Abaqus
Version(s) installed: abaqus/2018, abaqus/2021
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.
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, ampl/20210226
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
Version(s) installed: ansys/2019R3, ansys/2021R1
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/2020.2
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/3.18.4
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.
Developer Website
COMSOL
Version(s) installed: comsol/5.4, comsol/5.6 (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.
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.
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.
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.
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/8.8
IDL is the trusted scientific programming language used across disciplines to extract meaningful visualizations from complex numerical data.
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.
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.
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/12.3.0
Mathematica is a fully integrated software environment for technical and scientific computing.
Developer Website
MATLAB
Version(s) installed: matlab/R2019b, matlab/R2020b (update 5), matlab/R2021a
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.
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.
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.
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
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, schrodinger/2021.2
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
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, starccm/15.06.008-R8, starccm/16.02.009-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
SUBREAD
Version(s) installed: 2.0.0
The Subread package comprises a suite of software programs for processing next-gen sequencing read 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/2021r1
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.
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.
