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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
@@ Line 1: / Line 1: @@
 ====== Introduction to GPU accelerated jobs ======
+<note info>This information is severely outdated</note>
 Currently we have 31 nodes in the yoshi cluster (ygpu01-ygpu31) equipped with GPU boards. The exact hardware config is:
@@ Line 131: / Line 133: @@
 </xterm>
+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:
+<xterm>
+#!/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=01:00:00
+#SBATCH --gres=gpu:2
+#SBATCH --nodes=1
+#SBATCH --partition=gpu-main
+module load gromacs/non-mpi/4.6.7-cuda
+TAG="${SLURM_JOB_ID}-$(hostname -s)-cuda"
+grompp -f run.mdp -c waterbox.gro -p topol.top -o output-$TAG
+mdrun -nt ${SLURM_CPUS_ON_NODE} -testverlet -v -deffnm output-$TAG
+</xterm>
+Please make sure you change the email if you use this for your own tests ;)