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 anytime software is either added or updated on Talon2.
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: Amber14 cuda-parallel, parallel, series
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, 2017-02-28 11:08
Bio
Version: 6.4
Webpage:

Unknown

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

Bio

Research Area:
Linux Library
Last Updated: Tue, 2017-02-28 11:04
BLAST+
Version: 2.2.28
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: Thu, 2016-04-21 10:37
BLAT
Version: 10.24.13
Description:

Blat produces two major classes of alignments:

Compilation Notes:

For compilation and build notes, visit http://genome.ucsc.edu/admin/git.html

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

BLAT

Research Area:
Biology
Last Updated: Wed, 2016-02-10 12:07
BOOST
Version: 1.54.0
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: Wed, 2016-02-10 12:29
BOWTIE
Version: 2.2.5
Description:

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

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: Tue, 2017-02-28 11:08
CAFEMOL
Version: 2.1
Description:

CafeMol is a general-purpose coarse-grained(CG) biomolecular modeling and simulation software.It can simulate proteins,nucleic acids,lipids and their mixture with various CG models.

Compilation Notes:

Compiled with intel-mpif90

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

Cafemol

Research Area:
Biology, Chemistry
Last Updated: Wed, 2016-02-03 12:13
CAMX
Version: 6.10
Description:

An open-source modeling system for multi-scale integrated assessment of gaseous and particulate air pollution.

Compilation Notes:

openmpi/intel/14

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

CAMX

Research Area:
Mechanical Engineering
Last Updated: Mon, 2016-02-08 12:33
Circos
Version: 0.67
Description:

Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries.

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

Circos

Research Area:
Biology
Last Updated: Mon, 2016-02-08 12:37
CMAKE
Version: 3.5.0-rc1
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, 2016-02-03 13:42
CP2K
Version: 2.3-gfort-s, 2.3-intel-p, 2.4-intel-p
Description:

CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. It provides a general framework for different methods such as e.g., density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) and classical pair and many-body potentials.

Compilation Notes:

Serial version is compiles using gfortran.

Parallel version compiled using intel/mkl (13.1)

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

CP2K

Research Area:
Chemistry, Material Science
Last Updated: Thu, 2016-04-21 10:40
CPMD
Version: 3.15.3
Description:

The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
CPMD is jointly copyrighted by IBM Corporation and Max-Planck Institut, Stuttgart. 

Compilation Notes:

Parallel version is compiled with Intel/MKL 13.1

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

CPMD

Research Area:
Chemistry, Material Science, Physics
Last Updated: Wed, 2016-02-03 15:16
CUDA
Version: 5.0.35
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

Research Area:
Linux Library
Last Updated: Tue, 2017-02-28 11:10
CUFFLINKS
Version: 2.2.1, 2.1.1
Description:

Cufflinks is a reference-guided assembler for RNA-Seq experiments. It simultaneously assembles transcripts from reads and estimates their relative abundances, without using a reference annotation.

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: Tue, 2017-02-28 11:57
dDocent
Version: 1.2, 1.0
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: Tue, 2017-02-28 11:59
DFTB+
Version: 1.2.2, mpi, negf
Description:

DFTB+ is a fast and efficient versatile quantum mechanical simulation package.

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

DFTB+

Research Area:
Chemistry, Material Science
Last Updated: Tue, 2017-02-28 12:00
DIRAC
Version: 13.1
Description:

DIRAC is a powerful electronic structure program that is compatible of using various relativistic treatments onto atomic and molecular systems. This includes a full 4-component Dirac Hamiltonian, many types of approximate 2-component methods, and more. DIRAC is able to use relativistic Hamiltonian to various methods such as HF, DFT, and various other electron correlation methods.

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

DIRAC

Research Area:
Chemistry, Physics
Last Updated: Tue, 2017-02-28 12:01
DL_POLY
Version: 4.08
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: Tue, 2017-02-28 11:21
Eleven
Version: Eleven
Webpage:

Unknown

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

Eleven

Research Area:
Linux Library
Last Updated: Tue, 2017-02-28 11:11
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
FastTree
Version: 2.1.8
Description:

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

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

FastTree

Research Area:
Biology
Last Updated: Tue, 2017-02-28 11:11
FFTW
Version: 3.3.3 (Intel 13), 3.3.3 (Intel 14)
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, 2016-02-03 15:47
GAMESS
Version: 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: Tue, 2017-02-28 11:24
GAP
Version: 4
Description:

GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. GAP provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic objects.

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

GAP

Research Area:
Mathematics
Last Updated: Tue, 2017-02-28 12:03
Gaussian
Version: 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: Tue, 2017-02-28 11:26
GNU compiler
Version: 6.3
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: Tue, 2017-02-28 11:27
Gromacs
Version: 4.6.3-fftw (default), 4.6.3-cuda, 4.6.3-mpi-cuda
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: Tue, 2017-02-28 12:04
HDF5
Version: 1.8.13-s-ifort, 1.8.13-p-ifort
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: Tue, 2017-02-28 11:11
HTSeq
Version: 0.6.1p1
Description:

HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

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

HTSeq

Research Area:
Linux Utility
Last Updated: Tue, 2017-02-28 11:11
Human
Version: 0.99
Webpage:

Unknown

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

Human

Research Area:
Linux Library
Last Updated: Tue, 2017-02-28 11:11
Intel
Version: Parallel Studio 2017(Includes Intel MPI)
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: Tue, 2017-02-28 11:30
Isolation with Migration
Version: IMa2-8.27.12
Description:

IM is a program, written with Rasmus Nielsen, for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations.  IM is based on a method originally developed by Rasmus Nielsen and John Wakeley (Nielsen and Wakeley 2001 Genetics 158:885).  Large numbers of loci can be studied simultaneously, and different mutation models can be used.

Compilation Notes:

Compiled with gfortran for only single node (SMP) parallelization.

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

Isolation with Migration

Research Area:
Biology
Last Updated: Tue, 2017-02-28 12:05
JAGS
Version: 3.4.0
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: Fri, 2016-02-05 12:45
LAMMPS
Version: 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: Tue, 2017-02-28 11:31
MaSuRCA assembler
Version: 2.2.1
Description:

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454).

Compilation Notes:

Compiled with gcc/g++.  Will only run parallel threads on a single compute node.
The following parameters are mandatory:
NUM_THREADS=16
set it to the number of cores in the computer to be used for assembly.sh
The number of threads should match the number you request in your UGE parallel environment "-pe openmpi_16 16"

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

MaSuRCA assembler

Research Area:
Biology
Last Updated: Mon, 2016-04-04 15:06
MATHEMATICA
Version: 10.0.2
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: Tue, 2017-02-28 12:06
MATLAB
Version: R2016a, 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: Tue, 2017-02-28 12:07
MIRA
Version: 4
Description:

MIRA 4 is able to perform true hybrid de-novo assemblies using reads gathered through Sanger, 454, Solexa, IonTorrent or PacBio sequencing technologies. That is, it assembles reads instead of a mix of (eventually shredded) consensus sequence and reads. See an example on how it looks like for Sanger and 454 in the documentation introduction, but it also works with any other combination of sequencing technologies. Only restriction at the moment: reads must be <= 32 kilobases and for PacBio, MIRA must get CCS reads or error-corrected CLR data.

Compilation Notes:

Came as statically compiled binary.

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

MIRA

Research Area:
Biology
Last Updated: Fri, 2016-02-05 10:22
MKL
Version: 14.0.1 (default), 13.1.1, 11.0.3
Description:

Intel® Math Kernel Library (Intel® MKL) accelerates math processing routines that increase application performance and reduce development time. Intel® MKL includes highly vectorized and threaded Linear Algebra, Fast Fourier Transforms (FFT), Vector Math and Statistics functions.

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

MKL

Research Area:
Linux Library
Last Updated: Tue, 2017-02-28 12:09
Molcas
Version: 7.8
Description:

Molcas is an ab initio quantum chemistry software package developed by scientists to be used by scientists.

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

Molcas

Research Area:
Linux Library
Last Updated: Tue, 2017-02-28 11:13
MOLDEN
Version: 5.1
Description:

Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS andGAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden FormatMolden reads all the required information from the GAMESS / GAUSSIAN outputfile.

Compilation Notes:

This visualization software is only availble from the vis-login nodes and requires X11 forwarding to a client Xwin server to work.
molden, gmolden, surf, ambfor, and ambmd are all compiled with gcc/gfortran 4.4.7

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

MOLDEN

Research Area:
Biology
Last Updated: Mon, 2016-02-08 13:18
Molpro
Version: 2010-1.44
Description:

Molpro is a electronic structure calculation with a complete capability of ab initio methods. The code has implemented various method for highly accurate calculation for electron correlation.

Compilation Notes:

intel/13.1

mkl/13.1.1

global array v5.1.1

 

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

Molpro

Research Area:
Chemistry
Last Updated: Tue, 2017-02-28 12:10
MPICH
Version: 3.1.2
Description:

MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.

Compilation Notes:

Compiled with Intel14

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

MPICH

Research Area:
Linux Library
Last Updated: Wed, 2016-02-10 12:18
MUMmer
Version: 3.23
Description:

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.

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

MUMmer

Research Area:
Linux Library
Last Updated: Tue, 2017-02-28 11:13
NCL
Version: 6.2.0
Description:

NCL is an interpreted language designed specifically for scientific data analysis and visualization.

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

NCL

Research Area:
Linux Library
Last Updated: Tue, 2017-02-28 11:13
Newbler
Version: 2.9
Description:

Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Sciences, a Roche Diagnostics company. Newbler is a useful tool for assembling your 454 (or other pyrosequencing) data.

Compilation Notes:

Came as statically linked binary.

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

NEWBLER

Research Area:
Biology
Last Updated: Fri, 2016-02-05 10:41
NWChem
Version: 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: Tue, 2017-02-28 11:33
Oases
Version: 0.2.09, 0.2
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.

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

Oases

Research Area:
Biology
Last Updated: Tue, 2017-02-28 12:11
Openbabel
Version: 2.3.2
Description:

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

Compilation Notes:

gnu.

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

Openbabel

Research Area:
Biology, Chemistry
Last Updated: Mon, 2016-02-08 13:24
OpenMPI
Version: 1.10.2, gcc/mlx/1.6.4;1.6.5, gige/gcc1.6.4;1.6.5, gige/intel/1.6.4;1.6.5, intel/13/mlx1.6.4;1.6.5, intel/14/1.6.5 (default), pgi/mlx/1.6.5, gcc/mlx*, intel/mlx*
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: Tue, 2017-02-28 12:13
ORCA
Version: 3.0.2
Description:

The program ORCA is a modern electronic structure program package written by F. Neese, with contributions from many current and former coworkers and several collaborating groups. The binaries of ORCA are available free of charge for academic users for a variety of platforms.

Compilation Notes:

The linux version was inflated. The module loads openmpi/intel/14/1.6.5 for necessary parallel libraries. 
You must use "PAL#" in your ORCA input line to run in parallel, where # = 2 - 8.  Ex: ! HF PAL8

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

ORCA

Research Area:
Chemistry, Material Science, Physics
Last Updated: Mon, 2016-02-08 13:26
PAML
Version: 4.7a (default), X/1.1 (vis-node)
Description:

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.

Compilation Notes:

Compiled with intel/13.1

The command-line version can be run cluster wide.

The GUI version (PamlX) is only avaible on vis-nodes.

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

PAML

Research Area:
Biology
Last Updated: Mon, 2016-02-08 15:54
PGI
Version: 14.9
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: Tue, 2017-02-28 11:13
PSI4
Version: 0b5/6.5
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: Tue, 2017-02-28 11:13
python
Version: 2.7.3, 2.7.x, 3.2.1, 3.5.x
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.

Compilation Notes:

These are additional versions added to compute nodes from rocks python roll 6.1

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

python

Research Area:
Linux Utility
Last Updated: Tue, 2017-02-28 12:23
QIIME
Version: 1.8.0
Description:

QIIME (canonically pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data).

Compilation Notes:

python is used to download and compile the code. GPL 32bit version of "usearch" was used. 

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

QIIME

Research Area:
Biology, Chemistry, Health Science
Last Updated: Tue, 2017-02-28 12:24
R
Version: 3.3.2
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: Tue, 2017-02-28 11:34
RAxML
Version: 8.2.4
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: Tue, 2017-02-28 11:13
RSEM
Version: 1.2.23
Description:

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation.

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

RSEM

Research Area:
Biology
Last Updated: Tue, 2017-02-28 11:13
Rstudio
Version: 0.98.970
Description:

RStudio is an IDE that makes R easier to use and more productive. RStudio combines a set of productivity tools into a single environment including:

  • Code Editor – syntax highlighting, code completion, indenting, and definitions
  • Debugging – debugging console, breakpoints, environment panel, and tracebacks
  • Visualization – data display, data plotting, and data manipulation
for the full HPC Team page on this software, click the link below

Rstudio

Research Area:
Education, Statistics
Last Updated: Tue, 2017-02-28 12:24
Sage
Version: 5.11
Description:

Sage is a free open-source mathematics software system licensed under the GPL. It combines the power of many existing open-source packages into a common Python-based interface.

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

Compilation Notes:

Compiled with gcc.  Optional packages gap_packages-4.6.4.p1 and database_gap-4.6.4 have been installed too.

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SAGE

Research Area:
Mathematics
Last Updated: Fri, 2016-02-05 11:51
SAMTOOLS
Version: 1.2
Description:

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

Compilation Notes:

gcc make file.

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

samtools

Research Area:
Biology, Linux Utility
Last Updated: Tue, 2017-02-28 12:25
SCons
Version: 2.3.4
Description:

SCons is an Open Source software construction tool—that is, a next-generation build tool. Think of SCons as an improved, cross-platform substitute for the classic Make utility with integrated functionality similar to autoconf/automake and compiler caches such as ccache. In short, SCons is an easier, more reliable and faster way to build software.

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

SCons

Research Area:
Linux Utility
Last Updated: Tue, 2017-02-28 11:13
SOAPdenovo
Version: 2-rev240
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: Mon, 2016-04-04 15:42
SplitsTree
Version: 4.0
Description:

SplitsTree4 is the leading application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.

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

SplitsTree

Research Area:
Biology
Last Updated: Tue, 2017-02-28 11:13
SRA Toolkit
Version: 2.3.4
Description:

The Sequence Read Archive (SRA) stores raw sequence data from "next-generation" sequencing technologies including 454, IonTorrent, Illumina, SOLiD, Helicos and Complete Genomics. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence.

HOMEPAGE LINK DOES NOT WORK...

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

SRA Toolkit

Research Area:
Biology
Last Updated: Mon, 2016-02-08 13:48
tbl2asn
Version: linux64
Description:

Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank. Additional manual editing is not required before submission.

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

tbl2asn

Research Area:
Biology
Last Updated: Tue, 2017-02-28 11:13
TOPHAT
Version: 2.1.0
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:

Compiled via GNU compilers.

Prerequisites: bowtie and samtools

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

tophat

Research Area:
Biology
Last Updated: Tue, 2017-02-28 12:27
trinity
Version: 20131113
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: Mon, 2016-02-08 13:50
VASP
Version: 5.4.1
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: Tue, 2017-02-28 11:36
VERDI
Version: 1.4.1
Description:

VERDI is a Java program for visualizing meteorology, emissions, and air quality modeling data.

Compilation Notes:

java script.

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

VERDI

Research Area:
Mechanical Engineering
Last Updated: Mon, 2016-02-08 13:51
VirtualGL
Version: 2.3.3
Description:

VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the ability to run OpenGL applications with full 3D hardware acceleration. Some remote display solutions cannot be used with OpenGL applications at all.

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

VirtualGL

Research Area:
Linux Utility
Last Updated: Tue, 2017-02-28 11:13
VMD
Version: 1.9.1
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: Tue, 2017-02-28 11:13
VORO++
Version: voro++0.4.5
Description:

Voro++ is a open source software library for the computation of theVoronoi diagram, a widely-used tessellation that has applications in many scientific fields. The main design features are Cell-based computations, 3D calculation and C++ architecture.

Compilation Notes:

The voro++ utility package is added to LAMMPS so that users can access it directly from inside the LAMMPS.

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

VORO++

Research Area:
Biology, Chemistry, Computer Science, Electrical Engineering, Mathematics, Physics, Statistics
Last Updated: Mon, 2016-04-04 15:53
WARP
Version: warp-mpi
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: Tue, 2016-05-03 09:33
WRF
Version: gcc
Description:

The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting needs.

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

WRF

Research Area:
Linux Library
Last Updated: Tue, 2017-02-28 11:13