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Name | Version | Location / Module | Category |
|---|---|---|---|
| Apptainer | 1.2.5-1.el9 | (installed directly on all compute nodes) | Run Docker-like containers |
cmake | 3.20.2 | (installed directly on all compute nodes) | |
cuda | 12.3 | (installed directly on GPU nodes) | GPU Computing |
| gcc | 11.4.1 | (installed directly on all compute nodes) | Compiler - C / C++ |
gdal, gdal-devel libraries | 3.4.3 | (installed directly on all compute nodes) | |
gsl/gsl-devel libraries | 2.6-7 | (installed directly 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 | (installed directly 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 | (installed directly on all compute nodes) | |
| Mathematica | 14.0 | (installed directly 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 | (installed directly on all compute nodes) | Python for Scientific Computing |
Qt 5 | 5.15.9-1 | (installed directly on all compute nodes) | |
| R | 4.3.2 | (installed directly 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) | installed directly on compute nodes | ||
| 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 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:
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Once done, you will be able to open files in your Insomnia folder the same as you do ones on your local computer.
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It's possible that the next time you try to use the tunnel you've just made, you may not be able to re-connect. The connection may keep trying endlessly, or finally fail with an error. This is because the srun session in the first step has placed you on another node different from the one where you created the tunnel. IF that happens, follow the steps below: 1) In your local VSCode app (if you use a local copy of VS Code and not the browser-based window version), unregister/delete all of your existing tunnels. We’ll be making a new one. 2) Login to Insomnia. Do not start an srun session yet. 3) Delete your invisible vscode settings folders in your home directory (" 4) Start an srun session as described above, type "code tunnel", and follow all of the directions as normal. Open VScode in the web browser first. It will take a moment as the new tunnel is created. If you only use VS Code in the browser, you are now done. 5) If you prefer to use a local copy of VS Code on your computer, you can now connect to this tunnel in it. WINDOWS USERS, additionally you may need to downgrade your local copy of Visual Studio Code to version 1.8.1 due to a bug existing as of this writing (8/28/2024). |