REMINDER : allo-psmn is only a connection server; it allows you to have access to your files and to transfer them, and that's all. To work, you must connect, from
allo-psmn, to one of the compilation servers
The batch system currently in use at the PSMN is Sun Grid Engine (SGE).
It's 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.
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
More examples are avalaible here
OpenMPI 1.5.4 and above BEWARE of hostfile syntax
Surveiller un job
See corresponding the documentation and the examples.