The following software is available for use on Roar Collab.
Software
Software Available on the Roar-Collab Cluster
Abaqus
Roar-Collab Version(s) installed: abaqus/2022
Abaqus is a software suite for finite element analysis and computer-aided engineering.
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.
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.
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.
Avizo
Roar-Collab Version(s) installed: avizo/2021.1
Avizo is a 3D analysis software for scientific and industrial data
BamTools
Roar-Collab Version(s) installed: bamtools/2.5.1
A fast, flexible C++ API and toolkit for reading, writing, and managing BAM files.
Bedtools
Roar-Collab Version(s) installed: bedtools/2.30.0
A powerful toolset for genome arithmetic.
Boost
Roar-Collab Version(s) installed: boost/1.77.0
Boost provides free peer-reviewed portable C++ source libraries.
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.
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.
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
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
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.
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
FastQC
Roar-Collab Version(s) installed: fastqc/0.11.9
A quality control application for FastQ files.
FFmpeg
Roar-Collab Version(s) installed: ffmpeg/4.3.2
Multimedia framework to decode, encode, transcode, mux, demux, stream, and filter video and audio.
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.
FreeSurfer
Roar-Collab Version(s) installed: freesurfer/7.2.0
An open-source software suite for processing and analyzing (human) brain MRI images.
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
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
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.
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.
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.
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.
Julia
Roar-Collab Version(s) installed: julia/1.6.2
Julia is a high-level, high-performance dynamic programming language for numerical computing.
LS-PrePost
Roar-Collab Version(s) installed: lsprepost/4.8.21
LS-PrePost is a pre- and post-processor for LS-DYNA.
MAFFT
Roar-Collab Version(s) installed: mafft/7.481
Multiple alignment program for amino acid or nucleotide sequences
Mathematica
Roar-Collab Version(s) installed: mathematica/13.0.1
Mathematica is a fully integrated software environment for technical and scientific computing.
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
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.
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.
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>
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.
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.
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.
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.
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
Parallel
Roar-Collab Version(s) installed: parallel/20210922
GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
Paraview
Roar-Collab Version(s) installed: paraview/5.5.2
ParaView is an open-source, multi-platform data analysis and visualization application.
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.
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).
SAM
Roar-Collab Version(s) installed: samtools/1.13
SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
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.
Schrodinger
Roar-Collab Version(s) installed: schrodinger/2022.2
A suite of chemical simulation software.
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.
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.
Stata
Roar-Collab Version(s) installed: Stata/17
Stata is a statistical package for managing, analyzing, and graphing data.
TBB
Roar-Collab Version(s) installed: tbb/2021.4.0
TBB is a widely used C++ template library for task parallelism.
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.
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.