Différences

Ci-dessous, les différences entre deux révisions de la page.

--- logiciels:amber [2016/06/10 15:05]
164.81.157.90
+++ logiciels:amber [2016/06/10 15:08] (Version actuelle)
164.81.157.90
@@ Ligne 89: / Ligne 89: @@
   #!/bin/bash
-  **#SBATCH --nodes=1-X**
+  #SBATCH --nodes=1-X
-  **#SBATCH --ntasks=X**
+  #SBATCH --ntasks=X
-  **#SBATCH --time=XX:00:00**
+  #SBATCH --time=XX:00:00
   #SBATCH --partition=normal
   #SBATCH --cpus-per-task=1
@@ Ligne 128: / Ligne 128: @@
       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
+      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=02:00:00
+  #SBATCH --partition=gpu
+  #SBATCH --cpus-per-task=1
+  #SBATCH --gres=gpu
+  topname=del
+  crdname=del
+  CURR=$(pwd)
+  RESTART=YES
+  STEP=0
+  FINAL=1
+  module load amber/16-patched-10062016
+  module load nvidia/cuda/7.5
+  # MD are performed in Scratch
+  # Export running directectory
+  export RUN_DIR="${HOME}/scratch/Amber/run.${SLURM_JOB_ID}.amber16.${topname}"
+  # 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 = 'YES' ]; then
+      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

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