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Software

KLC Software

The Kellogg Linux Cluster (KLC) has access to all of the site-licensed software packages that Northwestern Quest does. Most KLC software can be run interactively using a graphical interface by connecting to KLC with X11 forwarding enabled:

 

On a Mac:  Terminal with  ssh –Y yournetid@klc.northwestern.edu

On Windows:  Connect with ssh client such as MobaXterm

Both Mac and Windows:  Open the application using FastX.

 

You might also prefer to run your programs in batch mode from the command line.

 

Availability

From the KLC command line, you can check to see the available software modules:


[~]$ module avail 

You can add a keyword to check for available versions of a specific application:


[~]$ module avail matlab
-------------------/software/Modules/3.2.9/modulefiles-------------------
   matlab/r2013a    matlab/r2014b (D)    matlab/r2015b    matlab/r2017a
   matlab/r2014a    matlab/r2015a        matlab/r2016a    matlab/r2018a


NUIT also maintains a full list of the Software on Quest along with brief descriptions of what those applications are.

 

Usage Notes

Below are useful reference information for how to call some of the most popular applications on KLC.

 

Matlab

Syntax for running “my_program” in batch mode:


[~]$ module load matlab
[~]$ matlab -nodisplay -nodesktop -nosplash -r "run(my_program.m);exit;" &

Remember: The KLC is public resource shared by dozens of others. Please exercise restraint when using the Parallel Computing Toolbox, and limit yourself to no more than 16 concurrent processes across all the nodes.

 

R / RStudio

You can run R in three different ways: with the graphical RStudio, by submitting an R program in batch mode, or even by issuing commands interactively on the command line if you want. To use any of these methods, first you must load R:


[~]$ module load R

To launch RStudio:


[~]$ rstudio &

Syntax for running “my_program” in batch mode:


[~]$ Rscript my_program.R &

SAS

Please note that the default memory allocation for SAS on Quest is quite low while the amount of available memory on KLC is quite high.  When running SAS in batch mode, use the –memsize option to request the amount of memory you want.

Syntax for running “my_program” in batch mode, with 175 GB of RAM:


[~]$ module load sas
[~]$ sas –memsize 175G my_program.sas  &
   

Stata

Please note that calling “stata” will open Stata/IC by default.   For batch jobs, we suggest using stata-se or stata-mp.

Syntax for running “my_program” in batch mode:


[~]$ module load stata
[~]$ stata-se –b do my_program.do &

Also note that Stata MP is only licensed for 4 cores; please do not request more than 4 cores when using Stata MP as the resources will be wasted.

To run Stata with a graphical interface, add “x” to the beginning of your command:


[~]$ module load stata
[~]$ xstata-se &

KAP02 Software

The KAP02 Windows server contains many software titles that are not available on the Kellogg Linux machines.  These include:

  • ArcGIS
  • Mathematica
  • Tableau Desktop
  • Visual Studio

The KAP02 Windows server also has many of the same analytical software packages (Matlab, R/RStudio, Stata, SAS) as the KLC. Please note: The Windows server has fewer CPU cores and less RAM than the KLC. In addition to greater scale, KLC also is more convenient if you want to script or schedule the running of your jobs.

That said, there are occasions where it makes sense to use these programs on KAP02. For example, if you are working with restricted data on the H:\ drive, you will need to use the software on KAP02. Also, during periods when KLC is down for maintenance, KAP02 is probably going to be your best alternative.

 

Personal Software

NUIT Software lists several titles available for you to download either for no charge or for a discounted fee.

The Kellogg On The Hub store also contains software for sale, such as SPSS.