Lammps

In progress. don't rely on this yet for GPU - CPU should be OK.

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator

LAMMPS was compiled using Intel 2013 compilers and the CUDA 6.5 libraries.

The following instructions are for running the LAMMPS in parallel on kong using cpu and gpu.

Create a directory for this run:

<pre=code>mkdir lammps_test cd lammps_test</pre>

Get an example lammps input file: <pre=code>cp /afs/cad/linux/lammps/30Jul16/lammps-30Jul16/bench/in.lj .</pre>

Edit the submit script as directed: <pre=code>

1. !/bin/bash
3. EXAMPLE LAMMPS PARALLEL SCRIPT FOR SGE
4. lammps_submit.sh
5. To use, change all of the following to real values:
6. JOB_NAME, QUEUE, UCID, NUMBER_OF_CPUS
8. Please see https://wiki.hpc.arcs.njit.edu/ for additional information.
10. Modified by Basement Supercomputing 1/2/2006 DJE
11. Modified for NJIT - AM 18Apr06
12. Updated for modules, QRSH_PORT, additional documentation. 31-Aug-2015 /KJW
13. Updated for LAMMPS 28-Sep-2016/GW
15. Change JOB_NAME to a one-word alphanumeric description. This will be used for
16. part of output file name and in status listings.
17. $ -N JOB_NAME

2. Change QUEUE to a valid queue. On kong this would be one of "short",
3. "medium", "long, or gpu." See https://wiki.hpc.arcs.njit.edu/index.php/KongQueues
4. To run on GPU you mus use the gpu queue
5. or https://wiki.hpc.arcs.njit.edu/index.php/SthenoQueues for more info
6. $ -q QUEUE

2. Send email when jobs starts and again when it finishes or if it aborts.
3. $ -M UCID@njit.edu
4. $ -m abe

2. Use current working directory where "qsub" was invoked.
3. $ -cwd

2. Join stdout and stderr
3. $ -j y

2. Set your number of processors here by changing NUMBER_OF_CPUS to an integer
3. value.
5. LAMMPS uses the intel mpich2 MPI
6. Do not select more than 16 CPUS if using the GPU node
7. $ -pe mpich2 NUMBER_OF_CPUS

2. Uncomment to request one gpu (max two)
3. Note that uncomment means to remove the first "#" and leave "#$."
   2. $ -l gpu=1

2. Run job through bash shell
3. $ -S /bin/bash

2. Load the correct lammps module.
3. Uncomment the one to use.
4. module load lammps/cpu/30Jul16
5. module load lammps/gpu/30Jul16

2. The following are for reporting only and not really needed to run the job;
3. their results will show up in your output file.

echo "Got $NSLOTS processors." echo "cwd=$(pwd)"

2. For CPU uncomment the following.
3. mpirun -np $NSLOTS lmp_intel_cpu_intelmpi -v x 16 -v y 16 -v z 16 -v t 100 < in.lj

2. For GPU uncomment the following.
3. mpirun -np $NSLOTS lmp_intel_cpu_intelmpi -sf gpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj

</pre>

Submit the script: <pre=code>qsub lammps_submit.sh</pre>