REMNDER : allo-psmn is just a connexion server; it allows you to have access to your files and to transfer them, and that's all. To work, you must to connect, from allo-psmn, to one of compilation servers

The batch system currently used at the PSMN is Sun Grid Engine (SGE).

Its documentation is on this page as well as in the F.A.Q..

Submit a job

We use the command qsub to submit a job to the batch system of PSMN. For exemple :

qsub submission_script

Submission scripts

Here are some scripts for submitting a job to the PSMN batch system.

Some variables have to be modified according to the actual configurations of the queues.

Other exemples of submission scripts , exemples of submission scripts as well as tutorials.

for parallel job (shell bash)

You can submit your job using the following command:

 qsub submission_script 
submission_script
#!/bin/bash
#
### variables SGE
### shell of the job
#$ -S /bin/bash
### job name (to change)
#$ -N SommeVecVecPAR
### queue (to change)
#$ -q E5_test
### parallel environment & nb cpu (NSLOTS) (to change)
#$ -pe test_debian 2
### load the user environment for SGE
#$ -cwd
### to export environment variables to all runtime nodes
#$ -V
### mails at the beginning and end of execution
#$ -m be
 
# given by the batch system
HOSTFILE=${TMPDIR}/machines
 
# go to the work / submission directory
# important, otherwise the program is running since ~/
cd ${SGE_O_WORKDIR}
 
# init env (should be in ~/.profile)
source /usr/share/lmod/lmod/init/bash
 
### configure the environment (to change)
module load iccifort/2017.4
module load intel/2017.4b/OpenMPI/3.0.0
 
### au besoin, forcer l'env OpenMPI
PREFIX="/applis/PSMN/debian9/software/Compiler/intel/2017.4b/OpenMPI/3.0.0/"
MPIRUN=${PREFIX}/bin/mpirun
 
### program execution (to change with your executable)
###EXECDIR=${HOME}/Formations/Parallel
###${MPIRUN} -v -prefix ${PREFIX} -mca btl vader,openib,self -hostfile ${HOSTFILE} -np ${NSLOTS} ${EXECDIR}/SommeVecVecPAR.exe
 
${MPIRUN} -v -prefix ${PREFIX} -mca btl vader,openib,self -np ${NSLOTS} SommeVecVecPAR.exe
 
# fin
:!: OpenMPI 1.5.4 et supérieures
ATTENTION au hostfile :!:

Surveiller un job

See corresponding the documentation and the examples.

en/documentation/tutorials/submit.txt · Dernière modification: 2019/01/15 11:12 par cicaluga