add batch scripts for gromacs gpu

Author: mariojmdavid

udocker-files/compile-gromacs-gpu.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+#SBATCH --job-name=run_gromacs
+#SBATCH --ntasks=64
+#SBATCH --partition=gpu
+#SBATCH --output=gromacs-%j.out
+#SBATCH --error=gromacs-%j.err
+
+export TUT_DIR=$HOME/udocker-tutorial
+export PATH=$HOME/udocker-1.3.17/udocker:$PATH
+export UDOCKER_DIR=$TUT_DIR/.udocker
+export OUT_NAME=output/ud-tutorial
+module load python
+cd $TUT_DIR
+
+echo "###############################"
+udocker run -v=$TUT_DIR/gromacs:/home/user -w=/home/user grom_gpu /home/user/compile.sh

udocker-files/prep-gromacs-gpu.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+#SBATCH --job-name=prep_gromacs
+#SBATCH --ntasks=1
+#SBATCH --partition=gpu
+#SBATCH --output=gromacs-gpu-prep-%j.out
+#SBATCH --error=gromacs-gpu-prep-%j.err
+
+export TUT_DIR=$HOME/udocker-tutorial
+export PATH=$HOME/udocker-1.3.10/udocker:$PATH
+cd $TUT_DIR
+export UDOCKER_DIR=$TUT_DIR/.udocker
+module load python
+
+echo "###############################"
+hostname
+echo ">> udocker command"
+which udocker
+echo
+echo ">> List images"
+udocker images
+echo
+echo ">> Create container"
+udocker create --name=grom_gpu nvidia/cuda:13.1.0-devel-ubuntu24.04
+echo
+echo ">> Set nvidia mode"
+udocker setup --nvidia --force grom_gpu
+echo ">> List containers"
+udocker ps -m -p