ARCHIVED: Use GAUSS on Big Red II at IU
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Big Red II was retired from service on December 15, 2019; for more, see ARCHIVED: About Big Red II at Indiana University (Retired).
Overview
On Big Red II at Indiana University, you can use GAUSS interactively from the command line or in batch mode using a TORQUE job script. If your interactive session will require more than 20 minutes of processor time, you must run it as an interactive job on one of Big Red II's compute nodes in the Cluster Compatibility Mode (CCM) execution environment.
Set up your user environment
On the research supercomputers at Indiana University, the Modules environment management system provides a convenient method for dynamically customizing your software environment.
To use GAUSS on Big Red II, you must first add the
gauss
module to your user environment. To run GAUSS jobs on Big Red II's compute nodes in the CCM execution environment, you also must add the ccm
module to your user environment. To make sure both modules are loaded every time you log into Big Red II, add the following lines to your
~/.modules
file:
module load gauss module load ccm
For more, see Use modules to manage your software environment on IU research supercomputers.
Submit a GAUSS batch job
To submit a GAUSS batch job that will run on Big Red II's compute nodes in the CCM execution environment:
- Create a GUASS program (for example,
program.e
) containing the commands GUASS should run. - Create a job script (for example,
gauss_job
) for the TORQUE resource manager on Big Red II. Your job script must include theccmrun
command, which will launch GAUSS on a compute node in the CCM environment, and the-l gres=ccm
flag.For example (replace
username
with your IU username andusername@iu.edu
with your IU email address):#!/bin/bash #PBS -l nodes=1:ppn=32 #PBS -l walltime=00:10:00 #PBS -l gres=ccm #PBS -m ae #PBS -M username@iu.edu #PBS -N gauss_job_name #PBS -V cd /N/u/username/BigRed2/new_directory ccmrun tgauss -b program.e
The above example job script will:
- Change the working directory to the directory where the
program.e
m-file is located. - Invoke
ccmrun
to launch GAUSS. - Have GAUSS run the commands in the program.
- Have Big Red II email you when the job is complete.
- Change the working directory to the directory where the
- Submit the job script to the TORQUE resource manager; on the command prompt, enter:
qsub gauss_job
- To check the status of your job, use the
qstat
command (replaceusername
with your IU username):qstat -u username
Run GAUSS interactively
If your interactive session will require less than 20 minutes of processor time, you can load the gauss
module and launch the application from the Big Red II command line; for example:
jajbinks@login1:~> module load gauss jajbinks@login1:~> tgauss
Interactive sessions requiring more than 20 minutes of processor time must be run as interactive jobs on a Big Red II compute nodes in the CCM execution environment. This method of interactive execution is strongly recommended, as the login nodes are not intended for computational work.
To run an interactive GAUSS job on Big Red II:
- Make sure your user environment is configured properly; see Set up your user environment above.
- From the command line, enter the
qsub
command with the-I
(interactive),-l gres=ccm
, and-q cpu
(CPU queue) flags added; for example:jajbinks@login1:~> qsub -I -l walltime=01:00:00 -l nodes=1:ppn=32 -l gres=ccm -q cpu
When the resources needed to run your job are available, your job will start. Once the CCM execution environment is initialized, you'll be placed on one of Big Red II's
aprun
nodes:qsub: waiting for job 79064 to start qsub: job 79064 ready In CCM JOB: 79064 JID 79064 USER jajbinks GROUP uits Initializing CCM environment, Please Wait waiting for jid.... CCM Start success, 1 of 1 responses Directory: /N/u/jajbinks/BigRed2 Tue Sep 10 15:29:21 EDT 2013 jajbinks@aprun1:~>
- From the
aprun
command line, enter theccmlogin
command:jajbinks@aprun1:~> ccmlogin
This will place you on a Big Red II compute node (for example,
nid00885
):Warning: Permanently added '[nid00885]:203' (RSA) to the list of known hosts. jajbinks@nid00885:~>
- From the compute node command prompt, enter
tgauss
to launch GAUSS:jajbinks@nid00885:~> tgauss GAUSS 14.0.1 (Oct 23 2013, 3493) 64-bit (C)Copyright 1984-2012 Aptech Systems, Inc. All Rights Reserved Worldwide. (gauss)
Get help
If you need help or have questions regarding the use of GAUSS on IU's research supercomputers, contact the UITS Research Applications and Deep Learning team.
Research computing support at IU is provided by the Research Technologies division of UITS. To ask a question or get help regarding Research Technologies services, including IU's research supercomputers and research storage systems, and the scientific, statistical, and mathematical applications available on those systems, contact UITS Research Technologies. For service-specific support contact information, see Research computing support at IU.
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Last modified on 2023-05-09 14:42:38.