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:mpiprocs=8  　← Specify the required resources（in this example 8 parallel MPI processors） 
#PBS -N my-job　　　　　　　　　　　　　　← Specify a job name

cd ${PBS_O_WORKDIR} 　　　　　　　← Change the working directory

mpirun -r ssh  -machinefile ${PBS_NODEFILE} -np 8 ./hello_mpi　　　           　← Run the complied executable

Job-script sample

Other samples of various job-scripts are shown here．

• MPI
• OpenMP
• Hybrid(MPI+OpenMP)
• MaterialsStudio

In addition to pcc login, please have copy the sample PBS script below and use it.

pcc:/work/Samples

How to calculate the resources needed in chunks

Default chunk size of this system is:

1 Chunk:
0.5 CPU (8 CPU Core/ncpus= 8 ) + 16GB Memory

If PBS is set as below,  2Chunks, + 16 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, 32 CPU Core is set as one chunk, 16 CPU Core.

#PBS -l select=2:ncpus=16

1CPU (16CPU Core, 32GB Mem), 16 MPI parallelized job with 0.5 node.

#!/bin/csh
#PBS -l select=2:ncpus=8:mpiprocs=8
#PBS -j oe
#PBS -N MPI-job

cd $PBS_O_WORKDIR

mpirun -machinefile ${PBS_NODEFILE} -np 8 ./hello_mpi

2CPU (32CPU Core, 64GB Mem), 16 MPI parallelized job with 1 node. (16 CPU will be free)

#!/bin/csh
#PBS -l select=4:ncpus=8:mpiprocs=4
#PBS -j oe
#PBS -N MPI-job

cd $PBS_O_WORKDIR

mpirun -machinefile ${PBS_NODEFILE} -np 4 ./hello_mpi

0.5CPU (8CPU Core) 8 Threads parallelized job

#!/bin/csh
#PBS -l select=1
#PBS -j oe
#PBS -N OpenMP-job

cd $PBS_O_WORKDIR
setenv OMP_NUM_THREADS 8

./a.out

Using 2CPU (32CPU Core) , 2 (MPI) process x 4 (OpenMP) threads per 8 Core

#!/bin/bash
#PBS -l select=4:ncpus=8:mpiprocs=2　　　<-- Two processes per CPU
#PBS -j oe
#PBS -N hybrid-job

cd $PBS_O_WORKDIR

export OMP_NUM_THREADS=4    <-- 4 threads per process

mpirun -machinefile ${PBS_NODEFILE} -np 2 ./hello_hyb　<-- 2 Process generation

Using 2CPU (32CPU Core), 1 process x 4 threads　

#!/bin/bash
#PBS -l select=4:mpiprocs=2　　　<-- 2CPU, Per CPU, 2 processes ( = in total 8 processes )
#PBS -j oe
#PBS -N hybrid-job

cd $PBS_O_WORKDIR

export OMP_NUM_THREADS=4    <--  4threads per process

mpirun -machinefile ${PBS_NODEFILE} -np 4 ./hello_hyb　<-- 4 process generation

1 CPU = 8 Cores running 8 parallel Dmol3 jobs

#!/bin/csh
#PBS -l select=1
#PBS -j oe
#PBS -N DMOL3

cd $PBS_O_WORKDIR
setenv PATH ${PATH}:/work/opt/Accelrys/MaterialsStudio6.1/etc/DMol3/bin

RunDMol3.sh -np 8 test  <--　(1 chunk : Specify a number less than 10 parallel Cores)