Below is a list of guides for popular subjects. It is not comprehensive so please search our site if you do not find what you are looking for. If that fails then please write to [email protected]. A.I. Sandbox Secure environment for using LLMs via chat or API Apptainer Container platform specifically for HPC Checkquota Checking your quota, requesting quota increases and dealing with large Conda environments Connect by SSH Connecting to the Clusters via SSH Connect by Web Connecting to the Clusters via a Web Browser (using OnDemand) Custom Modules Creating your own environment modules Data Storage Available on all clusters via various filesystems Data Transfer How to get files on and off the clusters Datasets Available on Della for popular cases like imagenet and alphafold DDT A graphical parallel debugger Environment Modules Make using pre-installed software packages and libraries easy Gaussian Software package for quantum chemistry calculations Globus An infrastructure for transferring large amounts of data. GPU Computing Covers the hardware at Princeton and related tools GROMACS A biomolecular simulation package on the HPC Clusters GUI Applications Working with Visualizations and GUI Applications on the Research Computing Clusters Hugging Face A machine learning community with a focus on natural language processing JAX A flexible Python library for machine learning research Jenkins Automatic testing typically for continuous integration Job Priority Job Priority of Slurm jobs Jobstats stats.rc provides detailed metrics about actively running and completed jobs Julia A programming language for scientific and numerical computing Jupyter Running Jupyter on the Research Computing Systems LAMMPS Molecular dynamics simulation package on the HCP clusters MAP Performance profiler for parallel and GPU codes Mathematica An integrated environment for numerical computing MATLAB Environment for scientific computing on the Research Computing clusters Memory Allocation for Slurm script explained mpi4py Provides a Python interface to MPI on HPC Clusters NAMD A molecular dynamics simulation package on the HPC Clusters OnDemand Portal Using the Clusters via a Web Browser Parallel Basic introduction into the concepts behind parallel programming PETSc Provides data structures and routines for the scalable solution of scientific applications Ports and proxy/default Module which enables internet access on compute nodes for specific software as well as general port configuration tips Python The most popular scripting language in the computational sciences PyTorch A popular deep learning framework Quantum Espresso Software suite for electronic structure calculations R/RStudio Popular environment for data analysis, statistics and machine learning Recover Files Recover accidentally deleted files Scaling Analysis How to determine the optimal number of nodes, CPU-cores, etc. Sharing Data Sharing data with other Research Computing users and external collaborators Singularity A secure alternative to Docker that is specifically for HPC Slurm The job scheduler used on the HPC clusters Snakemake A popular workflow manager Spark A cluster computing framework for large-scale data processing on the HPC Clusters Stata A general-purpose statistical software package on the Research Computing Clusters and Nobel Suppressing Duo Using VPN or SSH keys TensorFlow A popular deep learning framework tigress-web Allows one to make files in /tigress available on the internet TurboVNC A graphical desktop sharing system that allows users to connect to remote computers Using tigress-cifs Makes it possible to mount /tigress and /projects on your local machine VASP A popular simulation package for ab initio calculations Visual Studio Code (VS Code) is a popular IDE
