $PBS_O_WORKDIR/. && cd ../ + cp * $SLURM_SUBMIT_DIR/. && cd ../ # delete scratch directory rm -rf $GAUSS_SCRDIR -- GitLab