Ci-dessous, les différences entre deux révisions de la page.
Prochaine révision | Révision précédente | ||
faq:chimie:namd [2018/07/23 13:43] – créée tjiang | faq:chimie:namd [2022/03/03 16:30] (Version actuelle) – [Submission script NAMD] tjiang | ||
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====== NAMD ====== | ====== NAMD ====== | ||
+ | ===== Submission script NAMD ===== | ||
+ | <code bash sub_namd.sh> | ||
+ | #!/bin/bash | ||
+ | #$ -S /bin/bash | ||
+ | #$ -N mutm_ap-oxog | ||
+ | #$ -q E5-2670gpuK20deb128 | ||
+ | #$ -pe mpi_debian 16 | ||
+ | #$ -cwd | ||
+ | #$ -V | ||
+ | # Loading modules to set up environment | ||
+ | module load NAMD/ | ||
+ | |||
+ | # Setting up home and scratch directories | ||
+ | HOMEDIR=" | ||
+ | cd " | ||
+ | |||
+ | if [[ -d "/ | ||
+ | then | ||
+ | SCRATCHDIR="/ | ||
+ | elif [[ -d "/ | ||
+ | then | ||
+ | SCRATCHDIR="/ | ||
+ | elif [[ -d "/ | ||
+ | then | ||
+ | SCRATCHDIR="/ | ||
+ | |||
+ | else | ||
+ | echo "/ | ||
+ | exit 1 | ||
+ | fi | ||
+ | |||
+ | echo " | ||
+ | /bin/mkdir -p " | ||
+ | HOSTFILE=" | ||
+ | cp " | ||
+ | sed -i -e ' | ||
+ | |||
+ | # Please provide the following files for namd | ||
+ | CONFIGFILE=" | ||
+ | TOPFILE=" | ||
+ | PDBFILE=" | ||
+ | FIXFILE=" | ||
+ | COLVARSFILE=" | ||
+ | LOGFILE=" | ||
+ | |||
+ | # Copying files to scratchdir | ||
+ | rsync -c " | ||
+ | |||
+ | # The executables for mpirun and namd2 | ||
+ | MPIRUN=" | ||
+ | |||
+ | # Go to scratch directory and run calculation there | ||
+ | cd " | ||
+ | echo 'group main ++shell ssh' > nodelist | ||
+ | cat machines >> nodelist | ||
+ | |||
+ | namd2 +idlepoll +p " | ||
+ | |||
+ | # Copy back data | ||
+ | rsync -c --exclude " | ||
+ | cd " | ||
+ | |||
+ | # Cleaning up scratch directory and hostfile | ||
+ | rm -fr " | ||
+ | |||
+ | </ |