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job.80s_ray_192x192_dpi96.sh 1.74 KiB
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#!/bin/bash
#
# fast running test script
#
#
#SBATCH --job-name pymol_ray_8core_192x192_96dpi
#SBATCH --ntasks=1                          ##Number of PROCESSES
# ====== entire hi-mem node ======
#SBATCH --cpus-per-task=8                   ##Number of CPUs per task
#SBATCH --mem-per-cpu=1000                  ##Memory specified for each core used (in MB) (no cores, use --mem=)
##SBATCH --mem-per-cpu=15000                  ##Memory specified for each core used (in MB) (no cores, use --mem=)
#                                            ##Runtime in D-HH:MM:SS
#SBATCH --partition=medium -t 2-02:00:00       ## express(2h), short(12h), medium(2d2h), long(6d6h), interactive(2h)
#--share                                     ## !!!don't share!!!
#
##SBATCH --mail-user=BLAZERID@uab.edu
#SBATCH --mail-type=ALL                     ## BEGIN, END, ERROR, ALL
#
#SBATCH --error=logs/%j.%N.err.txt               ##File to which STDERR will be written
#SBATCH --output=logs/%j.%N.out.txt              ## File to which STDOUT will be written

PSE_FILE="test_1aon_struct_spectrum.pse"
PNG_FILE=$(basename $SESS_FILE .pse).ray.192x192.96dpi.png

module purge
module load shared rc-base
module load Anaconda3/5.3.0

. /share/apps/rc/software/Anaconda3/5.3.0/etc/profile.d/conda.sh

# this assumes you have created a pymol2 conda environment previously via :
if [ ! -e ~/.conda/envs/pymol2 ]; then
    # install pymol2, if necessary (only first time run, for each users)
    echo "# INSTALLING pymol into ~/$USER/.conda/envs/pymol2 using Anaconda"
    conda create --name pymol2 -c schrodinger pymol
fi
conda activate pymol2

date;
pymol -c -d "set max_threads, $SLURM_JOB_CPUS_PER_NODE; load $PSE_FILE; set antialias, 2; ray 192,192; png $PNG_FILE, width=2in, height=2in, dpi=96; quit;"
date