View source for Sample batch job submission scripts on the teaching cluster

[[Category:Teaching]]

====Serial (single-processor) Job====

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

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testserial         # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=yourMyID@uga.edu  # Where to send mail	
#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=%x.%j.out            # Standard output log
#SBATCH --error=%x.%j.err             # Standard error log

cd $SLURM_SUBMIT_DIR

module load R/4.3.1-foss-2022a

R CMD BATCH add.R
</pre>
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 and %x by the jobname.

====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:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=mpitest             # Job name
#SBATCH --partition=batch              # Partition (queue) name
#SBATCH --mail-type=END,FAIL           # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=yourMyID@uga.edu   # Where to send mail	
#SBATCH --ntasks=16                    # Number of MPI ranks
#SBATCH --cpus-per-task=1              # Number of cores per MPI rank 
#SBATCH --nodes=2                      # Number of nodes
#SBATCH --ntasks-per-node=8            # How many tasks on each node
#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


cd $SLURM_SUBMIT_DIR

module load foss/2022a

mpirun ./mympi.exe

</pre>

====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.

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=mctest             # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=yourMyID@uga.edu  # Where to send mail	
#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

cd $SLURM_SUBMIT_DIR

export OMP_NUM_THREADS=6  

module load foss/2022a

time ./a.out

</pre>

====High Memory Job====

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

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=highmemtest         # Job name
#SBATCH --partition=highmem            # Partition (queue) name
#SBATCH --mail-type=END,FAIL           # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=yourMyID@uga.edu   # Where to send mail	
#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

cd $SLURM_SUBMIT_DIR

export OMP_NUM_THREADS=4

module load Velvet

velvetg [options]

</pre>

====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:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=hybridtest
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=yourMyID@uga.edu  # Where to send mail	
#SBATCH --nodes=2                     # Number of nodes
#SBATCH --ntasks=4                    # Number of MPI ranks
#SBATCH --ntasks-per-node=2           # 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
 
cd $SLURM_SUBMIT_DIR
 
ml foss/2022a

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

mpirun ./myhybridprog.exe

</pre>

====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. 
<pre class="gscript">
#!/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/2022a

time ./a.out < input_$SLURM_ARRAY_TASK_ID

</pre>

====GPU/CUDA====

Sample script to run Amber on a GPU node using one node, 2 CPU cores, and 1 GPU card:
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=amber              # Job name
#SBATCH --partition=gpu               # 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=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
</pre>

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