Batch jobs on OSC are initiated through the Portable Batch System (PBS).  This is the recommended way to run stuff on OSC clusters.
Attached is a sample PBS script that copies files to temporary storage on the OSC cluster (also recommended) and runs an analysis program.
Info on batch processing is at https://www.osc.edu/supercomputing/batch-processing-at-osc.
     This will tell you how to submit and manage batch jobs.
More resources are available at www.osc.edu.

PBS web site: /www.pbsworks.com

The PBS user manual is at www.pbsworks.com/documentation/support/PBSProUserGuide10.4.pdf.

Jacob Here, Just want to add how I got AnitaTools to see FFTW:

1) echo $FFTW3_HOME to find where the lib and include dir is.

2) Next add the following line to the start of cmake/modules/FindFFTW.cmake

'set ( FFTW_ROOT full/path/you/got/from/step/1)'

Brief, experience-based instructions on installing the AnitaTools package on the Oakley OSC cluster.

These scripts allow you to do thousands of ShelfMC runs while varying certain parameters of your choice. As is, the attenuation length, reflection, ice thickness, firn depth, station depth is varied over certain rages; in total, the whole Parameter Space Scan does 5250 runs on a cluster like Ruby or KingBee. The scripts and instructions are attached below. 

Doing large runs of ShelfMC can be time intensive. However, if you have access to a computing cluster like Ruby or KingBee, where you are given a node with multiple processors, ShelfMC runs can be optimized by utilizing all available processors on a node. The multithread_shelfmc.sh script automates these runs for you. The script and instructions are attached below.

Here is an old email thread about how to ship a station to Pole.

Instructions on installing simulation software prerequisites (ROOT, Boost, etc) on Linux computers.

If you are trying to use the Ray Trace Correlator with AraRoot, you will probably encounter some issues as you go. Here is some advice that Carl Pfendner found, and Brian Clark compiled.

Please note that it is extremely important that your AntennaInfo.sqlite table in araROOT contain the ICRR versions of both Testbed and Station1. Testbed seems to have fallen out of practice of being included in the SQL table. Also, Station1 is the ICRR (earliest) version of A1, unlike the ATRI version which is logged as ARA01. This will cause seg faults in the intial setup of the timing and geometry arrays that seem unrelated to pure geometry files. If you get a seg-fault in the "setupSizes" function or the Detector call of the "setupPairs" function, checking your SQL file is a good idea. araROOT branch 3.13 has such a source table with Testbed and Station1 included.

Which combination of Makefile/Makefile.arch/StandardDefinitions.mk works can be machine specific (frustratingly). Sometimes the best StandardDefinitions.mk is found int he make_timing_arrays example.

Common Things to Check

1: Did you "make install" the Ray Trace Correlator after you made it?

2: Do you have the setup.txt file?

3: Do you have the "data" directory?

Common Errors

1: If the Ray Trace Correlator compiles, and you execute a binary, and get the following:

     ******** Begin Correlator ********, this one!
     Pre-icemodel test
     terminate called after throwing an instance of 'std::out_of_range'
     what():  basic_string::substr
     Aborted

Check to make sure have the "data" directory.
 

For Mac and Windows:

https://osuasc.teamdynamix.com/TDClient/KB/ArticleDet?ID=14542
For Linux, in case some of your students need it:

https://osuasc.teamdynamix.com/TDClient/KB/ArticleDet?ID=17908

From Sam 01/25/17:  It doesn't work from my Ubuntu 14 machine.  My VPN setup in 14 does not have the "Software Token Authentication" option on the screen as shown in the instructions.  It fails on connection attempt.  
The instructions specify Ubuntu 16; perhaps there is a way to make it work on 14, but I don't know what it is.

Log into kingbee.mps.ohio-state.edu first, then log into radiorm.physics.ohio-state.edu.

From Keith Stewart 03/16/17:  It appears that radiorm SSH from offsite is closed. So you will need to be on an OSU network physically or via VPN. fox is also blocked from offsite as well. Kingbee should still be available for now. If you want to use it as a jump host to get to radiorm without VPN. However, you will want to get comfortable with the VPN before it is a requirement.

Carl 03/16/17:  I could log in even while using a hard line and plugged in directly to the network.

From Bryan Dunlap 12/16/17:  I have set up the group permissions on the elog directory so you and your other designated people can edit files.  I have configured sudo to allow you all to restart the elogd service.  Once you have edited the file [/home/elog/elog.cfg I think], you can then type

sudo /sbin/service elogd restart

to restart the daemon so it re-reads the config. Sudo will prompt you for your password before it executes the command.