Apps for All Your Research Needs

The ICDS team operates and maintains a wide-range computing software stack selected with researchers and students in mind. In addition to the software required for the Roar system (formerly known as ICDS-ACI) system to function (e.g., operating systems and batch job schedulers), the stack includes application-driving software (e.g., compilers and communication libraries) and commonly used research applications such as MATLAB, R, and COMSOL.

Software Updates and Additions

Our software stack undergoes biannual baseline-delivery updates to install new software or newer versions of existing software.

If you would like to use an application that is not part of our software stack, you may

  • install and maintain it on your own storage space, or
  • request that it be added to the stack in the next update by submitting a ticket to the ICDS i-ASK Center.

Please review our software policy on installing your own software and requesting additions to the software stack.

Current Software in the Stack (as of May 2020)

NOTE: This list reflects the software available for use with the RHEL6 operating system on Roar. For the RHEL7 software stack, many older point releases have been retired to make way for for recent versions. For a complete list of these changes, see the FAQ Regarding the Transition to RHEL7.

The following is a list of the modules currently available in the RHEL6 software stack:



Version(s) installed: abaqus/2017, abaqus/2018

Abaqus is a software suite for finite element analysis and computer-aided engineering.

Developer Website


Version(s) installed: abinit/8.0.8b

ABINIT is a software suite to calculate the optical, mechanical, vibrational, and other observable properties of materials.

Developer Website


Version(s) installed: adf/2019.103, adf/2019.303

ADF (Amsterdam Density Functional) is a DFT program particularly strong in understanding and predicting structure, reactivity, and spectra of molecules.

Developer Website | User Guide


Version(s) installed: afni/17.2.05

AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.

Developer Website


Version(s) installed: amber/14, amber/18

Assisted Model Building with Energy Refinement (AMBER) is a software package for simulating force fields for molecular dynamics of biomolecules.

Developer Website


Version(s) installed: ampl/20170731, ampl/20190529

The AMPL system supports the entire optimization modeling lifecycle formulation, testing, deployment, and maintenance in an integrated way promotes rapid development and reliable results.


Version(s) installed: ansys/19.1, ansys/2019R3

The Ansys software suite provides engineering simulation software for structural mechanics, fluid dynamics, and electromagnetics, as well as pre- and post-processing.

Developer Website


Version(s) installed: arpack-ng/3.4.0

ARPACK is a collection of Fortran77 subroutines designed to solve large-scale eigenvalue problems

Developer Website


Version(s) installed: avizo/9.4.0, avizo/9.5.0

Avizo is a 3D analysis software for scientific and industrial data

Developer Website


Version(s) installed: bamtools/2.4.1

A fast, flexible C++ API and toolkit for reading, writing, and managing BAM files.

Developer Website


Version(s) installed: beast/1.15

BEaST stands for "Brain Extraction based on nonlocal Segmentation Technique."

Developer Website


Version(s) installed: bedtools/2.26.0, bedtools/2.27.1

A powerful toolset for genome arithmetic.

Developer Website


Version(s) installed: 3.6.0

The BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations.

Developer Website


Version(s) installed: blat/36

BLAT is a program that compares strings of DNA and is used for comparing SNP barcodes in this identity program.

Developer Website


Version(s) installed: boost/1.61.0, boost/1.63.0

Boost provides free peer-reviewed portable C++ source libraries.

Developer Website

BWA (Burrows-Wheeler Aligner)

Version(s) installed: bwa/0.7.15

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.

Developer Website


Version(s) installed: campari/2.2015.05.29

Software for molecular simulations and trajectory analysis.

Developer Website


Version(s) installed: charmxx/6.8.0

Charm++ is a machine independent parallel programming system.

Developer Website


Version(s) installed: clang/3.9.1

A C language family front-end for LLVM.

Developer Website


Version(s) installed: clustalw2/2.1

Multiple Sequence Alignment Program.

Developer Website


Version(s) installed: cmake/3.9.1

CMake is a family of tools designed to build, test, and package software

Developer Website


Version(s) installed: comsol/5.2a, comsol/5.3, comsol/5.4

COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating  physics-based problems.

Developer Website


Version(s) installed: cplex/12.8.0

The IBM ILOG CPLEX Optimization Studio consists of the CPLEX Optimizer for mathematical programming, the IBM ILOG CPLEX CP Optimizer for constraint programming, the Optimization Programming Language (OPL), and an integrated IDE.

Developer Website


Version(s) installed: ddt/7.1

Parallel debugger supporting a wide range of parallel architectures and models, including MPI, UPC, CUDA, and OpenMP

Developer Website


Version(s) installed: dl_poly/4.08

DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.

Developer Website


Version(s) installed: express/1.5.1

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.

Developer Website


Version(s) installed: fastqc/0.11.2

A quality control application for FastQ files.

Developer Website


Version(s) installed: fastx_toolkit/0.0.14

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files pre-processing.

Developer Website


Version(s) installed: ffmpeg/3.1.1, ffmpeg/3.3.3

Multimedia framework to decode, encode, transcode, mux, demux, stream, and filter video and audio.

Developer Website


Version(s) installed: 3.3.5

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.

Developer Website


Version(s) installed: freebayes/1.1.0, freebayes/1.2.0

Freebayes is a Bayesian genetic variant detector.


Version(s) installed: freesurfer/5.3.0, freesurfer/6.0.0

An open-source software suite for processing and analyzing (human) brain MRI images.

Developer Website


Version(s) installed: fsl/5.0.10

FSL is a functional MRI of the brain (FMRIB) software library.

Developer Website


Version(s) installed: gams/24.8.5, gams/28.2.0

The General Algebraic Modeling System (GAMS) is a high-level modeling system for mathematical programming and optimization.

Developer Website


Version(s) installed: gauss/19.2.0

An easy-to-use data analysis, mathematical and statistical environment based on the powerful, fast and efficient GAUSS Matrix Programming Language.

Developer Website


Version(s) installed: gaussian/g03e1, gaussian/g09d01

Gaussian is a general-purpose computational chemistry software package.

Developer Website


Version(s) installed: gcc/5.3.1, gcc/7.3.1

GNU Compiler Collection (GCC)

Developer Website


Version(s) installed: git/1.9.4 (RedHat SCL version)

Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

Developer Website


Version(s) installed: gromacs/5.1.4

GROMACS is a versatile package to perform molecular dynamics.

Developer Website


Version(s) installed: hdf5/1.8.18

HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.

Developer Website


Version(s) installed: htslib/1.1

An implementation of a unified C library for accessing common file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools.

Developer Website


Version(s) installed: idl/8.5

IDL is the trusted scientific programming language used across disciplines to extract meaningful visualizations from complex numerical data.

Developer Website


Version(s) installed: impi/5.1.3, impi/2019.5

Intel MPI library.

Developer Website


Version(s) installed: intel/16.0.3, intel/19.0.5

Intel C, C++ and Fortran compilers.

Developer Website


Version(s) installed: jags/4.2.0

JAGS (Just Another Gibbs Sampler) is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.

Developer Website


Version(s) installed: julia/0.6.0, julia/1.3.1

Julia is a high-level, high-performance dynamic programming language for numerical computing.

Developer Website


Version(s) installed: kim-api/1.8.2

The KIM API is an Application Programming Interface for atomistic simulations.

Developer Website


Version(s) installed: knitro/10.2.1, knitro/12.0.0

Knitro is an optimization software library for finding solutions of both continuous optimization models, as well as discrete optimization models.

Developer Website


Version(s) installed: lammps/20150210, lammps/20160827

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

Developer Website


Version(s) installed: lapack/3.6.0

LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.

Developer Website


Version(s) installed: lmod/6.5.1

Lmod is a Lua based module system that easily handles the MODULEPATH Hierarchical problem. Environment Modules provide a convenient way to dynamically change the users’ environment through modulefiles.

Developer Website


Version(s) installed: lsdyna/R9.0.1

LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems.

Developer Website


Version(s) installed: lsprepost/4.3

LS-PrePost is a pre- and post-processor for LS-DYNA.

Developer Website


Version(s) installed: mafft/7.310

Multiple alignment program for amino acid or nucleotide sequences

Developer Website


Version(s) installed: mathematica/11.0.1

Mathematica is a fully integrated software environment for technical and scientific computing.

Developer Website


Version(s) installed: matlab/R2016a, matlab/R2017b, matlab/R2019a

MATLAB (r) is a high-level language and interactive environment for numerical computation, visualization, and programming.

Developer Website


Version(s) installed: 5.1.0

METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices.

Developer Website


Version(s) installed: mkl/11.3.3, mkl/2019.5

Intel® Math Kernel Library (Intel® MKL) optimizes code with minimal effort for future generations of Intel® processors.

Developer Website


Version(s) installed: mpich/3.2

MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.

Developer Website


Version(s) installed: mugsy/1.2.3

Mugsy is a multiple whole genome aligner.

Developer Website


Version(s) installed: muscle/3.8.31

Popular multiple alignment software.

Developer Website


Version(s) installed: ncbi-blast/2.6.0

The BLAST+ package offers three categories of applications: 1 - search tools, 2 - BLAST database tools, and 3 - sequence filtering tools.

Developer Website


Version(s) installed: netcdf/4.4.1

NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Developer Website


Version(s) installed: netcdf-cxx/4.3.0

NetCDF-CXX is the cxx specific version of a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Developer Website


Version(s) installed: netcdf-fortran/4.4.4

NetCDF-Fortran is the fortran specific version of a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Developer Website


Version(s) installed: openjdk/1.8.0

Open Java Development Kit.

Developer Website


Version(s) installed: openmpi/1.10.1

A powerful implementation of MPI/SHMEM.

Developer Website


Version(s) installed: oraclejdk/1.8.0

Oracle Java Development Kit.

Developer Website


Version(s) installed: parallel/20170522

GNU parallel is a shell tool for executing jobs in parallel using one or more computers.

Developer Website


Version(s) installed: paraview/5.4.0

ParaView is an open-source, multi-platform data analysis and visualization application.

Developer Website


Version(s) installed: parmetis/4.0.3

ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.

Developer Website


Version(s) installed: petsc/3.7.3, petsc/3.8.3

PETSC is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.

Developer Website


Version(s) installed: pgi/16.4, pgi/18.5

Portland Group (PGI) is a premier supplier of software compilers and tool for parallel computing, known as PGI products. The Portland Group offers optimizing parallel FORTRAN 2003, C99, and C++ compilers and tools for workstations, servers and clusters running Linux, MacOS, and Windows.

Developer Website


Version(s) installed: picard/2.5.0

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Developer Website


Version(s) installed: ploticus/2.42

Ploticus is a free GPL software utility that can produce various types of plots and graphs.

Developer Website


Version(s) installed: pointwise/18.2R2

Pointwise is a software system for the generation of 3D grids and meshes, and preprocessing for computational fluid dynamics (CFD)

Developer Website | User Guide


Version(s) installed: python/2.7.14-anaconda5.0.1, python/3.6.3-anaconda5.0.1

Python 2.7.14 (Anaconda 5.0.1)

Developer Website

Quantum Espresso

Version(s) installed: quantum_espresso/5.4.0

Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale.

Developer Website


Version(s) installed: r/3.4

R is a free software environment for statistical computing and graphics.

Developer Website


Version(s) installed: samtools/0.1.19, samtools/1.5

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.

Developer Website


Version(s) installed: sas/9.4

SAS is a software suite for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.

Developer Website


Version(s) installed: schrodinger/2016.4, schrodinger/2019.4

A suite of chemical simulation software.

Developer Website


Version(s) installed: settarg/6.5.1

The Settarg module works with Lmod to help developers manage their compiled software projects.

Developer Website


Version(s) installed: spm/8, spm/12

The SPM software is a suite of MATLAB functions and subroutines with some externally compiled C routines. SPM was written to organise and interpret functional neuroimaging data.

Developer Website


Version(s) installed: spss/25

The IBM SPSS® software platform offers advanced statistical analysis.

Developer Website


Version(s) installed: ssake/4.0

SSAKE is a de novo assembler for short DNA sequence reads.

Developer Website


Version(s) installed: starccm/12.04.010, starccm/14.04.011

STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface.

Developer Website


Version(s) installed: Stata/14.2

Stata is a statistical package for managing, analyzing, and graphing data.

Developer Website


Version(s) installed: tau/2.27

TAU is a program and performance analysis tool framework being developed for the DOE and ASC program at the University of Oregon.

Developer Website


Version(s) installed: tbb/4.4.4, tbb/2017, tbb/2019.8

TBB is a widely used C++ template library for task parallelism.

Developer Website


Version(s) installed: tecplot/2017r1

Tecplot is a suite of visual data analysis software used in post-processing CFD, simulation and experimental results – Tecplot 360EX, Tecplot Chorus and Tecplot RS.

Developer Website


Version(s) installed: totalview/2017.1.21

Parallel debugger supporting a wide range of parallel architectures and models, including MPI, UPC, CUDA and OpenMP.

Developer Website


Version(s) installed: trinity/2.2.0

Trinity is a package for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

Developer Website


Version(s) installed: varscan/2.4.2

VarScan is a platform-independent genome software tool.


Version(s) installed: vmd/1.9.3

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Developer Website | User Guide

VTune Amplifier

Version(s) installed: vtune-amplifier/16.4, vtune-amplifier/2018.1

A performance profiler for HPC code.

Developer Website


Version(s) installed: wgs/8.3

Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler.

Developer Website


Version(s) installed: xblas/1.0.248

This library of routines is part of a reference implementation for the Dense and Banded BLAS routines, along with their Extended and Mixed Precision versions.

Developer Website


Version(s) installed: xdrf/1.2

A portable data compression library.

Developer Website


Version(s) installed: zlib/1.2.11

zlib is a software library used for data compression.