Launching software from Andes, Polaris:
See https://services.dartmouth.edu/TDClient/KB/ArticleDet?ID=64641 for more details on running research software on our Linux HPC's such as Andes and Polaris.
Begin by ensuring that you have FastX installed on your Mac/Win system: https://services.dartmouth.edu/TDClient/KB/ArticleDet?ID=81595
and that you are able to open an Xterm session on andes.dartmouth.edu or polaris.dartmouth.edu. These can be done using an ssh connection with the -Y option, for example ssh -Y netid@polaris.dartmouth.edu
Once you get the Xterm window open and the '$' prompt, do a quick test to make sure your terminal command line can also open up an external X window by typing xclock& at the command line:
$ xclock&
In a few seconds, you should see a new window open with a small clock in it. 
Close the clock window when it appears. If not, re-install your X Window software (FastX, MobaXterm, XQuartz)
Click back inside the terminal window, and press the Enter/Return key to get a new command prompt ($). Then, type the following command below to load the software you'd like to use (matlab, stata, R, etc) at the "$" prompt in your terminal window:
$ module load matlab
And then the software name to launch the interactive software in a new terminal X Window.
$ matlab
Some software packages have more than one version installed. Stata is one example. Type module avail stata to see available versions
$ module avail stata
$ module load stata/15
$ xstata
$ spss
$ sas
Note: to use the "Discovery" HPC, there are extra steps involved to create a "batch submission" script. See https://services.dartmouth.edu/TDClient/1806/Portal/KB/?CategoryID=21754 and https://services.dartmouth.edu/TDClient/1806/Portal/KB/ArticleDet?ID=132372)
Your DartFS file storage system is available at this same command prompt. You can drag and drop files in, or use a Unix cp or mv command. Type ls to view files:
$ ls
mydata_on_dartfs_netid.csv
myRscript.R
myMatlabMfiles.M
You can run R script files using the Rscript command.
$ Rscript myRscript.R
Note: MATLAB .m files can be run using MATLAB without the graphical interface (the MATLAB GUI does not run on Discovery with srun)
Matlab can be run without the graphical interface
$ matlab -nodisplay -nojvm -nosplash -nodesktop
< M A T L A B >
>>>
Matlab scripts can be run at the prompt without the graphical interface
Author a script on your desktop installation of Matlab, and save it to DartFS. Samlpe script titled "testmfile.m", which contains the following code:
This script can then be run by logging with your DartFS account and navigating to the directory
$ module load matlab
$ matlab -nodisplay -nodesktop -nosplash -nojvm -r "run testmfile.m"
Scripts can be written to accept parameters and write to files
$ matlab -nodisplay -nodesktop -nosplash -nojvm -r "matlabfunctionwritefile(25)"
Scripts can also be written to export data out to your DartFS file storage:
Example: a script called "script.m" containing the following:
A = magic(5);
outputfile1 = 'output1.xlsx';
writematrix(A,outputfile1,'Sheet',1,'Range','E1:I5');
outputfile2 = '//dartfs-hpc/rc/home/2/username2/output2.xlsx';
writematrix(A,outputfile2,'Sheet',1,'Range','E1:I5');
Then run on Polaris at the command line like this:
[usrname@polaris ~]$ module load matlab
[usrname@polaris ~]$ matlab -nodisplay -nodesktop -nosplash -nojvm -r "run script.m"
This will output files "output1.xlsx" and "output2.xlsx" to the user's home directory. Note the use of the full file path in the second file - this method could be used to write to subfolders on your DartFS file system.
Syntax examples for submitting a regular job:
$ matlab -nodisplay -nodesktop -nosplash -nojvm -r "run jobname.m"
Syntax example with Try-Catch-End statement:
$ matlab -nodisplay -nodesktop -nosplash -nojvm -r "try; run('YourScriptName.m'); catch; end; exit";
Mathematica
[usrname@polaris ~]$ module load mathematica
[usrname@polaris ~]$ module avail mathematica
SSH Terminal and X Window Clients
Windows / Mac / Linux "FastX" https://services.dartmouth.edu/TDClient/KB/ArticleDet?ID=81595
Windows: Gitbash https://git-scm.com/downloads
Mac: use built-in 'Terminal' Unix Shell
See this link for more help with the Andes Polaris Linux HPC machines: https://services.dartmouth.edu/TDClient/KB/ArticleDet?ID=64641
RStudio
Create a FastX connection to andes.dartmouth.edu on the Open Connections page, using the + button, Port 22 and your Dartmouth NetID
Double-click the connection and when prompted, enter your NetID password.
After logging in, click the large + button ('Start a new Session')
Click the xterm button
At the prompt, (username@andes$) type rstudio
R Studio will launch in a new window
