services:cluster:gpunodes
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services:cluster:gpunodes [2015/06/18 12:48] – [GROMACS example using GPU acceleration] dreger | services:cluster:gpunodes [2024/04/26 14:37] (current) – hoffmac00 | ||
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====== Introduction to GPU accelerated jobs ====== | ====== Introduction to GPU accelerated jobs ====== | ||
+ | |||
+ | <note info> | ||
Currently we have 31 nodes in the yoshi cluster (ygpu01-ygpu31) equipped with GPU boards. The exact hardware config is: | Currently we have 31 nodes in the yoshi cluster (ygpu01-ygpu31) equipped with GPU boards. The exact hardware config is: | ||
Line 131: | Line 133: | ||
</ | </ | ||
+ | So in this case the calculation runs about three times faster with two GPU cards. | ||
+ | |||
+ | ===== Example batch file ===== | ||
+ | |||
+ | A job script for the example given above could look like: | ||
+ | |||
+ | < | ||
+ | #!/bin/bash | ||
+ | |||
+ | #SBATCH --mail-user=dreger@physik.fu-berlin.de | ||
+ | #SBATCH --mail-type=end | ||
+ | |||
+ | #SBATCH --output=job%j.out | ||
+ | #SBATCH --error=job%j.err | ||
+ | #SBATCH --ntasks=8 | ||
+ | #SBATCH --mem-per-cpu=1024 | ||
+ | #SBATCH --time=01: | ||
+ | #SBATCH --gres=gpu: | ||
+ | #SBATCH --nodes=1 | ||
+ | #SBATCH --partition=gpu-main | ||
+ | |||
+ | module load gromacs/ | ||
+ | |||
+ | TAG=" | ||
+ | |||
+ | grompp -f run.mdp -c waterbox.gro -p topol.top -o output-$TAG | ||
+ | mdrun -nt ${SLURM_CPUS_ON_NODE} -testverlet -v -deffnm output-$TAG | ||
+ | </ | ||
+ | |||
+ | Please make sure you change the email if you use this for your own tests ;) | ||
services/cluster/gpunodes.1434631693.txt.gz · Last modified: 2015/06/18 12:48 by dreger