ICS@PSU: Institute for CyberScience

ICS-ACI Research Software

Apps for All Your Research Needs

The ICS-ACI team operates and maintains a wide-ranging 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.

Please review our policy on installing your own software and requesting additions to the software stack: ICS-ACI-P040 Software Policy.

Current Software in the Stack (as of October 2017)

The following is a list of the modules currently available:

Software: Version Description
abinit: abinit/8.0.8b ABINIT
afni: afni/17.0.02 Analysis of Functional NeuroImages (AFNI)
amber: amber/14 Assisted Model Building with Energy Refinement
ansys: ansys/18.1 The Ansys software suite provides engineering simulation software for structural mechanics; fluid dynamics; electromagnetics; as well as pre- and post-processing.
arpack-ng: arpack-ng/3.4.0 ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
bamtools: bamtools/2.4.1 A fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.
bedtools: bedtools/2.26.0 A powerful toolset for genome arithmetic.
blas: blas/3.6.0 BLAS – Basic Linear Algebra Subprograms
boost: boost/1.41.0; boost/1.61.0; boost/1.63.0 Boost provides free peer-reviewed portable C++ source libraries.
clang: clang/3.9.1  "A C language family front-end for LLVM"
comsol: comsol/5.2a COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems.
ddt: ddt/6.1 Parallel debugger supporting a wide range of parallel architectures and models, including MPI, UPC, CUDA and OpenMP
express: express/1.5.1 eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.
fastqc: fastqc/0.11.2 A Quality Control application for FastQ files
ffmpeg: ffmpeg/3.1.1 Multimedia framework to decode, encode, transcode, mux, demux, stream, filter video and audio
fftw: fftw/3.3.5 FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
freesurfer: freesurfer/5.3.0 An open source software suite for processing and analyzing (human) brain MRI images
gams: gams/24.8.5 The General Algebraic Modeling System (GAMS) is a high-level modeling system for mathematical programming and optimization.
gaussian: gaussian/g03e1, gaussian/g09d01 Gaussian 03 e1
gcc: gcc/5.3.1 GNU Compiler Collection (GCC)
git: git/1.9.4 Git 1.9.4 (RedHat SCL version)
gromacs: gromacs/5.1.4 gromacs
hdf5: hdf5/1.8.18 HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
htslib: 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.
idl: idl/8.5 Exelis IDL Package
impi: impi/5.1.3 Intel MPI library
intel: intel/16.0.3 Intel C, C++ and Fortran compilers
jags: jags/4.2.0 Just Another Gibbs Sampler
julia: julia/0.5.0 Julia programming language
knitro: knitro/10.2.1 KNITRO is an optimization software library for finding solutions of both continuous optimization models, as well as discrete optimization models.
lammps: lammps/20150210, lammps/20160827 Large-scale Atomic/Molecular Massively Parallel Simulator
lapack: lapack/3.6.0 Numerical linear algebra package libraries
lmod: lmod/6.5.1 Lmod: An Environment Module System
lsdyna: lsdyna/R9.0.1 LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems.
lsprepost: lsprepost/4.3 LS-PrePost is a pre and post-processor for LS-DYNA.
mathematica: mathematica/11.0.1 Mathematica is a fully integrated software environment for technical and scientific computing.
matlab: matlab/R2016a MATLAB(R) is a high-level language and interactive environment for numerical computation,visualization, and programming.
metis: metis/5.1.0 Serial Graph Partitioning and Fill-reducing Matrix Ordering
mkl: mkl/11.3.3 Intel Math Kernel Library (MKL)
mpich: mpich/3.2 A high-performance implementation of MPI
muscle: muscle/3.8.31 Popular multiple alignment software
ncbi-blast: 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.
netcdf: 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.
netcdf-cxx: 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.
netcdf-fortran: 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.
openjdk: openjdk/1.8.0 Open Java Development Kit
openmpi: openmpi/1.10.1 A powerful implementation of MPI/SHMEM
oraclejdk: oraclejdk/1.8.0 Oracle Java
parmetis: parmetis/4.0.3 Parallel Graph Partitioning and Fill-reducing Matrix Ordering
petsc: petsc/3.7.3 Portable, Extensible Toolkit for Scientific Computation
pgi: 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
picard: picard/2.5.0 A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF
ploticus: ploticus/2.42 Ploticus Data Display Engine
pointwise: 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).
python: python/2.7, python/2.7.8, python/3.3, python/3.3.2 Python 2.7.8 (RedHat SCL version)
quantum_espresso: quantum_espresso/5.4.0 Quantum Espresso 5.4.0
r: r/3.4 R is a free software environment for statistical computing and graphics
samtools: samtools/0.1.19 SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
sas: sas/9.4 SAS is a software suite for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.
schrodinger: schrodinger/2016.4 Schrodinger Suite
settarg: settarg/6.5.1 settarg
spm: spm/8 The Statistical Parametric Mapping (SPM) software package has been designed for the analysis of brain imaging data sequences.
starccm: 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."
stata: stata/14.2 Stata is a statistical package for managing, analyzing, and graphing data.
tbb: tbb/4.4.4, tbb/2017 Widely used C++ template library for task parallelism
tecplot: 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.
totalview: totalview/2017.1.21 Parallel debugger supporting a wide range of parallel architectures and models, including MPI, UPC, CUDA and OpenMP
trinity: trinity/2.2.0 Trinity RNA-Seq de novo transcriptome assembly
vasp: vasp/5.4.1.05Feb16 Vienna Ab Initio Simulation Package
vasp_vtst: vasp_vtst/5.4.1.05Feb16 Vienna Ab Initio Simulation Package with TST
vtune-amplifier: vtune-amplifier/16.4 Intel VTune Amplifier
xblas: xblas/1.0.248 Extra Precise Basic Linear Algebra Subroutines
xdrf: xdrf/1.2 A portable data compression library
Penn State Institute for CyberScience

Help us build the future. Contact ICS at Penn State.

  • email: ics@psu.edu
  • phone: ICS-ACI Support (i-ASK Center): 814-865-4275 | General Inquiries: 814-867-1467

November 2017

SuMoTuWeThFrSa
 1234
567891011
12131415161718
19202122232425
2627282930 
  • Nov 7, 201711:00 am - 5:00 pm

    XSEDE HPC Workshop: GPU Programming Using OpenACC

    OpenACC is the accepted standard using compiler directives t…

    More Info
  • Nov 6, 201710:00 am - 3:00 pm

    NIIMBL Teaming Event with Celgene

    Celgene, a biotechnology company, invites researchers to a m…

    More Info
  • Nov 8, 20178:30 am - 4:30 pm

    Amazon Web Services Research Immersion Day

    Come and learn how to do science on the cloud! From scaling …

    More Info
  • Nov 9, 20171:30 pm - 2:30 pm

    SIRO Proposal Development Workshop: Perspectives on Graduate Education

    Dean Evasius, Director, NSF Division of Graduate Education, …

    More Info
  • Nov 2, 201712:00 pm - 1:00 pm

    Introduction to Data Science with R Workshop 8: Managing Multiple Datasets

    In this workshop, we will begin to synthesize what we have l…

    More Info
  • Nov 10, 20172:00 pm - 3:00 pm

    SIRO Proposal Development Workshop: NSF Research Traineeship Program-Limited Submission Opportunity

    The NSF Research Traineeship (NRT) program (NSF 18-507) is d…

    More Info
  • Nov 14, 20179:00 am - 5:00 pm

    GIS Day 2017

    Penn State GIS Day strives to bring together those who are w…

    More Info
  • Nov 9, 201712:00 pm - 1:00 pm

    Introduction to Data Science with R: Working with Text Data in R

    In this workshop, we will cover the basics of manipulating a…

    More Info
  • Nov 14, 20175:00 pm

    Paul Hawken, “Drawdown, the Most Comprehensive Plan Ever Proposed to Reverse Global Warming”

    Environmentalist and entrepreneur Paul Hawken will be the ke…

    More Info
  • Nov 16, 20172:00 pm - 3:30 pm

    Ari Fertig of “The Conversation”

    Penn State will host editor Ari Fertig from the academic med…

    More Info
  • Nov 17, 20174:00 pm - 5:00 pm

    Stochastic Computations Working Group: “Parameter estimation using linear response statistics: Theory and numerical scheme”

    Join ICS Associate John Harlim and Xiantao Li for their bi-w…

    More Info