Job submission to run Amber PMEMD.cuda on GPU node on Spruce:
#!/bin/bash
#PBS -q jbmertz_gpu
#PBS -m ae
#PBS -M [YOUR EMAIL HERE] #change
#PBS -N [YOUR JOB NAME HERE] #change
#PBS -l walltime=3999:00:00 #change
#PBS -l gpus=1
module load chemistry/amber14
GPUSLOT=$(cat $PBS_GPUFILE | tail -c 2)
export CUDA_VISIBLE_DEVICES="$GPUSLOT"
scratch=/scratch/jufeng/bpr-run1 #change
cd $scratch
pmemd.cuda ....# your job command
#!/bin/bash
#PBS -q jbmertz_gpu
#PBS -m ae
#PBS -M [YOUR EMAIL HERE] #change
#PBS -N [YOUR JOB NAME HERE] #change
#PBS -l walltime=3999:00:00 #change
#PBS -l gpus=1
module load chemistry/amber14
GPUSLOT=$(cat $PBS_GPUFILE | tail -c 2)
export CUDA_VISIBLE_DEVICES="$GPUSLOT"
scratch=/scratch/jufeng/bpr-run1 #change
cd $scratch
pmemd.cuda ....# your job command
Job submission to run Gromacs on Spruce:
#!/bin/bash
#PBS -q jbmertz
#PBS -m ae
#PBS -M [xx] # ur email address here
#PBS -N [xx] # put ur job name here
#PBS -l walltime=99:00:00 #change according to how long ur job is
#PBS -l nodes=1:ppn=16 #change according to how many cores u want to request
module load chemistry/gromacs/5.0.5
cd xx #go to directory where u want to run ur job
mdrun_mpi -s top13.tpr # change according to ur gromacs command
#!/bin/bash
#PBS -q jbmertz
#PBS -m ae
#PBS -M [xx] # ur email address here
#PBS -N [xx] # put ur job name here
#PBS -l walltime=99:00:00 #change according to how long ur job is
#PBS -l nodes=1:ppn=16 #change according to how many cores u want to request
module load chemistry/gromacs/5.0.5
cd xx #go to directory where u want to run ur job
mdrun_mpi -s top13.tpr # change according to ur gromacs command
