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The environment modules package controls access to the software. Use "module avail pymolpy" to find all available versions of PyMOL installed at LRZ. The output could look as follows:

Code Block
languagebash
themeConfluence
~> module av py
---------------------------------------- /lrz/sys/spack/release/21.1.1/modules/x86_64/linux-sles15-x86_64 ---------------
py-pymol/2.3.0  python/3.7.10-base  python/3.7.10-extended  python/3.8.8-base  python/3.8.8-extended
---------------------------------------- /lrz/sys/share/modules/files_sles15/tools --------------------------------------

From here you can learn, that the current version of PyMOL in SPACK software distribution system is obviously named "py-pymol/2.3.0". To use the default version of PyMOL, please type:

Code Block
languagebash
> module load py-pymol/2.3.0

Visualization using the PyMOL GUI

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When a new batch session is returned to you, simply type

Code Block
languagebash
> module load py-pymol/2.3.0
> srun pymol -c PML_FILE_NAME.pml

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Linux Cluster

SuperMUC-NG

#!/bin/bash
#SBATCH -o /dss/dsshome1/<group>/<user>/mydir/%x.%j.out
#SBATCH -e /dss/dsshome1/<group>/<user>/mydir/%x.%j.err
#SBATCH -D /dss/dsshome1/<group>/<user>/mydir
#SBATCH -J <job_name>
#SBATCH --time=24:00:00
#SBATCH --clusters=cm2
#SBATCH --partition=cm2_tiny
#SBATCH --qos=cm2_tiny
#SBATCH --nodes=1
#SBATCH --export=NONE
#SBATCH --get-user-env
#SBATCH --mail-type=end
#SBATCH --mail-user=<email_address>@<domain>

module load slurm_setup
module load py-pymol/2.3.0

pymol -c PML_FILE_NAME.pml
#!/bin/bash
#SBATCH -o /dss/dsshome1/<group>/<user>/mydir/%x.%j.out
#SBATCH -e /dss/dsshome1/<group>/<user>/mydir/%x.%j.err
#SBATCH -D /dss/dsshome1/<group>/<user>/mydir
#SBATCH -J <job name>
#SBATCH --time=24:00:00
#SBATCH --partition=micro
#SBATCH --nodes=1
#SBATCH --export=NONE
#SBATCH --get-user-env
#SBATCH --mail-type=END
#SBATCH --mail-user=<email_address>@<domain>
#SBATCH --account=<project id>

module load slurm_setup
module load py-pymol/2.3.0

pymol -c PML_FILE_NAME.pml

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