Apps for All Your Research Needs

The ICS-ACI 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 ICS-ACI 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 ICS 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 (as of May 2018)

The following is a list of the modules currently available:

 

Abaqus

Version(s) installed: abaqus/2017

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.

Developer Website

AFNI

Version(s) installed: afni/17.2.05

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/14

Assisted Model Building with Energy Refinement (AMBER) is a software package for simulating force fields for molecular dynamics of biomolecules.

Developer Website

Ansys

Version(s) installed: ansys/18.1, ansys/19.1

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

Avizo

Version(s) installed: avizo/9.4.0, avizo/9.5.0

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

Developer Website

BamTools

Version(s) installed: bamtools/2.4.1

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

Developer Website

Bedtools

Version(s) installed: bedtools/2.26.0

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

Boost

Version(s) installed: boost/1.61.0, boost/1.63.0

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

Developer Website

Campari

Version(s) installed: campari/2.2015.05.29

Software for molecular simulations and trajectory analysis.

Developer Website

Clang

Version(s) installed: clang/3.9.1

A C language family front-end for LLVM.

Developer Website

CMake

Version(s) installed: cmake/3.9.1

CMake is a family of tools designed to build, test, and package software

Developer Website

COMSOL

Version(s) installed: comsol/5.2a, comsol/5.3

COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating  physics-based problems.

Developer Website

CPLEX

Version(s) installed: cplex/12.8.0

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/6.1, ddt/7.1

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

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/0.11.2

A quality control application for FastQ files.

Developer Website

FFmpeg

Version(s) installed: ffmpeg/3.1.1, ffmpeg/3.3.3

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/5.3.0, freesurfer/6.0.0

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/24.8.5

The General Algebraic Modeling System (GAMS) is a high-level modeling system for mathematical programming and optimization.

Developer Website

Gaussian

Version(s) installed: gaussian/g03e1, gaussian/g09d01

Gaussian is a general-purpose computational chemistry software package.

Developer Website

GCC

Version(s) installed: gcc/5.3.1, gcc/7.3.1

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.

Developer Website

GROMACS

Version(s) installed: gromacs/5.1.4

GROMACS is a versatile package to perform molecular dynamics.

Developer Website

HDF5

Version(s) installed: hdf5/1.8.18

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/1.1

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

Developer Website

IMPI

Version(s) installed: impi/5.1.3

Intel MPI library.

Developer Website

Intel

Version(s) installed: intel/16.0.3

Intel C, C++ and Fortran compilers.

Developer Website

JAGS

Version(s) installed: jags/4.2.0

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/0.6.0

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

Developer Website

KIM-API

Version(s) installed: kim-api/1.8.2

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

Developer Website

KNITRO

Version(s) installed: knitro/10.2.1

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/20150210, lammps/20160827

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

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.

Developer Website

Lmod

Version(s) installed: lmod/6.5.1

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

Mathematica

Version(s) installed: mathematica/11.0.1

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

Developer Website

MATLAB

Version(s) installed: matlab/R2016a, matlab/R2017b

MATLAB (r) is a high-level language and interactive environment for numerical computation, visualization, and programming.

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/11.3.3

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.

Developer Website

MUSCLE

Version(s) installed: muscle/3.8.31

Popular multiple alignment software.

Developer Website

NCBI-BLAST

Version(s) installed: ncbi-blast/2.6.0

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/4.3.0

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

OpenJDK

Version(s) installed: openjdk/1.8.0

Open Java Development Kit.

Developer Website

OpenMPI

Version(s) installed: openmpi/1.10.1

A powerful implementation of MPI/SHMEM.

Developer Website

OracleJDK

Version(s) installed: oraclejdk/1.8.0

Oracle Java Development Kit.

Developer Website

Parallel

Version(s) installed: parallel/20170522

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/3.7.3, 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/16.4

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

Version(s) installed: picard/2.5.0

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/17.3R5

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

Version(s) installed: python/2.7.14-anaconda5.0.1, python/3.6.3-anaconda5.0.1

Python 2.7 (Anaconda 5.0.0.1)

Developer Website

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.

Developer Website

R

Version(s) installed: r/3.4

R is a free software environment for statistical computing and graphics.

Developer Website

SAM

Version(s) installed: samtools/0.1.19, 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/2016.4

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

SPM

Version(s) installed: spm/8

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+

Version(s) installed: starccm/12.04.010

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/14.2

Stata is a statistical package for managing, analyzing, and graphing 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/4.4.4, tbb/2017

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

Developer Website

Tecplot

Version(s) installed: tecplot/2017r1

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/2017.1.21

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

Developer Website

Trinity

Version(s) installed: trinity/2.2.0

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

Developer Website

VASP

Version(s) installed: vasp/5.4.1.05Feb16

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.

Developer Website

VASP_VTST

Version(s) installed: vasp_vtst/5.4.1.05Feb16

Vienna Ab Initio Simulation Package with TST.

VTune Amplifier

Version(s) installed: vtune-amplifier/16.4, vtune-amplifier/2018.1

A performance profiler for HPC code.

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

XDRF

Version(s) installed: xdrf/1.2

A portable data compression library.

Developer Website