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.
For a list of all software installed on Bridges-2, type module spider. For a list of biological science software, type bioinformatics.
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 |
| Abinit | Calculates electronic density and derived properties of materials (incl. molecules, surfaces & solids) within DFT using pseudopotentials and a planewave or wavelet basis | Bridges-2 |
| ABySS | Parallel assembler for short read sequence data | Bridges-2 |
| AMBER | Package of molecular simulation programs | You must have your own license. PSC can help with installation. |
| Anaconda | Open data science platform, includes popular Python, R and SCALA packages | Bridges-2 |
| ANSYS | General purpose finite element modeling package | Bridges-2 |
| AOCL | Numerical library suite optimized for AMD processors | Bridges-2 |
| asciinema | Allows recording and sharing terminal sessions | Bridges-2 |
| AUGUSTUS | Predicts genes in eucaryotic genomic sequences | Bridges-2 |
| BAMTools | C++ API and toolkit for analyzing and managing BAM files | Bridges-2 |
| BCFTools | Utilities for variant calling and manipulating VCFs and BCFs | Bridges-2 |
| Bedops | Tools to address common questions raised in genomics studies | Bridges-2 |
| Bedtools | Utilities for comparing, summarizing and intersecting genomic features in the UCSC Genome Browser BED format | Bridges-2 |
| Bismark | Bisulfite read mapper and methylation caller | Bridges-2 |
| BLAST | Search tool that finds regions of local similarity between nucleotide or protein sequences | Bridges-2 |
| BLAT | Alignment tool like BLAST, but structured differently | 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. | Bridges-2 |
| BUSCO | Assesses genome assembly and annotation completeness | Bridges-2 |
| BWA | Fast light-weight tool that aligns relatively short sequences to a sequence database | Bridges-2 |
| C, C++ See the Bridges-2 User Guide for documentation on C and C++ |
Programming languages | Bridges-2 |
| Caffe | Deep learning framework | Bridges-2 |
| CheckM | Tools to assess the quality of genomes recovered from isolates, single cells, or metagenomes | Bridges-2 |
| Circos | Displays data in a circular layout | 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 |
| 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 | Bridges-2 |
| DDT | Debugger for C, C++ and Fortran 90 threaded and parallel codes | Bridges-2 |
| deal.ii | C++ library for finite element codes | Bridges-2 |
| DReAMM | Designs, renders and animates the output from a MCell simulation | |
| FastANI | Fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI) | Bridges-2 |
| FASTA-Splitter | Divides a single FASTA file into multiple files | Bridges-2 |
| FASTQ-Splitter | Divides a single FASTQ file into multiple files | Bridges-2 |
| FastQC | Quality control tool for high throughput sequence data | Bridges-2 |
| FASTX Toolkit | Command line tools for Short-Reads FASTA/FASTQ files preprocessing | 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 |
| Fortran See the Bridges-2 User Guide for documentation on Fortran |
Programming language | Bridges-2 |
| Funannotate | Genome prediction, annotation and comparison | Bridges-2 |
| GATK | Genome Analysis Toolkit, for high-throughput sequencing data | Bridges-2 |
| Gaussian | Electronic structure program | Bridges-2 |
| GCC
See theBridges-2 User Guide for documentation on the GNU compilers |
(GNU Compiler Collection) Compiler system supporting various programming languages | Bridges-2 |
| GeneMark-ES | Gene prediction in eukaryotes | Bridges-2 |
| GeNT | Computes the cross entropy for groups of sequences that have been assigned to groups on the basis of biochemical, physiological, or another biological property | 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-2 |
| GROMACS | Molecular dynamics software primarily designed for biomolecular systems | Bridges-2 |
| Guppy | Data processing toolkit containing the Oxford Nanopore Technologies’ basecalling algorithms | Bridges-2 |
| Gurobi | Mathematical programming solver | Bridges-2 |
| hashdeep | Computes hash files, or message digests, for any number of files | Bridges-2 |
| 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 | |
| HTSlib | C library for reading and writing high-throughput sequence data | Bridges-2 |
| iCommands | Library of commands to access iRODS servers | Bridges-2 |
| Infernal | Searches DNA sequence databases for RNA structure and sequence similarities | Bridges-2 |
| ICC (Intel)
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-2 |
| Kracken2 | Taxonomic sequence classifier that assigns taxonomic labels to DNA sequences | Bridges-2 |
| LAMMPS | Classical molecular dynamics code | Bridges-2 |
| lazygit | Simple terminal UI for git commands | Bridges-2 |
| lowcharts | Tool to draw low-resolution charts in the terminal | 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 | |
| MEME Suite | Collection of tools for the discovery and analysis of sequence motifs | Bridges-2 |
| 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. |
Bridges-2 |
| 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 |
| ncview | Viewer for netCDF format files | Bridges-2 |
| NVHPC
See the Bridges-2 User Guide for documentation on the NVHPC (formerly named PGI) compilers |
NVHPC (formerly called PGI) compilers and Tools | Bridges-2 |
| NWCHEM | Computes the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density | Bridges-2 |
| Octave | High-level programming language, intended for computation | Bridges-2 |
| OnDemand | Web browser interface to manage files, submit and track jobs on Bridges-2 | 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 |
| OpenMPI 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 |
| PGI
See the Bridges-2 User Guide for documentation on the PGI, now named NVHPC compilers |
NVHPC (formerly called PGI) compilers and Tools | Bridges-2 |
| PHYLIP | Package for inferring phylogenies | 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 |
| PLUMED | Library of enhanced sampling methods, free energy methods, tools to analyze data for MD simulations | Bridges-2 |
| pnetCDF | High-performance, parallel library for files compatible with netCDF | Bridges-2 |
| Prodigal | Open source lightweight microbial genefinding program | Bridges-2 |
| Prokka | Software tool for rapid annotation of prokaryotic genomes | Bridges-2 |
| Python (including 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 |
| Rclone | Tool for managing files in cloud storage | Bridges-2 |
| RNAview | Generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions | 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 |
| TIGER | Precisely maps IGEs in bacterial and archaeal genomes | 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 |
| tRNAscan-se | Program for improved detection of transfer RNA genes in genomic sequence | 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. |
| VCF2MAF | Tool to convert VCFs to MAFs | Bridges-2 |
| VCFtools | Tool providing easily accessible methods for working with complex genetic variation data in the form of VCF files | Bridges-2 |
| VisiData | Interactive tool to manage tabula data | 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:
Email: grants@psc.edu
Phone: 412/ 268-4960
Fax: 412/ 268-5831
Bridges-2
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