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.

Also, the -5g sufixed and non-suffixed commands are the same. Thus, the following two commands are equivalent:

#these two are the same command
mathematica
mathematica-5g

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 additional 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.

Where possible and if it makes sense, we've engineered the wrapper to allow an input file and an output file. The output file will be handled as the bsub -o option to the job submission command.

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

 

Resource

Batch
(Background)

Interactive, no GUI (X11)

Interactive, with GUI (X11)

Emacs - emacs -nw emacs
Mathematica - - mathematica[-RAM]
MATLAB matlab[-RAM] [-n #] myfile.m [outfile] MATLAB can be run interactively
in the shell without a GUI,
but custom bsub commands
must be used.
matlab[-RAM] [-n #]
 
Perl perl[-RAM] [-n #] myfile.pl - -
Python2 python[-RAM] [-n #] myfile.py [outfile] python[-RAM] [-n #] -
Python3 python3[-RAM] [-n #] myfile.py [outfile] python3[-RAM] [-n #] -
R R[-RAM] CMD BATCH [-n #] myfile.R [outfile] R[-RAM] [-n #] Rstudio[-RAM] [-n #]
Rscript Rscript[-RAM] [-n #] myfile.R [outfile] - -
SAS sas[-5g] myfile.sas sas[-5g] sas[-5g]
Spyder (Python2 IDE) - - spyder[-RAM] [-n #] [myfile.py]
Spyder3 (Python3 IDE) - - spyder3[-RAM] [-n #] [myfile.py]
Stata/SE stata-se[-RAM] -b do myfile.do stata-se[-RAM] xstata-se[-RAM] [myfile.do]
Stata/MP4 stata-mp4[-RAM] -b do myfile.do stata-mp4[-RAM] xstata-mp4[-RAM] [myfile.do]
Stata/MP8 stata-mp8[-RAM] -b do myfile.do stata-mp8[-RAM] xstata-mp8[-RAM] [myfile.do]
Stat/Transfer st myfile new-file stattransfer stattransfer

Updated 5/9/19