Apps for the Roar Software stack
Browse the Roar software and versions
Software
Roar Software
Abaqus
Roar Version(s) installed: abaqus/2018, abaqus/2021, abaqus/2022
Abaqus is a software suite for finite element analysis and computer-aided engineering.
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
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.
AFNI
Roar Version(s) installed: afni/20.2.11, 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.
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.
AMPL
Roar Version(s) installed: ampl/20190529, ampl/20210226, 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 Version(s) installed: ansys/2021R1, ansys/2021R2, ansys/2022R1
The Ansys software suite provides engineering simulation software for structural mechanics, fluid dynamics, and electromagnetics, as well as pre- and post-processing.
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.
Avizo
Roar Version(s) installed: avizo/2021.1
Avizo is a 3D analysis software for scientific and industrial data
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.
BamTools
Roar Version(s) installed: bamtools/2.4.1, bamtools/2.5.1
A fast, flexible C++ API and toolkit for reading, writing, and managing BAM files.
Bedtools
Roar Version(s) installed: bedtools/2.27.1, bedtools/2.30.0
A powerful toolset for genome arithmetic.
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.
Boost
Roar Version(s) installed: boost/1.63.0, boost/1.74.0, boost/1.77.0
Boost provides free peer-reviewed portable C++ source libraries.
Bowtie 2
Roar 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 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.
Campari
Roar Version(s) installed: campari/2.2015.05.29
Software for molecular simulations and trajectory analysis.
Clang
Roar Version(s) installed: clang/3.9.1
A C language family front-end for LLVM.
CMake
Roar Version(s) installed: cmake/3.18.4, 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 Version(s) installed: comsol/5.4, comsol/5.6 (update 2), 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
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.
CPLEX
Roar 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 Version(s) installed: ddt/22.0.2
Parallel debugger supporting a wide range of parallel architectures and models, including MPI, UPC, CUDA, and OpenMP
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.
FastQC
Roar Version(s) installed: fastqc/0.11.7, fastqc/0.11.9
A quality control application for FastQ files.
FFmpeg
Roar Version(s) installed: ffmpeg/4.1.1, ffmpeg/4.2.2
Multimedia framework to decode, encode, transcode, mux, demux, stream, and filter video and audio.
FFTW
Roar Version(s) installed: 3.3.5, 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 Version(s) installed: freesurfer/7.1.1, freesurfer/7.2.0
An open-source software suite for processing and analyzing (human) brain MRI images.
fsl
Roar Version(s) installed: fsl/5.0.10
FSL is a functional MRI of the brain (FMRIB) software library.
GAMS
Roar Version(s) installed: gams/33.2, gams/36.2, 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
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
GROMACS
Roar Version(s) installed: gromacs/2020.2, gromacs/2020.4, 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 Version(s) installed: hdf5/1.10.7, hdf5/1.12.0
HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
HTSLib
Roar Version(s) installed: htslib/1.10.2, 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 Version(s) installed: idl/8.8, idl/8.8.1
IDL is the trusted scientific programming language used across disciplines to extract meaningful visualizations from complex numerical data.
JAGS
Roar 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 Version(s) installed: julia/1.3.1, julia/1.5.3, julia/1.6.2
Julia is a high-level, high-performance dynamic programming language for numerical computing.
KIM-API
Roar Version(s) installed: kim-api/2.1.3
The KIM API is an Application Programming Interface for atomistic simulations.
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
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
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.
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.
LS-PrePost
Roar Version(s) installed: lsprepost/4.3, lsprepost/4.8.21
LS-PrePost is a pre- and post-processor for LS-DYNA.
MAFFT
Roar Version(s) installed: mafft/7.453, mafft/7.481
Multiple alignment program for amino acid or nucleotide sequences
Mathematica
Roar Version(s) installed: mathematica/12.3.0, mathematica/12.3.1, mathematica/13.0.1
Mathematica is a fully integrated software environment for technical and scientific computing.
MATLAB
Roar Version(s) installed: matlab/R2021a, matlab/R2021b, 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 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 Version(s) installed: mkl/2020.3
Intel® Math Kernel Library (Intel® MKL) optimizes code with minimal effort for future generations of Intel® processors.
MPICH
Roar Version(s) installed: mpich/3.2, 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 Version(s) installed: ncbi-rmblastn/2.9.0, 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 Version(s) installed: netcdf/4.4.1, netcdf/4.7.4, 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 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 Version(s) installed: netcdf-fortran/4.4.4, 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.
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.
OpenMPI
Roar Version(s) installed: openmpi/3.1.6, 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 Version(s) installed: parallel/20190222, parallel/20200822
GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
Paraview
Roar Version(s) installed: paraview/5.4.0, paraview/5.5.2
ParaView is an open-source, multi-platform data analysis and visualization application.
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.
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.
Picard
Roar 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.
Pointwise
Roar Version(s) installed: pointwise/18.4R2, 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).
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)
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
SAM
Roar Version(s) installed: samtools/1.5, samtools/1.10, samtools/1.13
SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
SAS
Roar 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 Version(s) installed: schrodinger/2019.4, schrodinger/2021.2, schrodinger/2022.2
A suite of chemical simulation software.
Settarg
Roar Version(s) installed: settarg/6.5.1
The Settarg module works with Lmod to help developers manage their compiled software projects.
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.
SPM
Roar 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 Version(s) installed: starccm/16.02.009-R8, starccm/16.06.008-R8, 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 Version(s) installed: Stata/16, Stata/17
Stata is a statistical package for managing, analyzing, and graphing data.
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.
TBB
Roar Version(s) installed: tbb/2020.8
TBB is a widely used C++ template library for task parallelism.
Tecplot
Roar Version(s) installed: tecplot/2021r1, 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 Version(s) installed: totalview/2019.2.12, totalview/2021.2.14, totalview/2022.1.11
Parallel debugger supporting a wide range of parallel architectures and models, including MPI, UPC, CUDA and OpenMP.
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.
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
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
VTune Amplifier
Roar Version(s) installed: vtune-amplifier/2020.3
A performance profiler for HPC code.
WGS
Roar Version(s) installed: wgs/8.3rc2
Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler.
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.
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.
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.
zlib
Roar Version(s) installed: zlib/1.2.11
zlib is a software library used for data compression.