Software and Packages
- Software and Applications
- Schrodinger Suite
- MATLAB, Simulink and MATLAB Distributed Compute Server
- Jupyter Notebook
Queues and Resources
- LSF Queues And Policies
- GPU Etiquette
- Access TSM with GUI
- Access TSM with Command Line
- Checkpoint Restart
- Disaster Recovery Plan
Both the MATLAB client and the MATLAB Distributed Compute Server (MDCS) products from Mathworks are available on Minerva.The current version for both is R2014b.
Accessing the MATLAB and SIMULINK client on Minerva
Users can use the MATLAB client on Minerva as part of the MATLAB Total Academic Headcount license administered by Academic IT. Users are required to purchase an activation for Minerva just as they must for a local desktop copy. This is done by filling out the Mathworks Software Distribution Form found here and checking the “Minerva” box. Once the Scientific Computing staff is notified by Academic IT, the user will be given permission to use MATLAB on Minerva.
The license on Minerva is a network floating license and allows a user to run on any node in the Minerva complex but only on one node at a time. One can have multiple installations of MATLAB on the same node just as they can on a local installation. Access to the MATLAB program on Minerva is by way of the module system so the user does not download a personal copy:
module load matlab
The MATLAB client can be run in either graphics mode or command line mode. If one wants to run in graphics mode, you must use X-forwarding when you log in:
ssh -X <userid>@minerva.hpc.mssm.edu
Because one should never use the login node for computing, you will need to open a session on an interactive node.
or submit a batch interactive job to a compute node:
bsub -q express -Ip -XF -W 2:00 /bin/bash
The -Ip option will create an interactive job with a pseudo-terminal; the -XF will allow X-forwarding. The command above starts the interactive session with only one cpu. The Parallel Toolkit(PTK) of MATLAB allows the user to start up 12 additional workers for parallel work. If you plan on using the PTK, then you should also use the -n option to specify that additional cores need to be allocated to your job.
bsub -q low -n 4 -Ip -XF -W 2:00 /bin/bash
or however many cpu’s you will be using.