Ceci est une ancienne révision du document !
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
D'autres exemples sont disponibles ici
OpenMPI 1.5.4 et supérieures ATTENTION au hostfile
Surveiller un job
See corresponding the documentation and the examples.