Thursday Exercise 1.3: Try an OSG Connect Software Module

In this exercise, you'll use a software package called GROMACS that was already installed on OASIS. GROMACS is a molecular dynamics simulation program.

Setup

Make sure you are logged into training.osgconnect.net (the OSG Connect submit server for this workshop).

Practice loading the GROMACS module on OSG Connect submit host

Before proceeding, make sure to read over the OSG Connect help desk guide on Accessing Software using Distributed Environment Modules.

  1. Run the module avail command to see available modules and determine which gromacs version will be the default (designated by a (D)).

  2. Before loading the gromacs module, check your "PATH" variable with:

[email protected] $ echo $PATH
  1. Now load the gromacs module, which will give you the default version, and check your list of modules:
[email protected] $ module load gromacs
[email protected] $ module list
  1. Recheck your "PATH" variable. What has changed? Is the default version of gromacs visible?

  2. When you're done, unload the module and check that you no longer have the module loaded:

[email protected] $ module unload gromacs
[email protected] $ module list
[email protected] $ echo $PATH

Submit a job that uses GROMACS from OASIS

Now let us see how to do a job submission on the OSG that uses GROMACS on OASIS (you don't have to transfer GROMACS source or the binary along with the job).

We will get the example files using the tutorial command.

[email protected] $ tutorial gromacs

This creates a directory tutorial-gromacs. Go inside the directory and see what is inside.

[email protected] $ cd tutorial-gromacs
[email protected] $ ls -F 

You will see the following files:

1cta_nvt.tpr  Figs/  gromacs_job.sh  gromacs_job.submit  README.md

Take a look at the job description file

[email protected] $ cat gromacs_job.submit 

The modules are loaded in the wrapper script before executing the actual job. In this example, gromacs is loaded before running the actual simulation.

[email protected] $ cat gromacs_job.sh

The following requirement is added to find a machine that has the modules:

requirements = HAS_MODULES == True

Check the job description file.

[email protected] $ cat gromacs_job.submit 

Let's submit the job.

[email protected] $ condor_submit gromacs_job.submit 

After the job completed, you will see the output files (including gro, cpt and trr files) from GROMACS in your work directory.