Sample Scripts

Sample batch job submission scripts on Sapelo2

OpenMPI

Sample job submission script (sub.sh) to run an OpenMPI application:

#PBS -S /bin/bash
#PBS -q batch
#PBS -N testjob
#PBS -l nodes=2:ppn=48:AMD
#PBS -l walltime=48:00:00
#PBS -l mem=2gb
#PBS -M username@uga.edu 
#PBS -m abe

cd $PBS_O_WORKDIR

ml OpenMPI/2.1.1-GCC-6.4.0-2.28

echo
echo "Job ID: $PBS_JOBID"
echo "Queue:  $PBS_QUEUE"
echo "Cores:  $PBS_NP"
echo "Nodes:  $(cat $PBS_NODEFILE | sort -u | tr '\n' ' ')"
echo "mpirun: $(which mpirun)"
echo

mpirun ./a.out > outputfile

OpenMP

Sample job submission script (sub.sh) to run an OpenMP (threaded) large memory application:

#PBS -S /bin/bash
#PBS -q batch
#PBS -N testjob
#PBS -l nodes=1:ppn=10:HIGHMEM
#PBS -l walltime=48:00:00
#PBS -l mem=300gb
#PBS -M username@uga.edu 
#PBS -m abe

cd $PBS_O_WORKDIR

export OMP_NUM_THREADS=10

echo
echo "Job ID: $PBS_JOBID"
echo "Queue:  $PBS_QUEUE"
echo "Cores:  $PBS_NP"
echo "Nodes:  $(cat $PBS_NODEFILE | sort -u | tr '\n' ' ')"
echo

time ./a.out > outputfile

A high memory job

Sample job submission script (sub.sh) to run an application that needs to use an Intel HIGHMEM node:

#PBS -S /bin/bash
#PBS -q highmem_q
#PBS -N testjob
#PBS -l nodes=1:ppn=12:Intel
#PBS -l walltime=48:00:00
#PBS -l mem=400gb
#PBS -M username@uga.edu 
#PBS -m abe

cd $PBS_O_WORKDIR

ml Velvet 

velvetg [options] > outputfile

GPU/CUDA

Sample job submission script (sub.sh) to run a GPU-enabled (e.g. CUDA) application:

#PBS -S /bin/bash
#PBS -q gpu_q
#PBS -N testjob
#PBS -l nodes=1:ppn=4:gpus=1:GPU
#PBS -l walltime=48:00:00
#PBS -l mem=2gb
#PBS -M username@uga.edu 
#PBS -m abe

cd $PBS_O_WORKDIR

ml CUDA/9.0.176

echo
echo "Job ID: $PBS_JOBID"
echo "Queue:  $PBS_QUEUE"
echo "Cores:  $PBS_NP"
echo "Nodes:  $(cat $PBS_NODEFILE | sort -u | tr '\n' ' ')"
echo

time ./a.out > outputfile

Note: Please note the additional gpus=1 option in the header line. This option should be used to request the number of GPU cards to be used (e.g. to request 2 GPU cards, use gpus=2).

The GPU devices allocated to a job are listed in a file whose name is stored in the queueing system environment variable PBS_GPUFILE. You can print what this file name is with the command (add it to your job submission file):

echo $PBS_GPUFILE

To get a list of the numbers of the GPU devices allocated to your job, separated by a blank space, use the command:

CUDADEV=$(cat $PBS_GPUFILE | rev | cut -d"u" -f1)

echo "List of devices allocated to this job:"

echo $CUDADEV

To remove the blank space between two device numbers in the CUDADEV variable above, use the command:

CUDADEV=$(cat $PBS_GPUFILE | rev | cut -d"u" -f1)

GPULIST=$(echo $CUDADEV | sed 's/ //')

echo "List of devices allocated to this job (no blank spaces between devices):"

echo $GPULIST

Some GPU/CUDA applications require that a list of the GPU devices be given as an argument to the application. If the application needs a blank space separated device number list, use the $CUDADEV variable as an argument. If no blank space is allowed in the list, you can use the $GPULIST variable as an argument to the application.

Hybrid MPI/shared-memory using OpenMPI

Sample job submission script (sub.sh) to run a parallel job that uses 3 MPI processes with OpenMPI and each MPI process runs with 12 threads:

#PBS -S /bin/bash
#PBS -j oe
#PBS -q batch
#PBS -N testhybrid
#PBS -l nodes=3:ppn=12:AMD
#PBS -l mem=60g
#PBS -l walltime=4:00:00
#PBS -M username@uga.edu 
#PBS -m abe

ml OpenMPI/2.1.1-GCC-6.4.0-2.28

echo
echo "Job ID: $PBS_JOBID"
echo "Queue:  $PBS_QUEUE"
echo "Cores:  $PBS_NP"
echo "Nodes:  $(cat $PBS_NODEFILE | sort -u | tr '\n' ' ')"
echo "mpirun: $(which mpirun)"
echo

cd $PBS_O_WORKDIR

export OMP_NUM_THREADS=12

perl /usr/local/bin/makehostlist.pl $PBS_NODEFILE $PBS_NUM_PPN $PBS_JOBID

mpirun -machinefile  host.$PBS_JOBID.list ./a.out

Running an 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.

#PBS -S /bin/bash
#PBS -j oe
#PBS -q batch
#PBS -N myarrayjob
#PBS -l nodes=1:ppn=1:AMD
#PBS -l walltime=4:00:00
#PBS -t 0-9

cd $PBS_O_WORKDIR

time ./a.out < input_$PBS_ARRAYID

Running a singularity job

For example, to run Trinity using the singularity image:

#PBS -S /bin/bash
#PBS -N j_s_trinity
#PBS -q highmem_q
#PBS -l nodes=1:ppn=1
#PBS -l walltime=480:00:00
#PBS -l mem=100gb
 
cd $PBS_O_WORKDIR

singularity exec /usr/local/singularity-images/trinity-2.5.1--0.simg COMMAND OPTION

where COMMAND should be replaced by the specific command and options, such as:

#PBS -S /bin/bash
#PBS -N j_s_trinity
#PBS -q highmem_q
#PBS -l nodes=1:ppn=16
#PBS -l walltime=480:00:00
#PBS -l mem=100gb
 
cd $PBS_O_WORKDIR

singularity exec /usr/local/singularity-images/trinity-2.5.1--0.simg Trinity --seqType <string> --max_memory 100G --CPU 8 --no_version_check 1>job.out 2>job.err   

Sample batch job submission scripts on zcluster

In all these sample scripts, the working_directory refers to your working directory. For example, your working directory could be a subdirectory called projectA in your home directory.

Notes about the job submission script

• You can use the pound sign # to start comment lines in your script, but # cannot be immediately followed by a dollar sign $. The combination #$ is reserved to indicate a qsub option defined in the script.
• The job submission script does not need to have execution permission.

To run a serial job

#!/bin/bash
cd working_directory
time ./myprog < myin > myout

Note that the 'time' command included in the sample script above is optional (this command measures the amount of time it takes to run an executable). Entering a standard input file (myin) and standard output file (myout) is only necessary if your executable requires input from standard input and if it outputs data to standard output.

You can specify the working_directory as in the example below:

#!/bin/bash
cd ${HOME}/projectA
time ./myprog < myin > myout

If the job is submitted from within the working directory, you can use the following sample script:

#!/bin/bash
cd `pwd`
time ./myprog < myin > myout

To run a Parallel job

#!/bin/bash
cd working_directory
time ./myprog -number-of-thread 4

Note that the '-number-of-thread' in the sample script above is an example of thread number parameter. Each program has own name of such parameter.

To submit a parallel job using 4 threads with script sub.sh to the rcc-30d batch queue and have the standard output and error go to the files sub.sh.ojobid and sub.sh.ejobid, respectively, in the directory from which the job was submitted, use

qsub -q rcc-30d -pe thread 4 sub.sh

To run an R program

Sample script to run an R program called program.R:

#!/bin/bash
cd `pwd`
time /usr/local/R/2.15.2/bin/R CMD BATCH program.R

To run a Matlab program

Sample script to run a Matlab program called plotsin.m:

#!/bin/bash
cd `pwd`
matlab -nodisplay < plotsin.m > matlab.out
exit

Parallel Jobs using MPI libraries

To run a parallel MPI job using MPICH/PGI

#!/bin/bash
cd working_directory
echo "Got $NSLOTS processors."
echo "Machines:"
cat $TMPDIR/machines
/usr/local/pgi/linux86-64/2012/mpi/mpich/bin/mpirun -np $NSLOTS -machinefile $TMPDIR/machines ./myprog

Note that lines 3, 4, and 5 in this script are optional.

To run a parallel MPI job using the default MPICH2 (PGI) compilers. For example, if you compiled the code with mpicc or mpif90, etc, without full path.

#!/bin/bash
cd working_directory
export LD_LIBRARY_PATH=/usr/local/mpich2/1.4.1p1/pgi123/lib:${LD_LIBRARY_PATH}
mpirun -np $NSLOTS ./myprog

To run a parallel MPI job using MPICH2 and e.g. GNU 4.4.4 compilers

#!/bin/bash
cd working_directory
export LD_LIBRARY_PATH=/usr/local/mpich2/1.4.1p1/gcc_4.4.4/lib:${LD_LIBRARY_PATH}
/usr/local/mpich2/1.4.1p1/gcc_4.4.4/bin/mpirun -np $NSLOTS ./myprog

Note that with MPICH2 it is not necessary to include the -machinefile option when submitting the job to a batch queue. When using other MPICH2 compilations, such as for PGI compilers, users need to adjust the path to the libraries and to mpirun appropriately in the script.

To run a parallel MPI job using OpenMPI 1.4.4 and e.g. GNU 4.1.2 compilers

#!/bin/bash
cd working_directory
export LD_LIBRARY_PATH=/usr/local/openmpi/1.4.4/gcc412/lib:${LD_LIBRARY_PATH}
/usr/local/openmpi/1.4.4/gcc412/bin/mpirun ––mca btl "tcp,self" -np $NSLOTS ./myprog

To run a parallel MPI job using OpenMPI 1.6.2 and e.g. GNU 4.7.1 compilers

#!/bin/bash
cd working_directory
export LD_LIBRARY_PATH=/usr/local/gcc/4.7.1/lib64:/usr/local/openmpi/1.6.2/gcc471/lib:${LD_LIBRARY_PATH}
/usr/local/openmpi/1.6.2/gcc471/bin/mpirun ––mca btl "tcp,self" -np $NSLOTS ./myprog

Note that with OpenMPI you can use the mpirun command and there is no need to include the -machinefile option. When using other OpenMPI compilations, such as the one for PGI compilers, users need to adjust the path to the libraries and to mpirun appropriately in the script. To use OpenMPI over Infiniband, remove the mpirun option

––mca btl "tcp,self"

from the script.

To run a parallel MPI job using MVAPICH2/GNU over Infiniband

#!/bin/bash
cd working_directory
export LD_LIBRARY_PATH=/usr/local/mvapich2/1.8/gcc444/lib:${LD_LIBRARY_PATH}
/usr/local/mvapich2/1.8/gcc444/bin/mpirun -np $NSLOTS ./myprog

To run a shared memory job using OpenMP

Sample script to run a program that uses 4 OpenMP threads:

#!/bin/bash
cd working_directory
export OMP_NUM_THREADS=4
time ./myprog