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SLURM Submit script example
More information about the submit script can be found using the Job Script Generator.
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#!/bin/bash
#SBATCH -J amber_example
#SBATCH -e amber_example.%j.err
#SBATCH -o amber_example.%j.out
#SBATCH -p std
#SBATCH -n 1
#SBATCH -t 0-02:00
module load apps/amber/18
##
# Modify the input and output files!
cp -r ${SLURM_SUBMIT_DIR}/{*.inp,*.top,*.crd} ${SCRATCH}
cd ${SCRATCH}
srun pmemd.MPI -O \
-i amber_example.inp \
-p amber_example.top \
-c amber_example.crd \
-o amber_example.out
cp ./*.out ${SLURM_SUBMIT_DIR} |
Sbatch options:
The options shown in the example are detailed below. For more information and a more comprehensive list of available options, see the sbatch command page.
- -J: Name for the job's allocation.
- -e: Name of the sterr redirection filename.
- -o: Name of the stdout redirection filename.
- -p: Name of the partition (queue) where the job will be submited.
-n: Number of tasks.
- -t: Set the job's time limit. If the job don't finish before the time runs out, it will be killed.
Software execution information:
The pmemd program is the comercial-high-performance version of sander, general purpose MD engine of Amber. Here is a summary of the command line options for them:
- -O: Overwrite output files if they exist.
- -A: Append output files if they exist.
- -i: Input file. Default input name: mdin.
- Contains control data for the min/md run.
- -p: Input file. Default input name: prmtop.
- Contains molecular topology, force field, periodic box type, atom and residue names.
- -c: Input file. Default input name: inpcrd.
- Contains initial coordinates and (optionally) velocities and periodic box size.
- -r: Output structure file. Default input name: restrt.
- Contains final coordinates, velocity, and box dimensions for restarting run.
- -o: Output energy file. Default input name: mdout.
- Contains user readable state info and diagnostics.
- -o stdout will send output to stdout (to the terminal) instead of to a file.
- -x: Output energy file. Default input name: mdcrd.
- Contains coordinate sets saved over trajectory.
- -e: Output energy file. Default input name: mden.
- Contains extensive energy data over trajectory (not synchronized with mdcrd or mdvel).
- -inf: Output energy file. Default input name: mdinfo.
- Latest mdout-format energy info.