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

The following is a list of the modules currently available in the RHEL7 software stack:

 

Abaqus

Version(s) installed: abaqus/2018

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

Developer Website

ABINIT

Version(s) installed: abinit/8.0.8b

ABINIT is a software suite to calculate the optical, mechanical, vibrational, and other observable properties of materials. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • ABINIT 8.10.3

Developer Website

ADF

Version(s) installed: 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

AFNI

Version(s) installed: afni/20.2.11

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

AMBER

Version(s) installed: amber/18

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

Developer Website

AMPL

Version(s) installed: 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.

Anaconda

Version(s) installed: anaconda3/2020.07

Anaconda

Developer Website

Ansys

Version(s) installed: 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

ARPACK-NG

Version(s) installed: arpack-ng/3.4.0

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

Developer Website

Aspera

Version(s) installed: aspera-cli/3.9.6

Aspera is a data transport and streaming technology company that provides high speed data transfer services. Aspera belongs to the hybrid cloud business unit of IBM. Note: This software is located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

Developer Website

Avizo

Version(s) installed: avizo/9.7.0, avizo/2020.1

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

Developer Website

Avogadro

Version(s) installed: avogadro/1.2

Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. Note: This software is located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

Developer Website | User Guide

BamTools

Version(s) installed: bamtools/2.4.1

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

Developer Website

BEaST

Version(s) installed: beast/1.10.4, beast2/2.5.2

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

Developer Website

Bedtools

Version(s) installed: bedtools/2.27.1

A powerful toolset for genome arithmetic.

Developer Website

BLAS

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

BLAT

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

Boost

Version(s) installed: 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

Campari

Version(s) installed: campari/2.2015.05.29

Software for molecular simulations and trajectory analysis.

Developer Website

Charm++

Version(s) installed: charmxx/6.8.0

Charm++ is a machine independent parallel programming system.

Developer Website

Clang

Version(s) installed: clang/3.9.1

A C language family front-end for LLVM.

Developer Website

ClustalW2

Version(s) installed: clustalw2/2.1

Multiple Sequence Alignment Program.

Developer Website

CMake

Version(s) installed: cmake/3.16.2

CMake is a family of tools designed to build, test, and package software. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • CMAKE 3.19

Developer Website

COMSOL

Version(s) installed: comsol/5.4

COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating  physics-based problems. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • comsol/5.6

Developer Website

CP2K

Version(s) installed: CP2K 7.1

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. Note: This software is located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

Developer Website | User Guide

CPLEX

Version(s) installed: cplex/12.10.0

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

DDT

Version(s) installed: ddt/20.1.1

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

Developer Website

DL_POLY

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

eXpress

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

FastQC

Version(s) installed: fastqc/0.11.7

A quality control application for FastQ files.

Developer Website

FASTX-Toolkit

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

FFmpeg

Version(s) installed: ffmpeg/4.1.1

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

Developer Website

FFTW

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

freebayes

Version(s) installed: freebayes/1.1.0

Freebayes is a Bayesian genetic variant detector.

FreeSurfer

Version(s) installed: freesurfer/7.1.1

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

Developer Website

fsl

Version(s) installed: fsl/5.0.10

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

Developer Website

GAMS

Version(s) installed: gams/28.2.0

The General Algebraic Modeling System (GAMS) is a high-level modeling system for mathematical programming and optimization. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • gams/33.2-s

Developer Website

Gaussian

Version(s) installed: gaussian/g09c01

Gaussian is a general-purpose computational chemistry software package. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • Gaussian 16 c01

Developer Website

GCC

Version(s) installed: gcc/8.3.1, gcc/9.3.1

GNU Compiler Collection (GCC)

Developer Website

Git

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. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • git/2.30.0-gcc-8.3.1

Developer Website

GROMACS

Version(s) installed: gromacs/2019.5

GROMACS is a versatile package to perform molecular dynamics. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • gromacs/5.1.5-gcc-8.3.1-openmpi-3.1.6-cuda-10.2.89
  • gromacs/5.1.5
  • gromacs/2020.5-gcc-8.3.1-openmpi-3.1.6-cuda-10.2.89
  • gromacs/2020.5

Developer Website

HDF5

Version(s) installed: hdf5/1.10.7

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

Developer Website

HTSLib

Version(s) installed: htslib/1.10.2

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

IDL

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

IMPI

Version(s) installed: impi/2019.8

Intel MPI library.

Developer Website

Intel

Version(s) installed: intel/19.1.2

Intel C, C++ and Fortran compilers.

Developer Website

JAGS

Version(s) installed: jags/4.3.0

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

Developer Website

Julia

Version(s) installed: julia/1.3.1

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

Developer Website

KIM-API

Version(s) installed: kim-api/2.1.3

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

Developer Website

Knitro

Version(s) installed: knitro/12.2.2

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

Developer Website

LAMMPS

Version(s) installed: lammps/20190807

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • lammps/20200303

Developer Website

LAPACK

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. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • lapack/3.9.0-gcc

Developer Website

Lmod

Version(s) installed: lmod/8.2.7

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

LS-DYNA

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

LS-PrePost

Version(s) installed: lsprepost/4.3

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

Developer Website

MAFFT

Version(s) installed: mafft/7.453

Multiple alignment program for amino acid or nucleotide sequences

Developer Website

Mathematica

Version(s) installed: mathematica/12.0.0

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

Developer Website

MATLAB

Version(s) installed: matlab/R2019b

MATLAB (r) is a high-level language and interactive environment for numerical computation, visualization, and programming. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • matlab/R2017b

Developer Website

METIS

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

MKL

Version(s) installed: mkl/2020.3

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

Developer Website

MPICH

Version(s) installed: mpich/3.2

MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • mpich/3.4-gcc-4.8.5 /li>

Developer Website

Mugsy

Version(s) installed: mugsy/1.2.3

Mugsy is a multiple whole genome aligner.

Developer Website

MUSCLE

Version(s) installed: muscle/3.8.1551

Popular multiple alignment software.

Developer Website

NCBI-RMBLASTN

Version(s) installed: ncbi-rmblastn/2.9.0

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

Developer Website

NetCDF

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

NetCDF-CXX

Version(s) installed: netcdf-cxx/4.2

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

NetCDF-Fortan

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

Openfoam

Version(s) installed: openfoam/v2012-gcc-8.3.1

OpenFOAM is the free, open source CFD software developed primarily by OpenCFD Ltd since 2004. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.

Developer Website

OpenJDK

Version(s) installed: openjdk/11.0.6.10

Open Java Development Kit.

Developer Website

OpenMPI

Version(s) installed: openmpi/3.1.5

A powerful implementation of MPI/SHMEM. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • openmpi/4.1.0-gcc-4.8.5

Developer Website

OracleJDK

Version(s) installed: oraclejdk/1.8.0

Oracle Java Development Kit.

Developer Website

Parallel

Version(s) installed: parallel/20190222

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

Developer Website

Paraview

Version(s) installed: paraview/5.4.0

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

Developer Website

ParMETIS

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

PETSC

Version(s) installed: 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

PGI

Version(s) installed: pgi/18.10

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

Picard

Version(s) installed: picard/2.20.8

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

Ploticus

Version(s) installed: ploticus/2.42

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

Developer Website

Pointwise

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

Python

Version(s) installed: python/2.7.5, python/3.6.8

Python

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. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • qe/6.3-intel-19.1.2, qe/6.4.1-intel-19.1.2

Developer Website

R

Version(s) installed: r/4.0.3

R is a free software environment for statistical computing and graphics. Note: This software is located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

Developer Website

SAM

Version(s) installed: samtools/1.5

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

Developer Website

SAS

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

Schrodinger

Version(s) installed: schrodinger/2019.4

A suite of chemical simulation software.

Developer Website

Settarg

Version(s) installed: settarg/6.5.1

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

Developer Website

Spark

Version(s) installed: spark/3.0.2

Apache Spark is an open-source unified analytics engine for large-scale data processing. Note: This software is located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

Developer Website | User Guide

SPM

Version(s) installed: 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

SPSS

Version(s) installed: spss/25

The IBM SPSS® software platform offers advanced statistical analysis.

Developer Website

SSAKE

Version(s) installed: ssake/4.0

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

Developer Website

STAR-CCM+

Version(s) installed: starccm/14.04.011-R8

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

Developer Website

Stata

Version(s) installed: Stata/16

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

Developer Website

TAU

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

TBB

Version(s) installed: tbb/2020.8

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

Developer Website

Tecplot

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

TotalView

Version(s) installed: totalview/2019.2.12

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

Developer Website

Trinity

Version(s) installed: trinity/2.6.6

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

Developer Website

VarScan

Version(s) installed: varscan/2.4.2

VarScan is a platform-independent genome software tool.

VASP

Version(s) installed: vasp/5.4.4

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • vasp/vasp-5.4.1a
  • vasp/vasp-5.4.1v
  • vasp/vasp-5.4.4a-vtst
  • vasp/vasp-5.4.4v
  • vasp/vasp-5.4.4vtst

Developer Website

VASP_VTST

Version(s) installed: vasp_vtst/5.4.4

Vienna Ab Initio Simulation Package with TST.

VMD

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. Note: The following additional versions of this software are located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

  • vmd/1.9.3

Developer Website | User Guide

VTune Amplifier

Version(s) installed: vtune-amplifier/2020.3

A performance profiler for HPC code.

Developer Website

WGS

Version(s) installed: wgs/8.3rc2

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

Developer Website

XBLAS

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

XCRYSDEN

Version(s) installed: xcrysden/1.6.2

XCrySDen is a crystalline and molecular structure visualization program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. Note: This software is located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

Developer Website | User Guide

XDRF

Version(s) installed: xdrf/1.2

A portable data compression library.

Developer Website

XMGRACE

Version(s) installed: xmgrace

Xmgrace is a 2D plotting tool which allows you to interactively modify plots, to set all kind of plot parameters, change the appearance of your figure, and to save the figure in the format of your choice. Note: This software is located in the supplemental software stack at “/gpfs/group/RISE/sw7”. Access to some items in this stack is limited due to licensing restrictions; contact the i-ASK helpdesk for access.

Developer Website | User Guide

zlib

Version(s) installed: zlib/1.2.11

zlib is a software library used for data compression.