Available Software

Contents

  1. The tap and module commands
    1. The tap command
    2. The modules command
    3. Library packages
    4. Common errors
  2. Software packages available
    1. Unclassified by field
    2. Classified by field, etc
      1. Software related to Biology
      2. Software related to Chemistry
      3. Software related to Meteorology
      4. Software related to Numerical Analysis
      5. Software related to Program Development
      6. GPU-enabled software packages
  3. Packages for scripting languages
    1. Perl packages
    2. Python packages
    3. R modules

tap and module commands

A large number of software packages are available on each of the clusters, and for some of them, multiple versions of the same package. Not all of them like to co-exist with each other, so many of the packages are not available by default. You need to tell the system you want to use them with the tap and/or module.

Please note that the HPC compute nodes have abridged copies of the software directories available on other Glue/TerpConnect systems. The HPC login nodes have the full software directories. Please look at software lists below, and in particular click on the software package name for the full breakdown by version number to see which, if any, HPC clusters a specific version of the package is on.

WARNING
The tap command is deprecated on Glue, and does not work on either of the Deepthought clusters. Use the module command instead.

For example, matlab is available on all Glued systems, but only after you module load it. E.g.

login-1: matlab
matlab: Command not found.
login-1: module load matlab
login-1: module help matlab

----------- Module Specific Help for 'matlab/2014b' ---------------


    This is Matlab Release 2014b

    Releases after 2009 require Red Hat 5 or later.
    Releases after 2013 require Red Hat 6 or later.
    Matlab 2009b is the last release supported under Solaris.

    Run command 'matlab' to start up the program,
    or 'matlab -h' to see various command-line options.

    ***  To see all releases, issue the command
	module avail matlab

login-1: matlab
                              < M A T L A B >
                  Copyright 1984-2014 The MathWorks, Inc.
                   R2014b (8.4.0.150421) 64-bit (glnxa64)
                             September 15, 2014


  To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit www.mathworks.com.

>> 

You can use the module help and module whatis commands before (or without) loading the package.

The tap command

Historically, GLUE has used the tap command. It is fairly simple to use. Each package has a tag, like matlab in the example above.

WARNING
The tap command is deprecated on Glue, and does not work on either of the Deepthought clusters. Use the module command instead.
WARNING
This section is no longer applicable to the Deepthought clusters. It is being retained for historical reasons.

For example, matlab is available on all Glued systems, but

To enable a package, you simple issue the command

tap PACKAGE_TAG

This version of the command will set up your environment for using the software, and print a brief message about the package. Usually things like what version, very basic usage instructions, and maybe where to find help. You can add the -q flag to suppress this message. NOTE: If you put tap commands in your startup scripts, e.g ~/.cshrc.mine, be sure to include the -q flag. Otherwise, the extraneous output from the tap message when you log in might break file transfer protocols like scp or sftp.

We encourage you to read the message at least once when you start to use a new package. There might be something useful in it.

WARNING
NOTE: If you are submitting a job using a bourne style shell (e.g. sh or bash), your dot files will not be read automatically if your default shell is something else (e.g. csh or tcsh). So you will need to include a . ~/.profile line near the top of your script, after the #SBATCH lines but before you try to use tap or module commands.

You can also give the commands

tap -h
tap -l
to get a brief usage summary, and a list of known application tags. The -l also give a little description with the application tags.

We are planning to phase out the tap command, and switch entirely to the module, as it is more flexible and has a broad user base outside of UMD. Some commands will be available via both mechanisms for a while, although in many cases not all options will be available via tap, and even when an application is available, the number of versions avaialable through tap will be restricted.

WARNING
The tap command is NOT available on the two Deepthought HPC clusters. Please switch to the module command. If there is an application you need which is only available via tap, please open a help ticket.

The module command

The module is replacing the tap command across Glue, and has already replaced it on the Deepthought HPC clusters. The module command is community supported, and used at many other institutions, and has some features that are lacking in the tap command.

Just like the tap command, the module command associates a tag with the various packages. Unlike the tap command, the module tag has a hierarchical nature, so we have tags like matlab/2013b and matlab/2011a in addition to plain old matlab. The former specify a specific version of matlab, whereas the latter will enable the default version of matlab.

In almost all cases, you need only specify a portion of the tag, the system will try to default it properly. For some more complicated cases, like packages which depend on compiler and MPI libraries, it can figure out which compiler and MPI library to use based on what you previously loaded, and find the correct variant for you. You may need to specify the version of the package if the default version was not built for that compiler/MPI library combination.

Alternatively, if you specify the full path to a package which depends on a specific compiler and MPI library, these will be loaded for you if not already loaded. In general, if the package has dependencies, they will be loaded automatically for you if needed.

WARNING
NOTE: If you are submitting a job using a bourne style shell (e.g. sh or bash), your dot files will not be read automatically if your default shell is something else (e.g. csh or tcsh). So you will need to include a . ~/.profile line near the top of your script, after the #SBATCH lines but before you try to use tap or module commands.

The module command allows you to issue commands of the form module SUBCOMMAND OPTIONAL_ARGUMENT. Recognized subcommands include:

  • list: This will list the packages you currently have loaded. Note that if a tap entry was migrated to modules, it will show up here if you loaded it using tap.
  • avail OPTIONAL_TAG: this will list all the packages available. If a tag is given, it will list all packages which match the tag.
  • load TAG: this is the most common usage, and it sets up the environment for the application associated with TAG. Again, if you do not specify the full tag, the system will attempt to default it, and usually it can do that with some success. Most of our application definitions will pull in any dependencies as well. Note that unlike tap, this is a silent operation when it succeeds.
  • help TAG: This displays a brief intro message about the package. Generally the same message you see when you tap a package. It is advised that you read this once for each package you use.
  • unload TAG: This unloads the package; i.e. all the environment that was set up for the package is returned to what it was before you loaded it. This is not 100% successful all the time, but for the most part works. You generally do not need this unless you which to change the version of an application you are using.
  • Please note that the HPC compute nodes have abridged copies of the software directories available on other Glue/TerpConnect systems. The HPC login nodes have the full software directories. Please look at software lists below, and in particular click on the software package name for the full breakdown by version number to see which, if any, HPC clusters a specific version of the package is on.

Library packages

Some packages are not so much applications as libraries; i.e. they provide libraries which your code can use, and might or might not have any binaries that you can run directly. To make use of these libraries in your code takes a little bit of work. Please see the section on compiling codes for more information on how to do this.

Common errors from module/tap commands

As stated early, not all packages co-exist nicely. This is particularly true of different versions of the same package, or related libraries (e.g. the various MPI libraries). The module command will generate an error if you try to load a package which does not play well with packages you have previously loaded; if this occurs you will need to unload the previous package and reload the new package. E.g.

login-1: module load matlab/2012b
login-1:~: module load matlab/2013b
matlab/2013b(8):ERROR:150: Module 'matlab/2013b' conflicts with the currently loaded module(s) 'matlab/2012b'
matlab/2013b(8):ERROR:102: Tcl command execution failed: source $moduledir/common
login-1: module unload matlab
login-1:~: module load matlab/2013b

Although not as user friendly as one would like, you can see that the first time I tried to load matlab/2013b it complained because matlab/2012b was already loaded. Also note that I did not need to specify the full tag to unload matlab/2012b, as there was only one matlab package loaded, so it could default it.

You can also run into similar incompatibillity problems if you mix packages (especially library packages) built for one compiler/MPI library/etc with a different compiler/MPI library/etc. For example

login-1: module avail fftw/3.3.3

------------------- /cell_root/system/common/modulefiles/sys -------------------
fftw/3.3.3/gnu/4.6.1/openmpi/1.6/shared
fftw/3.3.3/gnu/4.6.1/openmpi/1.6/static
fftw/3.3.3/gnu/4.6.1/openmpi/1.6.5/shared
fftw/3.3.3/gnu/4.6.1/openmpi/1.6.5/static
fftw/3.3.3/intel/2013.1.039/openmpi/1.6.5/shared
fftw/3.3.3/intel/2013.1.039/openmpi/1.6.5/static

login-1: module load intel/2013.1.039

login-1: module load fftw/3.3.3/gnu

***** Compiler mismatch

You have loaded compiler intel/2013.1.039
This package wants compiler gnu/4.6.1
login-1: 

In the above, we show that there are various builds of fftw/3.3.3 available. We then load the intel compiler module, and try to load a GNU compiler build of fftw/3.3.3, and get an error. That is because using a GNU build of fftw/3.3.3 with the intel compiler suite is likely not to work and cause you headaches. In general, you should not be specifying more than fftw/3.3.3 anyway, and the module command will figure out which build to load based on which compilers you already have loaded. Alternatively, you can give the full path (e.g. module load fftw/3.3.3/intel/2013.1.039/openmpi/1.6.5) and the module command will auto-load the appropriate intel compiler and openmpi module for if, if it can. If you have a conflicting module already loaded, you will still get the error.

For the most part, tap is just a wrapper around the module command for backwards compatibility, and so you will get the same errors with tap if you try to load conflicting modules. The tap command is limited, so you generally do NOT get a whole lot of choice as to which builds of packages get loaded, so it is less likely to be a problem, but it can still arise. Some packages have not been migrated from tap to module command, and these will NOT generate such errors when you tap incompatible modules. But things will probably NOT work as you expected; the incompatibility is REAL, not an artifact of the module command.

List of available software packages

Please note that the HPC compute nodes have abridged copies of the software directories available on other Glue/TerpConnect systems. The HPC login nodes have the full software directories. Please look at software lists below, and in particular click on the software package name for the full breakdown by version number to see which, if any, HPC clusters a specific version of the package is on.

All categories

The following shows all the software available on the HPC systems, unsorted by category.

Package Name Description Categories Comments
abaqus Abaqus: Finite Element Analysis and Computer aided engineering Engineering,
Numerical Analysis,
Research
afni AFNI-New Biology,
Research,
Science
AFNI
ansys Ansys: Computer-aided engineering software Engineering,
Numerical Analysis,
Research
aria Aria Biology,
Research,
Science
Automated NOE assignment and NMR structure calculation
arpack ARnoldi PACKage for solving large scale eigenvalue problems Numerical Analysis
beagle general purpose library for evaluating the likelihood of sequence evolution on trees Biology,
Research,
Science
BESST BESST: scaffolder for genomic assemblies Biology,
Research,
Science
bfc BFC: high-performance tool for correcting sequencing errors from Illumina sequencing data Biology,
Research,
Science
bio-bwa Burrows-Wheeler Aligner Biology,
Research,
Science
biojava Java framework for processing biological data. Biology,
Research,
Science
blast BLAST (Basic Local Alignment Search Tool) from NCBI (National Center for Biotechnology Information) Biology,
Research,
Science
blcr Berkeley Lab Checkpoint/Restart BLCR Progamming/Development Berkeley Lab Checkpoint/Restart BLCR
boost Boost portable C++ source libraries Progamming/Development
bowtie Fast short read DNA aligner Biology,
Research,
Science
caffe Caffe deep learning framework Computerscience,
Research
cap3 CAP3 Biology,
Research,
Science
Small-scale assemby of EST sequences
cdf Libraries for handling CDF (Common Data Format) Progamming/Development,
Research
cdftools Tools for the analysis of NEMO model output Meteorology,
Progamming/Development,
Research
cdo Climate Data Operators toolkit Meteorology,
Progamming/Development,
Research
celera Celera Whole-Genome Shotgun Assembler Biology,
Research,
Science
cgal The Computational Geometry Algorithms Library Graphics,
Progamming/Development
charm Charm++ parallel OO programming language Progamming/Development
clblas OpenCL versions of BLAS libraries Numerical Analysis,
Progamming/Development
clustalw ClustalW 1.83 Biology,
Research,
Science
Multiple sequence alignment
cmake Opensource cross-platform build platform Progamming/Development
cmor Climate Model Output Rewriter Meteorology,
Progamming/Development,
Research
cns CNS 1.2.1 Biology,
Research,
Science
Crystallography and NMR System
cpc cpc: Coding Potential Calculator Biology,
Research,
Science
cuda CUDA programming toolkit Progamming/Development CUDA parallel computing platform for GPUs
cuDNN NVIDIA CUDA Deep Neural Network library Progamming/Development
cufflinks Transcript assembly, differential expression/regulation for RNA-Seq Biology,
Research,
Science
dart DART Data Assimilation Research Testbed Progamming/Development,
Research
dcw Digital Chart of the World Geoscience,
Research
dellomsa Dell OpenManage/ ServerAdmin tools Misc,
Miscellaneous
energyplus EnergyPlus Research EneryPlus package (most current installed version)
envi ENVI package for processing and analyzing geospatial data Progamming/Development,
Research
esbtl Easy Structural Biology Template Library: C++ headers for PDB data Biology,
Progamming/Development,
Research,
Science
esmf Earth System Modeling Framework Geoscience,
Meteorology,
Progamming/Development,
Research
espresso Espresso (customized) Biology,
Chemistry,
Physics,
Research,
Science
Extensible Simulation Package for Research on Soft Matter
exonerate Generic bioinformatics tool for pairwise sequence comparison Biology,
Research,
Science
fastqc Quality control for FastQ files Biology,
Research,
Science
FDS FDS 5.5.0 Research FDS Fire Dynamics Simulator
fdtd Lumerical FDTD Solutions: 3D Maxwell Solver Chemistry,
Numerical Analysis,
Science
fftw FFTW Discrete Fourier Transform libraries Numerical Analysis
flame Flame Progamming/Development,
Research
Flame (Flexible Large-scale Agent Modelling System)
freesurfer FreeSurfer Biology,
Numerical Analysis,
Progamming/Development,
Research,
Science
Suite for processing/analyzing human brain MRI image
fsl FSL Biology,
Research,
Science
Analysis Tools for FMRI, MRI, DTI brain imaging data
g2clib C library for handling GRIB/GRIB-2 data formats Progamming/Development,
Research
GapCloser GapCloser: closes gap emerging during scaffolding process of genome assembly Biology,
Research,
Science
garli GARLI 0.942 MPI Misc Phylogenetic inference using maximum-likelihood criterion
gatk GATK: Genome Analysis Toolkit Biology,
Research,
Science
gaussian Gaussian: electronic structure modeling software Chemistry,
Numerical Analysis,
Science
gblocks Eliminates poorly aligned/divergent regions of DNA sequences Biology,
Research,
Science
gcc Gnu Compiler Collection Progamming/Development
gdal Geospatial Data Abstraction Library Geoscience,
Research
geomview Geomview interactive Graphics,
Progamming/Development,
Research
geos Geomerty Engine --- Open Source Progamming/Development,
Research
gf2x gf2x: C/C++ libraries for fast arithmetic on Galios field GF(2) Progamming/Development
gflags Google Commandline Flags Progamming/Development
globus Globus Toolkit for GRID computing Research
glog Google Logging Library Progamming/Development
gmt The Generic Mapping Tools Geoscience,
Research
gold Gold Cluster Allocation Manager for HPC Research
grads Grid Analysis and Display System toolkit Meteorology,
Progamming/Development,
Research
grib-api Libraries for handling GRIB meteorological data file format Meteorology,
Progamming/Development,
Research
gromacs Gromacs Moleculer Dynamics Package Chemistry,
Research,
Science
gshhg A Global Self-consistent, Hierarchical, High-resolution Geography Database Geoscience,
Research
gsl GNU Scientific Library Numerical Analysis GNU Scientific Library
gulp GULP (General Utility Lattice Program) Chemistry,
Research,
Science
General Utility Lattice Program
h5py Python interface to HDF v5 libraries Progamming/Development,
Research
hdf HDF5 1.8.6 (pgi) Misc,
Progamming/Development,
Research
Set environment variables for HDF5, new version, for pgi compilers
hdf4 Libraries for handling HDF scientific data file format v4 Progamming/Development,
Research
HDF hierarchal data format libraries v4
hdf5 Libraries for handling HDF scientific data file format (v5) Progamming/Development,
Research
hdfeos2 Libraries for handling EOS data in HDF4 format Progamming/Development,
Research
helpdesk_hpcc Utilities for helpdesk to support HPC Misc,
Miscellaneous
htslib High throughput I/O for sequencing data Biology,
Research,
Science
idl IDL interactive data language Progamming/Development,
Research
intel Intel(R) MPI Library for Linux 3.1 Misc,
Progamming/Development
ioapi The EDSS/Models-3 I/O API and utilities Enviromentalsciences,
Research,
Science
java Java Programming Language Progamming/Development
jellyfish Jellyfish: Fast, parallel k-mer counting for DNA Biology,
Research,
Science
lammps LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) Chemistry,
Research,
Science
lapack LAPACK/BLAS numerical linear algebra routines Numerical Analysis
leda LEDA: C++ class library for efficient data types/algorithms Progamming/Development
lev00 lev00: pre/post-processing utilities for VASP/DFT codes Chemistry,
Science
leveldb Lexicographically sorted key based persistence library Progamming/Development
libqglviewer C++ library for creation of OpenGL 3D viewers Graphics,
Multimedia,
Progamming/Development
librs librs: Libraries for real roots of polynomial systems Progamming/Development
libsx Lightweight wrappers around Athena widget set (DEPRECATED) Progamming/Development
lis Land Information System Geoscience,
Meteorology,
Progamming/Development,
Research
lncRNApipe lncRNApipe: pipeline to identify non-coding RNAs Biology,
Research,
Science
lucy Lucy 1.19 Biology,
Research,
Science
DNA sequence quality and vector trimming tool
mafft Multiple Sequence Alignment Program Biology,
Research,
Science
maker MAKER: Portable genome annotation pipeline Biology,
Research,
Science
mathematica Mathematica Numerical Analysis,
Research
System for doing numerical analysis and symbolic math
matlab Matlab Numerical Analysis
matlab-extras Addons for Matlab Numerical Analysis
mcl Suite of tools for the Markov Cluster algorithm Biology,
Research,
Science
metis METIS Graph Partitioning and Fill-reducing Matrix Ordering Numerical Analysis
migrate estimation of population sizes and gene flow using the coalescent Biology,
Research,
Science
minpack MINPACK Routines for solving systems of non-linear equations Numerical Analysis
moab Moab Cluster Manager Research
modeltest MODELTEST 3.7 Biology,
Research,
Science
MODELTEST selects best-fit nucleotide substitution model
mpfi MPFI: Multiprecision interval library based on MPFR Progamming/Development
mpfr MPFI: Multiprecision floating point library based on GMP Progamming/Development
mpiblast Parallel, mpi-enabled BLAST (Basic Local Alignment Search Tool) Biology,
Research,
Science
mpiJava mpiJava Progamming/Development Java interface to MPI (Message Passing Interface)
mrbayes Bayesian Inference of Phylogeny Biology,
Research,
Science
mumps MUMPS MUltifrontal Massively Parallel sparse direct Solver Numerical Analysis
muscle MUltiple Sequence Comparison by Log-Expectation Biology,
Research,
Science
Multiple sequence comparison by log-expectation
mvapich MVAPICH Progamming/Development MVAPICH implementation of MPI libraries
namd namd: Scalable molecular dynamics Biology,
Chemistry,
Research,
Science
ncarg NCL/NCAR graphics utilities Research,
Science
ncl NCL/NCAR graphics utilities Research,
Science
nco netCDF operator toolkit Meteorology,
Progamming/Development,
Research
NCO: NetCDF operators
ncview visual browser of netCDF files Graphics,
Meteorology,
Multimedia,
Research
netcdf Intel NetCDF 4.1.1 Misc,
Progamming/Development,
Research
Set environment variables for NetCDF compiled with Intel compilers
netcdf-cxx C++ API to the NetCDF data format libraries Progamming/Development,
Research
netcdf-fortran Fortran API to the NetCDF data format libraries Progamming/Development,
Research
netlogo Netlogo programming language Progamming/Development
nifticlib C Libraries for handling nifti1 neuroimage data format Progamming/Development,
Research
nvidia-gdk nVidia GPU Development Kit/nVidia Management Library Progamming/Development
nwchem NWChem: Open-source high-performance chemistry Chemistry,
Research,
Science
octave GNU Octave Numerical Analysis
ofed OpenFabrics Enterprise Distribution Research
openblas OpenBLAS basic linear algebra subprograms (+lapack) Numerical Analysis
opencv OpenCV computer vision library Computerscience,
Research
opendx OpenDX Data Explorer Graphics,
Progamming/Development,
Research
openfoam OpenFOAM Physics,
Progamming/Development,
Research,
Science
openFOAM CFD (computational Fluid Dynamics) Toolbox
openkim OpenKIM Knowledgebase of Interactomic Models API Chemistry,
Research,
Science
openmm OpenMM v4 Chemistry,
Research,
Science
openMM molecular modeling softwareD, v4
openmpi OpenMPI Message Passing Libraries for HPC Progamming/Development,
Research
paml phylogenetic analyses using maximum likelihood Biology,
Research,
Reserach,
Science
Phylogenetic Analysis by Maximum Likelihood
paraview Paraview visualization application for scientific data Research,
Science
perl Perl Progamming/Development
pgi PGI Compiler Suite Progamming/Development
povray povray - Persistance of Vision Ray Tracer Graphics,
Multimedia,
Research
Persistance of Vision Ray Tracer
proj Libraries for converting between cartographic projections Meteorology,
Progamming/Development,
Research
protobuf Google Protocol Buffers Progamming/Development
pysam Python API for reading/writin gSAM (Sequence/Alignment Mapping) files Biology,
Research,
Science
python Python Progamming/Development
quantum-espresso Quantum Espresso (Suite for electronic-structure calc/nanoscale materials modeling) Chemistry,
Research,
Science
R R 2.8.0 Numerical Analysis,
Research
Statistical Analyzer just like SPlus
RAxML RAxML 7.0.4 Biology,
Research,
Science
Randomized Axelerated Maximum Likelihood inference for phylogenetic trees
repeatmasker RepeatMasker: screens DNA sequences for interspersed repeats Biology,
Research,
Science
sage Sage mathematical software package Numerical Analysis,
Research
samtools SAM Sequence/Alignment Mapping Biology,
Research,
Science
scalapack Scalable LAPACK/BLAS numerical linear algebra routines Numerical Analysis
scalasca Scalasca Parallel Programming Analysis package Compilers,
Progamming/Development
scotch SCOTCH graph partitioning, static mapping and clustering libraries Numerical Analysis
sctk Speech Recognition Scoring Toolkit Research,
Speechrecognition
NIST Speech Recognition Scoring Toolkit v2.3
shapelib C library for handling ESRI Shapefiles Progamming/Development,
Research
siesta Siesta v2.0.2 Chemistry,
Physics,
Research
Siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms)
silo Mesh and Field I/O library Progamming/Development,
Research
singularity Singularity software containers Progamming/Development
slurm Slurm HPC Scheduler Research
snack snack Audio,
Multimedia
The Snack Sound Toolkit (http://www.speech.kth.se/snack/)
snap snap: Semi-HMM-based Nucleic Acid Parser Biology,
Research,
Science
Snap: Scalable Nucelotide Alignment Program
snappy High speed compression/decompression library Progamming/Development
SOAPdenovo SOAPdenovo: Short Oligonucleotide Analysis Package de novo assembly Biology,
Research,
Science
sparsehash Google SparseHash template library for hash_maps Progamming/Development
speech_tools Edinburgh Speech Tools Research,
Speechrecognition
Edinburgh Speech Tools Library (ver =1.2.96-beta+64bit patches)
stacks Stacks pipeline for building loci from short-read sequences Biology,
Research,
Science
star Spliced Transcripts Alignment to a Reference Biology,
Research,
Science
structure Population structure analysis using multi-locus genotype data Biology,
Research,
Science
Structure 2.3.3 Genetic Population Structure Software
sunstudio Sun Studio/Oracle Solaris Studio Compiler/Development Suite Progamming/Development
szip SZIP compression libraries for data defined on a sphere Progamming/Development
tensorflow TensorFlow library for Machine Intelligence Computerscience,
Research
tetr tetr: pre/post-processing utilities for VASP/DFT codes Chemistry,
Science
tophat RNA-Seq aligner for identifying exon-exon splice junctions Biology,
Research,
Science
torch Torch scientific framework/machine learning Computerscience,
Research
totalview Parallel Debugger Progamming/Development
trf trf: Tandem Repeats Finder Biology,
Research,
Science
trimmomatic Flexible trimmer for illumina sequence data Biology,
Research,
Science
trinity RNA-Seq de novo assembly Biology,
Research,
Science
udunits UDUNITS (Unit conversion/manipulation libraries) Progamming/Development
unio Unio 08 Biology,
Chemistry,
Research,
Science
Unio NMR Data analysis and Protein Structure Determination
uniref90 UniRef90 Protein Database Biology,
Research,
Science
uspex USPEX: Universal Structure Predictor: Evolutionary Xtallography Chemistry,
Numerical Analysis,
Science
vasp VASP: Vienna Ab-initio Simulation Package Chemistry,
Numerical Analysis,
Science
vesta VESTA 3d visualization for structural models Chemistry,
Research,
Science
visit ViSit Visualization and Graphical Analysis tool Graphics,
Progamming/Development,
Research
ViSit Visualization and Graphical Analysis tool
vmd Visual Molecular Dynamics Biology,
Chemistry,
Research,
Science
Molecular visualization program for displaying, animating, and analyzing large biomolecular systems
vtk Visualization Toolkit 5.0.0c Graphics,
Research
Visualizaton Toolkit 5.0.0c, somewhat old but needed for ViSit
wgrib Utilities for handling GRIB/GRIB-2 data formats Progamming/Development,
Research
wrf-hydro WRF-Hydro hydrological modeling architecture Meteorology,
Research
xplor-nih XPLOR-NIH 2.19 Biology,
Chemistry,
Research,
Science
Structure determination program
xz XZ utils: General purpose data compression supporting LZMA Progamming/Development
zeromq High-performance async messaging libraries Progamming/Development,
Research

Categorized by field, etc

The following tables basically contain the same information as above, but are filtered by field of research and other criteria to make them easier to browse.

  1. Biology
  2. Chemistry
  3. Meteorology
  4. Numerical Analysis
  5. Program Development
  6. GPU-enabled software packages

Biology

In addition to the packages listed below, Dr. Ian Misner maintains a large collection of bioinformatics packages, most of which are available for use (although with no promises of support) by anyone with access to the Deepthought2 HPC cluster. You will need to module load dept/bioinfo to get access to them, and then you can use the module avail bioinfo command to list what is available. Again, these were installed by Dr. Misner for his own research, and no claims are made that they are usable for anyone else's research, or that they will be maintained, but with these caveats you are free to use them. Also, access to some applications might be restricted due to licensing, etc.

Package Name Description Categories Comments
afni AFNI-New Biology,
Research,
Science
AFNI
aria Aria Biology,
Research,
Science
Automated NOE assignment and NMR structure calculation
beagle general purpose library for evaluating the likelihood of sequence evolution on trees Biology,
Research,
Science
BESST BESST: scaffolder for genomic assemblies Biology,
Research,
Science
bfc BFC: high-performance tool for correcting sequencing errors from Illumina sequencing data Biology,
Research,
Science
bio-bwa Burrows-Wheeler Aligner Biology,
Research,
Science
biojava Java framework for processing biological data. Biology,
Research,
Science
blast BLAST (Basic Local Alignment Search Tool) from NCBI (National Center for Biotechnology Information) Biology,
Research,
Science
bowtie Fast short read DNA aligner Biology,
Research,
Science
cap3 CAP3 Biology,
Research,
Science
Small-scale assemby of EST sequences
celera Celera Whole-Genome Shotgun Assembler Biology,
Research,
Science
clustalw ClustalW 1.83 Biology,
Research,
Science
Multiple sequence alignment
cns CNS 1.2.1 Biology,
Research,
Science
Crystallography and NMR System
cpc cpc: Coding Potential Calculator Biology,
Research,
Science
cufflinks Transcript assembly, differential expression/regulation for RNA-Seq Biology,
Research,
Science
esbtl Easy Structural Biology Template Library: C++ headers for PDB data Biology,
Progamming/Development,
Research,
Science
espresso Espresso (customized) Biology,
Chemistry,
Physics,
Research,
Science
Extensible Simulation Package for Research on Soft Matter
exonerate Generic bioinformatics tool for pairwise sequence comparison Biology,
Research,
Science
fastqc Quality control for FastQ files Biology,
Research,
Science
freesurfer FreeSurfer Biology,
Research,
Science
Suite for processing/analyzing human brain MRI images
fsl FSL Biology,
Research,
Science
Analysis Tools for FMRI, MRI, DTI brain imaging data
GapCloser GapCloser: closes gap emerging during scaffolding process of genome assembly Biology,
Research,
Science
gatk GATK: Genome Analysis Toolkit Biology,
Research,
Science
gblocks Eliminates poorly aligned/divergent regions of DNA sequences Biology,
Research,
Science
htslib High throughput I/O for sequencing data Biology,
Research,
Science
jellyfish Jellyfish: Fast, parallel k-mer counting for DNA Biology,
Research,
Science
lncRNApipe lncRNApipe: pipeline to identify non-coding RNAs Biology,
Research,
Science
lucy Lucy 1.19 Biology,
Research,
Science
DNA sequence quality and vector trimming tool
mafft Multiple Sequence Alignment Program Biology,
Research,
Science
maker MAKER: Portable genome annotation pipeline Biology,
Research,
Science
mcl Suite of tools for the Markov Cluster algorithm Biology,
Research,
Science
migrate estimation of population sizes and gene flow using the coalescent Biology,
Research,
Science
modeltest MODELTEST 3.7 Biology,
Research,
Science
MODELTEST selects best-fit nucleotide substitution model
mpiblast Parallel, mpi-enabled BLAST (Basic Local Alignment Search Tool) Biology,
Research,
Science
mrbayes Bayesian Inference of Phylogeny Biology,
Research,
Science
muscle MUltiple Sequence Comparison by Log-Expectation Biology,
Research,
Science
Multiple sequence comparison by log-expectation
namd namd: Scalable molecular dynamics Biology,
Chemistry,
Research,
Science
paml phylogenetic analyses using maximum likelihood Biology,
Research,
Reserach,
Science
Phylogenetic Analysis by Maximum Likelihood
pysam Python API for reading/writin gSAM (Sequence/Alignment Mapping) files Biology,
Research,
Science
RAxML RAxML 7.0.4 Biology,
Research,
Science
Randomized Axelerated Maximum Likelihood inference for phylogenetic trees
repeatmasker RepeatMasker: screens DNA sequences for interspersed repeats Biology,
Research,
Science
samtools SAM Sequence/Alignment Mapping Biology,
Research,
Science
snap snap: Semi-HMM-based Nucleic Acid Parser Biology,
Research,
Science
Snap: Scalable Nucelotide Alignment Program
SOAPdenovo SOAPdenovo: Short Oligonucleotide Analysis Package de novo assembly Biology,
Research,
Science
stacks Stacks pipeline for building loci from short-read sequences Biology,
Research,
Science
star Spliced Transcripts Alignment to a Reference Biology,
Research,
Science
structure Population structure analysis using multi-locus genotype data Biology,
Research,
Science
Structure 2.3.3 Genetic Population Structure Software
tophat RNA-Seq aligner for identifying exon-exon splice junctions Biology,
Research,
Science
trf trf: Tandem Repeats Finder Biology,
Research,
Science
trimmomatic Flexible trimmer for illumina sequence data Biology,
Research,
Science
trinity RNA-Seq de novo assembly Biology,
Research,
Science
unio Unio 08 Biology,
Chemistry,
Research,
Science
Unio NMR Data analysis and Protein Structure Determination
uniref90 UniRef90 Protein Database Biology,
Research,
Science
vmd Visual Molecular Dynamics Biology,
Chemistry,
Research,
Science
Molecular visualization program for displaying, animating, and analyzing large biomolecular systems
xplor-nih XPLOR-NIH 2.19 Biology,
Chemistry,
Research,
Science
Structure determination program

Chemistry

Package Name Description Categories Comments
espresso Espresso (customized) Biology,
Chemistry,
Physics,
Research,
Science
Extensible Simulation Package for Research on Soft Matter
fdtd Lumerical FDTD Solutions: 3D Maxwell Solver Chemistry,
Numerical Analysis,
Science
gaussian Gaussian: electronic structure modeling software Chemistry,
Numerical Analysis,
Science
gromacs Gromacs Moleculer Dynamics Package Chemistry,
Research,
Science
gulp GULP (General Utility Lattice Program) Chemistry,
Research,
Science
General Utility Lattice Program
lammps LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) Chemistry,
Research,
Science
lev00 lev00: pre/post-processing utilities for VASP/DFT codes Chemistry,
Science
namd namd: Scalable molecular dynamics Biology,
Chemistry,
Research,
Science
nwchem NWChem: Open-source high-performance chemistry Chemistry,
Research,
Science
openkim OpenKIM Knowledgebase of Interactomic Models API Chemistry,
Research,
Science
openmm OpenMM v4 Chemistry,
Research,
Science
openMM molecular modeling softwareD, v4
quantum-espresso Quantum Espresso (Suite for electronic-structure calc/nanoscale materials modeling) Chemistry,
Research,
Science
siesta Siesta v2.0.2 Chemistry,
Physics,
Research
Siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms)
tetr tetr: pre/post-processing utilities for VASP/DFT codes Chemistry,
Science
unio Unio 08 Biology,
Chemistry,
Research,
Science
Unio NMR Data analysis and Protein Structure Determination
uspex USPEX: Universal Structure Predictor: Evolutionary Xtallography Chemistry,
Numerical Analysis,
Science
vasp VASP: Vienna Ab-initio Simulation Package Chemistry,
Numerical Analysis,
Science
vesta VESTA 3d visualization for structural models Chemistry,
Research,
Science
vmd Visual Molecular Dynamics Biology,
Chemistry,
Research,
Science
Molecular visualization program for displaying, animating, and analyzing large biomolecular systems
xplor-nih XPLOR-NIH 2.19 Biology,
Chemistry,
Research,
Science
Structure determination program

Meteorology

Package Name Description Categories Comments
cdftools Tools for the analysis of NEMO model output Meteorology,
Progamming/Development,
Research
cdo Climate Data Operators toolkit Meteorology,
Progamming/Development,
Research
cmor Climate Model Output Rewriter Meteorology,
Progamming/Development,
Research
esmf Earth System Modeling Framework Geoscience,
Meteorology,
Progamming/Development,
Research
grads Grid Analysis and Display System toolkit Meteorology,
Progamming/Development,
Research
grib-api Libraries for handling GRIB meteorological data file format Meteorology,
Progamming/Development,
Research
lis Land Information System Geoscience,
Meteorology,
Progamming/Development,
Research
nco netCDF operator toolkit Meteorology,
Progamming/Development,
Research
NCO: NetCDF operators
ncview visual browser of netCDF files Graphics,
Meteorology,
Multimedia,
Research
proj Libraries for converting between cartographic projections Meteorology,
Progamming/Development,
Research
wrf-hydro WRF-Hydro hydrological modeling architecture Meteorology,
Research

Numerical Analysis

Package Name Description Categories Comments
abaqus Abaqus: Finite Element Analysis and Computer aided engineering Engineering,
Numerical Analysis,
Research
ansys Ansys: Computer-aided engineering software Engineering,
Numerical Analysis,
Research
arpack ARnoldi PACKage for solving large scale eigenvalue problems Numerical Analysis
clblas OpenCL versions of BLAS libraries Numerical Analysis,
Progamming/Development
fdtd Lumerical FDTD Solutions: 3D Maxwell Solver Chemistry,
Numerical Analysis,
Science
fftw FFTW Discrete Fourier Transform libraries Numerical Analysis
freesurfer FreeSurfer-new Numerical Analysis,
Progamming/Development,
Research
Suite for processing/analyzing human brain MRI image
gaussian Gaussian: electronic structure modeling software Chemistry,
Numerical Analysis,
Science
gsl GNU Scientific Library Numerical Analysis GNU Scientific Library
lapack LAPACK/BLAS numerical linear algebra routines Numerical Analysis
mathematica Mathematica Numerical Analysis,
Research
System for doing numerical analysis and symbolic math
matlab Matlab Numerical Analysis
matlab-extras Addons for Matlab Numerical Analysis
metis METIS Graph Partitioning and Fill-reducing Matrix Ordering Numerical Analysis
minpack MINPACK Routines for solving systems of non-linear equations Numerical Analysis
mumps MUMPS MUltifrontal Massively Parallel sparse direct Solver Numerical Analysis
octave GNU Octave Numerical Analysis
openblas OpenBLAS basic linear algebra subprograms (+lapack) Numerical Analysis
R R 2.8.0 Numerical Analysis,
Research
Statistical Analyzer just like SPlus
sage Sage mathematical software package Numerical Analysis,
Research
scalapack Scalable LAPACK/BLAS numerical linear algebra routines Numerical Analysis
scotch SCOTCH graph partitioning, static mapping and clustering libraries Numerical Analysis
uspex USPEX: Universal Structure Predictor: Evolutionary Xtallography Chemistry,
Numerical Analysis,
Science
vasp VASP: Vienna Ab-initio Simulation Package Chemistry,
Numerical Analysis,
Science

Program Development

Package Name Description Categories Comments
blcr Berkeley Lab Checkpoint/Restart BLCR Progamming/Development Berkeley Lab Checkpoint/Restart BLCR
boost Boost portable C++ source libraries Progamming/Development
cdf Libraries for handling CDF (Common Data Format) Progamming/Development,
Research
cdftools Tools for the analysis of NEMO model output Meteorology,
Progamming/Development,
Research
cdo Climate Data Operators toolkit Meteorology,
Progamming/Development,
Research
cgal The Computational Geometry Algorithms Library Graphics,
Progamming/Development
charm Charm++ parallel OO programming language Progamming/Development
clblas OpenCL versions of BLAS libraries Numerical Analysis,
Progamming/Development
cmake Opensource cross-platform build platform Progamming/Development
cmor Climate Model Output Rewriter Meteorology,
Progamming/Development,
Research
cuda CUDA programming toolkit Progamming/Development CUDA parallel computing platform for GPUs
cuDNN NVIDIA CUDA Deep Neural Network library Progamming/Development
dart DART Data Assimilation Research Testbed Progamming/Development,
Research
envi ENVI package for processing and analyzing geospatial data Progamming/Development,
Research
esbtl Easy Structural Biology Template Library: C++ headers for PDB data Biology,
Progamming/Development,
Research,
Science
esmf Earth System Modeling Framework Geoscience,
Meteorology,
Progamming/Development,
Research
flame Flame Progamming/Development,
Research
Flame (Flexible Large-scale Agent Modelling System)
freesurfer FreeSurfer-new Numerical Analysis,
Progamming/Development,
Research
Suite for processing/analyzing human brain MRI image
g2clib C library for handling GRIB/GRIB-2 data formats Progamming/Development,
Research
gcc Gnu Compiler Collection Progamming/Development
geomview Geomview interactive Graphics,
Progamming/Development,
Research
geos Geomerty Engine --- Open Source Progamming/Development,
Research
gf2x gf2x: C/C++ libraries for fast arithmetic on Galios field GF(2) Progamming/Development
gflags Google Commandline Flags Progamming/Development
glog Google Logging Library Progamming/Development
grads Grid Analysis and Display System toolkit Meteorology,
Progamming/Development,
Research
grib-api Libraries for handling GRIB meteorological data file format Meteorology,
Progamming/Development,
Research
h5py Python interface to HDF v5 libraries Progamming/Development,
Research
hdf Libraries for handling HDF scientific data file format Progamming/Development,
Research
hdf4 Libraries for handling HDF scientific data file format v4 Progamming/Development,
Research
HDF hierarchal data format libraries v4
hdf5 Libraries for handling HDF scientific data file format (v5) Progamming/Development,
Research
hdfeos2 Libraries for handling EOS data in HDF4 format Progamming/Development,
Research
idl IDL interactive data language Progamming/Development,
Research
intel Intel Compiler Suite Progamming/Development
java Java Programming Language Progamming/Development
leda LEDA: C++ class library for efficient data types/algorithms Progamming/Development
leveldb Lexicographically sorted key based persistence library Progamming/Development
libqglviewer C++ library for creation of OpenGL 3D viewers Graphics,
Multimedia,
Progamming/Development
librs librs: Libraries for real roots of polynomial systems Progamming/Development
libsx Lightweight wrappers around Athena widget set (DEPRECATED) Progamming/Development
lis Land Information System Geoscience,
Meteorology,
Progamming/Development,
Research
mpfi MPFI: Multiprecision interval library based on MPFR Progamming/Development
mpfr MPFI: Multiprecision floating point library based on GMP Progamming/Development
mpiJava mpiJava Progamming/Development Java interface to MPI (Message Passing Interface)
nco netCDF operator toolkit Meteorology,
Progamming/Development,
Research
NCO: NetCDF operators
netcdf Libraries for handling NetCDF scientific data file format Progamming/Development,
Research
Libraries for handling NetCDF scientific data file format
netcdf-cxx C++ API to the NetCDF data format libraries Progamming/Development,
Research
netcdf-fortran Fortran API to the NetCDF data format libraries Progamming/Development,
Research
netlogo Netlogo programming language Progamming/Development
nifticlib C Libraries for handling nifti1 neuroimage data format Progamming/Development,
Research
nvidia-gdk nVidia GPU Development Kit/nVidia Management Library Progamming/Development
opendx OpenDX Data Explorer Graphics,
Progamming/Development,
Research
openfoam The Open Source CFD Toolbox Progamming/Development,
Research
openmpi OpenMPI Message Passing Libraries for HPC Progamming/Development,
Research
perl Perl Progamming/Development
pgi PGI Compiler Suite Progamming/Development
proj Libraries for converting between cartographic projections Meteorology,
Progamming/Development,
Research
protobuf Google Protocol Buffers Progamming/Development
python Python Progamming/Development
scalasca Scalasca Parallel Programming Analysis package Compilers,
Progamming/Development
shapelib C library for handling ESRI Shapefiles Progamming/Development,
Research
silo Mesh and Field I/O library Progamming/Development,
Research
singularity Singularity software containers Progamming/Development
snappy High speed compression/decompression library Progamming/Development
sparsehash Google SparseHash template library for hash_maps Progamming/Development
sunstudio Sun Studio/Oracle Solaris Studio Compiler/Development Suite Progamming/Development
szip SZIP compression libraries for data defined on a sphere Progamming/Development
totalview Parallel Debugger Progamming/Development
udunits UDUNITS (Unit conversion/manipulation libraries) Progamming/Development
visit ViSit Visualization and Graphical Analysis tool Graphics,
Progamming/Development,
Research
ViSit Visualization and Graphical Analysis tool
wgrib Utilities for handling GRIB/GRIB-2 data formats Progamming/Development,
Research
xz XZ utils: General purpose data compression supporting LZMA Progamming/Development
zeromq High-performance async messaging libraries Progamming/Development,
Research

GPU-enabled software packages

The following lists shows packages available on the HPC clusters for which at least one version of the package has been built to be able to make use of the GPUs available on some nodes. Typically, there will be special builds of the package (i.e. special module load commands needed) which can use the GPUs, and those versions will typically ONLY run on nodes with GPUs.

You should follow the link to the package specific page for more information on which versions of the package are built to support GPUs, and how to use them.

This list is quite small right now. If there is a package on one of the Deepthought HPCCs that you use that can support using GPUs but is not on the list, let us know and we will look into building a GPU aware version. NOTE: The Division of Information Technology does not have the expertise or resources to adapt codes to take advantage of GPUs; the above is for packages to which the software authors have already added GPU support, and only need a fresh build on the Deepthought HPCCs to take advantage of that support.

Package Name Description Categories Comments
caffe Caffe deep learning framework Computerscience,
Research
gromacs Gromacs Moleculer Dynamics Package Chemistry,
Research,
Science
matlab Matlab Numerical Analysis
namd namd: Scalable molecular dynamics Biology,
Chemistry,
Research,
Science
opencv OpenCV computer vision library Computerscience,
Research
torch Torch scientific framework/machine learning Computerscience,
Research

Packages installed for scripting languages

The Division of Information Technology maintains several versions of several scripting languages on the clusters. These scripting languages can be enhanced by the addition of packages/modules/etc, and the Division of IT maintains a collection of packages for these. In cases where the package/module is large, tightly coupled to a specific version of an installed library, and/or is not applicable to many fields, we tend to install the packages/modules/etc as entities which need to be separately module loaded. These will be listed in the application tables above.

The tables below are primarily for packages stored in the standard location for the specific scripting language. We also do NOT list any packages/modules/etc. that come as part of the standard library for the particular scripting language. Note also that packages/modules/etc. are not necessarily available on all versions of the particular scripting language installed, and you might need to module load a specific version of the scripting language to get a specific package.

Perl packages

We have many perl modules installed; this is NOT a complete list.

Package Name Perl Versions Description Categories
BioPerl 5.8.7
5.16.3
Perl modules for Biology research Biology
DBI 5.8.7
5.10.1
5.16.3
Interface with various Databases Development
GO 5.8.7
5.16.3
Gene ontology package Biology

You should also look at the Perl page for more information, including information re installing your own modules.

Python packages

This is NOT a complete list of python modules available

Package Name Python Versions Description Categories
BioPython 2.7.3
2.7.8
modules for Biology research Biology
matplotlib 2.6.1
2.7.3
2.7.8
 
mpi4py 2.6.1
2.7.3
2.7.8
MPI inteface
Numdifftools 2.7.3
2.7.8
  Numerical Analysis
numpy 2.6.1
2.7.3
2.7.8
Numerical analysis Numerical Analysis
PyOpenMM 2.6.1
2.7.3
2.7.8
OpenMM interface Chemistry
scipy 2.6.1
2.7.3
2.7.8
base package for scientific computing Physics
Chemistry
Mathematics
theano 2.7.8 define and evaluate multidimensional expressions Mathematics

NOTE: There have been some issues noted with theano on HPC nodes with Qlogic Infiniband cards. On such nodes (including DT1 login nodes), you will need to set the environmental variable OMPI_MCA_mtl to ^psm, e.g.

	setenv OMPI_MCA_mtl ^psm
for c-style shells or
	OMPI_MCA_mtl=^psm
	export OMPI_MCA_mtl
for bourne style shells.

You should also look at the Python page for more information, including information re installing your own modules.

R packages

This is NOT a complete list of R modules available

Package Name R Versions Description Categories
Bioconductor 2.8.0
2.11.1
2.13.1
2.15.0
3.0.3
modules for Biology research Biology
biovizBase 2.15.0
3.0.3
  Biology
cummeRbund 2.15.0
3.0.3
  Biology
DESeq 2.15.0
3.0.3
  Biology
genealogicalSorting 2.8.0
2.11.1
2.13.1
2.15.0
3.0.3
  Biology
GenomicFeatures 2.15.0
3.0.3
  Biology
Gviz 2.15.0
3.0.3
  Biology
HiddenMarkov 2.8.0
2.11.1
2.13.1
2.15.0
3.0.3
  Biology
Rmpi 2.8.0
2.11.1
2.13.1
2.15.0
3.0.3
Interface to OpenMPI Development

You should also look at the R page for more information, including information re installing your own modules.