Difference between revisions of "LAMMPS Guide"
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'''mkdir lammpstest''' && ls
'''mkdir lammpstest''' && ls
Revision as of 09:25, 14 September 2015
|LAMMPS Molecular Dynamics Simulator|
|Author||Sandia National Labs and Temple University|
LAMMPS is a program for simulating large scale atomic / molecular dynamics leveraging parallel hardware.
- 1 Loading / Unloading LAMMPS module
- 2 Running a LAMMPS job in the Hornet Cluster
Loading / Unloading LAMMPS module
Check Module Availability
To see which LAMMPS modules are available to the system, use the following command:
$ module avail lammps
You should see all available modules in
----------------------- /apps2/Modules/3.2.6/modulefiles ----------------------- lammps/1Feb14 lammps/23Sep13 lammps/28Jun14 lammps/28Jun14MoS2
If the module list is empty please contact your administrators.
Loading a LAMMPS Module
You can load the default LAMMPS module as follows:
$ module load lammps
To see which version is being used, do the following:
$ which lammps /apps2/lammps/28Jun14MoS2/bin/lammps
If your program needs a specific versin e.g.,
lammps/28Jun14, do the following:
$ module load lammps/28Jun14
After you load a module you can use it until you log out; you will need to load it again the next time you log in and run your program.
Automatically Loading a LAMMPS Module
If you frequently use a particular module (which is usual) you can do the following:
$ module initadd lammps
Or, if you need a specific version,
$ module initadd lammps/28Jun14
Note that this auto-loading of the module will start from your next login session. Therefore if you need the module at the present session you will need to load the module using the
module load command.
Unloading a LAMMPS Module
You can unload an already-loaded module as follows:
$ module unload lammps
Or, to unload a specific version,
$ module unload lammps/28Jun14
To make sure that a module is unloaded, use the command
which lammps which should say
/usr/bin/which: no lammps in ...
Running a LAMMPS job in the Hornet Cluster
If possible, you should always first run your code in your local machine just to ensure that your code is correct. You can do it on a small dataset and a small configuration (single processor, etc.). This way you would be able to catch any errors not related to the cluster even before submitting your job.
Below we show a step by step example on how to run a simple LAMMPS simulation in the cluster. We have used one of the examples bundled with LAMMPS distribution, namely
Copy your code and data into the cluster
We are assuming that you are using the terminal to copy your data. If you are using a GUI client such as  you should be able to do it in a visual way.
Open a terminal to connect to the cluster and create a directory for the experiment.
$ mkdir lammpstest && ls lammpstest
Our code / data is located in the directory
~/Downloads/lammps-10Aug15/examples/flow in the local machine.
$ ls ~/Downloads/lammps-10Aug15/examples/flow in.flow.couette log.15May15.flow.couette.g++.1 log.15May15.flow.pois.g++.1 in.flow.pois log.15May15.flow.couette.g++.4 log.15May15.flow.pois.g++.4
Let us copy everything in this folder to the cluster using the  command. Because we are using secure protocol you will be asked for your the password of your cluster account. In the snippet below remember to replace the word hronetuser with your actual account name.
$ cd ~/Downloads/lammps-10Aug15/examples $ ls | grep flow flow $ scp -r flow firstname.lastname@example.org:~/lammpstest/flow in.flow.pois 100% 1503 1.5KB/s 00:00 in.flow.couette 100% 1505 1.5KB/s 00:00 log.15May15.flow.couette.g++.1 100% 4559 4.5KB/s 00:00 log.15May15.flow.pois.g++.4 100% 4561 4.5KB/s 00:00 log.15May15.flow.pois.g++.1 100% 4559 4.5KB/s 00:00 log.15May15.flow.couette.g++.4 100% 4560 4.5KB/s 00:00
-r switch tells the
scp command to copy everything recursively. You can of course selectively copy the files you need by omitting this switch. See the manual for
scp for details.
Now let's make sure our files are copied to the cluster. For this we switch back to the cluster's terminal and do the following:
$ ls ~/lammpstest flow $ cd ~/lammpstest/flow && ls in.flow.couette log.15May15.flow.couette.g++.1 log.15May15.flow.pois.g++.1 in.flow.pois log.15May15.flow.couette.g++.4 log.15May15.flow.pois.g++.4
Create a SLURM script to run your job
SLURM is the scheduler program for our cluster. In the cluster we need to create a simple script which would tell
SLURM how to run your job. For details see the SLURM Guide.
You can either create this script in the terminal using any editor such as
nano, or you can create it in your local machine and use the
scp command to copy it into the cluster. We can put this script in the
lammpstest directory, and it would contain the following lines:
$ cd ~/lammpstest $ cat lammps_job.sh #!/bin/bash #SBATCH -n2 #SBATCH -o ~/lammpstest/lammps_sim_out.txt #SBATCH -e ~/lammpstest/lammps_sim_out.txt #SBATCH --mail-type=ALL #SBATCH --email@example.com
lammps < ~/lammpstest/flow/in.flow.couette
This script is telling how many processors we need as well as which files the output (and errors) should be written to. Basically, the lines starting with
#SBATCH provide the switches for the  command, which submits a job to
SLURM. Note that we have told
SLURM to email us at every event for this job such as begin / queued / end / error etc.
The last line is the command that would be run as the job. It invokes the
lammps module with the input
Submitting your job
Before you submit your job make sure that the
LAMMPS module is loaded, as described at the first part of this guide. When you are ready, simple do the following:
$ sbatch < ~/lammpstest/lammps_job.sh Submitted batch job 24703
When the job is done we would get email notifications. You can also check your job status using the
bjobs command. If we check the directory where we expect the output we would see the following:
$ ls -l ~/lammpstest total 64 drwxr-xr-x 2 hpc-saad hpc-saad 512 Sep 10 15:43 flow -rw-rw-r-- 1 hpc-saad hpc-saad 186 Sep 14 09:11 lammps_job.sh -rw-rw-r-- 1 hpc-saad hpc-saad 3064 Sep 14 09:16 lammps_sim_out.txt -rw-rw-r-- 1 hpc-saad hpc-saad 4419 Sep 14 09:16 log.lammps