Updated 2019-06-26

Running ASE on the Cluster

Overview

  • ASE (Atomic Simulation Environment) is a set of tools and Python modules for setting up, steering, and anlyzing atomistic simulations.
  • This guide will cover how to run a Python script using ASE on the Cluster

Tips

  • The latest version of ASE that PACE offers is ase/3.9.1, so please be wary of what ASE modules you are using and whether they are a part of version 3.9.1.
  • You must load python/2.7 and intel/15.0 before trying to load ase/3.9.1.

Walkthrough: Run ASE on the Cluster

  • This walkthrough will run a Python 2 script that uses ASE to create and print the positions of 4 Ni atoms.
  • The Python script can be found here
  • PBS script can be found here
  • You can transfer the files to your account on the cluster to follow along. The file transfer guide may be helpful.

Part 1: The PBS Script

#PBS -N aseTest
#PBS -l nodes=1:ppn=2
#PBS -l pmem=2gb
#PBS -l walltime=3:00
#PBS -q force-6
#PBS -j oe
#PBS -o aseTest.out

cd $PBS_O_WORKDIR
module load python/2.7
module load intel/15.0
module load ase/3.9.1

python aseTest.py

  • The #PBS directives are standard, requesting just 3 minutes of walltime and 1 node with 2 cores. More on #PBS directives can be found in the PBS guide
  • $PBS_O_WORKDIR is a variable that represents the directory you submit the PBS script from. Make sure the files you want to use are in the same directory you put the PBS script.
  • Output Files will also show up in this dir as well
  • module load ase/3.9.1 loads the 3.9.1 version of ASE. To see what ASE versions are available, run module avail ase, and load the one you want. The other module are dependencies that must be loaded before ASE is loaded.
  • python aseTest.py runs the Python 2 script using ASE. Make sure that the only version of Python loaded is Python 2 or else you will recieve errors about the syntax of the aseTest.py script.

Part 2: Submit Job and Check Status

  • Be sure to change to the directory that contains the PBS Script
  • qsub aseTest.pbs
  • Check job status with qstat -t <jobid>, replacing the number with the job id returned after running qsub
  • You can delete the job with qdel <jobid> , again replacing the number with the jobid returned after running qsub

Part 3: Collecting Results

  • In the directory where you submitted the PBS script, you should see a aseTest.out file, which contains the results of the job. Use cat aseTest.out or open the file in a text editor to take a look.
  • aseTest.out should look like this:
---------------------------------------
Begin PBS Prologue Wed Jun 19 15:50:26 EDT 2019
Job ID:     26094907.shared-sched.pace.gatech.edu
User ID:    svemuri8
Job name:   aseTest
Queue:      force-6
End PBS Prologue Wed Jun 19 15:50:26 EDT 2019
---------------------------------------
Atom('Ni', [0.0, 0.0, 0.0], index=0)
Atom('Ni', [0.5, 0.0, 0.0], index=1)
Atom('Ni', [0.0, 0.5, 0.0], index=2)
Atom('Ni', [0.5, 0.5, 0.0], index=3)
[[ 0.   0.   0. ]
 [ 0.5  0.   0. ]
 [ 0.   0.5  0. ]
 [ 0.5  0.5  0. ]]
[[ 0.   0.   0. ]
 [ 0.6  0.   0. ]
 [ 0.   0.5  0. ]
 [ 0.5  0.5  0. ]]
[[ 1.  0.  0.]
 [ 0.  1.  0.]
 [ 0.  0.  1.]]
---------------------------------------
Begin PBS Epilogue Wed Jun 19 15:50:27 EDT 2019
Job ID:     26094907.shared-sched.pace.gatech.edu
User ID:    svemuri8
Job name:   aseTest
Resources:  neednodes=1:ppn=2,nodes=1:ppn=2,pmem=2gb,walltime=00:03:00
Rsrc Used:  cput=00:00:00,energy_used=0,mem=0kb,vmem=0kb,walltime=00:00:01
Queue:      force-6
Nodes:
iw-h43-9.pace.gatech.edu
End PBS Epilogue Wed Jun 19 15:50:27 EDT 2019
---------------------------------------
  • After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
  • Congratulations! You successfully ran a Python script using ASE on the cluster.