On Thu, Apr 1, 2021 at 21:57 Satyen Dhamankar <[email protected]> wrote:
> Hello,
>
> I have been running the propane IBI tutorial for propane. The IBI for
> propane takes quite some time to run. Step_001 has taken more than an hour
> to complete.
>
> This is the slurm script I have used to run this job:
>
> #!/bin/bash
> #
> #SBATCH --job-name=R1.5-CG # create a short name for your job
> #SBATCH --qos=vshort # _quality of service_
> #SBATCH --nodes=1 # node count
> #SBATCH --ntasks-per-node=12 # number of tasks per node
> #SBATCH --cpus-per-task=1 # cpu-cores per task (>1 if multi-threaded tasks)
> #SBATCH --mem=10GB # total memory requested
> ##SBATCH --mem-per-cpu=4G # memory per cpu-core (4G per cpu-core is
> default)
> #SBATCH --gres=gpu:1 # number of gpurs per node
> #SBATCH --time=2:30:00 # total run time limit (HH:MM:SS)
> #SBATCH --mail-type=all # send email on job start, end, and fail
> module purge
> module load intel/19.0/64/19.0.5.281 # for running gromacs
> module load rh/devtoolset/7
> module load intel-mkl/2019.5/5/64
> module load cmake/3.x
> # run the job
> set -e
> # keep track of the last executed command
> trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
> # echo an error message before exiting
> #trap 'echo "\"${last_command\" command filed with exit code $?." ' EXIT
> bash run.sh
>
> Is taking such a long time for a sample IBI run normal?
>
Where does it get stuck? In the gromacs run or after that?
Christoph
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>
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Christoph Junghans
Web: http://www.compphys.de
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