Updated 2021-05-17
Run LAMMPS on the Cluster¶
Summary¶
- Use
module avail lammps
to see all available versions of LAMMPS on the cluster. - To load LAMMPS in your
PBS
script:module load lammps/22Aug18
. Replace the date with the version you want to load.
- To run LAMMPS:
- In your
PBS
script, put all the lines to execute LAMMPS after themodule load
lines that load LAMMPS
- In your
Warning
If using mpirun
to execute LAMMPS, you must set the number of processors to the number you requested in your PBS
script. Example: if you requested 8 nodes (2 nodes and 4 proc. per node), you would set the -np
option as -np 8
Example PBS Script¶
#PBS -N lammpsTest
#PBS -A [Account]
#PBS -l nodes=2:ppn=4
#PBS -l walltime=10:00
#PBS -q inferno
#PBS -j oe
#PBS -o lammpsResult.out
cd $PBS_O_WORKDIR
module load lammps/22Aug18
mpirun -np 8 lmp < filename.in
- The
#PBS
directives are standard, requesting 10 min of walltime and 2 nodes with 4 cores per node. More on#PBS
directives can be found in the PBS guide $PBS_O_WORKDIR
is simply a variable that represents the folder you submit the PBS script from. Make sure the.in
file, and any other files you need are in the same directory you put thePBS
script in. This line tells the cluster to enter this directory where you have stored thePBS
script, and look for all the files for the job. If you use$PBS_O_WORKDIR
, you need to have all your files in the same folder as yourPBS
script otherwise the cluster won't be able to find the files it needs.- Output Files, such as the
lammps.log
file will also show up in the same folder as thePBS
script - The
module load
lines loads LAMMPS mpirun -np 8 lmp < filename.in
executes LAMMPS with a.in
file. Note, this is just a general example line, and there are many more options to run LAMMPS. For more options, check out the LAMMPS documentation.- The point with the example line is to show how the
-np
flag is used. Here, 8 processors are specified after-np
, as 8 processors were requested (2 nodes x 4 proc per node)
Submit Job and Check Status¶
- Make sure you're in the directory that contains the
PBS
script, the sequence files, and any other files you need. - Submit as normal, with
qsub <pbs script name>
. In this caseqsub lammps.pbs
or whatever you called thePBS
script. You can name thePBS
scripts whatever you want, just keep the.pbs
at the end - Check job status with
qstat -u username3 -n
, replacing "username3" with your gt username - You can delete the job with
qdel 22182721
, replacing the number with the jobid returned after running qsub - Depending on the resources requested and queue the job is run on, it may take varying amounts of time for the job to start. To estimate the time until the job executes, run
showstart 22182721
, replacing the number with the jobid returned after running qsub. More helpful commands can be found in this guide
Collecting Results¶
- All files created will be in the same folder where your
PBS
script is (same directory you ranqsub
from) - The
.out
file will be found here as well. It contains the results of the job, as well as diagnostics and a report of resources used during the job. If the job fails or doesn't produce the result your were hoping for, the.out
file is a great debugging tool. - You can transfer the resulting files off the cluster using scp or a file transfer service