MATLAB scripts already exist for our lab to run jobs on Karst. You can find these scripts in Dropbox under Dropbox (NewmanLab) > scripts > utils > utils_cluster. The necessary scripts are ClusterSubmit_IU.m and a unique jobSubmit_*.m function.
If you don't already have a computing account on Karst, sign up for one here: https://access.iu.edu/Accounts/Create. You can also use the lab group account.
There are a couple different ways to conect to Karst, which will be outlined below.
If you're comfortable with Unix commands, you can SSH into Karst using a supported SSH client. Available software for Windows and Mac OS X can be found here: https://kb.iu.edu/d/ahjh.
The login command is as follows (replace <username> with your IU account name):
ssh <username>@karst.uits.iu.edu
The password will be your IU account password.
Starting MATLAB
To start MATLAB on Karst, you need to make sure the program is loaded into your software environment. To add the default verstion of MATLAB, enter the following command:
module load matlab
Now you can open matlab by typing matlab into the terminal window. Note that this will only open a MATLAB terminal, not the GUI.
To have matlab automatically load when you connect to Karst, you will need to edit you .modules file in your home directory on Karst. Instruction on how to edit this file can be found here: https://kb.iu.edu/d/bcxp.
Opening the MATLAB graphical interface
To open the MATLAB graphical interface in an SSH client, you will need an SSH client that allows X forwarding. A good, free client for Windows is MobaXterm, found here: http://mobaxterm.mobatek.net/. An SSH client like PuTTy doesn't have X forwarding built in, so you would need to install secondary software to allow X forwarding. MobaXterm has the SSH terminal and X forwarding in the same interface, simplifying the process. More on X forwarding here: https://kb.iu.edu/d/bdnt.
Transferring files
To transfer files, you will need to connect to karst via SCP or SFTP.
If you're unfamiliar with Unix commands and command processors, you can use Karst Desktop to connect to Karst. Karst Desktop is a remote desktop service for Karst that allows you to simulate a desktop environment to interact with Karst. https://kb.iu.edu/d/bfwp
Both of the files below can be found in Dropbox at the following location: Dropbox > scripts >utils > utils_cluster.
This is the script you will edit to hold the necessary variables for submitting a job. Start with the file "jobSubmit_EXAMPLE.m" and save a copy, replacing "EXAMPLE" with the title of the function you're trying to run or some other unique identifier. This function has comments with instructions for how to edit and run it.
This is the function that actually submits the job to Karst. You should not have to edit ClusterSumbit_IU.m. However, if changes need to be made specific to your job, please re-save the script as a new file.