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 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

Roar Version(s) installed: abaqus/2018, abaqus/2021, abaqus/2022

Roar-Collab Version(s) installed: abaqus/2022

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

Developer Website

ABINIT

Roar 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

Roar 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

Roar Version(s) installed: afni/20.2.11, afni/21.3.04

Roar-Collab Version(s) installed: afni/21.3.04

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

Roar 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

Roar Version(s) installed: ampl/20190529, ampl/20210226, ampl/20220525

Roar-Collab Version(s) installed: ampl/20220525

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

Roar Version(s) installed: anaconda3/2020.07, anaconda3/2021.05

Roar-Collab Version(s) installed: anaconda3/2021.05

Anaconda

Developer Website

Ansys

Roar Version(s) installed: ansys/2021R1, ansys/2021R2, ansys/2022R1

Roar-Collab Version(s) installed: ansys/2022R1

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

Developer Website

Aspera

Roar 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

Roar Version(s) installed: avizo/2021.1

Roar-Collab Version(s) installed: avizo/2021.1

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

Developer Website

Avogadro

Roar 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

Roar Version(s) installed: bamtools/2.4.1, bamtools/2.5.1

Roar-Collab Version(s) installed: bamtools/2.5.1

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

Developer Website

Bedtools

Roar Version(s) installed: bedtools/2.27.1, bedtools/2.30.0

Roar-Collab Version(s) installed: bedtools/2.30.0

A powerful toolset for genome arithmetic.

Developer Website

BLAS

Roar 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

Boost

Roar Version(s) installed: boost/1.63.0, boost/1.74.0, boost/1.77.0

Roar-Collab Version(s) installed: boost/1.77.0

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

Developer Website

Bowtie 2

Roar Version(s) installed: bowtie2/2.4.2

Roar-Collab Version(s) installed: bowtie2/2.4.2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Developer Website | User Guide

BWA (Burrows-Wheeler Aligner)

Roar Version(s) installed: bwa/0.7.15

Roar-Collab Version(s) installed: bwa/0.7.17

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

Developer Website

Campari

Roar Version(s) installed: campari/2.2015.05.29

Software for molecular simulations and trajectory analysis.

Developer Website

Clang

Roar Version(s) installed: clang/3.9.1

A C language family front-end for LLVM.

Developer Website

CMake

Roar Version(s) installed: cmake/3.18.4, cmake/3.21.4

Roar-Collab Version(s) installed: cmake/3.21.4

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

Roar Version(s) installed: comsol/5.4, comsol/5.6 (update 2), comsol/6.0 (update 2)

Roar-Collab Version(s) installed: comsol/6.0 (update 2)

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

Roar 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

Roar Version(s) installed: cplex/12.10.0

Roar-Collab 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

cuda

Roar Version(s) installed: cuda/10.2.89, cuda/11.1.0, cuda/11.5.0

Roar-Collab Version(s) installed: cuda/10.1.243, cuda/11.5.0

Developer Website

DDT

Roar Version(s) installed: ddt/22.0.2

Roar-Collab Version(s) installed: ddt/22.0.2

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

Developer Website

DL_POLY

Roar 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

FastQC

Roar Version(s) installed: fastqc/0.11.7, fastqc/0.11.9

Roar-Collab Version(s) installed: fastqc/0.11.9

A quality control application for FastQ files.

Developer Website

FFmpeg

Roar Version(s) installed: ffmpeg/4.1.1, ffmpeg/4.2.2

Roar-Collab Version(s) installed: ffmpeg/4.3.2

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

Developer Website

FFTW

Roar Version(s) installed: 3.3.5, 3.3.10

Roar-Collab Version(s) installed: 3.3.10

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

FreeSurfer

Roar Version(s) installed: freesurfer/7.1.1, freesurfer/7.2.0

Roar-Collab Version(s) installed: freesurfer/7.2.0

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

Developer Website

fsl

Roar Version(s) installed: fsl/5.0.10

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

Developer Website

GAMS

Roar Version(s) installed: gams/33.2, gams/36.2, gams/39.1

Roar-Collab Version(s) installed: gams/39.1

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

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

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

Roar-Collab Version(s) installed: gcc/8.5.0

GNU Compiler Collection (GCC)

Developer Website

Git

Roar 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

Roar Version(s) installed: gromacs/2020.2, gromacs/2020.4, gromacs/2021.3

Roar-Collab Version(s) installed: gromacs/2021.3

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

Roar Version(s) installed: hdf5/1.10.7, hdf5/1.12.0

Roar-Collab Version(s) installed: hdf5/1.12.1

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

Developer Website

HTSLib

Roar Version(s) installed: htslib/1.10.2, htslib/1.13

Roar-Collab Version(s) installed: htslib/1.13

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

Roar Version(s) installed: idl/8.8, idl/8.8.1

Roar-Collab Version(s) installed: idl/8.8.1

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

Developer Website

IMPI

Roar Version(s) installed: impi/2019.8

Roar-Collab Version(s) installed: impi/2019.8

Intel MPI library.

Developer Website

Intel

Roar Version(s) installed: intel/19.1.2

Intel C, C++ and Fortran compilers.

Developer Website

JAGS

Roar Version(s) installed: jags/4.3.0

Roar-Collab 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

Roar Version(s) installed: julia/1.3.1, julia/1.5.3, julia/1.6.2

Roar-Collab Version(s) installed: julia/1.6.2

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

Developer Website

KIM-API

Roar Version(s) installed: kim-api/2.1.3

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

Developer Website

Knitro

Roar Version(s) installed: knitro/12.2.2, knitro/12.4.0

Roar-Collab Version(s) installed: knitro/12.4.0

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

Developer Website

LAMMPS

Roar Version(s) installed: lammps/20190807, lammps/20200721

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

Roar 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

Roar 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

Roar 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

Roar Version(s) installed: lsprepost/4.3, lsprepost/4.8.21

Roar-Collab Version(s) installed: lsprepost/4.8.21

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

Developer Website

MAFFT

Roar Version(s) installed: mafft/7.453, mafft/7.481

Roar-Collab Version(s) installed: mafft/7.481

Multiple alignment program for amino acid or nucleotide sequences

Developer Website

Mathematica

Roar Version(s) installed: mathematica/12.3.0, mathematica/12.3.1, mathematica/13.0.1

Roar-Collab Version(s) installed: mathematica/13.0.1

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

Developer Website

MATLAB

Roar Version(s) installed: matlab/R2021a, matlab/R2021b, matlab/R2022a

Roar-Collab Version(s) installed: matlab/R2022a

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

Roar Version(s) installed: metis/5.1.0

Roar-Collab Version(s) installed: metis/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

Roar Version(s) installed: mkl/2020.3

Roar-Collab Version(s) installed: mkl/2021.4.0

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

Developer Website

MPICH

Roar Version(s) installed: mpich/3.2, mpich/3.4.2

Roar-Collab Version(s) installed: mpich/3.4.2

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

NCBI-RMBLASTN

Roar Version(s) installed: ncbi-rmblastn/2.9.0, ncbi-rmblastn/2.11.0

Roar-Collab Version(s) installed: ncbi-rmblastn/2.11.0

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

Developer Website

NetCDF

Roar Version(s) installed: netcdf/4.4.1, netcdf/4.7.4, netcdf/4.8.1

Roar-Collab Version(s) installed: netcdf/4.8.1

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

Roar Version(s) installed: netcdf-cxx/4.2

Roar-Collab 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-Fortran

Roar Version(s) installed: netcdf-fortran/4.4.4, netcdf-fortran/4.5.3

Roar-Collab Version(s) installed: netcdf-fortran/4.5.3

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

NVHPC

Roar Version(s) installed: nvhpc/20.9, nvhpc/21.9

Roar-Collab Version(s) installed: nvhpc/21.9

Developer Website

Openfoam

Roar 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

Roar Version(s) installed: openjdk/11.0.16

Open Java Development Kit.

Developer Website

OpenMPI

Roar Version(s) installed: openmpi/3.1.6, openmpi/4.1.1

Roar-Collab Version(s) installed: openmpi/4.1.1

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

Roar Version(s) installed: oraclejdk/1.8.0

Oracle Java Development Kit.

Developer Website

Parallel

Roar Version(s) installed: parallel/20190222, parallel/20200822

Roar-Collab Version(s) installed: parallel/20210922

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

Developer Website

Paraview

Roar Version(s) installed: paraview/5.4.0, paraview/5.5.2

Roar-Collab Version(s) installed: paraview/5.5.2

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

Developer Website

PETSC

Roar Version(s) installed: petsc/3.8.3, petsc/3.11.4

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

Roar Version(s) installed: pgi/18.10, pgi/20.4

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

Roar Version(s) installed: picard/2.20.8

Roar-Collab Version(s) installed: picard/2.26.2

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

Pointwise

Roar Version(s) installed: pointwise/18.4R2, pointwise/18.4R4

Roar-Collab Version(s) installed: pointwise/18.4R4

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

Developer Website

Pointwise

Roar 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

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

Roar-Collab Version(s) installed: python/3.6.8

Python

Developer Website

Quantum Espresso

Roar 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

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

Roar Version(s) installed: samtools/1.5, samtools/1.10, samtools/1.13

Roar-Collab Version(s) installed: samtools/1.13

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

Developer Website

SAS

Roar Version(s) installed: sas/9.4

Roar-Collab 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

Roar Version(s) installed: schrodinger/2019.4, schrodinger/2021.2, schrodinger/2022.2

Roar-Collab Version(s) installed: schrodinger/2022.2

A suite of chemical simulation software.

Developer Website

Settarg

Roar Version(s) installed: settarg/6.5.1

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

Developer Website

Spark

Roar 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

Roar Version(s) installed: spm/12

Roar-Collab 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

STAR-CCM+

Roar Version(s) installed: starccm/16.02.009-R8, starccm/16.06.008-R8, starccm/17.02.008-R8

Roar-Collab Version(s) installed: starccm/17.02.008-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

Roar Version(s) installed: Stata/16, Stata/17

Roar-Collab Version(s) installed: Stata/17

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

Developer Website

TAU

Roar 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

Roar Version(s) installed: tbb/2020.8

Roar-Collab Version(s) installed: tbb/2021.4.0

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

Developer Website

Tecplot

Roar Version(s) installed: tecplot/2021r1, tecplot/2021r2

Roar-Collab Version(s) installed: tecplot/2021r2

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

Roar Version(s) installed: totalview/2019.2.12, totalview/2021.2.14, totalview/2022.1.11

Roar-Collab Version(s) installed: totalview/2022.1.11

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

Developer Website

Trinity

Roar Version(s) installed: trinity/2.11.0

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

Developer Website

VASP

Roar 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

Roar Version(s) installed: vasp_vtst/5.4.4

Vienna Ab Initio Simulation Package with TST.

VMD

Roar 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

Roar Version(s) installed: vtune-amplifier/2020.3

A performance profiler for HPC code.

Developer Website

WGS

Roar Version(s) installed: wgs/8.3rc2

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

Developer Website

XBLAS

Roar 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

Roar 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

Roar Version(s) installed: xdrf/1.2

A portable data compression library.

Developer Website

XMGRACE

Roar 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

Roar Version(s) installed: zlib/1.2.11

zlib is a software library used for data compression.