Ci-dessous, les différences entre deux révisions de la page.
Les deux révisions précédentesRévision précédenteProchaine révision | Révision précédente | ||
faq:chimie:amber [2018/07/23 13:22] – cpetit | faq:chimie:amber [2022/03/03 16:27] (Version actuelle) – [Submission script] tjiang | ||
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====== AMBER ====== | ====== AMBER ====== | ||
+ | ===== Submission script ===== | ||
+ | <code bash sub_amber17.sh> | ||
+ | #!/bin/bash | ||
+ | #$ -S /bin/bash | ||
+ | #$ -N amber17 | ||
+ | #$ -cwd | ||
+ | #$ -V | ||
+ | #$ -o npt4.out | ||
+ | #$ -j y | ||
+ | ## | ||
+ | ##Choose between cpu queues and gpu queues, default gpu queues | ||
+ | ##cpu queues | ||
+ | ##$ -q M6*, | ||
+ | ##$ -pe mpi16_debian 16 | ||
+ | ##gpu queues | ||
+ | #$ -q E5-2670gpuK20deb128, | ||
+ | #$ -pe mpi_debian 1 | ||
+ | ## | ||
- | [[faq:accueil|Foire Aux Questions]] | + | # PSMN: $Id$ |
+ | # | ||
+ | |||
+ | export MODULEPATH="/ | ||
+ | module use " | ||
+ | |||
+ | #module file for gpu version of amber | ||
+ | module load amber/ | ||
+ | |||
+ | #module file for cpu only version of amber | ||
+ | #module load amber/ | ||
+ | |||
+ | ambermod=$(basename " | ||
+ | echo " | ||
+ | if [ " | ||
+ | amberexe=" | ||
+ | else | ||
+ | amberexe=" | ||
+ | fi | ||
+ | echo " | ||
+ | |||
+ | ulimit -v unlimited | ||
+ | ulimit -s unlimited | ||
+ | |||
+ | ######################" | ||
+ | HOMEDIR=" | ||
+ | HOSTFILE=" | ||
+ | |||
+ | cd " | ||
+ | |||
+ | echo NSLOTS=" | ||
+ | |||
+ | if [[ -d "/ | ||
+ | then | ||
+ | SCRATCHDIR="/ | ||
+ | elif [[ -d "/ | ||
+ | then | ||
+ | SCRATCHDIR="/ | ||
+ | elif [[ -d "/ | ||
+ | then | ||
+ | SCRATCHDIR="/ | ||
+ | else | ||
+ | echo "/ | ||
+ | exit 1 | ||
+ | fi | ||
+ | # Using /tmp as scratch instead | ||
+ | # SCRATCHDIR="/ | ||
+ | |||
+ | echo " | ||
+ | /bin/mkdir -p " | ||
+ | ################### | ||
+ | Mac=$(hostname | awk ' | ||
+ | |||
+ | NbMac=$(wc " | ||
+ | rm ./ | ||
+ | for i in $(seq 1 " | ||
+ | do | ||
+ | Mac=$(head -n " | ||
+ | Nb=$(head -n " | ||
+ | for j in $(seq 1 " | ||
+ | do | ||
+ | echo " | ||
+ | done | ||
+ | done | ||
+ | |||
+ | cp " | ||
+ | |||
+ | cd " | ||
+ | |||
+ | echo "start at" | ||
+ | date | ||
+ | |||
+ | echo -n " | ||
+ | date | ||
+ | " | ||
+ | -o " | ||
+ | -p " | ||
+ | -c " | ||
+ | -r " | ||
+ | -x " | ||
+ | |||
+ | echo "done at" | ||
+ | date | ||
+ | cp -rf -- outputfiles_only " | ||
+ | rm -rf " | ||
+ | |||
+ | |||
+ | </ |