Example  job-script


The job script includes the options (qsub option) to be passed to the job scheduler and the execution command.

qsub Option: Start with #PBS at the beginning of the line then the arguments to be passed to the executed command.Other parts: treated as a command to be executed by the shell.Job script example:Execute MPI program (compiled)

#!/bin/csh                  ← Specify the shell to use for execution
#PBS -q SINGLE              ← Specify the destination queue
#PBS -oe                   ← Direct standard output and error to the same file
#PBS -l select=1:ncpus=16:mpiprocs=16   ← Specify the required resources(in this example 16 parallel MPI processors) 
#PBS -N my-job              ← Specify a job name

cd ${PBS_O_WORKDIR}        ← Change the working directory

mpiexec_mpt dplace -s1 ./hello_mpi.exe           ← Run the complied executable with MPI

Job-script sample

Other samples of various job-scripts are shown here.

In addition to lmpcc login, the sample PBS script is available via the following path.


Resources specification example

The size of compute resource available for calculation is counted as "chunk"

Default chunk size of this system is:

1 Chunk:
1 CPU (16 CPU Core/ncpus= 16 ) + about 384GB Memory

If PBS is set as below,  2Chunks, + 32 CPU Core is provided.

#PBS -l select=2

If the resources are specified as below, the chunk size will change.In this example, 2 chunks, 64 CPU Core is set as one chunk, 32 CPU Core.

#PBS -l select=2:ncpus=32


1CPU ("16CPU Core, 384GB Mem"), 16 MPI parallelized job with 0.25 node.

#PBS -l select=1:npus=16:mpiprocs=16
#PBS -j oe
#PBS -N MPI-job


mpiexec_mpt dplace -s1 ./hello_mpi.exe

2CPU (32CPU Core, 768GB Mem), 16 MPI parallelized job with 0.5 node. (16 CPU will be free)

#PBS -l select=2:ncpus=16:mpiprocs=8
#PBS -j oe
#PBS -N MPI-job


mpiexec_mpt dplace -s1 ./hello_mpi.exe

OpenMP Job

0.5CPU (8CPU Core) 8 Threads parallelized job

#PBS -l select=1:ncpus=16
#PBS -j oe
#PBS -N OpenMP-job

setenv KMP_AFFINITY disabled

dplace ./a.out

Hybrid(MPI+OpenMP) Job

Using 2CPU (32CPU Core) , 4 (MPI) process x 4 (OpenMP) threads per 16 Core

#PBS -l select=2:ncpus=16:mpiprocs=4   <-- 4 processes per CPU
#PBS -j oe
#PBS -N hybrid-job


export OMP_NUM_THREADS=4    <-- 4 threads per process
export KMP_AFFINITY=disabled

mpiexec_mpt  omplace -nt ${OMP_NUM_THREADS} ./hello_hyb.exe <-- 実行

Materials Studio Job

1 CPU = 8 Cores running 8 parallel Dmol3 jobs

#PBS -l select=1
#PBS -j oe

setenv PATH ${PATH}:/work/opt/lm/BIOVIA/MaterialsStudio22.1/etc/DMol3/bin -np 8 test  <-- (1 chunk : Specify a number less than 10 parallel Cores)