Outils pour utilisateurs
logiciels:amber
Différences
Ci-dessous, les différences entre deux révisions de la page.
| Les deux révisions précédentes Révision précédente Prochaine révision | Révision précédente | ||
|
logiciels:amber [2016/06/10 15:03] 164.81.157.90 |
logiciels:amber [2016/06/10 15:08] (Version actuelle) 164.81.157.90 |
||
|---|---|---|---|
| Ligne 86: | Ligne 86: | ||
| done | done | ||
| + | ==== MPI ==== | ||
| + | #!/bin/bash | ||
| + | #SBATCH --nodes=1-X | ||
| + | #SBATCH --ntasks=X | ||
| + | #SBATCH --time=XX: | ||
| + | #SBATCH --partition=normal | ||
| + | #SBATCH --cpus-per-task=1 | ||
| + | #SBATCH --mem-per-cpu=XXX | ||
| + | topname=del | ||
| + | crdname=del | ||
| + | CURR=$(pwd) | ||
| + | RESTART=YES | ||
| + | STEP=0 | ||
| + | FINAL=1 | ||
| + | module load amber/ | ||
| + | # MD are performed in Scratch | ||
| + | # Export running directectory | ||
| + | export RUN_DIR=" | ||
| + | # Link the scratch directory to the current directory | ||
| + | # Link name is related to JOB ID and NOT TO JOBNAME --> Prevent issues related to new MDs with same name | ||
| + | ln -sfn ${RUN_DIR} ${SLURM_JOB_ID}.results | ||
| + | echo ${RUN_DIR} | ||
| + | # Create Scratch directory | ||
| + | mkdir -p ${RUN_DIR} | ||
| + | # Copy Topology and CRD names into Scratch directory | ||
| + | cp ${topname}.prmtop *.in ${RUN_DIR} | ||
| + | # Copy starting CRD files according to restart procedure or not | ||
| + | if [ $RESTART = ' | ||
| + | cp ${topname}_md${STEP}.rst ${RUN_DIR}/ | ||
| + | else | ||
| + | STEP=0 | ||
| + | cp ${topname}.inpcrd ${RUN_DIR}/ | ||
| + | fi | ||
| + | # Enter into Scratch directory | ||
| + | cd ${RUN_DIR} | ||
| + | # Run calculation | ||
| + | # Keep in mind: Never run a long MD into a single trajectory file - Split it into several trajectories | ||
| + | for i in `seq $STEP 1 $FINAL` | ||
| + | do | ||
| + | j=$(( $i + 1 )) | ||
| + | # Run MD | ||
| + | srun premed.MPI -O -i md.in -o ${crdname}_md${j}.out -p $topname.prmtop -c ${crdname}_md${i}.rst -r ${crdname}_md${j}.rst -x ${crdname}_${j}.mdcrd | ||
| + | # Compress mdcrd file to prevent storage issues and remove the uncompressed trajectory | ||
| + | tar -zcvf ${crdname}_${j}.mdcrd.tar.gz ${crdname}_${j}.mdcrd | ||
| + | rm -rf ${crdname}_${j}.mdcrd | ||
| + | done | ||
| + | |||
| + | ==== GPU ==== | ||
| + | |||
| + | #!/bin/bash | ||
| + | #SBATCH --nodes=1 | ||
| + | #SBATCH --time=02: | ||
| + | #SBATCH --partition=gpu | ||
| + | #SBATCH --cpus-per-task=1 | ||
| + | #SBATCH --gres=gpu | ||
| + | topname=del | ||
| + | crdname=del | ||
| + | CURR=$(pwd) | ||
| + | RESTART=YES | ||
| + | STEP=0 | ||
| + | FINAL=1 | ||
| + | module load amber/ | ||
| + | module load nvidia/ | ||
| + | # MD are performed in Scratch | ||
| + | # Export running directectory | ||
| + | export RUN_DIR=" | ||
| + | # Link the scratch directory to the current directory | ||
| + | # Link name is related to JOB ID and NOT TO JOBNAME --> Prevent issues related to new MDs with same name | ||
| + | ln -sfn ${RUN_DIR} ${SLURM_JOB_ID}.results | ||
| + | echo ${RUN_DIR} | ||
| + | # Create Scratch directory | ||
| + | mkdir -p ${RUN_DIR} | ||
| + | # Copy Topology and CRD names into Scratch directory | ||
| + | cp ${topname}.prmtop *.in ${RUN_DIR} | ||
| + | # Copy starting CRD files according to restart procedure or not | ||
| + | if [ $RESTART = ' | ||
| + | cp ${topname}_md${STEP}.rst ${RUN_DIR}/ | ||
| + | else | ||
| + | STEP=0 | ||
| + | cp ${topname}.inpcrd ${RUN_DIR}/ | ||
| + | fi | ||
| + | # Enter into Scratch directory | ||
| + | cd ${RUN_DIR} | ||
| + | # Run calculation | ||
| + | # Keep in mind: Never run a long MD into a single trajectory file - Split it into several trajectories | ||
| + | for i in `seq $STEP 1 $FINAL` | ||
| + | do | ||
| + | j=$(( $i + 1 )) | ||
| + | # Run MD | ||
| + | pmemd.cuda -O -i md.in -o ${crdname}_md${j}.out -p $topname.prmtop -c ${crdname}_md${i}.rst -r ${crdname}_md${j}.rst -x ${crdname}_${j}.mdcrd | ||
| + | # Compress mdcrd file to prevent storage issues and remove the uncompressed trajectory | ||
| + | tar -zcvf ${crdname}_${j}.mdcrd.tar.gz ${crdname}_${j}.mdcrd | ||
| + | rm -rf ${crdname}_${j}.mdcrd | ||
| + | done | ||
logiciels/amber.1465563838.txt.gz · Dernière modification: 2016/06/10 15:03 de 164.81.157.90
Outils de la page
Sauf mention contraire, le contenu de ce wiki est placé sous les termes de la licence suivante : CC Attribution-Share Alike 4.0 International
