ARCHIVED: Use Stata Big Red II at IU

• Overview
• Set up your user environment
• Submit a Stata batch job
• Run Stata interactively
• Get help

Overview

On Big Red II at Indiana University, you can use Stata interactively from the command line or in batch mode using a 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

To use Stata on Big Red II, you first must add the stata module to your user environment. To run Stata 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 stata
module load ccm

Submit a Stata batch job

To submit a Stata batch job that will run on Big Red II's compute nodes in the CCM execution environment:

1. Create a do-file (for example, stata_input.do) containing the commands Stata should run.
2. Create a job script (for example, stata_job) for the TORQUE resource manager on Big Red II. Your job script must include the ccmrun command, which will launch Stata on a compute node in the CCM environment, and the -l gres=ccm flag; for example (replace username with your IU username and username@iu.edu with your IU email address):

   #!/bin/bash
   #PBS -l nodes=1:ppn=32
   #PBS -l walltime=01:00:00
   #PBS -l gres=ccm
   #PBS -m ae
   #PBS -M username@iu.edu
   #PBS -N stata_job_name
   #PBS -V
   
   cd /N/u/username/BigRed2/new_directory
   
   ccmrun stata -b do stata_input.do
   

   The above example job script will:

   • Change the working directory to the directory where the do-file is located.
   • Invoke ccmrun to launch Stata.
   • Have Stata run the commands in the do-file.
   • Have Big Red II email you when the job is complete.
3. Submit the job script (for example, stata_job to the TORQUE resource manager; on the command prompt, enter:

   qsub stata_job
   

4. To check the status of your job, use the qstat command (replace username with your IU username):

   qstat -u username
   

Run Stata interactively

If your interactive session will require less than 20 minutes of processor time, you can load the stata module and launch the application from the Big Red II command line; for example:

username@login1:~> module load stata
username@login1:~> stata

If your interactive session will require more than 20 minutes of processor time, you must run it as an interactive job on a Big Red II compute node in the CCM execution environment. UITS Research Technologies strongly recommends this method of interactive execution, as the login nodes are not intended for computational work.

To run an interactive Stata job on Big Red II:

1. Make sure your user environment is configured properly; see Set up your user environment above.
2. From the command line, enter the qsub command with the -I (interactive), -l gres=ccm, and -q cpu (CPU queue) flags added; for example:

   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 at the command prompt on one of Big Red II's aprun nodes (where username is your IU username):

   qsub: waiting for job 79064 to start
   qsub: job 79064 ready
   
   In CCM JOB:  79064  JID  79064  USER  statmath  GROUP  uits
   Initializing CCM environment, Please Wait
   waiting for jid....
   CCM Start success, 1 of 1 responses
   Directory: /N/u/username/BigRed2
   Tue May 14 15:29:21 EDT 2019
   username@aprun1:~>

3. On the aprun command line, enter:

   ccmlogin
   

   This will place you at the command prompt on a Big Red II compute node (for example, nid00885, where username is your IU username):

   Warning: Permanently added '[nid00885]:203' (RSA) to the list of known hosts.
   username@nid00885:~>
   

4. To launch Stata, on the compute node command line, enter:

   stata
   

To use the features of the Stata graphical user interface (GUI), you must SSH to Big Red II with X forwarding enabled, and then use qsub with the -I (interactive) and -X (X forwarding) switches, as well as the -l gres=ccm switch; for example:

qsub -I -X -l walltime=01:00:00 -l nodes=1:ppn=32 -l gres=ccm -q cpu

Get help

If you need help or have questions regarding the use of Stata on Big Red II, contact the UITS Research Applications and Deep Learning team.