Différences
Ci-dessous, les différences entre deux révisions de la page.
| Prochaine révision | Révision précédenteDernière révisionLes deux révisions suivantes | ||
| en:documentation:tutorials:submit:jobsequentielbash [2018/01/17 06:25] – créée cicaluga | en:documentation:tutorials:submit:jobsequentielbash [2020/08/25 15:58] – modification externe 127.0.0.1 | ||
|---|---|---|---|
| Ligne 2: | Ligne 2: | ||
| - | The batch system currently used at the PSMN is Sun Grid Engine (SGE). Its documentation is [[documentation: | + | The batch system currently used at the PSMN is Sun Grid Engine (SGE). Its documentation is [[documentation: |
| Ligne 20: | Ligne 20: | ||
| <note warning> Some variables have to be updated, for exemple, according to [[documentation: | <note warning> Some variables have to be updated, for exemple, according to [[documentation: | ||
| - | Othere | + | Other [[documentation: |
| ======for sequential programs | ======for sequential programs | ||
| Ligne 32: | Ligne 32: | ||
| # | # | ||
| ### variables SGE | ### variables SGE | ||
| - | ### shell du job | + | ### shell of the job |
| #$ -S /bin/bash | #$ -S /bin/bash | ||
| ### job name (to change): | ### job name (to change): | ||
| #$ -N SommeVecVecSEQ | #$ -N SommeVecVecSEQ | ||
| ### queue (to change) | ### queue (to change) | ||
| - | #$ -q E5-2670_test | + | #$ -q E5_test |
| ### load the user environment for SGE | ### load the user environment for SGE | ||
| #$ -cwd | #$ -cwd | ||
| Ligne 56: | Ligne 56: | ||
| ### | ### | ||
| ### | ### | ||
| - | ./ | + | ./ |
| - | # fin | + | # end |
| </ | </ | ||
| - | Travailler dans le /scratch | + | Work in the |
| - | <code bash batch.sh> | + | <code bash script_seq> |
| #!/bin/bash | #!/bin/bash | ||
| # | # | ||
| ### variables SGE | ### variables SGE | ||
| # | # | ||
| - | ### shell du job | + | ### shell of the job |
| #$ -S /bin/bash | #$ -S /bin/bash | ||
| - | ### nom du job (a changer) | + | ### job name (to change): |
| #$ -N SommeVecVecSEQ | #$ -N SommeVecVecSEQ | ||
| - | ### file d' | + | ### queue (to change) |
| #$ -q E5-2670_test | #$ -q E5-2670_test | ||
| - | ### charger l' | + | ### load the user environment for SGE |
| #$ -cwd | #$ -cwd | ||
| - | ### exporter les variables | + | ### export environment |
| #$ -V | #$ -V | ||
| - | ### mails en debut et fin d'execution | + | ### start and end of execution |
| #$ -m be | #$ -m be | ||
| - | # aller dans le repertoire de travail/soumission | + | # go to the work / submission directory |
| - | # important, | + | # important, |
| cd ${SGE_O_WORKDIR} | cd ${SGE_O_WORKDIR} | ||
| - | ### configurer l' | + | ### configure the environment |
| - | module load iccifort/2017.4 | + | module load GCC/7.2.0 |
| - | # for bash: | + | ### SCRATCHDIR definition |
| - | SCRATCHDIR=${SGE_O_WORKDIR/ | + | SCRATCHDIR=/ |
| - | /bin/mkdir -p $SCRATCHDIR | + | ### SCRATCHDIR checking |
| + | echo " | ||
| - | /bin/ | + | ### creation of the working directory in /scratch |
| - | ###/bin/cp -rf $INPUT | + | if [[ ! -d "${SCRATCHDIR}" ]] |
| + | then | ||
| + | /bin/mkdir -p ${SCRATCHDIR} | ||
| + | fi | ||
| - | # go to scratch | + | ### copy source files to /scratch |
| + | /bin/cp ${SGE_O_WORKDIR}/ | ||
| + | |||
| + | ### move into the execution directory BEFORE launching the program | ||
| cd ${SCRATCHDIR} | cd ${SCRATCHDIR} | ||
| - | + | ||
| - | ### execution | + | ### program |
| ###### | ###### | ||
| EXECDIR=${SCRATCHDIR} | EXECDIR=${SCRATCHDIR} | ||
| - | ${EXECDIR}/ | + | ${EXECDIR}/ |
| - | #### | + | #### |
| + | |||
| # copy results from scratch to home | # copy results from scratch to home | ||
| - | /bin/cp -r $SCRATCHDIR/ | + | /bin/cp -r $SCRATCHDIR/ |
| - | + | ||
| - | rm -fr ${SCRATCHDIR}/ | + | # rm -fr ${SCRATCHDIR}/ |
| - | + | ||
| - | # fin | + | # end |
| </ | </ | ||
| - | |||
| - | |||
| ====== Surveiller un job ====== | ====== Surveiller un job ====== | ||
| Voir [[documentation: | Voir [[documentation: | ||