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Name | Version | Location / Module | Category |
|---|---|---|---|
| Apptainer | 1.2.5-1.el9 | (loaded automatically on all compute nodes) | Run Docker-like containers |
cmake | 3.20.2 | (loaded automatically on all compute nodes) | |
cuda | 12.3 | (loaded automatically on GPU nodes) | GPU Computing |
| gcc | 11.4.1 | (loaded automatically on all compute nodes) | Compiler - C / C++ |
gdal, gdal-devel libraries | 3.4.3 | (loaded automatically on all compute nodes) | |
gsl/gsl-devel libraries | 2.6-7 | (loaded automatically on all compute nodes) | GNU Scientific Library |
| gurobi | 10.0.3 | module load gurobi/10/0/3 | Prescriptive analytics platform and a decision-making technology |
| hdf5/hdf5-devel | 1.12.1-7 | (loaded automatically on all compute nodes) | Hierarchical Data Format version 5 |
hdf5p | 1.10.7 and 1.14.3 | module load hdf5p | Hierarchical Data Format version 5, PARALLEL version |
| Intel oneAPI toolkit | various | module load intel-oneAPI-toolkit <library> | Core set of tools and libraries for developing high-performance, data-centric applications across diverse architectures. |
| julia | 1.5.3 | module load julia/1.5.3 | Programming Language |
| knitro | 13.2.0 | module load knitro/13.2.0 | Software package for solving large scale nonlinear mathematical optimization problems; short for "Nonlinear Interior point Trust Region Optimization" |
| make | 4.3 | (loaded automatically on all compute nodes) | |
| Mathematica | 14.0 | (loaded automatically on all compute nodes) | Numerical Computing |
| MATLAB | R2023b | module load MATLAB/2023b | Numerical Computing |
| openmpi | 5.0.2 | module load openmpi/gcc/64/4.1.5a1 | OpenMPI Compiler (provided by Nvidia/Mellanox) |
Python (Incl many libraries such as numpy, torch, Tensorflow, scipy, and more) | 3.9.18 | (loaded automatically on all compute nodes) | Python for Scientific Computing |
Qt 5 | 5.15.9-1 | (loaded automatically on all compute nodes) | |
| R | 4.3.2 | (loaded automatically on all compute nodes) | Programming Language |
| Schrodinger | 2024-1 | module load schrodinger | A collection of software for chemical and biochemical use. It offers various tools that facilitate the investigation of the structures, reactivity and properties of chemical systems. |
| Singularity (now called Apptainer. see above) | |||
| Visual Studio Code Server | Not a module | A server side Integrated Development Environment hosted on Insomnia compute nodes |
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apptainer pull --name rstudio.simg docker://rocker/rstudio:4.3.1 |
In order for RStudio to start in a browser via an interactive session you will need the IP address of the compute node. Note that the IP below will likely be different for you:
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$ hostname -i 10.197.16.39 (REMEMBER, this is only an example IP. Yours will likely be different) |
From RStudio 4.2 and later, some added security features require binding of a locally created database file to the database in the container. Don't forget to change the password.
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mkdir -p run var-lib-rstudio-server printf 'provider=sqlite\ndirectory=/var/lib/rstudio-server\n' > database.conf PASSWORD='CHANGEME' singularity exec \ --bind run:/run,var-lib-rstudio-server:/var/lib/rstudio-server,database.conf:/etc/rstudio/database.conf \ rstudio.simg \ /usr/lib/rstudio-server/bin/rserver --auth-none=0 --auth-pam-helper-path=pam-helper --server-user=$USER |
This will run rserver in a Singularity container.
Now open another Terminal and start the RStudio rserver session using Port Forwarding to connect a local port on your computer to a remote one on Insomnia.
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Visual Studio Code Server
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A pre-existing Github account is now required to use the below instructions. |
Visual Studio Code is an Integrated Development Environment that some like to use on their laptops. If you are familiar with that, the HPC has a server-side version hosted on the compute nodes (NOT the login nodes) for users to create code directly on Insomnia with access to their files. connect their local VS Code application on their laptop to Insomnia and open files from their Insomnia folder directly. To use it, do the following:
After logging into Insomnia, start an srun session to a CPU or GPU node of your choice:
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A Github account is not required. Simply open a browser window and point it to the device login line in the last sentence. The browser window will ask for the unique code the line provides.
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When you use the device login url, you will first get a page asking you to use your GitHub credentials to login.
After using your GitHub login, then you will get a page asking you to input the device code given you above (represented as <###-###> here)
Next you will see a page requesting you to authorize VS Code studio's access permissions.
After that, when you use your local VS Code application on your computer, you will see a running ssh tunnel listed. Double click to connect to it. This can take a moment to finish.
Once done, you will be able to open files in your Insomnia folder the same as you do ones on your local computer.