AMBER job submission

Here is the job submission script for MD simulation on compute node.

#!/bin/bash -l
#SBATCH --partition=compute             # specific partition to compute node
#SBATCH -N 1 --ntasks-per-node=40       # for requset 1 compute node with 40 cpu-cores
#SBATCH --time=120:00:00                # job time limit <hr:min:sec>
#SBATCH --account=projXXXX              # change projXXXX  to your project account
#SBATCH --job-name=testMD

module purge                            # purge all module
module load bzip2/1.0.8-GCCcore-8.3.0
module load XZ/5.2.4-GCCcore-8.3.0
module load GCC/8.3.0
module load OpenMPI/3.1.4-GCC-8.3.0

WORKDIR=$SLURM_SUBMIT_DIR
######################################################
# nothing should need changed below here to run unless you do not
export AMBER_PREFIX="/tarafs/data/project/proj0XXXX/amber20_src"
export AMBERHOME=/tarafs/data/project/proj0XXXX/amber20_src
export PATH="${AMBER_PREFIX}/bin:${PATH}"

# Add location of Amber Python modules to default Python search path
if [ -z "$PYTHONPATH" ]; then
    export PYTHONPATH="${AMBER_PREFIX}/lib/python2.7/site-packages"
else
    export PYTHONPATH="${AMBER_PREFIX}/lib/python2.7/site-packages:${PYTHONPATH}"
fi
if [ -z "${LD_LIBRARY_PATH}" ]; then
   export LD_LIBRARY_PATH="${AMBER_PREFIX}/lib"
else
   export LD_LIBRARY_PATH="${AMBER_PREFIX}/lib:${LD_LIBRARY_PATH}"
fi

######################################################
cd $WORKDIR

srun pmemd.MPI -O -i input.in -o md.out -p system.top -c md_2.restrt -ref md_2.restrt -r md_1.restrt -x md_1.nc -v mdvel

Here is the job submission script for MD simulation on GPU node.

#!/bin/bash -l
#SBATCH --partition=compute             # specific partition to compute node
#SBATCH -N 1 --ntasks-per-node=40       # for requset 1 compute node with 40 cpu-cores
#SBATCH --time=120:00:00                # job time limit <hr:min:sec>
#SBATCH --account=projXXXX              # change projXXXX  to your project account
#SBATCH --job-name=testMD

module purge                            # purge all module
module load bzip2/1.0.8-GCCcore-8.3.0
module load XZ/5.2.4-GCCcore-8.3.0
module load CUDA/10.1.243-GCC-8.3.0
module load gcccuda/2019b
module load OpenMPI/3.1.4-gcccuda-2019b

WORKDIR=$SLURM_SUBMIT_DIR
######################################################
# nothing should need changed below here to run unless you do not
export AMBER_PREFIX="/tarafs/data/project/proj0XXXX/amber20_src"
export AMBERHOME=/tarafs/data/project/proj0XXXX/amber20_src
export PATH="${AMBER_PREFIX}/bin:${PATH}"

# Add location of Amber Python modules to default Python search path
if [ -z "$PYTHONPATH" ]; then
    export PYTHONPATH="${AMBER_PREFIX}/lib/python2.7/site-packages"
else
    export PYTHONPATH="${AMBER_PREFIX}/lib/python2.7/site-packages:${PYTHONPATH}"
fi
if [ -z "${LD_LIBRARY_PATH}" ]; then
   export LD_LIBRARY_PATH="${AMBER_PREFIX}/lib"
else
   export LD_LIBRARY_PATH="${AMBER_PREFIX}/lib:${LD_LIBRARY_PATH}"
fi

######################################################
cd $WORKDIR

srun pmemd.cuda.MPI -O -i input.in -o md.out -p system.top -c md_2.restrt -ref md_2.restrt -r md_1.restrt -x md_1.nc -v mdvel

Here is the job submission script for Trajectory analysis on compute node.

#!/bin/bash -l
#SBATCH --partition=devel               # specific partition to compute node
#SBATCH --nodes=1 --ntasks-per-node=1   # for requset 1 compute node with 1 cpu-core
#SBATCH --account=projXXXX              # change projXXXX  to your project account
#SBATCH --time=2:00:00                  # job time limit <hr:min:sec>
#SBATCH --account=projXXXX              # change projXXXX  to your project account
#SBATCH --job-name=mmpbsa

module purge                            # purge all module
module load bzip2/1.0.8-GCCcore-8.3.0
module load XZ/5.2.4-GCCcore-8.3.0
module load GCC/8.3.0
module load OpenMPI/3.1.4-GCC-8.3.0

WORKDIR=$SLURM_SUBMIT_DIR
######################################################
# nothing should need changed below here to run unless you do not
export AMBER_PREFIX="/tarafs/data/project/proj0XXXX/amber20_src"
export AMBERHOME=/tarafs/data/project/proj0XXXX/amber20_src
export PATH="${AMBER_PREFIX}/bin:${PATH}"

# Add location of Amber Python modules to default Python search path
if [ -z "$PYTHONPATH" ]; then
    export PYTHONPATH="${AMBER_PREFIX}/lib/python2.7/site-packages"
else
    export PYTHONPATH="${AMBER_PREFIX}/lib/python2.7/site-packages:${PYTHONPATH}"
fi
if [ -z "${LD_LIBRARY_PATH}" ]; then
   export LD_LIBRARY_PATH="${AMBER_PREFIX}/lib"
else
   export LD_LIBRARY_PATH="${AMBER_PREFIX}/lib:${LD_LIBRARY_PATH}"
fi

######################################################
cd $WORKDIR

cpptraj -i  rmsd.in   >  rmsd.out

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