Sample batch job submission scripts on SapSlurm

Serial (single-processor) Job

Sample job submission script (sub.sh) to run an R program called add.R using a single core:

#!/bin/bash
#SBATCH --job-name=testserial         # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --ntasks=1                    # Run on a single CPU
#SBATCH --mem=1gb                     # Job memory request
#SBATCH --time=02:00:00               # Time limit hrs:min:sec
#SBATCH --output=testserial.%j.out    # Standard output log
#SBATCH --error=testserial.%j.err     # Standard error log

#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu  # Where to send mail	

cd $SLURM_SUBMIT_DIR

module load R/3.6.2-foss-2019b

R CMD BATCH add.R

In this sample script, the standard output and error of the job will be saved into a file called testserial.o%j, where %j will be automatically replaced by the job id of the job.

MPI Job

Sample job submission script (sub.sh) to run an OpenMPI application. In this example the job requests 16 cores and further specifies that these 16 cores need to be divided equally on 2 nodes (8 cores per node) and the binary is called mympi.exe:

#!/bin/bash
#SBATCH --job-name=mpitest            # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --nodes=2                     # Number of nodes
#SBATCH --ntasks=16                   # Number of MPI ranks
#SBATCH --ntasks-per-node=8           # How many tasks on each node
#SBATCH --cpus-per-task=1             # Number of cores per MPI rank 
#SBATCH --mem-per-cpu=600mb           # Memory per processor
#SBATCH --time=02:00:00               # Time limit hrs:min:sec
#SBATCH --output=mpitest.%j.out       # Standard output log
#SBATCH --error=mpitest.%j.err        # Standard error log

#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu  # Where to send mail

cd $SLURM_SUBMIT_DIR

module load OpenMPI/3.1.4-GCC-8.3.0

mpirun ./mympi.exe

OpenMP (Multi-Thread) Job

Sample job submission script (sub.sh) to run a program that uses OpenMP with 6 threads. Please set --ntasks=1 and set --cpus-per-task to the number of threads you wish to use. The name of the binary in this example is a.out.

#!/bin/bash
#SBATCH --job-name=mctest             # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --ntasks=1                    # Run a single task	
#SBATCH --cpus-per-task=6             # Number of CPU cores per task
#SBATCH --mem=4gb                     # Job memory request
#SBATCH --time=02:00:00               # Time limit hrs:min:sec
#SBATCH --output=mctest.%j.out        # Standard output log
#SBATCH --error=mctest.%j.err         # Standard error log

#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu  # Where to send mail	

cd $SLURM_SUBMIT_DIR

export OMP_NUM_THREADS=6  

module load foss/2019b  # load the appropriate module file, e.g. foss/2019b

time ./a.out

High Memory Job

Sample job submission script (sub.sh) to run a velvet application that needs to use 50GB of memory and 4 threads:

#!/bin/bash
#SBATCH --job-name=highmemtest        # Job name
#SBATCH --partition=highmem           # Partition (queue) name
#SBATCH --ntasks=1                    # Run a single task	
#SBATCH --cpus-per-task=4             # Number of CPU cores per task
#SBATCH --mem=50gb                    # Job memory request
#SBATCH --time=02:00:00               # Time limit hrs:min:sec
#SBATCH --output=highmemtest.%j.out   # Standard output log
#SBATCH --error=highmemtest.%j.err    # Standard error log

#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu  # Where to send mail	

cd $SLURM_SUBMIT_DIR

export OMP_NUM_THREADS=4

module load Velvet

velvetg [options]

Hybrid MPI/shared-memory using OpenMPI

Sample job submission script (sub.sh) to run a parallel job that uses 4 MPI processes with OpenMPI and each MPI process runs with 3 threads:

#!/bin/bash
#SBATCH --job-name=hybridtest         # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --nodes=2                     # Number of nodes
#SBATCH --ntasks=8                    # Number of MPI ranks
#SBATCH --ntasks-per-node=4           # Number of MPI ranks per node
#SBATCH --cpus-per-task=3             # Number of OpenMP threads for each MPI process/rank
#SBATCH --mem-per-cpu=2000mb          # Per processor memory request
#SBATCH --time=2-00:00:00             # Walltime in hh:mm:ss or d-hh:mm:ss (2 days in the example)
#SBATCH --output=hybridtest.%j.out    # Standard output log
#SBATCH --error=hybridtest.%j.err     # Standard error log
 
#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu  # Where to send mail	

cd $SLURM_SUBMIT_DIR
 
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

mpirun ./myhybridprog.exe

Array job

Sample job submission script (sub.sh) to submit an array job with 10 elements. In this example, each array job element will run the a.out binary using an input file called input_0, input_1, ..., input_9.

#!/bin/bash
#SBATCH --job-name=arrayjobtest      # Job name
#SBATCH --partition=batch            # Partition (queue) name
#SBATCH --ntasks=1                   # Run a single task
#SBATCH --mem=1gb                    # Job Memory
#SBATCH --time=10:00:00              # Time limit hrs:min:sec
#SBATCH --output=array_%A-%a.out     # Standard output log
#SBATCH --error=array_%A-%a.err      # Standard error log
#SBATCH --array=0-9                  # Array range

cd $SLURM_SUBMIT_DIR

module load foss/2019b # load any needed module files, e.g. foss/2019b

time ./a.out < input_$SLURM_ARRAY_TASK_ID

GPU/CUDA

Sample script to run Amber on a GPU node using one node, 2 CPU cores, and 1 GPU card:

#!/bin/bash
#SBATCH --job-name=amber              # Job name
#SBATCH --partition=gpu_p             # Partition (queue) name
#SBATCH --gres=gpu:1                  # Requests one GPU device 
#SBATCH --ntasks=1                    # Run a single task	
#SBATCH --cpus-per-task=2             # Number of CPU cores per task
#SBATCH --mem=40gb                    # Job memory request
#SBATCH --time=10:00:00               # Time limit hrs:min:sec
#SBATCH --output=amber.%j.out         # Standard output log
#SBATCH --error=amber.%j.err          # Standard error log

#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu  # Where to send mail	

cd $SLURM_SUBMIT_DIR

ml Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8

mpiexec $AMBERHOME/bin/pmemd.cuda -O -i ./prod.in -o prod_c4-23.out  -p ./dimerFBP_GOL.prmtop -c ./restart.rst -r prod.rst -x prod.mdcrd