Software Examples
The RCD team maintains a repository of examples for how to use popular software on Palmetto.
Some of these software examples have not been updated recently. If you encounter issues or would like an updated example, please submit a support ticket.
ABAQUS
ABAQUS is a Finite Element Analysis software used for engineering simulations.
View the abaqus example on GitHub
Amber
Amber is a suite of biomolecular simulation programs.
View the amber example on GitHub
ANSYS
ANSYS is a general-purpose, finite-element modeling package for numerically solving a wide variety of mechanical problems. These problems include static/dynamic, structural analysis, heat transfer, and fluid problems, as well as acoustic and electromagnetic problems.
View the ansys example on GitHub
COMSOL
COMSOL Multiphysics is a finite element analysis, solver, and simulation software package for various physics and engineering applications, especially coupled phenomena and multiphysics. COMSOL provides an IDE and unified workflow for electrical, mechanical, fluid, acoustics, and chemical applications.
View the comsol example on GitHub
Gephi
Gephi is an interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs. At this time, we don't have Gephi setup as a software module on Palmetto, but downloading and installing it in your own home or scratch directory (and running it from that location) is easy to do.
View the gephi example on GitHub
GROMACS
A free and open-source software suite for high-performance molecular dynamics and output analysis. GROMACS is an architecture-specific software. It performs best when installed and configured for the specific hardware. This example shows how to run it optimally on Palmetto.
View the GROMACS example on GitHub
GROMACS Official Documentation
Java
The Java Runtime Environment (JRE) is currently available cluster-wide on Palmetto. If a user needs a different version of Java, or if the Java Development Kit (JDK, which includes the JRE) is needed, that user is encouraged to download and install Java (JRE or JDK) themselves.
This example shows how to manually install Java on Palmetto.
View the Java example on GitHub
Julia
Julia: high-level dynamic programming language that was originally designed to address the needs of high-performance numerical analysis and computational science.
View the julia example on GitHub
GNU Parallel
The GNU Parallel utility is useful for running several independent tasks simultaneously, e.g., for processing several files in parallel, or running batches of simulations.
In this example, we demonstrate how GNU parallel can be used to operate on several input files.
View the GNU Parallel example on GitHub
HOOMD
HOOMD-blue is a Python package that runs simulations of particle systems on CPUs and GPUs. It performs hard particle Monte Carlo simulations of a variety of shape classes and molecular dynamics simulations of particles with a range of pair, bond, angle, and other potentials. Many features are targeted at the soft matter research community, though the code is general and capable of many types of particle simulations.
View the hoodmd example on GitHub
LAMMPS
Performance of LAMMPS is sensitive to how the installation is configured relative to the running hardware and how lmp is called with different process/thread/gpu options. Given the heterogeneous nature of Palmetto, we do not maintain a baseline LAMMPS module, but encourage users to build their own LAMMPS. Please read the installation and benchmarking instructions on our example.
View the LAMMPS example on GitHub
MATLAB
MATLAB is a programming and numeric computing platform to analyze data, develop algorithms, and create models.
View the matlab example on GitHub
Mothur
This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
View the mothur example on GitHub
MrBayes
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
View the MrBayes example on GitHub
NAMD
NAMD is a molecular dynamics simulation software written in charm++. Currently
namd/2.14 is available on Palmetto.
View the namd example on GitHub
Open Babel
It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
View the Open Babel example on GitHub
Paraview
This example shows how Paraview can use multiple GPUs on Palmetto to visualize very large datasets.
View the paraview example on GitHub
PyTorch
We provide a number of examples on GitHub demonstrating how to setup and use PyTorch on Palmetto:
- Introduction: This example explains how to install the PyTorch package for use with GPUs on the cluster, and how to launch a JupyterLab Server with PyTorch environment on OpenOnDemand.
- Distributed Data Parallel: run your PyTorch code using multiple GPUs on single node or multiple nodes.
- Distributed ImageNet Training: this example demonstrates the power of Palmetto as a high-performance AI cluster by training imagenet at a rate of 45,000 images per second.
Also, see our instructional material on the workshop website: RCDE Pytorch Workshop Materials
Rclone
Rclone is a tool that can be used to copy local files to many cloud storage providers.
View the Rclone example on GitHub
Tensorflow
This example explains how to install the TensorFlow package for use with GPUs on the cluster, and how to use it from Jupyter Notebook via OpenOD.
View the tensorFlow example on GitHub
Apptainer / Singularity
Apptainer (formerly known as Singularity) is a tool for creating and running containers on HPC systems, similar to Docker. This example provides information about Apptainer specific to Palmetto.
View the old singularity example on GitHub
Simulator of Urban Mobility (SUMO)
SUMO (Simulation of Urban MObility)is an open source, highly portable, microscopic and continuous multi-modal traffic simulation package designed to handle large networks.
View the Simulator of Urban Mobility example on GitHub
TASSEL
TASSEL (Trait Analysis by Association, Evolution, and Linkage) is a software package used to evaluate genotype and trait associations with the tools of population and quantitative genetics. TASSEL can handle datasets commonly encountered in the plant community, e.g. replicated trials, inbred lines, and complex structured pedigrees.
View the TASSEL example on GitHub
tmux
If you would like to run multiple shells in a single window over the same connection, you can use a terminal multiplexer. One common program that provides this functionality is tmux.
This example shows how to load the must recent version of tmux on Palmetto and
how to use tmux.
View the tmux example on GitHub
Trinity
Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.