Software Installed on PSC Systems

Advancing state of the art high-performance computing, communications and data analytics.

This list includes software installed on most PSC computing resources. Anton runs specific software written for its specialized hardware and is not included here.  See the Anton document for specifics on Anton.

Supported vs. unsupported software

Most third-party software is supported by the PSC User Services staff. Sofware is updated regularly and a limited number of versions are maintained. Questions about usage or other issues for maintained software can be sent to the help desk at

On occasion, deprecated software or a deprecated version of a package may remain on the system by special request. In those cases, the software is retained on an as-is basis, and it may be used at the user’s own risk. It will not be updated or maintained. There is no expectation of support for this software, and questions about these packages will not be answered by the help desk.

Software that is unsupported or for which a deprecated version is available are highlighted in the table below in yellow, and it is noted in the Resource column that this software is unsupported.

The Module package

The environment management package Module is essential for running software on most PSC systems.  Be sure to check if there is a module for the software you want to use by typing module avail software-name

To load the environment for a software package, which defines paths and variables needed to use the software, type module load software-name.

The module spider software-name command lists any additional modules that must also be loaded.  Note that in some cases the order in which these additional modules are loaded matters. See documentation on the module command for more information.

Software Description Computing Resource
ABySS Parallel assembler for short read sequence data Unsupported – Bridges-2
Anaconda Open data science platform, includes popular Python, R and SCALA packages Bridges-2
ANSYS General purpose finite element modeling package Bridges-2
BAMTools C++ API and toolkit for analyzing and managing BAM files Unsupported – Bridges-2
BCFTools Utilities for variant calling and manipulating VCFs and BCFs Unsupported – Bridges-2
Bedops Tools to address common questions raised in genomics studies Unsupported – Bridges-2
Bedtools Utilities for comparing, summarizing and intersecting genomic features in the UCSC Genome Browser BED format Unsupported – Bridges-2
Bismark Bisulfite read mapper and methylation caller Unsupported – Bridges-2
BLAST Search tool that finds regions of local similarity between nucleotide or protein sequences Unsupported – Bridges-2
BLAT Alignment tool like BLAST, but structured differently Unsupported – Bridges-2
Boost Peer reviewed C++ source libraries Bridges-2
Bowtie2 Ultrafast, memory-efficient tool for aligning sequencing reads to long reference sequences. See related tool Bowtie. Unsupported – Bridges-2
BWA Fast light-weight tool that aligns relatively short sequences to a sequence database Unsupported – Bridges-2
C, C++
See the  Bridges-2 User Guide for documentation on C and C++
Programming languages Bridges-2
An unsupported version is available
Caffe Deep learning framework Bridges-2
CMake Tools to control the compilation process, build, test and package software Bridges-2
CP2K Atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems Bridges-2
An unsupported version is available
CUDA Parallel computing platform and API model Bridges-2
Cutadapt Reads a FASTA or FASTQ file, finds and removes adapters, writes the changed sequence to standard output Unsupported – Bridges-2
DDT Debugger for C, C++ and Fortran 90 threaded and parallel codes Bridges-2
DReAMM Designs, renders and animates the output from a MCell simulation
FASTA-Splitter Divides a single FASTA file into multiple files Unsupported – Bridges-2
FASTQ-Splitter Divides a single FASTQ file into multiple files Unsupported – Bridges-2
FastQC Quality control tool for high throughput sequence data Unsupported – Bridges-2
FASTX Toolkit Command line tools for Short-Reads FASTA/FASTQ files preprocessing Unsupported – Bridges-2
FFTW3 C subroutine library for computing the DFT in one or more dimensions, of arbitrary input size, of both real and complex data Bridges-2
FLASh Fast and accurate tool to merge paired-end reads from NGS experiments Bridges-2
Fluent Computational fluid dynamics, part of ANSYS Bridges-2
See the Bridges-2 User Guide for documentation on Fortran
Programming language Bridges-2
Galaxy Open, web-based platform for data intensive biomedical research. Bridges-2
GATK Genome Analysis Toolkit, for high-throughput sequencing data Bridges-2
Gaussian Electronic structure program Bridges-2

See theBridges-2 User Guide for documentation on the GNU compilers

(GNU Compiler Collection) Compiler system supporting various programming languages Bridges-2
Git Version control system for tracking changes in files and coordinating work on files among multiple people Bridges-2
GNU Parallel Shell tool for executing jobs in parallel using one or more computers Bridges
GROMACS Molecular dynamics software primarily designed for biomolecular systems Bridges-2
Gurobi Mathematical programming solver Bridges-2
Hadoop Big Data processing framework Bridges
HDF5/PHDF5 Data model, library, and file format for storing and managing data and its parallel version Bridges-2
HISAT2 Fast, sensitive alignment, mapping NGS reads (DNA & RNA) to a population of human genomes or against a single reference genome Bridges-2
HMMER Biosequence analysis using profile hidden Markov models Bridges-2
Homer Suite of tools for motif discovery and next-gen sequence analysis Bridges-2
HPN-SSH Series of patches for OpenSSH to provide improved performance and functionality




See the  Bridges-2 User Guide for documentation on the Intel compilers

Intel compilers, libraries and MPI implementation Bridges-2
Java Programming language Bridges-2
Julia High-level, high-performance dynamic programming language for numerical computing Bridges-2
Jupyter Create and share code, visualizations, equations, more Bridges-2
Keras Minimalist, highly modular neural networks library written in Python and capable of running on top of either TensorFlow or Theano Bridges
LAMMPS Classical molecular dynamics code Bridges-2
LSMS Locally Self-consistent Multiple Scattering method, an order-N approach to the calculating the electronic structure of large systems within the local density approximation
MATLAB High-level language and interactive environment, performs computationally intensive tasks faster than traditional languages Bridges-2
MCell Monte Carlo Cell, simulates the movements and reactions of molecules within and between cells
Methylpy Bisulfate sequencing data processing and differential methylation analysis Bridges-2
MKL Math Kernel Library, highly optimized and threaded routines for linear algebra, FFTs, vector math and random number generators Bridges-2
MPI Message Passing Interface. Both Intel MPI and Open MPI are available.

See the Bridges-2 User Guide for documentation on MPI.

MVAPICH Library exploiting novel features and mechanisms of high-performance networking technologies. Delivers improved performance and scalability to MPI applications. Bridges-2
NAMD Parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems Bridges-2
Ncdu Disk usage analyzer Bridges-2

See PnetCDF for Bridges-2

Software libraries and self-describing, machine-independent data formats supporting the creation, access, and sharing of array-oriented scientific data Bridges-2
NWCHEM Computes the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density Bridges-2
OnDemand Web browser interface to manage files, submit and track jobs on Briges Bridges-2
OpenBLAS Optimized BLAS library Bridges-2
OpenCV Open source library of several hundred computer vision algorithms Bridges-2
OpenFOAM Finite volume CFD package Bridges-2
An unsupported version is available
See the Bridges-2 User Guide for documentation on OpenMPI
High performance message passing library Bridges-2
ORCA Ab-initio quantum chemistry Bridges-2
Perl Programming language Bridges-2

See the  Bridges-2 User Guide for documentation on the PGI compilers

PGI compilers and Tools Bridges-2
An unsupported version is available
pnetCDF High-performance, parallel library for files compatible with netCDF Bridges-2
Picard Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files Bridges-2
Prodigal Open source lightweight microbial genefinding program Bridges-2
Python (including  matplotlib, numpy, scipy) Powerful, object-oriented programming language Bridges-2
Quantum Espresso Integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale Bridges-2
R Language and environment and an IDE for statistical computing and graphs Bridges-2
RAxML Maximum likelihood phylogeny estimation for interpreting relationships between sets of data Bridges-2
SAMtools Utilities for manipulating alignments in SAM format Bridges-2
Scikit-learn Simple and efficient tools for data mining and data analysis, built on NumPy, SciPy and matplotlib Bridges-2
Singularity Open-source software container platform Bridges-2
SPAdes St. Petersburg genome assembler – an assembly toolkit with various assembly pipelines Bridges-2
Spark Open source software web application framework and domain-specific language written in Java Bridges-2
SRA toolkit Collection of tools and libraries for using data in the INSDC Sequence Read Archives Bridges-2
STAR-Fusion Uses the STAR aligner to dentify candidate fusion transcripts supported by Illumina reads, maps junction and spanning reads to a reference annotation set Bridges-2
STAR Aligner Spliced Transcripts Alignment to Reference, an alignment tool for RNA sequences Bridges-2
TensorFlow Machine learning library for numerical computation using data flow graphs Bridges-2
Theano Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently Bridges-2
tmux Terminal multiplexer; create and control multiple terminals Bridges-2
Trinity Package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data Bridges-2
VASP Atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. You must have your own license. PSC can help with installation.
VCFtools Tool providing easily accessible methods for working with complex genetic variation data in the form of VCF files Bridges-2
Visit Interactive and scalable visualization, animation and analysis tool Bridges-2
VTune Performance analysis tool for serial, multithreaded or MPI applications Bridges-2
WIEN2k Electronic structure calculations of solids using DFT You must have your own license. PSC can help with installation.
Xfig and transfig Interactive drawing tools Bridges-2
Zoltan Data management services for unstructured, adaptive and dynamic applications Bridges-2

Allocations questions

Please see the Allocations FAQ page.

For questions not answered in the FAQ, contact the PSC Allocations department at:

Phone: 412/ 268-4960
Fax: 412/ 268-5831


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