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The environment modules for these packages are somewhat old at this point. However, there are packages in this stack that are not yet in the newer stacks. Work is ongoing to get packages updated and migrated to newer stacks. Please begin using newer versions whenever possible.

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ProgramVersionLink to main page
bamtools2.5.1pezmaster31/bamtools: C++ API & command-line toolkit for working with BAM data
augustus3.3.2Augustus: gene prediction
cmake

3.7.2
3.13.2

CMake - Cross Platform Make

RHash1.3.7rhash/RHash: Great utility for computing hash sums
FFTW3.3.6
3.3.7		FFTW Home Page
GCC

5.4.0
6.3.0
7.3.0
8.3.0

GCC, the GNU Compiler Collection - GNU Project - Free Software Foundation (FSF)
GMP6.1.2The GNU MP Bignum Library
grib_api1.19.0 Home - GRIB-API - ECMWF Confluence Wiki
GSL2.2.3GSL - GNU Scientific Library - GNU Project - Free Software Foundation (FSF)
Gurobi Optimizer

5.6.3
7.0.2
8.1.0
9.0.0

Gurobi Optimizer
HDF51.8.18HDF Group - HDF5
Intel Parallel Studio
  • Intel compilers
  • MKL
  • DAAL
  • IPP
  • TBB

2017.1
2017.4

Intel® Composer XE Suites
Intel-MKL2019.3.199Intel® Math Kernel Library (Intel® MKL) | Intel® Software
matlab

R2016b
2018a

MATLAB - The Language of Technical Computing
MPC1.0.3MPC
MPFR3.1.5

The GNU MPFR Library

NCO4.6.4NCO Homepage
netcdf4.4.1.1Unidata | NetCDF
netcdf-cxx4.3.0Unidata | NetCDF
netcdf-fortran4.4.4Unidata | NetCDF

openmpi

2.0.1
2.1.2		Open MPI: Open Source High Performance Computing
Python

see below

Welcome to Python.org
R

see below

The R Project for Statistical Computing
valgrind3.12.0Valgrind Home
ocaml4.04.0 OCaml
Ansys

17.2 

ANSYS - Simulation Driven Product Development
CFITSIO3.410FITSIO Home Page
Pythia8.223PYTHIA
Platypus0.8.1Platypus Variant Caller
Ruby

2.4.0

Ruby Programming Language
Julia0.5.0
0.5.1		The Julia Language
MOSEK8.0.0.53
8.0.0.80		MOSEK ApS
JDK8u121
8u172		Java SE | Oracle Technology Network | Oracle
RSL1.49RSL (Radar Software Library)
Perl5.24.1The Perl Programming Language
Postgresql11.2PostgreSQL: The world's most advanced open source database
Graphviz2.40.1

Graphviz - Graph Visualization Software

htslib1.3.2Releases · samtools/htslib
samtools1.3.1Releases · samtools/samtools
bcftools1.3.1Releases · samtools/bcftools
bedtools2.26.0bedtools: a powerful toolset for genome arithmetic
lzo2.09

LZO real-time data compression library

CUDA8.0.44
8.0.61
9.0.176.1
9.1.85.1
9.1.85.2		Parallel Programming and Computing Platform | CUDA | NVIDIA
Beagle-lib2.1.2
3.1.2		general purpose library for evaluating the likelihood of sequence evolution on trees
Tecplot3602016R2Tecplot 360 CFD post processing tools to analyze data
CDO1.8.0Overview - CDO
I/O API3.2CMAS: Community Modeling and Analysis System I/O API
Plink1.07PLINK: Whole genome data analysis toolset
CMAQ5.1Community Multi-scale Air Quality (CMAQ) Modeling System for Air Quality Management | Air Research | US EPA
NCL6.4.0NCL Overview
HDF-EOS22.19HDF-EOS Tools and Information Center
HDF-EOS51.15HDF-EOS Tools and Information Center
g2clib1.60

GRIB2

Gaussian 09D.01Gaussian.com | Expanding the limits of computational chemistry
NBO6.0NATURAL BOND ORBITAL 6.0 HOME
HDF4.2.1HDF Group - HDF4
AutoDock Vina1.1.2AutoDock Vina - molecular docking and virtual screening program
BEAST1.8.4BEAST Software - Bayesian Evolutionary Analysis Sampling Trees
XCrySDen1.5.60XCrySDen - (X-Window) Crystalline Structures and Densities
Mesa17.0.1The Mesa 3D Graphics Library
LLVM4.0.0The LLVM Compiler Infrastructure Project
Open Babel2.4.1Open Babel
Eigen3.3.3Eigen
Protobuf (C++)3.2.0Protocol Buffers  |  Google Developers
Snappy1.1.4Snappy by google
LevelDB1.20GitHub - google/leveldb: LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.
YASM1.3.0The Yasm Modular Assembler Project
FFMPEG3.2.4About FFmpeg
OpenCV3.2.0OpenCV library
JAGS4.2.0JAGS - Just Another Gibbs Sampler
STAR-CCM+

12.02.010 
13.04.010

STAR-CCM+® | CFD Simulation Software
Cufflinks2.2.1Cufflinks
PETSc
  • hpre
  • metis
  • parmetis
  • mpi4py
  • mumps
  • petsc4py
  • ptscotch
  • suitesparse
  • superlu_dist 
3.7.5
3.10.3		PETSc: Home Page
Wannier902.1.0wannier.org
Atompaw4.0.0.14Atompaw Web Page
Libxc2.2.3
3.0.0 		Libxc - OctopusWiki
ABINIT8.2.2ABINIT
c-blosc1.11.2Blosc, an extremely fast, multi-threaded, meta-compressor library | Blosc Main Page
MDTraj1.8.0MDTraj
lmfit6.1lmfit [MLZ Scientific Computing Group]
Gromacs2016.3Gromacs
ELPA2016.05.004
2018.11.001		About ELPA — Eigenvalue SoLvers for Petaflop-Applications (ELPA)
Quantum Espresso6.1Quantum ESPRESSO
BWA0.7.15Burrows-Wheeler Aligner
libcerf1.5libcerf [MLZ Scientific Computing Group]
Gnuplot5.0.6gnuplot homepage
GEOS3.6.1GEOS
Ncview2.1.7Ncview
git2.13.0Git
BLAST
databases: nt, nt, swissprot		2.6.0+BLAST: Basic Local Alignment Search Tool
ParaView5.4.0ParaView Home
cuDNN5.1
6.0
7.0.5		NVIDIA cuDNN | NVIDIA Developer
Leptonica1.74.4Leptonica
Tesseract3.05.01Tesseract Open Source OCR Engine
WebP0.6.0A new image format for the Web  |  WebP  |  Google Developers
giflib5.1.4The GIFLIB project
Subread1.5.2Subread
GLPK4.62

GLPK - GNU Project - Free Software Foundation (FSF)

Symphony5.6.16SYMPHONY
gavl1.4.0Gmerlin homepage - gavl
frei0r-plugins1.6.1Frei0r :: Free Video Effects collection
MPFI1.5.1InriaForge: MPFI: Project Home
ESBTL1.0-beta01ESBTL (Easy Structural Biology Template Library)
gf2x1.2InriaForge: gf2x: Project Home
NTL10.4.0NTL: A Library for doing Number Theory
CGAL4.10
4.13		The Computational Geometry Algorithms Library
SQLite3.16.2
3.30.0		SQLite Home Page
scotch6.0.4SCOTCH: Static Mapping, Graph, Mesh and Hypergraph Partitioning, and Parallel and Sequential Sparse Matrix Ordering Package
metis5.1.0METIS - Serial Graph Partitioning and Fill-reducing Matrix Ordering | Karypis Lab
parmetis4.0.3ParMETIS - Parallel Graph Partitioning and Fill-reducing Matrix Ordering | Karypis Lab
OpenFOAM4.1
5.0		OpenFOAM | Free CFD Software | The OpenFOAM Foundation
STAR2.5.3aSTAR | Spliced Transcripts Alignment to a Reference
libunwind1.2.1The libunwind project
glog0.3.5google/glog: C++ implementation of the Google logging module
gflags2.2.1How To Use Gflags (formerly Google Commandline Flags)
LMDB0.9.21LMDB/lmdb: Read-only mirror of official repo on openldap.org.
Caffe1.0Caffe | Deep Learning Framework
NCCL1.3.4
2.1.4		NVIDIA/nccl: Optimized primitives for collective multi-GPU communication

WIEN2K

Info

license required


17.1WIEN 2k
Turbomole

7.2.0

7.2.1

Turbomole: Program Package for ab initio Electronic Structure Calculations
Parallel NetCDF1.8.1parallel-netcdf
Amber2017 (Amber16 + AmberTools17)The Amber Molecular Dynamics Package
TransPS1.1.0TransPS
cusplibrary0.4.0
0.5.1		CUSP: Main Page
Mesquite2.3.0Mesquite – The Trilinos Project
foam-extend4.0foam-extend download | SourceForge.net
HPL2.2HPL - A Portable Implementation of the High-Performance Linpack Benchmark for Distributed-Memory Computers
PortAudio19.6.0PortAudio - an Open-Source Cross-Platform Audio API
openSMILE2.3.0audEERING | Intelligent Audio Engineering – openSMILE
log4j2.10.0Log4j – Apache Log4j 2 - Apache Log4j 2
flex2.6.4GitHub - westes/flex: The Fast Lexical Analyzer - scanner generator for lexing in C and C++
WRF
WRF-chem
WPS (WRF Preprocessing System)		3.9.1.1Weather Research and Forecasting Model | MMM: Mesoscale & Microscale Meteorology Laboratory
Darshan3.5.1Darshan
RngStreams1.0.1

RngStreams - multiple independent streams of pseudo-random numbers

UNU.RAN1.8.1UNU.RAN - Universal Non-Uniform RANdom number generators
LZ41.8.1.2LZ4 - Extremely fast compression
GL2PS1.4.0GL2PS: an OpenGL to PostScript printing library
XRootD4.8.1Home Page | XRootD
Z34.6.0GitHub - Z3Prover/z3: The Z3 Theorem Prover
Davix0.6.7GitHub - cern-it-sdc-id/davix: High-performance file management over WebDAV / HTTP
xxHash0.6.4GitHub - Cyan4973/xxHash
Oracle instantclient

12.2.0.1.0

Oracle Instant Client - Free tools and libraries for connecting to Oracle Database
ROOT6.12.06ROOT a Data analysis Framework
Praat6.0.37Praat: doing Phonetics by Computer
MKL-DNN0.12GitHub - intel/mkl-dnn: Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN)
NASM2.13.03NASM
Yeppp1.0.0MDukhan / Yeppp — Bitbucket
CNVnator0.3.3GitHub - abyzovlab/CNVnator: a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
CPLEX12.8.0ILOG CPLEX Optimization Studio | IBM

SAS

Info

License required
SAS | Information Technology Services


9.4_TS1M2Foundation Tools | SAS
Gentle0.10.1lowerquality/gentle: gentle forced aligner
Bazel0.12.0Bazel - a fast, scalable, multi-language and extensible build system - Bazel
TensorBoard1.7.0tensorflow/tensorboard: TensorFlow's Visualization Toolkit
TensorFlow1.7.0TensorFlow
libedit3.1-20170329Editline Library (libedit) - Port of NetBSD Command Line Editor Library
GEANT410.4.1Overview | geant4.web.cern.ch
Google Test1.8.0google/googletest: Google Test
InsightToolkit4.13.0
4.13.2		ITK - Segmentation & Registration Toolkit
RTK1.4.0RTK - Reconstruction Toolkit
Gate8.1Forewords | GATE
SimplElastix0.10.0SimpleElastix
Elastix4.9.0elastix
PGI Community Edition18.4PGI | Products | Community Edition
Nettle3.4Nettle - a low-level crypto library
libarchive3.3.2libarchive - C library and command-line tools for reading and writing tar, cpio, zip, ISO, and other archive formats
SRA-tools2.9.0ncbi/sra-tools: SRA Tools
NGS2.9.0ncbi/ngs: NGS Language Bindings
NCBI-VDB2.9.0-1ncbi/ncbi-vdb: ncbi-vdb
LASzip2.2.0
3.2.2		LASzip - free and lossless LiDAR compression
libLAS1.8.1libLAS - LAS 1.0/1.1/1.2 ASPRS LiDAR data translation toolset — liblas.org
libgeotiff1.4.2GeoTIFF
libgpuarray0.7.6Welcome to libgpuarray’s documentation!
GATK4.0.5.2GATK | Home
SNAP0.15SNAP Sequence Aligner
zstd1.3.5

Zstandard - Real-time data compression algorithm

magma2.4.0Magma
ZeroMQ4.2.5Distributed Messaging
CUB1.8.0CUB: Main Page
pybind112.2.3pybind/pybind11: Seamless operability between C++11 and Python
pytorch/caffe20.4.0PyTorch
torchvision0.2.1pytorch/vision: Datasets, Transforms and Models specific to Computer Vision
bowtie1.2.2Bowtie: An ultrafast, memory-efficient short read aligner
bowtie22.3.4.2Bowtie 2: fast and sensitive read alignment
WRF-Hydro5.0.0Overview | NCAR Research Applications Laboratory | RAL
libuuid1.0.3libuuid download | SourceForge.net
CZMQ4.1.1CZMQ - High-level C Binding for ZeroMQ - libzapi
cppzmq4.3.0zeromq/cppzmq: Header-only C++ binding for libzmq
libtool2.4.6GNU Libtool - GNU Project - Free Software Foundation
libunistring0.9.10libunistring - GNU Project - Free Software Foundation (FSF)
libatomic_ops7.6.4ivmai/libatomic_ops: The atomic_ops project (Atomic memory update operations portable implementation)
GC7.6.4A garbage collector for C and C++
Guile2.2.4GNU's programming and extension language — GNU Guile
libctl4.1.3Overview - libctl Documentation
OpenBUGS3.2.3FrontPage - OpenBUGS
TopHat2.1.1
2.1.2		TopHat
VCFtools0.1.16VCFtools
Jellyfish2.2.10gmarcais/Jellyfish: A fast multi-threaded k-mer counter
BLAT35Human BLAT Search
Mapsembler22.2.4mapsembler2
cortex_con0.04c (beta)CORTEX website (cortex_con)
cortex_var1.0.5.21CORTEX website (cortex_var)
CoNIFER0.2.2Conifer - COpy Number Inference From Exome Reads - Home
libgtextutils0.7agordon/libgtextutils: Gordon's Text utils Library
fastx_toolkit0.0.14agordon/fastx_toolkit: FASTA/FASTQ pre-processing programs

Abaqus

Info

license required


2018Abaqus Unified FEA - SIMULIA™ by Dassault Systèmes®
GMT5.4.4GenericMappingTools/gmt: The Generic Mapping Tools
RocksDB5.17.2RocksDB | A persistent key-value store | RocksDB
TeXLive20180414TeX Live - TeX Users Group
ARPACK-NG3.7.0opencollab/arpack-ng: Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
SuperLU5.2.1SuperLU: Home Page
Armadillo9.200.7Armadillo: C++ library for linear algebra & scientific computing
PEST13.6PESThomePage.org - HOME PAGE
FEniCS2018.1.0FEniCS Project
mpiP3.4.1mpiP: Lightweight, Scalable MPI Profiling
PAPI5.7.0PAPI
SimpleITK1.2.0SimpleITK
OpenJDK11.0.2OpenJDK
libogg1.3.3Xiph.org
flac1.3.2FLAC - Free Lossless Audio Codec
mpg1231.25.10mpg123, Fast MP3 Player for Linux and UNIX systems
libvorbis1.3.6Xiph.org
libsndfile1.0.28Libsndfile
lame3.100LAME MP3 Encoder
libmad0.15.1bUnderbit: MAD (MPEG Audio Decoder)
libid3tag0.15.1bUnderbit: MAD (MPEG Audio Decoder)
opus1.3.1Opus Codec
wavpack5.1.0WavPack Audio Compression
TwoLAME0.3.13TwoLAME - MPEG Audio Layer 2 Encoder
libao1.2.0Xiph.org: libao: a cross platform audio library
opencore-amr0.1.5opencore-amr download | SourceForge.net
opusfile0.11Opus Codec
SoX14.4.2http://sox.sourceforge.net/
SCons3.0.5SCons: A software construction tool - SCons
ISCE22.3.1

isce-framework/isce2: InSAR Scientific Computing Environment version 2

Mono5.18.0.240Home | Mono
VASP5.4.4VASP - Vienna Ab initio Simulation Package
zip3.0Info-ZIP Home Page



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