Software

The following are codes that have been built and are maintained by the HPC Team.
There is an RSS Feed available at https://hpc.unt.edu/softwareupdate that will update any time a new page is updated.
If you would like to request a software program that is not listed below, please fill out our Software Request Form at https://hpc.unt.edu/software-requests

AMBER
Version: Amber16-mpi, Amber16-gpu, AmberTools16
Description:

"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

Compilation Notes:

Compiled using Intel compiler and its MKL math libraries. Serial, parallel (openmpi-1.6.5/intel14), and cuda(5.0.35) versions are available.

AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers.

for the full HPC Team page on this software, click the link below

AMBER

Research Area:
Biology, Chemistry, Material Science, Physics
Last Updated: Tue, 2017-04-04 12:59
Armadillo
Version: #7.950.1#, 7.950.1
Description:
  • Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use 
  • Provides high-level syntax (API) deliberately similar to Matlab 
  • Useful for algorithm development directly in C++, or quick conversion of research code into production environments (eg. software & hardware products) 
  • Can be used for machine learning, pattern recognition, computer vision, signal processing, bioinformatics, statistics, finance, etc 
for the full HPC Team page on this software, click the link below

Armadillo

Research Area:
Biology, Computer Science, Health Science, Mathematics, Statistics, Linux Library
Last Updated: Mon, 2018-02-26 10:17
Bamtools
Version: 2.4.1
Description:

BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.

for the full HPC Team page on this software, click the link below

Bamtools

Research Area:
Biology, Linux Utility
Last Updated: Mon, 2018-02-26 10:19
Bcftools
Version: 1.6 (default), 1.4.1, 1.4
Description:

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

for the full HPC Team page on this software, click the link below

Bcftools

Research Area:
Linux Utility
Last Updated: Mon, 2018-02-26 10:20
Beast
Version: 2.4.5 (default), 1.8.4
Description:

Beast1:

for the full HPC Team page on this software, click the link below

Beast

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:28
BLAST+
Version: 2.6.0
Description:

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

for the full HPC Team page on this software, click the link below

BLAST+

Research Area:
Biology
Last Updated: Tue, 2017-04-11 10:59
BOOST
Version: 1.63.0
Description:

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

We emphasize libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.

Compilation Notes:

Compiled using gcc. 

for the full HPC Team page on this software, click the link below

boost

Research Area:
Biology, Linux Library
Last Updated: Tue, 2017-04-11 11:24
BOWTIE2
Version: 2.3.2 (default), 2.3.1
Description:

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 to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index (based on the Burrows-Wheeler Transform or BWT) to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 gigabytes of RAM. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Compilation Notes:

Binary installation.

Bowtie is a prerequisite for tophat.

for the full HPC Team page on this software, click the link below

bowtie

Research Area:
Biology
Last Updated: Wed, 2018-01-31 11:18
BWA
Version: 0.7.17
Description:

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate.

for the full HPC Team page on this software, click the link below

Bwa

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:29
Bzip2
Version: 1.0.6
Description:

bzip2 is a freely available, patent free (see below), high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.

for the full HPC Team page on this software, click the link below

Bzip2

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:30
Cairo
Version: 1.14.10
Description:

Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB.

Cairo is designed to produce consistent output on all output media while taking advantage of display hardware acceleration when available (eg. through the X Render Extension).

for the full HPC Team page on this software, click the link below

Cairo

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:32
CD-Hit
Version: 4.6.6-2016-0711
Description:

CD-HIT is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset.

for the full HPC Team page on this software, click the link below

CD-Hit

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:33
CMAKE
Version: 3.8.0
Description:

CMake is an open-source, cross-platform family of tools designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files, and generate native makefiles and workspaces that can be used in the compiler environment of your choice. The suite of CMake tools were created by Kitware in response to the need for a powerful, cross-platform build environment for open-source projects such as ITK and VTK.

Compilation Notes:

Installed using gcc.

for the full HPC Team page on this software, click the link below

cmake

Research Area:
Linux Utility
Last Updated: Wed, 2018-01-31 11:21
CUDA 75
Version: blas/7.5.18, fft/7.5.18, insight/7.5.18, profiler/7.5.18, toolkit/7.5.18
Webpage:

Unknown

Description:

CUDA is a parallel computing platform and programming model, which interfaces CPU and of the graphics processing unit (GPU).

for the full HPC Team page on this software, click the link below

CUDA 75

Research Area:
Linux Library
Last Updated: Wed, 2018-01-31 12:51
CUDA 80
Version: blas/8.0.61, fft/8.0.61, insight/8.0.61, profiler/8.0.61, toolkit/8.0.61
Webpage:

Unknown

Description:

CUDA is a parallel computing platform and programming model, which interfaces CPU and of the graphics processing unit (GPU).

for the full HPC Team page on this software, click the link below

CUDA 80

Research Area:
Linux Library
Last Updated: Wed, 2018-01-31 12:56
CUDA Neutral Network
Version: 6.0/cuda80, 6.0/cuda75, 5.1/cuda80, 5.1/cuda75
Webpage:

Unknown

Description:

CUDA is a parallel computing platform and programming model, which interfaces CPU and of the graphics processing unit (GPU).

for the full HPC Team page on this software, click the link below

CUDA Neutral Network

Research Area:
Linux Library
Last Updated: Wed, 2018-01-31 13:01
CUFFLINKS
Version: 2.2.1
Description:

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

Compilation Notes:

compiled using GCC suite.

for the full HPC Team page on this software, click the link below

cufflinks

Research Area:
Biology
Last Updated: Wed, 2018-01-31 11:22
Curl
Version: 7.54.1
Description:

curl is used in command lines or scripts to transfer data. It is also used in cars, television sets, routers, printers, audio equipment, mobile phones, tablets, settop boxes, media players and is the internet transfer backbone for thousands of software applications affecting billions of humans daily..

for the full HPC Team page on this software, click the link below

Curl

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:35
dDocent
Version: 2.2.16
Description:

dDocent’s purpose is to be a standalone laboratory protocol and analysis pipeline for double digest Restriction site Associated DNA (ddRAD) sequencing (the pipeline should also work with ezRAD).  The laboratory protocol largely follows Peterson et al. (2012), but is focused down to specifically what has worked best for us in the Gold lab.

Compilation Notes:

Self retriving and installing with gcc.

for the full HPC Team page on this software, click the link below

dDocent

Research Area:
Biology, Health Science
Last Updated: Wed, 2018-01-31 11:23
DL_POLY
Version: 4.08, class-1.10
Description:

DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.

for the full HPC Team page on this software, click the link below

DL_POLY

Research Area:
Chemistry, Material Science
Last Updated: Wed, 2018-01-31 11:24
Ea-Utils
Version: 2017
Description:

Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.

for the full HPC Team page on this software, click the link below

Ea-Utils

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:36
Eigen
Version: 3.3.3
Description:
  • Eigen is versatile.
    • It supports all matrix sizes, from small fixed-size matrices to arbitrarily large dense matrices, and even sparse matrices.
    • It supports all standard numeric types, including std::complex, integers, and is easily extensible to custom numeric types.
    • It supports various matrix decompositions and geometry features.
    • Its ecosystem of unsupported modules provides many specialized features such as non-linear optimization, matrix functions, a polynomial solver, FFT, and much more.
for the full HPC Team page on this software, click the link below

Eigen

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:42
ESPRESSO
Version: 6.0
Description:

Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

for the full HPC Team page on this software, click the link below

ESPRESSO

Research Area:
Material Science, Physics
Last Updated: Tue, 2017-02-28 11:23
FastxToolkit
Version: 0.0.13
Description:

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information).

for the full HPC Team page on this software, click the link below

FastxToolkit

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:44
FFTW
Version: 3.3.6 (default), 2.1.5
Description:

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 (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.

Compilation Notes:

Intel 13, icc/ifort compiled with openmpi/intel/mlx1.6.5 support.

Intel 14, icc/ifort compiled with openmpi/intel/14/mlx/1.6.5 support. (this is the recommended version).

for the full HPC Team page on this software, click the link below

FFTW

Research Area:
Linux Library
Last Updated: Wed, 2018-01-31 11:25
GAMESS
Version: October 30 2017, August 18 2016
Description:

The General Atomic and Molecular Electronic Structure System (GAMESS)
is a general ab initio quantum chemistry package.

for the full HPC Team page on this software, click the link below

GAMESS

Research Area:
Chemistry
Last Updated: Wed, 2018-01-31 11:26
Gatk
Version: 3.80
Description:

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

for the full HPC Team page on this software, click the link below

Gatk

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:46
Gaussian
Version: g16-RevA.03-ax2, g09-RevD, g09-RevA
Description:

Gaussian 09 is the latest version of the Gaussian® series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian 09 predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Gaussian 09’s models can be applied to both stable species and compounds which are difficult or impossible to observe experimentally (e.g., short-lived intermediates and transition structures).

Gaussian 09 provides the most advanced modeling capabilities available today, and it includes many new features and enhancements which significantly expand the range of problems and systems which can be studied. With Gaussian 09, you can model larger systems and more complex problems than ever before, even on modest computer hardware.

Compilation Notes:

Gaussian runs on shared memory and run single host.

for the full HPC Team page on this software, click the link below

Gaussian

Research Area:
Chemistry
Last Updated: Wed, 2018-01-31 11:27
Git
Version: 2.9.3
Description:

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.

Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCM tools like Subversion, CVS, Perforce, and ClearCase with features like cheap local branching, convenient staging areas, and multiple workflows.

for the full HPC Team page on this software, click the link below

Git

Research Area:
Linux Library
Last Updated: Mon, 2018-02-26 10:47
glibc
Version: 2.25
Description:

The GNU C Library project provides the core libraries for the GNU system and GNU/Linux systems, as well as many other systems that use Linux as the kernel. These libraries provide critical APIs including ISO C11, POSIX.1-2008, BSD, OS-specific APIs and more. These APIs include such foundational facilities as open, read, write, malloc, printf, getaddrinfo, dlopen, pthread_create,crypt, login, exit and more.

for the full HPC Team page on this software, click the link below

glibc

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:48
GNU compiler
Version: 6.3.0 (default), 6.1.0, 4.8.5
Description:

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages (libstdc++, libgcj,...). GCC is a key component of the GNU toolchain.GCC has been ported to a wide variety of processor architectures, and is widely deployed as a tool in the development of both free and proprietary software. GCC is also available for most embedded platforms including Symbian, AMCC and Freescale Power Architecture-based chips.It was originally written as the compiler for the GNU operating system.

for the full HPC Team page on this software, click the link below

GNU Complier

Research Area:
Linux Utility
Last Updated: Wed, 2018-01-31 11:30
GNU Plot
Version: 5.0.6
Description:

Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986.

for the full HPC Team page on this software, click the link below

GNU Plot

Research Area:
Linux Utility
Last Updated: Mon, 2018-02-26 10:49
Gromacs
Version: 5.1.4-fftw
Description:

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

Compilation Notes:

Makefile was made with cmake (2.8) and using gfortran.

 

for the full HPC Team page on this software, click the link below

GROMACS

Research Area:
Biology, Chemistry
Last Updated: Wed, 2018-01-31 11:49
GSL
Version: 2.4
Description:

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.

The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.

for the full HPC Team page on this software, click the link below

GSL

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:50
Gulp
Version: 4.5
Description:
  • Automation - gulp is a toolkit that helps you automate painful or time-consuming tasks in your development workflow.
  • Platform-agnostic - Integrations are built into all major IDEs and people are using gulp with PHP, .NET, Node.js, Java, and other platforms.
  • Strong Ecosystem - Use npm modules to do anything you want + over 2000 curated plugins for streaming file transformations
  • Simple - By providing only a minimal API surface, gulp is easy to learn and simple to use
for the full HPC Team page on this software, click the link below

Gulp

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:54
HDF5
Version: 1.8.18-gnu, 1.8.18-intel
Description:

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.

for the full HPC Team page on this software, click the link below

HDF5

Research Area:
Linux Library
Last Updated: Wed, 2018-01-31 11:31
Hisat
Version: 2.0.5 (default), 0.1.6
Description:

HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover the whole genome (each index represents a genomic region of ~64,000 bp and ~48,000 indexes are needed to cover the human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons.

for the full HPC Team page on this software, click the link below

Hisat

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:55
htslib
Version: 1.6 (default), 1.4.1, 1.4
Description:

HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang.

HTSlib implements a generalized BAM index, with file extension .csi (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent.

for the full HPC Team page on this software, click the link below

htslib

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:56
ICU
Version: 4c-59
Description:

ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU is widely portable and gives applications the same results on all platforms and between C/C++ and Java software.

ICU is released under a nonrestrictive open source license that is suitable for use with both commercial software and with other open source or free software.

for the full HPC Team page on this software, click the link below

ICU

Research Area:
Biology
Last Updated: Mon, 2018-02-26 10:58
Intel
Version: intel-tbb-oss/ia32/2017_20161128oss, intel-ode/1.0.0, PS2017-t2, PS2017-17.0.4-legacy, PS2017-17.0.4-compute, PS2017-17.0.4, PS2017, mkl/PS2017, compilers/17.0
Description:

Intel Fortran Compiler, also known as IFORT, is a group of Fortran compilers from Intel.

for the full HPC Team page on this software, click the link below

Intel

Research Area:
Linux Utility, Linux Library
Last Updated: Wed, 2018-01-31 12:37
JAGS
Version: 4.2.0
Description:

JAGS is Just Another Gibbs Sampler.  It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation  not wholly unlike BUGS.  JAGS was written with three aims in mind:

  • To have a cross-platform engine for the BUGS language
  • To be extensible, allowing users to write their own functions, distributions and samplers.
  • To be a plaftorm for experimentation with ideas in Bayesian modelling

JAGS is licensed under the GNU General Public License.

Compilation Notes:

Also availble within R package rjags by loading the library as follows:

> library(rjags)

Then you should see:
Loading required package: coda
Loading required package: lattice
Linked to JAGS 3.4.0
Loaded modules: basemod,bugs

for the full HPC Team page on this software, click the link below

JAGS

Research Area:
Education, Statistics
Last Updated: Wed, 2018-01-31 11:32
Java
Version: 1.8
Description:

Java is at the heart of our digital lifestyle. It's the platform for launching careers, exploring human-to-digital interfaces, architecting the world's best applications, and unlocking innovation everywhere—from garages to global organizations.

for the full HPC Team page on this software, click the link below

Java

Research Area:
Computer Science
Last Updated: Mon, 2018-02-26 10:59
Kallisto
Version: 0.43.1
Description:

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build.

for the full HPC Team page on this software, click the link below

Kallisto

Research Area:
Biology
Last Updated: Mon, 2018-02-26 11:03
Keras
Version: 2.0.3
Description:

Keras is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano. It was developed with a focus on enabling fast experimentation. Being able to go from idea to result with the least possible delay is key to doing good research.

Use Keras if you need a deep learning library that:

for the full HPC Team page on this software, click the link below

Keras

Research Area:
Computer Science
Last Updated: Mon, 2018-02-26 11:05
Kraken
Version: 0.10
Description:

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.

for the full HPC Team page on this software, click the link below

Kraken

Research Area:
Biology
Last Updated: Mon, 2018-02-26 11:06
LAMMPS
Version: August 11 2017, November 17 2016
Description:

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

for the full HPC Team page on this software, click the link below

LAMMPS

Research Area:
Chemistry, Material Science
Last Updated: Wed, 2018-01-31 11:37
Lapack
Version: 3.7.0
Description:

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. The associated matrix factorizations (LU, Cholesky, QR, SVD, Schur, generalized Schur) are also provided, as are related computations such as reordering of the Schur factorizations and estimating condition numbers. Dense and banded matrices are handled, but not general sparse matrices.

for the full HPC Team page on this software, click the link below

lapack

Research Area:
Biology
Last Updated: Mon, 2018-02-26 11:12
Libtool
Version: 2.4.6
Description:

GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.

for the full HPC Team page on this software, click the link below

Libtool

Research Area:
Biology
Last Updated: Mon, 2018-02-26 11:13
MATHEMATICA
Version: 10.0
Description:

Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields. It was conceived by Stephen Wolfram and is developed by Wolfram Research of Champaign, Illinois.

for the full HPC Team page on this software, click the link below

MATHEMATICA

Research Area:
Mathematics, Statistics
Last Updated: Mon, 2018-01-29 15:01
MATLAB
Version: 2017a, R2016b, R2014b
Description:

MATLAB® is a high-level language and interactive environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java™.

Compilation Notes:

The Linux distro of Matlab is installed. It includes distributed computing server that enables parallel execution of the code. 

 

for the full HPC Team page on this software, click the link below

MATLAB

Research Area:
Mathematics, Statistics
Last Updated: Mon, 2018-01-29 15:02
Minimac2
Version: September 15 2014
Description:

Genotype imputation is a key step in the analysis of genome-wide association studies. Upcoming very large reference panels, such as those from The 1000 Genomes Project and the Haplotype Consortium, will improve imputation quality of rare and less common variants, but will also increase the computational burden. Here, we demonstrate how the application of software engineering techniques can help to keep imputation broadly accessible. Overall, these improvements speed up imputation by an order of magnitude compared with our previous implementation.

for the full HPC Team page on this software, click the link below

Minimac2

Research Area:
Biology
Last Updated: Wed, 2018-01-31 13:23
Mpiblast
Version: 1.6.0
Description:

mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems.

for the full HPC Team page on this software, click the link below

mpiblast

Research Area:
Biology
Last Updated: Wed, 2018-01-31 13:27
Mplus
Version: 8
Description:

Mplus is a statistical modeling program that provides researchers with a flexible tool to analyze their data. Mplus offers researchers a wide choice of models, estimators, and algorithms in a program that has an easy-to-use interface and graphical displays of data and analysis results. Mplus allows the analysis of both cross-sectional and longitudinal data, single-level and multilevel data, data that come from different populations with either observed or unobserved heterogeneity, and data that contain missing values.

for the full HPC Team page on this software, click the link below

Mplus

Research Area:
Statistics
Last Updated: Wed, 2018-01-31 13:29
Namd
Version: 2.12-cuda, 2.12
Description:

NAMD, recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code.

for the full HPC Team page on this software, click the link below

Namd

Research Area:
Biology
Last Updated: Wed, 2018-01-31 13:31
Ncurses
Version: 6.0
Description:

The ncurses (new curses) library is a free software emulation of curses in System V Release 4.0 (SVr4), and more. It uses terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SVr4-curses enhancements over BSD curses. SVr4 curses became the basis of X/Open Curses.

for the full HPC Team page on this software, click the link below

Ncurses

Research Area:
Linux Utility
Last Updated: Wed, 2018-01-31 13:35
NWChem
Version: 6.6-gcc, 6.6-3, 6.6-2, 6.6
Description:

NWChem is actively developed by a consortium of developers and maintained by the EMSL located at the Pacific Northwest National Laboratory (PNNL) in Washington State. The code is distributed as open-source under the terms of the Educational Community License version 2.0

for the full HPC Team page on this software, click the link below

NWChem

Research Area:
Chemistry
Last Updated: Wed, 2018-01-31 11:33
Oases
Version: 0.2.8
Description:

Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. It was developed by Marcel Schulz (MPI for Molecular Genomics) and Daniel Zerbino (previously at the European Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz).

Compilation Notes:

requires the velvet module.

for the full HPC Team page on this software, click the link below

Oases

Research Area:
Biology
Last Updated: Thu, 2017-04-06 11:19
Openblas
Version: 0.2.19
Description:

OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

for the full HPC Team page on this software, click the link below

Openblas

Research Area:
Biology
Last Updated: Wed, 2018-01-31 13:36
Opencv
Version: 3.3
Description:

OpenCV (Open Source Computer Vision Library) is released under a BSD license and hence it’s free for both academic and commercial use. It has C++, C, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library can take advantage of multi-core processing. Enabled with OpenCL, it can take advantage of the hardware acceleration of the underlying heterogeneous compute platform.

for the full HPC Team page on this software, click the link below

Opencv

Research Area:
Computer Science
Last Updated: Wed, 2018-01-31 13:38
OpenMPI
Version: gcc/2.1.0, intel/2.1.0, intel/2.1.0-cuda, gcc/1.10.6, pgi/1.10.2
Description:

The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.

for the full HPC Team page on this software, click the link below

OpenMPI

Research Area:
Linux Library
Last Updated: Wed, 2018-01-31 12:12
Ovito
Version: 2.9.0
Description:

OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. It helps scientists gain better insights into materials phenomena and physical processes.

OVITO is being developed by Alexander Stukowski at Darmstadt University of Technology, Germany. The program is Open Source and freely available for all major platforms. It has served in a growing number of computational simulation studies as a useful tool to analyze, understand, and illustrate simulation results.

for the full HPC Team page on this software, click the link below

Ovito

Research Area:
Chemistry, Computer Science
Last Updated: Wed, 2018-01-31 13:40
Paraview
Version: 5.3.0
Description:

ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities.

for the full HPC Team page on this software, click the link below

Paraview

Research Area:
Linux Utility
Last Updated: Wed, 2018-01-31 13:41
perl
Version: 5.24.1
Description:

Practical Extraction and Report Language

for the full HPC Team page on this software, click the link below

perl

Research Area:
Linux Utility
Last Updated: Tue, 2017-04-11 10:21
PGI
Version: 17.5
Description:

PGI Unified Binary™ technology simplifies cross-platform support by combining into a single executable file, code sequences optimized for multi-core x64 processor families from Intel and AMD and GPU accelerators from NVIDIA. The PGI Unified Binary delivers all the benefits of a single x64 platform while enabling you to leverage the latest hardware innovations.

for the full HPC Team page on this software, click the link below

PGI

Research Area:
Linux Library
Last Updated: Wed, 2018-01-31 11:39
Picard
Version: 2.10
Description:

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification.

for the full HPC Team page on this software, click the link below

Picard

Research Area:
Computer Science
Last Updated: Wed, 2018-01-31 13:42
Plink
Version: 1.07
Description:

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

for the full HPC Team page on this software, click the link below

Plink

Research Area:
Biology
Last Updated: Wed, 2018-01-31 13:45
PSI4
Version: 1.0.0
Description:

Psi4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel.

for the full HPC Team page on this software, click the link below

PSI4

Research Area:
Chemistry
Last Updated: Wed, 2018-01-31 11:34
Pssh
Version: 2.3.1
Description:

pssh is a program for executing ssh in parallel on a number of hosts. It provides features such as sending input to all of the processes, passing a password to ssh, saving output to files, and timing out.

The PSSH_NODENUM and PSSH_HOST environment variables are sent to the remote host. The PSSH_NODENUM variable is assigned a unique number for each ssh connection, starting with 0 and counting up. The PSSH_HOST variable is assigned the name of the host as specified in the hosts list.

for the full HPC Team page on this software, click the link below

Pssh

Research Area:
Linux Utility, Linux Library
Last Updated: Wed, 2018-01-31 13:46
pyMPI
Version: 2.4
Description:

Welcome to the home of pyMPI, a project integrating the Message Passing Interface (MPI) into the Python interpreter. pyMPI is being developed primarily by researchers at Lawrence Livermore National Laboratory.

for the full HPC Team page on this software, click the link below

pyMPI

Research Area:
Biology
Last Updated: Wed, 2018-01-31 13:49
python
Version: 3.6.0-2, 3.6.0 (default), 2.7.14-pyCUDA, 2.7.13
Description:

Python is an interpreted, interactive, object-oriented programming language that combines remarkable power with very clear syntax.  For an introduction to programming in Python you are referred to the Python Tutorial.  The Python Library Reference documents built-in and standard types, constants, functions and modules.

for the full HPC Team page on this software, click the link below

python

Research Area:
Linux Utility
Last Updated: Wed, 2018-01-31 12:29
R
Version: 3.4.1, 3.3.2, R-devel
Description:

R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.

for the full HPC Team page on this software, click the link below

R

Research Area:
Education, Statistics
Last Updated: Wed, 2018-01-31 11:08
RAxML
Version: 8.2.10
Description:

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for postanalyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads. 

for the full HPC Team page on this software, click the link below

RAxML

Research Area:
Biology
Last Updated: Wed, 2018-01-31 11:09
Readline
Version: 7.0
Description:

The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.

for the full HPC Team page on this software, click the link below

Readline

Research Area:
Linux Utility, Linux Library
Last Updated: Wed, 2018-01-31 13:51
SageMath
Version: 7.6
Description:

SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib,Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers.

Mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.

Compilation Notes:

 

for the full HPC Team page on this software, click the link below

SageMath

Research Area:
Mathematics
Last Updated: Wed, 2018-01-31 12:27
SAMTOOLS
Version: 1.6 (default), 1.4.1, 1.4
Description:

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.

Compilation Notes:

required './configure', 'make', and 'make install' commands.

for the full HPC Team page on this software, click the link below

samtools

Research Area:
Biology, Linux Utility
Last Updated: Wed, 2018-01-31 11:10
seqprep
Version: 1.0
Description:

SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap. When an adapter sequence is present, that means that the two reads must overlap (in most cases) so they are forcefully merged. When reads do not have adapter sequence they must be treated with care when doing the merging, so a much more specific approach is taken.

for the full HPC Team page on this software, click the link below

seqprep

Research Area:
Biology
Last Updated: Wed, 2018-01-31 13:52
SKLearn
Version: 0.18.1
Description:
  • Simple and efficient tools for data mining and data analysis
  • Accessible to everybody, and reusable in various contexts
  • Built on NumPy, SciPy, and matplotlib
  • Open source, commercially usable - BSD license
for the full HPC Team page on this software, click the link below

SKLearn

Research Area:
Linux Utility, Linux Library
Last Updated: Wed, 2018-01-31 13:54
SLURM
Version: 16.05.8
Description:

The Slurm Workload Manager (formally known as Simple Linux Utility for Resource Management or SLURM), or Slurm, is a free and open-source job scheduler for Linux and Unix-like kernels, used by many of the world's supercomputers and computer clusters. It provides three key functions. First, it allocates exclusive and/or non-exclusive access to resources (computer nodes) to users for some duration of time so they can perform work.

for the full HPC Team page on this software, click the link below

SLURM

Research Area:
Linux Utility
Last Updated: Tue, 2017-02-28 11:41
SOAPdenovo
Version: 1.03
Description:

SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. Now the new version is available.

Compilation Notes:

This code is NOT compiled with MPI, and should only be used in parallel on a SINGLE node, via a threaded model.

for the full HPC Team page on this software, click the link below

SOAPdenovo

Research Area:
Biology
Last Updated: Wed, 2018-01-31 11:36
Spades
Version: 3.10.1
Description:

SPADES is an assembly toolkit containing various assembly pipelines.

SPADES works with Illumina or IonTorrent reads, and is capable of
providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger
reads. You can also provide additional contigs that will be used as
long reads.

for the full HPC Team page on this software, click the link below

Spades

Research Area:
Linux Utility, Linux Library
Last Updated: Wed, 2018-01-31 14:05
Spring
Version: spring5
Description:

Spring Boot is designed to get you up and running as quickly as possible, with minimal upfront configuration of Spring. Spring Boot takes an opinionated view of building production ready applications.

for the full HPC Team page on this software, click the link below

Spring

Research Area:
Computer Science
Last Updated: Mon, 2018-02-26 12:59
Stacks
Version: 1.46
Description:

Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

for the full HPC Team page on this software, click the link below

Stacks

Research Area:
Biology
Last Updated: Mon, 2018-02-26 13:00
Star
Version: 2.5.3a
Description:

The STAR program at MIT seeks to bridge the divide between scientific research and the classroom. Understanding and applying research methods in the classroom setting can be challenging due to time constraints and the need for advanced equipment and facilities. The multidisciplinary STAR team collaborates with faculty from MIT and other educational institutions to design software exploring core scientific research concepts. The goal of STAR is to develop innovative and intuitive teaching tools for classroom use.

for the full HPC Team page on this software, click the link below

Star

Research Area:
Computer Science
Last Updated: Mon, 2018-02-26 13:01
Stringtie
Version: 1.3.3b
Description:

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.

for the full HPC Team page on this software, click the link below

Stringtie

Research Area:
Biology
Last Updated: Mon, 2018-02-26 13:02
Szip
Version: 1.12b
Description:

Szip compression software, providing lossless compression of scientific data, has been provided with HDF software products as of HDF5 Release 1.6.0 and HDF4 Release 2.0.

for the full HPC Team page on this software, click the link below

Szip

Research Area:
Biology
Last Updated: Mon, 2018-02-26 13:04
Tensorflow
Version: 1.2.1-gpu, 1.2.1
Description:

TensorFlow™ is an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more CPUs or GPUs in a desktop, server, or mobile device with a single API.

for the full HPC Team page on this software, click the link below

Tensorflow

Research Area:
Computer Science
Last Updated: Mon, 2018-02-26 13:05
TOPHAT
Version: 2.1.1
Description:

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. 

Compilation Notes:

 

Prerequisites: bowtie and samtools

for the full HPC Team page on this software, click the link below

tophat

Research Area:
Biology
Last Updated: Wed, 2018-01-31 10:10
trinity
Version: 2.4.0 Released 02/05/2017
Description:

Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads.

Compilation Notes:

Trinity will run in SMP threaded model (i.e. parallel on a single node).

for the full HPC Team page on this software, click the link below

trinity

Research Area:
Biology
Last Updated: Wed, 2017-04-05 11:35
VASP
Version: 5.4.1-vtst, 5.4.1, 4.6-vtst
Description:

The Vienna Ab-initio Simulation Package, better known as VASP, is a package for performing ab initio quantum mechanical molecular dynamics using either Vanderbilt pseudopotentials, or the projector augmented wave method, and a plane wave basis set.

for the full HPC Team page on this software, click the link below

VASP

Research Area:
Chemistry, Material Science, Physics
Last Updated: Wed, 2018-01-31 10:09
Velvet
Version: 1.2.10
Description:

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.

Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

for the full HPC Team page on this software, click the link below

Velvet

Research Area:
Biology
Last Updated: Thu, 2017-04-06 11:19
Visit
Version: 2.12.2
Description:

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. From Unix, Windows or Mac workstations, users can interactively visualize and analyze data ranging in scale from small (<101 core) desktop-sized projects to large (>105 core) leadership-class computing facility simulation campaigns. Users can quickly generate visualizations, animate them through time, manipulate them with a

for the full HPC Team page on this software, click the link below

Visit

Research Area:
Computer Science
Last Updated: Mon, 2018-02-26 13:06
VMD
Version: 1.9.3
Description:

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

for the full HPC Team page on this software, click the link below

VMD

Research Area:
Biology
Last Updated: Wed, 2018-01-31 10:08
WARP
Version: 4.5
Description:

Warp is a extensively developed open-source particle-in-cell code designed to simulate
charged particle beams with high space-charge intensity. The name "Warp" stems from the
code's ability to simulate Warped (bent) Cartesian meshes. This bent-mesh capability
allows the code to efficiently simulate space-charge effects in bent accelerator lattices
(resolution can be placed where needed) associated with rings and beam transfer lines with
dipole bends. The code is setup around the interactive python interpreter with dynamically

for the full HPC Team page on this software, click the link below

WARP

Research Area:
Physics
Last Updated: Wed, 2018-01-31 10:07
Zlib
Version: 1.2.11
Description:

A Massively Spiffy Yet Delicately Unobtrusive Compression Library

for the full HPC Team page on this software, click the link below

zlib

Research Area:
Linux Utility
Last Updated: Mon, 2018-02-26 13:07