Sample batch job submission scripts on Sapelo2

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=yourMyID@uga.edu  # Where to send mail	

cd $SLURM_SUBMIT_DIR

module load R/4.3.1-foss-2022a

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.%j.out and testserial.%j.err, where %j will be automatically replaced by the job id of the job.

Serial (single-processor) Job on an AMD EPYC Milan processor

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 --constraint=Milan             # node feature
#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=yourMyID@uga.edu  # Where to send mail	

cd $SLURM_SUBMIT_DIR

module load R/4.3.1-foss-2022a

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=yourMyID@uga.edu  # Where to send mail

cd $SLURM_SUBMIT_DIR

module load OpenMPI/4.1.4-GCC-11.3.0

srun ./mympi.exe

Please note that you need to start the application with srun and not with mpirun or mpiexec.

MPI Job on nodes connected via the EDR IB fabric

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 --constraint=EDR              # node feature
#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=yourMyID@uga.edu  # Where to send mail

cd $SLURM_SUBMIT_DIR

module load OpenMPI/4.1.4-GCC-11.3.0

srun ./mympi.exe

Please note that you need to start the application with srun, and not with mpirun or mpiexec.

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=yourMyID@uga.edu  # Where to send mail	

cd $SLURM_SUBMIT_DIR

export OMP_NUM_THREADS=6  

module load foss/2022a  # load the appropriate module file, e.g. foss/2022a

time ./a.out

High Memory Job

Sample job submission script (sub.sh) to run a velvet application that needs to use 200GB of memory and 4 threads:

#!/bin/bash
#SBATCH --job-name=highmemtest        # Job name
#SBATCH --partition=highmem_p         # Partition (queue) name, i.e., highmem_p
#SBATCH --ntasks=1                    # Run a single task	
#SBATCH --cpus-per-task=4             # Number of CPU cores per task
#SBATCH --mem=200gb                    # 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=yourMyID@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=yourMyID@uga.edu  # Where to send mail	

cd $SLURM_SUBMIT_DIR
 
module load OpenMPI/4.1.4-GCC-11.3.0

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

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

cd $SLURM_SUBMIT_DIR

module load foss/2022a # load any needed module files, e.g. foss/2022a

time ./a.out < input_$SLURM_ARRAY_TASK_ID

Singularity job

Sample job submission script (sub.sh) to run a program (e.g. sortmerna) using a singularity container:

#!/bin/bash
#SBATCH --job-name=j_sortmerna        # 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=sortmerna.%j.out     # Standard output log
#SBATCH --error=sortmerna.%j.err      # Standard error log
#SBATCH --cpus-per-task=4             # Number of CPU cores per task
#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=yourMyID@uga.edu  # Where to send mail	

cd $SLURM_SUBMIT_DIR

singularity exec /apps/singularity-images/sortmerna-3.0.3.simg sortmerna \
--threads 4 --ref db.fasta,db.idx --reads file.fa --aligned base_name_output

For more information about software installed as singularity containers on the cluster, please see Software_on_Sapelo2#Singularity_Containers

GPU/CUDA

Sample script to run Amber on a GPU node using one node, 2 CPU cores, and 1 GPU A100 card:

#!/bin/bash
#SBATCH --job-name=amber              # Job name
#SBATCH --partition=gpu_p             # Partition (queue) name, i.e., gpu_p 
#SBATCH --gres=gpu:A100:1                  # 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=yourMyID@uga.edu  # Where to send mail	

cd $SLURM_SUBMIT_DIR

ml Amber/22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1

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

You can use the header #SBATCH --gres=gpu:P100:1 or #SBATCH --gres=gpu:A100:1 to specify using a P100 or an A100 GPU device. The compute mode of the GPU is set to Default.

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