Difference between revisions of "Amber Job Sample Scripts"
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| Line 5: | Line 5: | ||
<source lang=bash> | <source lang=bash> | ||
#!/bin/bash | #!/bin/bash | ||
| − | #SBATCH --job-name=< | + | #SBATCH --job-name=<JOBNAME> |
| − | #SBATCH --mail-user=< | + | #SBATCH --mail-user=<EMAIL> |
#SBATCH --mail-type=FAIL,END | #SBATCH --mail-type=FAIL,END | ||
| − | #SBATCH --output < | + | #SBATCH --output <my_job-%j.out> |
| − | #SBATCH --error < | + | #SBATCH --error <my_job-%j.err> |
#SBATCH --nodes=1 | #SBATCH --nodes=1 | ||
#SBATCH --ntasks=1 | #SBATCH --ntasks=1 | ||
| − | #SBATCH --mem-per-cpu= | + | #SBATCH --mem-per-cpu=2G |
#SBATCH --time=01:00:00 | #SBATCH --time=01:00:00 | ||
| + | #SBATCH --account=<GROUP> | ||
| + | #SBATCH --array=<BEGIN-END> | ||
module load intel/2016.0.109 amber/14 | module load intel/2016.0.109 amber/14 | ||
| Line 29: | Line 31: | ||
<source lang=bash> | <source lang=bash> | ||
#!/bin/bash | #!/bin/bash | ||
| − | #SBATCH --job-name=< | + | #SBATCH --job-name=<JOBNAME> |
| − | #SBATCH --mail-user=< | + | #SBATCH --mail-user=<EMAIL> |
#SBATCH --mail-type=FAIL,END | #SBATCH --mail-type=FAIL,END | ||
| − | #SBATCH --output < | + | #SBATCH --output <my_job-%j.out> |
| − | #SBATCH --error < | + | #SBATCH --error <my_job-%j.err> |
#SBATCH --nodes=1 | #SBATCH --nodes=1 | ||
| − | #SBATCH --ntasks= | + | #SBATCH --ntasks=<number of tasks> |
| − | #SBATCH --mem-per-cpu= | + | #SBATCH --mem-per-cpu=2G |
#SBATCH --time=01:00:00 | #SBATCH --time=01:00:00 | ||
| + | #SBATCH --account=<GROUP> | ||
| + | #SBATCH --array=<BEGIN-END> | ||
module load intel/2016.0.109 openmpi/1.10.2 amber/14 | module load intel/2016.0.109 openmpi/1.10.2 amber/14 | ||
Revision as of 15:23, 19 July 2016
Serial Submission Script
The following job script runs sander on a single processor.
#!/bin/bash
#SBATCH --job-name=<JOBNAME>
#SBATCH --mail-user=<EMAIL>
#SBATCH --mail-type=FAIL,END
#SBATCH --output <my_job-%j.out>
#SBATCH --error <my_job-%j.err>
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=2G
#SBATCH --time=01:00:00
#SBATCH --account=<GROUP>
#SBATCH --array=<BEGIN-END>
module load intel/2016.0.109 amber/14
echo $PBS_O_WORKDIR
cd $PBS_O_WORKDIR
sander -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd
MPI Submission Script
The following job script runs sander.MPI on two nodes with four processors each.
#!/bin/bash
#SBATCH --job-name=<JOBNAME>
#SBATCH --mail-user=<EMAIL>
#SBATCH --mail-type=FAIL,END
#SBATCH --output <my_job-%j.out>
#SBATCH --error <my_job-%j.err>
#SBATCH --nodes=1
#SBATCH --ntasks=<number of tasks>
#SBATCH --mem-per-cpu=2G
#SBATCH --time=01:00:00
#SBATCH --account=<GROUP>
#SBATCH --array=<BEGIN-END>
module load intel/2016.0.109 openmpi/1.10.2 amber/14
echo $PBS_O_WORKDIR
cd $PBS_O_WORKDIR
mpiexec sander.MPI -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd