ROAR User Guide

Software Available on the Roar Collab Cluster

Use the search box below to find software available through the Roar Collab cluster.

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Abaqus

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

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

Developer Website

AFNI

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

AMPL

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-Collab Version(s) installed: anaconda3/2021.05

Anaconda

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Ansys

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.

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Avizo

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

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

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BamTools

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

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

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Bedtools

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

A powerful toolset for genome arithmetic.

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Boost

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

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

Developer Website

Bowtie 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-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

CMake

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-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

CPLEX

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.

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cuda

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

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DDT

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

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FastQC

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

A quality control application for FastQ files.

Developer Website

FFmpeg

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

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

Developer Website

GAMS

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

GCC

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

GNU Compiler Collection (GCC)

Developer Website

GROMACS

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-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-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-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.

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IMPI

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

Intel MPI library.

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JAGS

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.

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Julia

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

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

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Knitro

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.

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LS-PrePost

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

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

Developer Website

MAFFT

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

Multiple alignment program for amino acid or nucleotide sequences

Developer Website

Mathematica

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

Developer Website

OpenMPI

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

Parallel

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-Collab Version(s) installed: paraview/5.5.2

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

Developer Website

Picard

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-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

Python

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

Python

Developer Website

SAM

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

A suite of chemical simulation software.

Developer Website

SPM

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

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

Developer Website

TBB

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

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

Developer Website

Tecplot

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-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