Command Line

The final method for running applications with the pre-defined, default submissions scripts is via the command line in your terminal application. These scripts can run applications and jobs either as interactive sessions or batch jobs.

In the table below, replace [RAM] with the amount of memory in GB you are requesting. Memory values are 5g, 10g, or 20g. For example, to run a 10 GB Mathematica job, the command would be mathematica-10g.

Please note that all commands listed should be entered on one line.  Please keep in mind that the RAM option -30g is not available for interactive sessions. 

Most wrapper scripts also include the optional core count flag -n. If included, (e.g. -n 2), this will reserve addtional cores for parallel processing for your session or job. If not included, the session or job will default to 1 (one) core. Note that your code has to be able to use multiple cores for this to be effective. Please see our document on Parallel Processing for more information.

 
  • To get help on a given command and its options, include only the -h flag with the command.

Resource

Command Line
(Batch)

Interactive
without X11

Interactive
with X11

Emacs

-

emacs -nw

emacs

Mathematica

-

-

mathematica[-RAM]

MATLAB

matlab[-RAM] [-n #] myfile.m [outfile]

N/A

MATLAB can be run interactively
in the shell without a GUI,
but custom bsub commands
must be used.

matlab[-RAM] [-n #]
 

Perl

perl [-n #] myfile.pl

-

-

Python

python [-n #] myfile.py [outfile]

python [-n #]

-

Python3 python3 [-n #] myfile.py [outfile] python3 [-n #]  -

R

R[-RAM] CMD BATCH [-n #] myfile.R [outfile]

R[-RAM] [-n #]

Rstudio[-RAM] [-n #]

SAS

sas myfile.sas

sas[-RAM]

sas[-RAM]

Stata/SE

stata-se[-RAM] -b do myfile.do

stata-se[-RAM]

xstata-se[-RAM]

Stata/MP4  

stata-mp4[-RAM] -b do myfile.do

stata-mp4[-RAM] 

xstata-mp4[-RAM]

Stata/MP8

stata-mp8[-RAM] -b do myfile.do

-

-

Stat/Transfer

st myfile new-file

stattransfer

stattransfer

Updated 1/15/19