SLURM Submit script example
For more configuration options use the Job Script Generator.
amber_example.slm
#!/bin/bash #SBATCH -J amber_example #SBATCH -e amber_example.err #SBATCH -o amber_example.out #SBATCH -p std #SBATCH --nodes=1 #SBATCH --ntasks=1 module load apps/amber/14 INPUT_DIR=$PWD OUTPUT_DIR=$PWD cd $SCRATCH cp -r $INPUT_DIR/* $SCRATCH mpirun -np $SLURM_NTASKS pmemd.MPI -O \ -i amber_example.inp \ -p amber_example.top \ -c amber_example.crd \ -o amber_example.out cp ./* $OUTPUT_DIR
Sbatch options:
- -J: Specify a name for the job allocation. The default is the name of the batch script.
- -e: Specify a name for the error output file.
- -o: Specify a name for the output file.
- -p: Specify the name of the partition (queue) where the job will be submited. The default is std.
- --nodes: Number of nodes requested for allocation.
- --ntasks: Number of processes requested for allocation.
- --mem-per-cpu: Memory allocated per core.
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.