CD task8 protocol

Preparation

• Load LRZ tools:

module load lrztools

• Load git

module load git

• clone git repository:

git clone git://github.com/offmarc/AGroS.git

• SetPath

export PATH=$PATH:$HOME/AGroS/
export PATH=$PATH:$HOME/software/scwrl/
rename Scwrl4 to scwrl

• Job script for testing: job.sh

#!/bin/bash
#SBATCH -o /home/hpc/pr58ni/di34fog/jobs/wt/wt_md.out
#SBATCH -D /home/hpc/pr58ni/di34fog/jobs/wt
#SBATCH -J wt_MD
#SBATCH --partition=mpp1_inter
#SBATCH --get-user-env
#SBATCH --ntasks=32
#SBATCH --mail-type=end
#SBATCH --mail-user=susann.vorberg@cmapus.lmu.de
#SBATCH --export=NONE
#SBATCH --time=02:00:00
source /etc/profile.d/modules.sh
module load gromacs
export PATH="$HOME/AGroS:$PATH"
export PATH="$HOME/apps/bin/:$PATH"
export PATH="$HOME/software/scwrl/:$PATH"
AGroS 2O4H_chainA.pdb --scwrlPATH /home/hpc/pr58ni/di34fog/software/scwrl -dir /home/hpc/pr58ni/di34fog/jobs/wt -threads 32

for real run:

--time 32:00:00
--partitition=mpp1

• Log in and submit job

ssh -X lxia4-1
sbatch job.sh

• Status:

squeue -u di34fog --cluster mpp1
squeue --cluster mpp1