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logiciels:amber

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Prochaine révision 		Révision précédente
logiciels:amber [2016/06/10 15:01]
164.81.157.90 		logiciels:amber [2016/06/10 15:08] (Version actuelle)
164.81.157.90
Ligne 38: Ligne 38:
  
 ==== Serial ==== ==== Serial ====
-<konsole> 
  
-#!/bin/bash 
  
-#SBATCH --nodes=1 +  #!/bin/bash 
-#SBATCH --ntasks=1 +  #SBATCH --nodes=1 
-#SBATCH --time=02:00:00 +  #SBATCH --ntasks=1 
-#SBATCH --partition=normal +  #SBATCH --time=02:00:00 
-#SBATCH --cpus-per-task=1 +  #SBATCH --partition=normal 
-#SBATCH --mem-per-cpu=2000+  #SBATCH --cpus-per-task=1 
 +  #SBATCH --mem-per-cpu=2000  
 +  topname=del 
 +  crdname=del 
 +  CURR=$(pwd) 
 +  RESTART=YES 
 +  STEP=0 
 +  FINAL=1 
 +  module load amber/16-patched-10062016 
 +  # MD are performed in Scratch  
 +  # Export running directectory 
 +  export RUN_DIR="${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 -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
  
-topname=del +==== MPI ====
-crdname=del +
-CURR=$(pwd) +
-RESTART=YES +
-STEP=0 +
-FINAL=1+
  
-module load amber/16-patched-10062016+  #!/bin/bash 
 +  #SBATCH --nodes=1-X 
 +  #SBATCH --ntasks=X 
 +  #SBATCH --time=XX:00:00 
 +  #SBATCH --partition=normal 
 +  #SBATCH --cpus-per-task=1 
 +  #SBATCH --mem-per-cpu=XXX  
 +  topname=del 
 +  crdname=del 
 +  CURR=$(pwd) 
 +  RESTART=YES 
 +  STEP=0 
 +  FINAL=1 
 +  module load amber/16-patched-10062016 
 +  # MD are performed in Scratch  
 +  # Export running directectory 
 +  export RUN_DIR="${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 
 +      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
  
-# MD are performed in Scratch  +==== GPU ====
-# 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 -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 +
-</konsole>+
  
 +  #!/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
 +      rm -rf ${crdname}_${j}.mdcrd
 +  done
  
logiciels/amber.1465563676.txt.gz · Dernière modification: 2016/06/10 15:01 de 164.81.157.90

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