BATCH Scripts in ARINA

Example SLURM Script (slurm.sl)

The following example shows a general BATCH script that can be modified or adapted to most of the common calculations ran in ARINA:

script slurm.sl

#!/bin/bash 
#SBATCH --ntasks=4
#SBATCH --mem-per-cpu=3760M
#SBATCH --time=4:00:00
#SBATCH --partition=vfast

# Required input files for the software execution,
# separated by a space
files="input.inp checkpoint.chk"

# Unload all possible present modules
module purge
# LOAD NOW REQUIRED MODULES
module load MYDESIREDMODULE/version-compiler

# Define the command line you will run
command=""

#######################################################
## Do not change below this line

. /home/users/slurm/etc/slurm_func.sh

# Signal trap to recover files
trap 'cleanup_function' EXIT

HOST=$(hostname)
echo "Job running on $HOST"

chooseScr

LDIR=$(pwd)
export LDIR

echo "cp ${files} $0 to $scr/."
cp ${files} $0 ${scr}/.

cd $scr

# CALL EXECUTABLE with SRUN
echo /usr/bin/time -p srun ${command}
eval /usr/bin/time -p srun ${command}

Once the script is generated or modified, the sbatch command has to be executed in order to send the job to the cluster queues.

Submitting a job

[user@agamede] sbatch slurm.sl

---

send commands

In the Scientific Computing Center of SGIker (EHU) we have prepared some commands that enable the user to submit jobs in the queue system by only requesting an input file. Those commands starts by the string "send_" following a specification of the software to be ran:

Software	command	Software	command
ADF :	send_adf	Amber:	send_amber
Blender:	send_blender	CP2K:	send_cp2k
Gaussian:	send_gauss16	GROMACS:	send_gmx
LAMMPS:	send_lmp	MModel :	send_mmodel
MOLCAS:	send_molcas	NCIPLOT:	send_nciplot
NWChem:	send_nwchem	ORCA:	send_orca
PSI4:	send_psi4	VASP:	send_vasp

Further explanation on the usage of the send_sw commands can be found at send commands .

Software Prepared Scripts

Our aim is to help researchers:

We prepared several BATCH scripts available in:

/home/users/slurm/batch-scripts/

SOFTWARE LIST

ABINIT	BLAST	generic	Lumerical
nf_core_eager	qespresso	scilab	starccm+
ams	CP2K	gromacs	matlab
nwchem	qiime2	shasta	Trinity
ANSYS	lammps	molcas
orca	R	siesta	vasp

---

Notes

• The scripts are designed for ARINA's SLURM-managed clusters.
• slurm_func.sh contains helper functions for scratch space and file recovery.
• chooseScr accepts the -g option to enforce to use the /gscratch/$USER directory.
• Always edit command and files variables according to the specific software you are running.
• Modules should be loaded as needed before execution.