Gromacs

Gromacs is a molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. originally developed in the University of Groningen, now maintained and extended at different places, including the University of Uppsala, University of Stockholm and the Max Planck Institute for Polymer Research. GROMACS is open source software released under the GPL.

The program is written for Unix-like operating systems; it can run on Windows machines if the Cygwin Unix layer is used. The program can be run in parallel on multiple CPU cores or a network of machines using the MPI library. The latest stable release on Cheaha is 4.0.7.

Using Gromacs

GROMACS is free software, licensed under the GNU General Public License. The details are available in the license text, but in short you can modify and redistribute the code as long as your version is licensed under the GPL too.

Gromacs on Your Desktop

Gromacs can be downloaded and installed on your desktop from http://www.gromacs.org/. Linux: Download and installation instructions for Gromacs are available at: http://www.gromacs.org/Downloads/Installation_Instructions Windows: Download and installation instructions for Gromacs on Windows are avialable at: http://www.gromacs.org/Downloads/Installation_Instructions/Windows

Gromacs on Cheaha

Gromacs is pre-installed on the Cheaha research computing system. This allows users to run Gromacs directly on the cluster without any need to install software.

Gromacs Versions

Use the 'module' command to view a list of available Gromacs versions. If the version that you require isn't listed, please open a help desk ticket to request the installation.

The following is an example output of the command and doesn't necessarily represent the currently installed versions:

$ module avail gromacs

---------------------------------------------- /etc/modulefiles 
-----------------------------------------------
gromacs/gromacs-4-gnu   
gromacs/gromacs-4-intel

Submitting Gromacs jobs to Cheaha

These instructions provide an example of how to create and submit a Gromacs job on Cheaha.

First, create the working directory for the job- Replace 'USERNAME' with the account associated username on Cheaha. You can create any directory to run your job. It is recommended that the job directory be on the scratch (i.e. lustre filesystem) instead of the user home directory.

$ mkdir -p /lustre/scratch/USERNAME/jobs/gromacs 
$ cd /lustre/scratch/USERNAME/jobs/gromacs

Next, Copy all the files required for Gromacs to the working directory.

Gromacs supports the following files: run parameters(*.mdp, m2p), structure(*.gro,g96,pdb), topolgy (*.top,itp,rtp,ndx), run input (*.tpr,tpa,tpb), trajectory (*.trj,trr,xtc,gro,g96,pdb), energy (*.ene,edr), and other (*.dat,edi,edo,eps,log,map,mtx,out,tex,xpm,xvg) files.

Eg. Copy the directory "d.dppc" from the local host to a remote host's directory "NAMD"

$ scp -r d.dppc USERNAME@cheaha.uabgrid.uab.edu:/lustre/scratch/USERNAME/jobs/gromacs 

Benchmarking

2011 Hardware

Benchmark data for running Gromacs on Cheaha will be developed leveraging the benchmark foundation of the NIH's Biowulf cluster Gromacs testing suite combined with local work flow characteristics.

2007 Hardware and Gromacs 3.x

Note: The Gromacs 3.x code base was severely limited in spanning multiple compute nodes. The limit for 1GigE network fabrics was 4 nodes. The following performance data is provided for historical reference only and does not reflect performance of the Gromacs 4.x code base currently install on Cheaha.

Two identical 4 CPU Gromacs runs and the jobs spread out as follows based on current queue load (the new nodes are using Infiniband, the old TCP for message passing):

Dell Blades: 4 cpu job running on 4 compute nodes

Job ID:    71566
Submitted: 14:11:40
Completed: 17:06:03
Wall Clock: 02:54:23

              NODE (s)   Real (s)      (%)
      Time:  10462.000  10462.000    100.0
                      2h54:22
              (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    238.044     16.164      4.129      5.812

Verari: 4 cpu job running on 2 compute nodes

Job ID:    71567
Submitted: 14:11:44
Completed: 23:13:01
Wall Clock: 09:01:17

              NODE (s)   Real (s)      (%)
      Time:  32473.000  32473.000    100.0
                      9h01:13
              (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:     76.705      5.208      1.330     18.040