Available Software

WARNING
Note: We are in the process of integrating the software documentation for the RHEL6 and RHEL8 environments on the Deepthought2 cluster and the RHEL7 environment on Juggernaut. This page mainly shows the RHEL7 and RHEL8 software, and we are in the process of migrating content from the old, RHEL6 software pages to the current pages. This process will be ongoing over fall of 2020. While this migration is underway, you might wish to check the old pages as well as the current pages.

Contents

  1. The module command
    1. The module command
    2. Library packages
    3. Common errors
  2. Software packages available
    1. Unclassified by field
    2. Classified by field, etc
      1. Packages related to Aeronautics
      2. Packages related to Astronomy
      3. Packages related to BrainImaging
      4. Packages related to CFD
      5. Packages related to Chemistry
      6. Packages related to ComputerVision
      7. Packages related to DataCompression
      8. Packages related to DataFormat
      9. Packages related to EarthScience
      10. Packages related to Engineering
      11. Packages related to Genomics
      12. Packages related to ImageProcessing
      13. Packages related to MachineLearning
      14. Packages related to MaterialScience
      15. Packages related to Mathematics
      16. Packages related to Meteorology
      17. Packages related to MolecularDynamics
      18. Packages related to MultiPhysics
      19. Packages related to NumericalMethods
      20. Packages related to PythonModule
      21. Packages related to SoftwareDevelopment
      22. Packages related to Utilities
      23. Packages related to Visualization
    3. Available by cluster
      1. All packages available on the Deepthought2 cluster (RHEL8)
      2. All packages available on the Juggernaut cluster
  3. Packages for scripting languages
    1. Packages/modules for Python
    2. Packages/modules for R
    3. Packages/modules for Perl

The module command

WARNING
Note: We are in the process of integrating the software documentation for the RHEL6 and RHEL8 environments on the Deepthought2 cluster and the RHEL7 environment on Juggernaut. This page mainly shows the RHEL7 and RHEL8 software, and we are in the process of migrating content from the old, RHEL6 software pages to the current pages. This process will be ongoing over fall of 2020. While this migration is underway, you might wish to check the old pages as well as the current pages.

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 module command.

For example, matlab is available on the HPC clusters, 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 module command

The module command associates a tag with the various packages. It 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.

WARNING

With the roleout of a new software library with the RHEL8 upgrade of the Deepthought2 HPC cluster, we are no longer keeping the "default" versions of software packages fixed over long periods of time. Instead, if you do not provide a version in your "module load" command, you will almost always get the latest installed version compatible with other modules you have loaded. (There will be rare and brief exceptions if we find problems in the latest version of a package). This is a change from the behavior of many packages on the RHEL6 version of Deepthought2.

For reproducibility over time, it is strongly recommended that in job submission batch scripts you provide the full version specification for any packages for which you care about the version number.

For many packages, the tag is basically just the base name of the package, followed by a slash (/) and a version number. E.g., the examples matlab/2013b and matlab/2011a refer to versions 2013b and 2011a, respectively, of matlab. You can also just use matlab as the tag when e.g. loading a module, in which case you will get one of the versions (usually the latest, sometimes we pin to an earlier version if the newest version is still being tested).

Many packages compiled from source will have different builds depending on what CPU microarchitecture they were compiled for. Running a code compiled for a more modern CPU than you are currently using will likely result in the code crashing; running a code compiled for a less modern CPU will generally work, but you might lose some of the optimizations available on the newer chip. Generally, these packages will have two equivalent module tags, one of the form "foo/VERSION/ARCHITECTURE" and one of the form "foo/ARCHITECTURE/VERSION"; both forms load foo version VERSION built for architecture ARCHITECTURE. The module load command will attempt to load the build for the most advanced architecture compatible with the CPU you are running on. If you omit the version, it will look for the latest version built for the most advanced CPU architecture compatible with the CPU you are running on.

Some packages are fussy about the compiler and/or MPI libraries they are used with. This is particularly true of libraries which have fortran90 and/or C++ components; some examples are openmpi, hdf5, and netcdf. In these cases, the package will again have multiple module tags referring to the same build of the software. The first starts like the simple case, with the base name of the package followed by the version of the package, but to this is appended the other dependencies (like compiler family and version, and perhaps MPI library family and version, etc.). For example, one tag for version 1.8.13 of hdf5, built with version 4.8.1 of the GNU compiler suite and version 1.8.1 of , with shared linkage would be:

hdf5/1.8.13/gnu/4.8.1/openmpi/1.8.1/shared  

There is also an alternative form giving the compiler, MPI library, and linkage portions of the tag immediately after the base package name, and ending with the version of the package, e.g.

hdf5/gnu/4.8.1/openmpi/1.8.1/shared/1.8.13

Both of these tags do exactly the same thing, and set up exactly the same build of hdf5, when loaded. You can use either.

The advantage of the module command is that you generally do NOT need to give these long tag names, but can leave off components on the right and it will try to do the right thing. In particular, if you try loading just the base package name, e.g. module load hdf5, the system will determine if you have previously loaded a compiler and/or MPI library. If so, then the system will see if there are any builds of any version of the package matching the compiler and MPI library versions you previously loaded, and if one is found load the build for the most recent version that matches. If no matching build is found, and error will be displayed and no module loaded.

The following except gives an example of this:

login-2:> module purge 
login-2:> module list 
No Modulefiles Currently Loaded.
login-2:> module load gcc/4.8.1
login-2:> module load openmpi/1.8.1
login-2:> module load hdf5
login-2:> module list
Currently Loaded Modulefiles:
  1) gcc/4.8.1(default)
  2) openmpi/1.8.1/gnu/4.8.1
  3) hdf5/gnu/4.8.1/openmpi/1.8.1/shared/1.8.13
login-2:> 
login-2:> module purge
login-2:> module list
No Modulefiles Currently Loaded.
login-2:> module load intel/2016
login-2:> module load openmpi/1.10.2
login-2:> module load hdf5
login-2:> module list
Currently Loaded Modulefiles:
  1) ofed/3.12(default)
  2) intel/2016.3.210(default)
  3) openmpi/1.10.2/intel/2016.3.210
  4) hdf5/intel/2016.3.210/openmpi/1.10.2/shared/1.10.0
login-2:> 
login-2:> module purge
login-2:> module list
No Modulefiles Currently Loaded.
login-2:> module load hdf5/1.8.15p1/sunstudio/12.4/openmpi/1.8.6/shared
login-2:> module list
Currently Loaded Modulefiles:
  1) sunstudio/12.4(default)
  2) openmpi/1.8.6/sunstudio/12.4
  3) hdf5/1.8.15p1/sunstudio/12.4/openmpi/1.8.6/shared

We start by issuing a module purge command to delete any previously loaded modules (in general, you should use this with caution. If you do use it, you should immediately load the modules hpcc/deepthought or hpcc/deepthought2, as appropriate for the cluster you are on, and slurm. These are the default modules on the Deepthought HPC clusters and things might not work properly without them). We then do a module list to confirm that there are no modules loaded. We then load a specific version of the gcc compiler (4.8.1) and the openmpi libraries (1.8.1) and then ask the system to load the best hdf5 module. We then list what was loaded, and note that the system loaded an openmpi build (version 1.8.1) for the compiler we loaded, and a hdf5 version (1.8.13) for the previously loaded compiler and MPI library.

In the second example above, we load the 2016 version of the intel compiler suite, and the 1.10.2 version of openmpi, and when we issue the simple module load hdf5, this time it loads hdf5 version 1.10.0 built for that compiler and openmpi library. (Note also that the openmpi library loaded was also built for the correct compiler.)

In the final example above, we do not explicitly load any compiler or MPI library, but instead give a full path the the hdf5 module, e.g. hdf5/1.8.15p1/sunstudio/12.4/openmpi/1.8.6/shared. In this case, we note that not only was the requested hdf5 module loaded, but we also loaded the corresponding compiler (sunstudio/12.4) and openmpi (openmpi/1.8.6) modules as well.

In summary, in almost all cases, you need only specify a portion of the tag, and the system will try to default it properly. Generally, you should load the compiler you wish to use first (or do not load anything if you want to use the default gcc 4.6.1 compiler) followed by the MPI library if needed. This will allow the system to pick the correct build of libraries which depend on such. 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.

However, if you want reproducable results, it is generally recommended that you fully specify version numbers when loading modules in your job scripts. I.e., the latest version of the foo package might be 1.5 when you run your job today, but if you run it again a month from today, the latest version might by 1.7 at that time, and that could change the results unexpectedly if your script merely did a module load foo. If you wish to ensure the same version is always used, specifying the version number in the module load command is advised, e.g. module load foo/1.5; this way you will get the same version of the foo package both today and a month from now. But if you always prefer to use the latest package available, then in general you should leave the version numbers off.

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. Note the matching is purely lexical, so module avail netcdf will pick up all netcdf modules, as well as netcdf-fortran and netcdf-cxx modules. To restrict to just netcdf modules, use something like module avail netcdf/ (note the final /)
  • 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.
  • purge: This unloads ALL currently loaded modules. This should be used sparingly. If you do use it, please follow it with the loading of either hpcc/deepthought or hpcc/deepthought2 (as appropriate for the cluster you are on) and slurm. These modules are loaded for you automatically when you log into the clusters, and if you remove them (e.g. with the purge command), things might not work as expected.
  • 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.

WARNING
Note: We are in the process of integrating the software documentation for the RHEL6 and RHEL8 environments on the Deepthought2 cluster and the RHEL7 environment on Juggernaut. This page mainly shows the RHEL7 and RHEL8 software, and we are in the process of migrating content from the old, RHEL6 software pages to the current pages. This process will be ongoing over fall of 2020. While this migration is underway, you might wish to check the old pages as well as the current pages.

List of available software packages

In this section we list the various software packages available on the UMD HPC clusters. We start with a list of all packages, unclassified by field of research, and follow with some shorter lists for various fields of research. If there is a mistake in the classification of software (e.g. a package is listed in the wrong category, or is missing from a category where it belongs), please contact systems staff so that we may correct the situation. Similarly, contact us if there is a category for software which is missing and you believe would be useful to have.

For each list, you can click on the name of the package to bring up a page with more detailed information on what versions are available on which clusters, and some basic (and sometimes not so basic) usage and help.

  1. All packages (unsorted by field)
  2. Software lists classified by field of research, etc
    1. Packages related to Aeronautics
    2. Packages related to Astronomy
    3. Packages related to BrainImaging
    4. Packages related to CFD
    5. Packages related to Chemistry
    6. Packages related to ComputerVision
    7. Packages related to DataCompression
    8. Packages related to DataFormat
    9. Packages related to EarthScience
    10. Packages related to Engineering
    11. Packages related to Genomics
    12. Packages related to ImageProcessing
    13. Packages related to MachineLearning
    14. Packages related to MaterialScience
    15. Packages related to Mathematics
    16. Packages related to Meteorology
    17. Packages related to MolecularDynamics
    18. Packages related to MultiPhysics
    19. Packages related to NumericalMethods
    20. Packages related to PythonModule
    21. Packages related to SoftwareDevelopment
    22. Packages related to Utilities
    23. Packages related to Visualization
  3. Software lists by cluster
    1. All packages available on the Deepthought2 cluster (RHEL8)
    2. All packages available on the Juggernaut cluster

All packages (unsorted by field)

This section list all installed research software, unsorted by field of research/category/etc.

All packages (unsorted by field)
Package Name Description Supported CPUs GPU ready?
adios2 adios2: The Adapatble Input/Output System, version 2 ivybridge, x86_64 Yes
ansys ANSYS: Computer-aided engineering software x86_64
ansys-em ANSYSEM: Computer-aided engineering software for electromagnetic systems x86_64
ansys.new ANSYS: Computer-aided engineering software x86_64
ansys.old ANSYS: Computer-aided engineering software x86_64
arpack-ng arpack-ng: Fortran77 subroutines designed to solve large scale eigenvalue problems ivybridge, x86_64, zen Yes
bcftools bcftools: BCFtools is a set of utilities that manipulate variant calls ivybridge
beagle beagle: package for phasing genotypes and for imputing ungenotyped markers ivybridge, x86_64
bedtools2 bedtools2: swiss-army knife of genomics analysis tasks ivybridge, x86_64
blast-plus blast-plus: Basic Local Alignment Search Tool ivybridge
bml bml: Basic Matrix Library ivybridge Yes
boost boost: free, portable C++ source libraries ivybridge, sandybridge, x86_64, zen Yes
bowtie bowtie: ultrafast sequence aligner ivybridge
bowtie2 bowtie2: ultrafast sequence aligner ivybridge
bwa bwa: Burrows-Wheeler Aligner ivybridge
bzip2 bzip2: patent-free high quality data compression libraries ivybridge, sandybridge, x86_64, zen
c-blosc c-blosc: A blocking, shuffling, and loss-less compression library ivybridge, x86_64, zen
caffe caffe: Deep learning framework ivybridge, x86_64
cdo cdo: Climate Data Operators ivybridge Yes
cfitsio cfitsio: Libraries for Flexible Image Transport System (FITS) data format ivybridge
cfour cfour: Software for quantum chemical modeling x86_64
cgal cgal: Computations Geometry Algorithms Library ivybridge, x86_64 Yes
cgns cgns: CFD General notation system ivybridge Yes
charm4py Charm4py: distributed/parallel programing framework for Python ivybridge Yes
charmpp Charm++: parallel programming framework in C++ ivybridge
cmake cmake: cross-platform, open-source build system ivybridge, x86_64, zen
cminpack cminpack: Library for solving nonlinear equations and nonlinear least squares problems ivybridge
cosma COSMA: Distributed Communication-Optimal Matrix-Matrix Multiplication Library ivybridge Yes
cp2k CP2K: quantum chemistry and solid state physics package ivybridge
cuda cuda: parallel computing platform/programming model for NVIDIA GPUs ivybridge, x86_64, zen
cudnn cudnn: Library of deep learning/neural network primitives for GPUs ivybridge, x86_64, zen Yes
cufflinks cufflinks: Transcriptome assembly and differential expression analysis for RNA-Seq. ivybridge
curl curl: command line tool for transferring data ivybridge, x86_64, zen
deepthought2 deepthought2: Default env setting for the Deepthought2 (DT2) cluster x86_64
dmtcp dmtcp: Distributed Multithreaded Checkpointing ivybridge
dplr dplr: Hypersonic Continuum CFD Code skylake_avx512, x86_64
dyninst dyninst: API for dynamic binary instrumentation ivybridge, x86_64 Yes
eccodes eccodes: Libraries for encoding/decoding weather related data formats ivybridge, x86_64 Yes
eigen eigen: C++ template library for matrix and vector operations, ivybridge, x86_64
elpa elpa: Eigenvalue solvers for Petaflop Applications ivybridge, x86_64 Yes
embree Embree: High performance ray tracing kernels x86_64
envi ENVI: ENVI software for processing and analyzing geospatial data x86_64
esmf esmf: The Earth System Modeling Framework ivybridge Yes
exonerate Exonerate: generic tool for pairwise sequence comparison ivybridge
fastqc fastqc: quality control tool for high throughput sequence data. ivybridge
ffmpeg FFmpeg: ivybridge, x86_64
fftw fftw: Discrete Fourier Transform library ivybridge, x86_64, zen Yes
fsl fsl: the FMRIB Software Library ivybridge
fun3d fun3d: FUN3d (Fully Unstructured Navier-Stokes) CFD suite skylake_avx512
gaussian Gaussian: Software for electronic structure modeling sandybridge
gcam GCAM: The Global Change Analysis Model ivybridge Yes
gcc gcc: GNU Compiler Suite x86_64
gdb gdb: GNU Project Debugger ivybridge Yes
geos geos: C++ Geometry Engine Open Source ivybridge
gloo gloo: Gloo collective communications package ivybridge, x86_64, zen
gnuplot gnuplot: command-line driven graphing utility ivybridge, x86_64
go go: Go programming language ivybridge, x86_64
gromacs gromacs: Chemical simulation/Molecular dynamics package ivybridge Yes
gsl gsl: GNU Scientific Library ivybridge, x86_64, zen
h5utils h5utils: Utilities for visualization/conversion of HDF5 data ivybridge, x86_64, zen
hdf-eos2 HDF-EOS2: HDF for Earth Observing System (hdf4) ivybridge
hdf-eos5 HDF-EOS5: HDF for Earth Observing System (hdf5) ivybridge Yes
hdf4 hdf4: Libraries for Hierarchical Data Format v4 ivybridge, x86_64, zen
hdf5 hdf5: Libraries for Hierarchical Data Format v5 ivybridge, x86_64, zen Yes
hector hector: Simple Global Climate Carbon-Cycle model ivybridge Yes
hello-umd hello-umd: Simple Hello world binary ivybridge Yes
hisat2 hisat2: graph-based alignment of next generation sequencing reads to a population of genomes ivybridge
hmmer hmmer: biosequence analyser using profile hidden Markov models ivybridge, x86_64 Yes
hpcc hpcc: Default env setting for the various clusters x86_64
hpctoolkit hpctoolkit: toolkit for performance measurement and analysis ivybridge, x86_64 Yes
hpx hpx: C++ runtime for parallel and distributed applications ivybridge Yes
hypre hypre: Scalable Linear Solvers and Multigrid Methods ivybridge Yes
igv igv: Integrative Genomics Viewer ivybridge
intel Intel: Intel Parallel Studio collection (compilers, MPI, tools, etc) x86_64
intel-tbb intel-tbb: Intel Threaded Building Blocks ivybridge, x86_64, zen
ioapi ioapi: Models-3/EDSS Input/Output Applications Programming Interface ivybridge Yes
jasper jasper: Library for manipulating JPEG-2000 images ivybridge, x86_64
jellyfish jellyfish: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. ivybridge
jn jn: Default env setting for the Juggernaut (JN) cluster x86_64
json-c JSON-C: JSON library implemented in C ivybridge, x86_64
jsoncpp JsonCpp: JSON library implemented in C++ ivybridge, x86_64
julia julia: Julia programming language: A fresh approach to technical computing ivybridge
jupyter jupyter: The Jupyter Notebook application ivybridge
kahip kahip: Karlsruhe High Quality Graph Partitioning Framework ivybridge, x86_64 Yes
kallisto kallisto: Program for RNA-sequence quantification ivybridge, x86_64 Yes
lammps lammps: LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator ivybridge
latte latte: Open source density functional tight binding molecular dynamics. ivybridge Yes
lftp lftp: multiprotocolfile transfer program ivybridge
libint libint: library to evaluate molecular integrals ivybridge Yes
libvdwxc Libvdwxc: library for vdW-DF exchange-correlation functionals ivybridge Yes
libxsmm LIBXSMM: library for specialized dense and sparse matrix operations ivybridge
libzmq libzmq: ZeroMQ networking/concurrency library and core API ivybridge, x86_64
lz4 lz4: Lossless compression utility and library ivybridge, x86_64, zen
magics magics: meteorological plotting software ivybridge, x86_64 Yes
magma magma: Matrix Algebra on GPU and Multicore Architectures ivybridge, x86_64, zen Yes
mathematica Mathematica: Mathematica symbolic and computational mathematics package. x86_64
matio matio: MATLAB MAT file I/O library ivybridge, x86_64, zen Yes
matlab matlab: Matlab numerical computing environment x86_64
matplotlib matplotlib: Open-source software library for creating visualizations in Python ivybridge, x86_64
mercurial mercurial: Mercurial source control management system ivybridge
metis metis: Metis unstructured graph partitioner ivybridge, x86_64, zen
mgridgen mgridgen: Multilevel Serial & Parallel Coarse Grid Construction Library ivybridge, x86_64 Yes
mt-metis mt-metis: Metis unstructured graph partitioner ivybridge, x86_64, zen
mumps mumps: MUltifrontal Massively Parallel sparse direct Solver ivybridge, x86_64 Yes
namd NAMD: Nanoscale Molecular Dynamics ivybridge Yes
ncl NCL: NCAR Command Language ivybridge Yes
nco nco: Toolkits for manipulating data in NetCDF formats ivybridge Yes
ncview ncview: Viewer for NetCDF files ivybridge Yes
netcdf netcdf: C Libraries for NetCDF data format ivybridge, x86_64, zen Yes
netcdf-cxx netcdf-cxx: C++ Libraries for NetCDF data format ivybridge, zen
netcdf-fortran netcdf-fortran: Fortran Libraries for NetCDF data format ivybridge, zen Yes
nvhpc nvhpc: Nvidia HPC SDK Compiler suite x86_64
nvmpi nvmpi: MPI libraries from the Nvidia HPC SDK Compiler suite x86_64
openblas openblas: Optimized BLAS libraries ivybridge, x86_64, zen
opencv opencv: Open-source Computer Vision Library ivybridge, x86_64
openfoam openfoam: Opensource C++ CFD toolbox ivybridge Yes
openjdk openjdk: Open-source implementation of Java ivybridge, x86_64, zen
openmm openmm: A high-performance toolkit for molecular simulation. ivybridge Yes
openmpi openmpi: OpenMPI implementation of Message Passing Interface ivybridge, x86_64 Yes
osu-micro-benchmarks osu-micro-benchmarks: Microbenchmarks for MPI ivybridge, x86_64
parallel-netcdf parallel-netcdf: Parallel I/O library for NetCDF file format ivybridge, x86_64 Yes
paraview paraview: data analysis and visualization application ivybridge
pari-gp pari-gp: computer algebra system for computations in number theory ivybridge Yes
parmetis parmetis: Parallel Metis ivybridge, x86_64 Yes
parmgridgen ParMGridGen: Multilevel Serial & Parallel Coarse Grid Construction Library ivybridge, x86_64 Yes
perl perl: Perl scripting language ivybridge, x86_64, zen
petsc PETSc: PETSc (Portable, Extensible Toolkit for Scientific Computation) ivybridge Yes
pexsi PEXSI: electronic structure calculation based on Kohn-Sham density functional theory ivybridge Yes
pfft pfft: Parallel Fast Fourier Transform library ivybridge, x86_64 Yes
plink PLINK: genome association analysis toolset ivybridge
pointwise pointwise: Pointwise mesh generation software for CFD x86_64
popoolation2 popoolation2: PoPoolation2 allows to compare allele frequencies for single-nucleotide polymorphisms. ivybridge
povray POV-Ray: Persistence of Vision Ray tracer ivybridge
python python: Python scripting language ivybridge, x86_64
pytorch pytorch: Open-source machine learning library ivybridge, x86_64 Yes
qbox Qbox: first-principles molecular dynamics code. ivybridge Yes
qmd-progress qmd-progress: PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver ivybridge Yes
qnnpack qnnpack: Quantized Neural Networks PACKage ivybridge, x86_64, zen
quantum-espresso quantum-espresso: Electronic-structure calculations at the nanoscale. ivybridge Yes
r r: R statistical computing scripting language ivybridge, x86_64
rclone Rclone: command line tool for managing cloud storage ivybridge
rust rust: Rust programming language ivybridge
samtools samtools: SAM (Sequence/Alignment Mapping) Tools ivybridge
scalapack scalapack: Scalable linear algebra package ivybridge, x86_64 Yes
scons SCons: SCons open-source software construction tool ivybridge, x86_64
scorep scorep: suite for profiling, event tracing, and analysis of HPC applications ivybridge Yes
scotch scotch: Package for graph and mesh partitioning, graph clustering, and sparse matrix ordering ivybridge, x86_64 Yes
silo silo: libraries for reading/writing a variety of scientific data ivybridge, x86_64, zen Yes
singularity singularity: Singularity container utilities x86_64
sirius SIRIUS: domain specific library for electronic structure calculations ivybridge
spfft SpFFT: 3D FFT library for sparse frequency domain data ivybridge
spglib spglib: C library for finding and handling crystal symmetries ivybridge, zen
suite-sparse suite-sparse: Suite of Sparse Matrix algorithms ivybridge, x86_64, zen Yes
superlu superlu: Sparse Linear system solver (sequential) ivybridge, x86_64, zen
superlu-dist superlu-dist: Sparse Linear system solver (distributed mem/MPI) ivybridge, x86_64 Yes
superlu-mt superlu-mt: Sparse Linear system solver (multithreaded) ivybridge, x86_64, zen
swig swig: compiler to interface C/C++ libraries to Perl, Python, etc ivybridge, x86_64
sz sz: Error-bounded Lossy Compressor for HPC Data ivybridge, x86_64 Yes
tecplot360 Tecplot360: CFD visualization software x86_64
tensorflow tensorflow: Open-source software library for machine intelligence ivybridge, x86_64 Yes
tophat tophat: Spliced read mapper for RNA-Seq x86_64
trilinos Trilinos: Solvers collection including linear, non-linear, optimization, and transient solvers ivybridge Yes
trimmomatic trimmomatic: Trimming tool for Illumina NGS data. ivybridge
trinity trinity: trinity is a novel method to reconstruct transcriptomes for RNA-seq data. ivybridge Yes
us3d us3d: Aeordynamic and Aerothermodynamic Simulations Software skylake_avx512, x86_64
vasp vasp: VASP: Vienna Ab-initio Simulation Package x86_64
virtualgl virtualgl: Toolkit to allow remote display to run OpenGL applications with full hardware acceleration ivybridge
visit visit: interactive, scalable, visualization, animation and analysis tool x86_64
vmd VMD: Visual Molecular Dynamics x86_64
voropp Voro++: library for 3D computations of the Voronoi tessellation ivybridge
vtk vtk: 3D computer graphics, image processing and visualization library ivybridge, x86_64 Yes
wannier90 Wannier90: tool to calculate maximally-localized Wannier functions ivybridge Yes
xerces-c xerces-c: validating XML parser in C++ ivybridge, x86_64
xssp xssp: Secondary structure assignments for entries in the Protein Data Bank ivybridge Yes
xz xz: Lossless compression utility and library ivybridge, x86_64, zen
zfp zfp: Library for lossy compression of multidimensional arrays ivybridge, x86_64, zen
zlib zlib: General purpose, patent-free compression ibrary ivybridge, sandybridge, x86_64, zen
zoltan zoltan: Toolkit for parallel combinatorial algorithms ivybridge, x86_64 Yes
zstd zstd: Fast, lossless compression algorithm ivybridge, x86_64, zen

Software packages related to Aeronautics

This section lists various software packages related to Aeronautics, Aviation, Aerospace Sciences and related fields (Astronautics, Hypersonics, Aerothermodynamics, etc.)

Software packages related to Aeronautics
Package Name Description Supported CPUs GPU ready?
dplr dplr: Hypersonic Continuum CFD Code skylake_avx512, x86_64
fun3d fun3d: FUN3d (Fully Unstructured Navier-Stokes) CFD suite skylake_avx512
pointwise pointwise: Pointwise mesh generation software for CFD x86_64
us3d us3d: Aeordynamic and Aerothermodynamic Simulations Software skylake_avx512, x86_64

Software packages related to Astronomy

This section lists various software packages related to Astronomy and related fields.

Software packages related to Astronomy
Package Name Description Supported CPUs GPU ready?
cfitsio cfitsio: Libraries for Flexible Image Transport System (FITS) data format ivybridge

Packages related to BrainImaging

This section lists various software packages related to $cat.

Packages related to BrainImaging
Package Name Description Supported CPUs GPU ready?
fsl fsl: the FMRIB Software Library ivybridge

Software packages related to CFD

This section lists various software packages related to Computational Fluid Dynamics (CFD).

Software packages related to CFD
Package Name Description Supported CPUs GPU ready?
cgns cgns: CFD General notation system ivybridge Yes
dplr dplr: Hypersonic Continuum CFD Code skylake_avx512, x86_64
fun3d fun3d: FUN3d (Fully Unstructured Navier-Stokes) CFD suite skylake_avx512
openfoam openfoam: Opensource C++ CFD toolbox ivybridge Yes
pointwise pointwise: Pointwise mesh generation software for CFD x86_64
tecplot360 Tecplot360: CFD visualization software x86_64

Software packages related to Chemistry

This section lists various software packages related to Chemistry, Computational Chemistry, Quantum Chemistry, etc. See also MolecularDynamics and MaterialScience.

Software packages related to Chemistry
Package Name Description Supported CPUs GPU ready?
cfour cfour: Software for quantum chemical modeling x86_64
cp2k CP2K: quantum chemistry and solid state physics package ivybridge
gaussian Gaussian: Software for electronic structure modeling sandybridge
gromacs gromacs: Chemical simulation/Molecular dynamics package ivybridge Yes
lammps lammps: LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator ivybridge
libint libint: library to evaluate molecular integrals ivybridge Yes
namd NAMD: Nanoscale Molecular Dynamics ivybridge Yes
openmm openmm: A high-performance toolkit for molecular simulation. ivybridge Yes
qbox Qbox: first-principles molecular dynamics code. ivybridge Yes
qmd-progress qmd-progress: PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver ivybridge Yes
sirius SIRIUS: domain specific library for electronic structure calculations ivybridge
vasp vasp: VASP: Vienna Ab-initio Simulation Package x86_64
vmd VMD: Visual Molecular Dynamics x86_64

Software packages related to ComputerVision

This section lists various software packages related to Computer Vision and related fields. You might also want to look at the section on packages related to Machine Learning.

Software packages related to ComputerVision
Package Name Description Supported CPUs GPU ready?
caffe caffe: Deep learning framework ivybridge, x86_64
opencv opencv: Open-source Computer Vision Library ivybridge, x86_64
pytorch pytorch: Open-source machine learning library ivybridge, x86_64 Yes
tensorflow tensorflow: Open-source software library for machine intelligence ivybridge, x86_64 Yes

Software packages related to DataCompression

This section lists various software packages related to Data Compression. Basically libraries and binaries for compressing and uncompressing data to/from various compressed formats and/or compression algorithms.

Software packages related to DataCompression
Package Name Description Supported CPUs GPU ready?
bzip2 bzip2: patent-free high quality data compression libraries ivybridge, sandybridge, x86_64, zen
c-blosc c-blosc: A blocking, shuffling, and loss-less compression library ivybridge, x86_64, zen
lz4 lz4: Lossless compression utility and library ivybridge, x86_64, zen
sz sz: Error-bounded Lossy Compressor for HPC Data ivybridge, x86_64 Yes
xerces-c xerces-c: validating XML parser in C++ ivybridge, x86_64
xz xz: Lossless compression utility and library ivybridge, x86_64, zen
zfp zfp: Library for lossy compression of multidimensional arrays ivybridge, x86_64, zen
zlib zlib: General purpose, patent-free compression ibrary ivybridge, sandybridge, x86_64, zen
zstd zstd: Fast, lossless compression algorithm ivybridge, x86_64, zen

Software packages related to DataFormat

This section lists various software packages related to various scientific or other data formats, including libraries and binaries for reading, writing, and manipulating data in specific formats.

Software packages related to DataFormat
Package Name Description Supported CPUs GPU ready?
adios2 adios2: The Adapatble Input/Output System, version 2 ivybridge, x86_64 Yes
cdo cdo: Climate Data Operators ivybridge Yes
cfitsio cfitsio: Libraries for Flexible Image Transport System (FITS) data format ivybridge
eccodes eccodes: Libraries for encoding/decoding weather related data formats ivybridge, x86_64 Yes
h5utils h5utils: Utilities for visualization/conversion of HDF5 data ivybridge, x86_64, zen
hdf-eos2 HDF-EOS2: HDF for Earth Observing System (hdf4) ivybridge
hdf-eos5 HDF-EOS5: HDF for Earth Observing System (hdf5) ivybridge Yes
hdf4 hdf4: Libraries for Hierarchical Data Format v4 ivybridge, x86_64, zen
hdf5 hdf5: Libraries for Hierarchical Data Format v5 ivybridge, x86_64, zen Yes
ioapi ioapi: Models-3/EDSS Input/Output Applications Programming Interface ivybridge Yes
matio matio: MATLAB MAT file I/O library ivybridge, x86_64, zen Yes
nco nco: Toolkits for manipulating data in NetCDF formats ivybridge Yes
ncview ncview: Viewer for NetCDF files ivybridge Yes
netcdf netcdf: C Libraries for NetCDF data format ivybridge, x86_64, zen Yes
netcdf-cxx netcdf-cxx: C++ Libraries for NetCDF data format ivybridge, zen
netcdf-fortran netcdf-fortran: Fortran Libraries for NetCDF data format ivybridge, zen Yes
parallel-netcdf parallel-netcdf: Parallel I/O library for NetCDF file format ivybridge, x86_64 Yes
silo silo: libraries for reading/writing a variety of scientific data ivybridge, x86_64, zen Yes

Software packages related to EarthScience

This section lists various software packages related to various Earth sciences. See also Meteorology.

Software packages related to EarthScience
Package Name Description Supported CPUs GPU ready?
esmf esmf: The Earth System Modeling Framework ivybridge Yes
gcam GCAM: The Global Change Analysis Model ivybridge Yes
geos geos: C++ Geometry Engine Open Source ivybridge
hdf-eos2 HDF-EOS2: HDF for Earth Observing System (hdf4) ivybridge
hdf-eos5 HDF-EOS5: HDF for Earth Observing System (hdf5) ivybridge Yes
hector hector: Simple Global Climate Carbon-Cycle model ivybridge Yes

Software packages related to Engineering

This section lists various software packages related to various Engineering fields.

Software packages related to Engineering
Package Name Description Supported CPUs GPU ready?
ansys ANSYS: Computer-aided engineering software x86_64
ansys-em ANSYSEM: Computer-aided engineering software for electromagnetic systems x86_64
ansys.new ANSYS: Computer-aided engineering software x86_64
ansys.old ANSYS: Computer-aided engineering software x86_64
petsc PETSc: PETSc (Portable, Extensible Toolkit for Scientific Computation) ivybridge Yes
trilinos Trilinos: Solvers collection including linear, non-linear, optimization, and transient solvers ivybridge Yes

Software packages related to Genomics

This section lists various software packages related to Genomics, Genetics, and related fields.

Software packages related to Genomics
Package Name Description Supported CPUs GPU ready?
bcftools bcftools: BCFtools is a set of utilities that manipulate variant calls ivybridge
beagle beagle: package for phasing genotypes and for imputing ungenotyped markers ivybridge, x86_64
bedtools2 bedtools2: swiss-army knife of genomics analysis tasks ivybridge, x86_64
blast-plus blast-plus: Basic Local Alignment Search Tool ivybridge
bowtie bowtie: ultrafast sequence aligner ivybridge
bowtie2 bowtie2: ultrafast sequence aligner ivybridge
bwa bwa: Burrows-Wheeler Aligner ivybridge
cufflinks cufflinks: Transcriptome assembly and differential expression analysis for RNA-Seq. ivybridge
exonerate Exonerate: generic tool for pairwise sequence comparison ivybridge
fastqc fastqc: quality control tool for high throughput sequence data. ivybridge
hisat2 hisat2: graph-based alignment of next generation sequencing reads to a population of genomes ivybridge
hmmer hmmer: biosequence analyser using profile hidden Markov models ivybridge, x86_64 Yes
igv igv: Integrative Genomics Viewer ivybridge
jellyfish jellyfish: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. ivybridge
kallisto kallisto: Program for RNA-sequence quantification ivybridge, x86_64 Yes
plink PLINK: genome association analysis toolset ivybridge
popoolation2 popoolation2: PoPoolation2 allows to compare allele frequencies for single-nucleotide polymorphisms. ivybridge
samtools samtools: SAM (Sequence/Alignment Mapping) Tools ivybridge
tophat tophat: Spliced read mapper for RNA-Seq x86_64
trimmomatic trimmomatic: Trimming tool for Illumina NGS data. ivybridge
trinity trinity: trinity is a novel method to reconstruct transcriptomes for RNA-seq data. ivybridge Yes

Software packages related to ImageProcessing

This section lists various software packages related to the processing/editting/manipulation/etc of image or video files.

Software packages related to ImageProcessing
Package Name Description Supported CPUs GPU ready?
embree Embree: High performance ray tracing kernels x86_64
ffmpeg FFmpeg: ivybridge, x86_64
fsl fsl: the FMRIB Software Library ivybridge
jasper jasper: Library for manipulating JPEG-2000 images ivybridge, x86_64

Software packages related to MachineLearning

This section lists various software packages related to Machine Learning, Deep Learning, Neural Nets and related fields. You might also wish to look at the section on Computer Vision

Software packages related to MachineLearning
Package Name Description Supported CPUs GPU ready?
caffe caffe: Deep learning framework ivybridge, x86_64
cudnn cudnn: Library of deep learning/neural network primitives for GPUs ivybridge, x86_64, zen Yes
gloo gloo: Gloo collective communications package ivybridge, x86_64, zen
libxsmm LIBXSMM: library for specialized dense and sparse matrix operations ivybridge
opencv opencv: Open-source Computer Vision Library ivybridge, x86_64
pytorch pytorch: Open-source machine learning library ivybridge, x86_64 Yes
qnnpack qnnpack: Quantized Neural Networks PACKage ivybridge, x86_64, zen
tensorflow tensorflow: Open-source software library for machine intelligence ivybridge, x86_64 Yes

Software packages related to MaterialScience

This section lists various software packages related to Material Science and related fields. See also Chemistry and SolidStatePhysics.

Software packages related to MaterialScience
Package Name Description Supported CPUs GPU ready?
cp2k CP2K: quantum chemistry and solid state physics package ivybridge
spglib spglib: C library for finding and handling crystal symmetries ivybridge, zen
vasp vasp: VASP: Vienna Ab-initio Simulation Package x86_64

Packages related to Mathematics

This section lists various software packages related to $cat.

Packages related to Mathematics
Package Name Description Supported CPUs GPU ready?
pari-gp pari-gp: computer algebra system for computations in number theory ivybridge Yes

Software packages related to Meteorology

This section lists various software packages related to Meteorology, Weather, Atmospheric and Oceanographic Sciences and related fields. See also Earth Sciences

Software packages related to Meteorology
Package Name Description Supported CPUs GPU ready?
cdo cdo: Climate Data Operators ivybridge Yes
eccodes eccodes: Libraries for encoding/decoding weather related data formats ivybridge, x86_64 Yes
magics magics: meteorological plotting software ivybridge, x86_64 Yes

Software packages related to MolecularDynamics

This section lists various software packages related to Molecular Dynamics and related fields. See also Chemistry and Material Science.

Software packages related to MolecularDynamics
Package Name Description Supported CPUs GPU ready?
gromacs gromacs: Chemical simulation/Molecular dynamics package ivybridge Yes
lammps lammps: LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator ivybridge
latte latte: Open source density functional tight binding molecular dynamics. ivybridge Yes
libint libint: library to evaluate molecular integrals ivybridge Yes
libvdwxc Libvdwxc: library for vdW-DF exchange-correlation functionals ivybridge Yes
namd NAMD: Nanoscale Molecular Dynamics ivybridge Yes
openmm openmm: A high-performance toolkit for molecular simulation. ivybridge Yes
qmd-progress qmd-progress: PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver ivybridge Yes
quantum-espresso quantum-espresso: Electronic-structure calculations at the nanoscale. ivybridge Yes
sirius SIRIUS: domain specific library for electronic structure calculations ivybridge
spglib spglib: C library for finding and handling crystal symmetries ivybridge, zen
vmd VMD: Visual Molecular Dynamics x86_64
wannier90 Wannier90: tool to calculate maximally-localized Wannier functions ivybridge Yes
xssp xssp: Secondary structure assignments for entries in the Protein Data Bank ivybridge Yes

Software packages related to MultiPhysics

This section lists various software packages related to Multiphysics.

Software packages related to MultiPhysics
Package Name Description Supported CPUs GPU ready?
petsc PETSc: PETSc (Portable, Extensible Toolkit for Scientific Computation) ivybridge Yes
trilinos Trilinos: Solvers collection including linear, non-linear, optimization, and transient solvers ivybridge Yes

Software packages related to NumericalMethods

This section lists various software packages related to Numerical Methods and Computational Mathematics. It includes both underlying numerical libraries as well as advanced computational (and often GUI) environments. These packages are generally useful across a wide range of disciplines.

Software packages related to NumericalMethods
Package Name Description Supported CPUs GPU ready?
arpack-ng arpack-ng: Fortran77 subroutines designed to solve large scale eigenvalue problems ivybridge, x86_64, zen Yes
bml bml: Basic Matrix Library ivybridge Yes
cgal cgal: Computations Geometry Algorithms Library ivybridge, x86_64 Yes
cminpack cminpack: Library for solving nonlinear equations and nonlinear least squares problems ivybridge
cosma COSMA: Distributed Communication-Optimal Matrix-Matrix Multiplication Library ivybridge Yes
eigen eigen: C++ template library for matrix and vector operations, ivybridge, x86_64
elpa elpa: Eigenvalue solvers for Petaflop Applications ivybridge, x86_64 Yes
envi ENVI: ENVI software for processing and analyzing geospatial data x86_64
fftw fftw: Discrete Fourier Transform library ivybridge, x86_64, zen Yes
gsl gsl: GNU Scientific Library ivybridge, x86_64, zen
hypre hypre: Scalable Linear Solvers and Multigrid Methods ivybridge Yes
kahip kahip: Karlsruhe High Quality Graph Partitioning Framework ivybridge, x86_64 Yes
magma magma: Matrix Algebra on GPU and Multicore Architectures ivybridge, x86_64, zen Yes
mathematica Mathematica: Mathematica symbolic and computational mathematics package. x86_64
matio matio: MATLAB MAT file I/O library ivybridge, x86_64, zen Yes
matlab matlab: Matlab numerical computing environment x86_64
metis metis: Metis unstructured graph partitioner ivybridge, x86_64, zen
mgridgen mgridgen: Multilevel Serial & Parallel Coarse Grid Construction Library ivybridge, x86_64 Yes
mt-metis mt-metis: Metis unstructured graph partitioner ivybridge, x86_64, zen
mumps mumps: MUltifrontal Massively Parallel sparse direct Solver ivybridge, x86_64 Yes
ncl NCL: NCAR Command Language ivybridge Yes
openblas openblas: Optimized BLAS libraries ivybridge, x86_64, zen
parmetis parmetis: Parallel Metis ivybridge, x86_64 Yes
parmgridgen ParMGridGen: Multilevel Serial & Parallel Coarse Grid Construction Library ivybridge, x86_64 Yes
pexsi PEXSI: electronic structure calculation based on Kohn-Sham density functional theory ivybridge Yes
pfft pfft: Parallel Fast Fourier Transform library ivybridge, x86_64 Yes
pytorch pytorch: Open-source machine learning library ivybridge, x86_64 Yes
scalapack scalapack: Scalable linear algebra package ivybridge, x86_64 Yes
scotch scotch: Package for graph and mesh partitioning, graph clustering, and sparse matrix ordering ivybridge, x86_64 Yes
spfft SpFFT: 3D FFT library for sparse frequency domain data ivybridge
suite-sparse suite-sparse: Suite of Sparse Matrix algorithms ivybridge, x86_64, zen Yes
superlu superlu: Sparse Linear system solver (sequential) ivybridge, x86_64, zen
superlu-dist superlu-dist: Sparse Linear system solver (distributed mem/MPI) ivybridge, x86_64 Yes
superlu-mt superlu-mt: Sparse Linear system solver (multithreaded) ivybridge, x86_64, zen
tensorflow tensorflow: Open-source software library for machine intelligence ivybridge, x86_64 Yes
voropp Voro++: library for 3D computations of the Voronoi tessellation ivybridge
zoltan zoltan: Toolkit for parallel combinatorial algorithms ivybridge, x86_64 Yes

Software packages related to PythonModule

This section lists various software packages containing python modules which can be imported in your python code, after the corresponding environmental module is loaded.

Software packages related to PythonModule
Package Name Description Supported CPUs GPU ready?
charm4py Charm4py: distributed/parallel programing framework for Python ivybridge Yes
jupyter jupyter: The Jupyter Notebook application ivybridge
magics magics: meteorological plotting software ivybridge, x86_64 Yes
matplotlib matplotlib: Open-source software library for creating visualizations in Python ivybridge, x86_64
openmm openmm: A high-performance toolkit for molecular simulation. ivybridge Yes
pytorch pytorch: Open-source machine learning library ivybridge, x86_64 Yes
tensorflow tensorflow: Open-source software library for machine intelligence ivybridge, x86_64 Yes
trilinos Trilinos: Solvers collection including linear, non-linear, optimization, and transient solvers ivybridge Yes

Software packages related to SoftwareDevelopment

This section lists various software packages related to the development and optimization, etc. of software and codes. It includes compilers, debuggers, profiling tools, as well as relatively low level libraries. It also includes various scripting languages.

Software packages related to SoftwareDevelopment
Package Name Description Supported CPUs GPU ready?
bml bml: Basic Matrix Library ivybridge Yes
boost boost: free, portable C++ source libraries ivybridge, sandybridge, x86_64, zen Yes
cgal cgal: Computations Geometry Algorithms Library ivybridge, x86_64 Yes
charm4py Charm4py: distributed/parallel programing framework for Python ivybridge Yes
charmpp Charm++: parallel programming framework in C++ ivybridge
cmake cmake: cross-platform, open-source build system ivybridge, x86_64, zen
cminpack cminpack: Library for solving nonlinear equations and nonlinear least squares problems ivybridge
cosma COSMA: Distributed Communication-Optimal Matrix-Matrix Multiplication Library ivybridge Yes
cuda cuda: parallel computing platform/programming model for NVIDIA GPUs ivybridge, x86_64, zen
cudnn cudnn: Library of deep learning/neural network primitives for GPUs ivybridge, x86_64, zen Yes
dmtcp dmtcp: Distributed Multithreaded Checkpointing ivybridge
dyninst dyninst: API for dynamic binary instrumentation ivybridge, x86_64 Yes
eccodes eccodes: Libraries for encoding/decoding weather related data formats ivybridge, x86_64 Yes
eigen eigen: C++ template library for matrix and vector operations, ivybridge, x86_64
elpa elpa: Eigenvalue solvers for Petaflop Applications ivybridge, x86_64 Yes
envi ENVI: ENVI software for processing and analyzing geospatial data x86_64
esmf esmf: The Earth System Modeling Framework ivybridge Yes
ffmpeg FFmpeg: ivybridge, x86_64
fftw fftw: Discrete Fourier Transform library ivybridge, x86_64, zen Yes
gcc gcc: GNU Compiler Suite x86_64
gdb gdb: GNU Project Debugger ivybridge Yes
geos geos: C++ Geometry Engine Open Source ivybridge
gloo gloo: Gloo collective communications package ivybridge, x86_64, zen
go go: Go programming language ivybridge, x86_64
gsl gsl: GNU Scientific Library ivybridge, x86_64, zen
hdf4 hdf4: Libraries for Hierarchical Data Format v4 ivybridge, x86_64, zen
hdf5 hdf5: Libraries for Hierarchical Data Format v5 ivybridge, x86_64, zen Yes
hello-umd hello-umd: Simple Hello world binary ivybridge Yes
hpctoolkit hpctoolkit: toolkit for performance measurement and analysis ivybridge, x86_64 Yes
hpx hpx: C++ runtime for parallel and distributed applications ivybridge Yes
hypre hypre: Scalable Linear Solvers and Multigrid Methods ivybridge Yes
intel Intel: Intel Parallel Studio collection (compilers, MPI, tools, etc) x86_64
intel-tbb intel-tbb: Intel Threaded Building Blocks ivybridge, x86_64, zen
ioapi ioapi: Models-3/EDSS Input/Output Applications Programming Interface ivybridge Yes
jasper jasper: Library for manipulating JPEG-2000 images ivybridge, x86_64
json-c JSON-C: JSON library implemented in C ivybridge, x86_64
jsoncpp JsonCpp: JSON library implemented in C++ ivybridge, x86_64
julia julia: Julia programming language: A fresh approach to technical computing ivybridge
kahip kahip: Karlsruhe High Quality Graph Partitioning Framework ivybridge, x86_64 Yes
libxsmm LIBXSMM: library for specialized dense and sparse matrix operations ivybridge
libzmq libzmq: ZeroMQ networking/concurrency library and core API ivybridge, x86_64
magma magma: Matrix Algebra on GPU and Multicore Architectures ivybridge, x86_64, zen Yes
mathematica Mathematica: Mathematica symbolic and computational mathematics package. x86_64
matio matio: MATLAB MAT file I/O library ivybridge, x86_64, zen Yes
matlab matlab: Matlab numerical computing environment x86_64
metis metis: Metis unstructured graph partitioner ivybridge, x86_64, zen
mgridgen mgridgen: Multilevel Serial & Parallel Coarse Grid Construction Library ivybridge, x86_64 Yes
mt-metis mt-metis: Metis unstructured graph partitioner ivybridge, x86_64, zen
mumps mumps: MUltifrontal Massively Parallel sparse direct Solver ivybridge, x86_64 Yes
ncl NCL: NCAR Command Language ivybridge Yes
nco nco: Toolkits for manipulating data in NetCDF formats ivybridge Yes
netcdf netcdf: C Libraries for NetCDF data format ivybridge, x86_64, zen Yes
netcdf-cxx netcdf-cxx: C++ Libraries for NetCDF data format ivybridge, zen
netcdf-fortran netcdf-fortran: Fortran Libraries for NetCDF data format ivybridge, zen Yes
nvhpc nvhpc: Nvidia HPC SDK Compiler suite x86_64
nvmpi nvmpi: MPI libraries from the Nvidia HPC SDK Compiler suite x86_64
openblas openblas: Optimized BLAS libraries ivybridge, x86_64, zen
opencv opencv: Open-source Computer Vision Library ivybridge, x86_64
openjdk openjdk: Open-source implementation of Java ivybridge, x86_64, zen
openmpi openmpi: OpenMPI implementation of Message Passing Interface ivybridge, x86_64 Yes
osu-micro-benchmarks osu-micro-benchmarks: Microbenchmarks for MPI ivybridge, x86_64
parallel-netcdf parallel-netcdf: Parallel I/O library for NetCDF file format ivybridge, x86_64 Yes
parmetis parmetis: Parallel Metis ivybridge, x86_64 Yes
perl perl: Perl scripting language ivybridge, x86_64, zen
pfft pfft: Parallel Fast Fourier Transform library ivybridge, x86_64 Yes
python python: Python scripting language ivybridge, x86_64
qnnpack qnnpack: Quantized Neural Networks PACKage ivybridge, x86_64, zen
r r: R statistical computing scripting language ivybridge, x86_64
rust rust: Rust programming language ivybridge
scalapack scalapack: Scalable linear algebra package ivybridge, x86_64 Yes
scons SCons: SCons open-source software construction tool ivybridge, x86_64
scorep scorep: suite for profiling, event tracing, and analysis of HPC applications ivybridge Yes
scotch scotch: Package for graph and mesh partitioning, graph clustering, and sparse matrix ordering ivybridge, x86_64 Yes
silo silo: libraries for reading/writing a variety of scientific data ivybridge, x86_64, zen Yes
singularity singularity: Singularity container utilities x86_64
suite-sparse suite-sparse: Suite of Sparse Matrix algorithms ivybridge, x86_64, zen Yes
superlu superlu: Sparse Linear system solver (sequential) ivybridge, x86_64, zen
superlu-dist superlu-dist: Sparse Linear system solver (distributed mem/MPI) ivybridge, x86_64 Yes
superlu-mt superlu-mt: Sparse Linear system solver (multithreaded) ivybridge, x86_64, zen
swig swig: compiler to interface C/C++ libraries to Perl, Python, etc ivybridge, x86_64
zlib zlib: General purpose, patent-free compression ibrary ivybridge, sandybridge, x86_64, zen
zoltan zoltan: Toolkit for parallel combinatorial algorithms ivybridge, x86_64 Yes

Software packages related to Utilities

This section lists various utility software packages, etc. This is sort of a catch-all category for packages which are useful across a wide range of disciplines but do not really fall into any discipline. These are often just newer versions of utilities supplied by the OS.

Software packages related to Utilities
Package Name Description Supported CPUs GPU ready?
curl curl: command line tool for transferring data ivybridge, x86_64, zen
deepthought2 deepthought2: Default env setting for the Deepthought2 (DT2) cluster x86_64
dmtcp dmtcp: Distributed Multithreaded Checkpointing ivybridge
hpcc hpcc: Default env setting for the various clusters x86_64
jn jn: Default env setting for the Juggernaut (JN) cluster x86_64
jupyter jupyter: The Jupyter Notebook application ivybridge
lftp lftp: multiprotocolfile transfer program ivybridge
mercurial mercurial: Mercurial source control management system ivybridge
rclone Rclone: command line tool for managing cloud storage ivybridge
singularity singularity: Singularity container utilities x86_64

Software packages related to Visualization

This section lists various software packages related to Visualization; basically packages to assist in visualizing data generated from other packages/codes. It includes both basic graphics libraries and high end (GUI) visualization platforms.

Software packages related to Visualization
Package Name Description Supported CPUs GPU ready?
envi ENVI: ENVI software for processing and analyzing geospatial data x86_64
gnuplot gnuplot: command-line driven graphing utility ivybridge, x86_64
magics magics: meteorological plotting software ivybridge, x86_64 Yes
ncl NCL: NCAR Command Language ivybridge Yes
paraview paraview: data analysis and visualization application ivybridge
povray POV-Ray: Persistence of Vision Ray tracer ivybridge
virtualgl virtualgl: Toolkit to allow remote display to run OpenGL applications with full hardware acceleration ivybridge
visit visit: interactive, scalable, visualization, animation and analysis tool x86_64
vmd VMD: Visual Molecular Dynamics x86_64
vtk vtk: 3D computer graphics, image processing and visualization library ivybridge, x86_64 Yes

All packages available on the Deepthought2 cluster (RHEL8)

This section lists all software packages available on the Deepthought2 cluster (RHEL8)

All packages available on the Deepthought2 cluster (RHEL8)
Package Name Description Supported CPUs GPU ready?
adios2 adios2: The Adapatble Input/Output System, version 2 ivybridge, x86_64 Yes
ansys ANSYS: Computer-aided engineering software x86_64
ansys-em ANSYSEM: Computer-aided engineering software for electromagnetic systems x86_64
ansys.new ANSYS: Computer-aided engineering software x86_64
arpack-ng arpack-ng: Fortran77 subroutines designed to solve large scale eigenvalue problems ivybridge, x86_64, zen Yes
bcftools bcftools: BCFtools is a set of utilities that manipulate variant calls ivybridge
beagle beagle: package for phasing genotypes and for imputing ungenotyped markers ivybridge, x86_64
bedtools2 bedtools2: swiss-army knife of genomics analysis tasks ivybridge, x86_64
blast-plus blast-plus: Basic Local Alignment Search Tool ivybridge
bml bml: Basic Matrix Library ivybridge Yes
boost boost: free, portable C++ source libraries ivybridge, sandybridge, x86_64, zen Yes
bowtie bowtie: ultrafast sequence aligner ivybridge
bowtie2 bowtie2: ultrafast sequence aligner ivybridge
bwa bwa: Burrows-Wheeler Aligner ivybridge
bzip2 bzip2: patent-free high quality data compression libraries ivybridge, sandybridge, x86_64, zen
c-blosc c-blosc: A blocking, shuffling, and loss-less compression library ivybridge, x86_64, zen
caffe caffe: Deep learning framework ivybridge, x86_64
cdo cdo: Climate Data Operators ivybridge Yes
cfitsio cfitsio: Libraries for Flexible Image Transport System (FITS) data format ivybridge
cfour cfour: Software for quantum chemical modeling x86_64
cgal cgal: Computations Geometry Algorithms Library ivybridge, x86_64 Yes
cgns cgns: CFD General notation system ivybridge Yes
charm4py Charm4py: distributed/parallel programing framework for Python ivybridge Yes
charmpp Charm++: parallel programming framework in C++ ivybridge
cmake cmake: cross-platform, open-source build system ivybridge, x86_64, zen
cminpack cminpack: Library for solving nonlinear equations and nonlinear least squares problems ivybridge
cosma COSMA: Distributed Communication-Optimal Matrix-Matrix Multiplication Library ivybridge Yes
cp2k CP2K: quantum chemistry and solid state physics package ivybridge
cuda cuda: parallel computing platform/programming model for NVIDIA GPUs ivybridge, x86_64, zen
cudnn cudnn: Library of deep learning/neural network primitives for GPUs ivybridge, x86_64, zen Yes
cufflinks cufflinks: Transcriptome assembly and differential expression analysis for RNA-Seq. ivybridge
curl curl: command line tool for transferring data ivybridge, x86_64, zen
dmtcp dmtcp: Distributed Multithreaded Checkpointing ivybridge
dplr dplr: Hypersonic Continuum CFD Code skylake_avx512, x86_64
dyninst dyninst: API for dynamic binary instrumentation ivybridge, x86_64 Yes
eccodes eccodes: Libraries for encoding/decoding weather related data formats ivybridge, x86_64 Yes
eigen eigen: C++ template library for matrix and vector operations, ivybridge, x86_64
elpa elpa: Eigenvalue solvers for Petaflop Applications ivybridge, x86_64 Yes
embree Embree: High performance ray tracing kernels x86_64
envi ENVI: ENVI software for processing and analyzing geospatial data x86_64
esmf esmf: The Earth System Modeling Framework ivybridge Yes
exonerate Exonerate: generic tool for pairwise sequence comparison ivybridge
fastqc fastqc: quality control tool for high throughput sequence data. ivybridge
ffmpeg FFmpeg: ivybridge, x86_64
fftw fftw: Discrete Fourier Transform library ivybridge, x86_64, zen Yes
fsl fsl: the FMRIB Software Library ivybridge
fun3d fun3d: FUN3d (Fully Unstructured Navier-Stokes) CFD suite skylake_avx512
gaussian Gaussian: Software for electronic structure modeling sandybridge
gcam GCAM: The Global Change Analysis Model ivybridge Yes
gcc gcc: GNU Compiler Suite x86_64
gdb gdb: GNU Project Debugger ivybridge Yes
geos geos: C++ Geometry Engine Open Source ivybridge
gloo gloo: Gloo collective communications package ivybridge, x86_64, zen
gnuplot gnuplot: command-line driven graphing utility ivybridge, x86_64
go go: Go programming language ivybridge, x86_64
gromacs gromacs: Chemical simulation/Molecular dynamics package ivybridge Yes
gsl gsl: GNU Scientific Library ivybridge, x86_64, zen
h5utils h5utils: Utilities for visualization/conversion of HDF5 data ivybridge, x86_64, zen
hdf-eos2 HDF-EOS2: HDF for Earth Observing System (hdf4) ivybridge
hdf-eos5 HDF-EOS5: HDF for Earth Observing System (hdf5) ivybridge Yes
hdf4 hdf4: Libraries for Hierarchical Data Format v4 ivybridge, x86_64, zen
hdf5 hdf5: Libraries for Hierarchical Data Format v5 ivybridge, x86_64, zen Yes
hector hector: Simple Global Climate Carbon-Cycle model ivybridge Yes
hello-umd hello-umd: Simple Hello world binary ivybridge Yes
hisat2 hisat2: graph-based alignment of next generation sequencing reads to a population of genomes ivybridge
hmmer hmmer: biosequence analyser using profile hidden Markov models ivybridge, x86_64 Yes
hpcc hpcc: Default env setting for the various clusters x86_64
deepthought2 deepthought2: Default env setting for the Deepthought2 (DT2) cluster x86_64
jn jn: Default env setting for the Juggernaut (JN) cluster x86_64
hpctoolkit hpctoolkit: toolkit for performance measurement and analysis ivybridge, x86_64 Yes
hpx hpx: C++ runtime for parallel and distributed applications ivybridge Yes
hypre hypre: Scalable Linear Solvers and Multigrid Methods ivybridge Yes
igv igv: Integrative Genomics Viewer ivybridge
intel Intel: Intel Parallel Studio collection (compilers, MPI, tools, etc) x86_64
intel-tbb intel-tbb: Intel Threaded Building Blocks ivybridge, x86_64, zen
ioapi ioapi: Models-3/EDSS Input/Output Applications Programming Interface ivybridge Yes
jasper jasper: Library for manipulating JPEG-2000 images ivybridge, x86_64
jellyfish jellyfish: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. ivybridge
json-c JSON-C: JSON library implemented in C ivybridge, x86_64
jsoncpp JsonCpp: JSON library implemented in C++ ivybridge, x86_64
julia julia: Julia programming language: A fresh approach to technical computing ivybridge
jupyter jupyter: The Jupyter Notebook application ivybridge
kahip kahip: Karlsruhe High Quality Graph Partitioning Framework ivybridge, x86_64 Yes
kallisto kallisto: Program for RNA-sequence quantification ivybridge, x86_64 Yes
lammps lammps: LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator ivybridge
latte latte: Open source density functional tight binding molecular dynamics. ivybridge Yes
lftp lftp: multiprotocolfile transfer program ivybridge
libint libint: library to evaluate molecular integrals ivybridge Yes
libvdwxc Libvdwxc: library for vdW-DF exchange-correlation functionals ivybridge Yes
libxsmm LIBXSMM: library for specialized dense and sparse matrix operations ivybridge
libzmq libzmq: ZeroMQ networking/concurrency library and core API ivybridge, x86_64
lz4 lz4: Lossless compression utility and library ivybridge, x86_64, zen
magics magics: meteorological plotting software ivybridge, x86_64 Yes
magma magma: Matrix Algebra on GPU and Multicore Architectures ivybridge, x86_64, zen Yes
mathematica Mathematica: Mathematica symbolic and computational mathematics package. x86_64
matio matio: MATLAB MAT file I/O library ivybridge, x86_64, zen Yes
matlab matlab: Matlab numerical computing environment x86_64
matplotlib matplotlib: Open-source software library for creating visualizations in Python ivybridge, x86_64
mercurial mercurial: Mercurial source control management system ivybridge
metis metis: Metis unstructured graph partitioner ivybridge, x86_64, zen
mgridgen mgridgen: Multilevel Serial & Parallel Coarse Grid Construction Library ivybridge, x86_64 Yes
mt-metis mt-metis: Metis unstructured graph partitioner ivybridge, x86_64, zen
mumps mumps: MUltifrontal Massively Parallel sparse direct Solver ivybridge, x86_64 Yes
namd NAMD: Nanoscale Molecular Dynamics ivybridge Yes
ncl NCL: NCAR Command Language ivybridge Yes
nco nco: Toolkits for manipulating data in NetCDF formats ivybridge Yes
ncview ncview: Viewer for NetCDF files ivybridge Yes
netcdf netcdf: C Libraries for NetCDF data format ivybridge, x86_64, zen Yes
netcdf-cxx netcdf-cxx: C++ Libraries for NetCDF data format ivybridge, zen
netcdf-fortran netcdf-fortran: Fortran Libraries for NetCDF data format ivybridge, zen Yes
nvhpc nvhpc: Nvidia HPC SDK Compiler suite x86_64
openblas openblas: Optimized BLAS libraries ivybridge, x86_64, zen
opencv opencv: Open-source Computer Vision Library ivybridge, x86_64
openfoam openfoam: Opensource C++ CFD toolbox ivybridge Yes
openjdk openjdk: Open-source implementation of Java ivybridge, x86_64, zen
openmm openmm: A high-performance toolkit for molecular simulation. ivybridge Yes
openmpi openmpi: OpenMPI implementation of Message Passing Interface ivybridge, x86_64 Yes
osu-micro-benchmarks osu-micro-benchmarks: Microbenchmarks for MPI ivybridge, x86_64
parallel-netcdf parallel-netcdf: Parallel I/O library for NetCDF file format ivybridge, x86_64 Yes
paraview paraview: data analysis and visualization application ivybridge
pari-gp pari-gp: computer algebra system for computations in number theory ivybridge Yes
parmetis parmetis: Parallel Metis ivybridge, x86_64 Yes
parmgridgen ParMGridGen: Multilevel Serial & Parallel Coarse Grid Construction Library ivybridge, x86_64 Yes
perl perl: Perl scripting language ivybridge, x86_64, zen
petsc PETSc: PETSc (Portable, Extensible Toolkit for Scientific Computation) ivybridge Yes
pexsi PEXSI: electronic structure calculation based on Kohn-Sham density functional theory ivybridge Yes
pfft pfft: Parallel Fast Fourier Transform library ivybridge, x86_64 Yes
plink PLINK: genome association analysis toolset ivybridge
pointwise pointwise: Pointwise mesh generation software for CFD x86_64
popoolation2 popoolation2: PoPoolation2 allows to compare allele frequencies for single-nucleotide polymorphisms. ivybridge
povray POV-Ray: Persistence of Vision Ray tracer ivybridge
python python: Python scripting language ivybridge, x86_64
pytorch pytorch: Open-source machine learning library ivybridge, x86_64 Yes
qbox Qbox: first-principles molecular dynamics code. ivybridge Yes
qmd-progress qmd-progress: PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver ivybridge Yes
qnnpack qnnpack: Quantized Neural Networks PACKage ivybridge, x86_64, zen
quantum-espresso quantum-espresso: Electronic-structure calculations at the nanoscale. ivybridge Yes
r r: R statistical computing scripting language ivybridge, x86_64
rclone Rclone: command line tool for managing cloud storage ivybridge
rust rust: Rust programming language ivybridge
samtools samtools: SAM (Sequence/Alignment Mapping) Tools ivybridge
scalapack scalapack: Scalable linear algebra package ivybridge, x86_64 Yes
scons SCons: SCons open-source software construction tool ivybridge, x86_64
scorep scorep: suite for profiling, event tracing, and analysis of HPC applications ivybridge Yes
scotch scotch: Package for graph and mesh partitioning, graph clustering, and sparse matrix ordering ivybridge, x86_64 Yes
silo silo: libraries for reading/writing a variety of scientific data ivybridge, x86_64, zen Yes
singularity singularity: Singularity container utilities x86_64
sirius SIRIUS: domain specific library for electronic structure calculations ivybridge
spfft SpFFT: 3D FFT library for sparse frequency domain data ivybridge
spglib spglib: C library for finding and handling crystal symmetries ivybridge, zen
suite-sparse suite-sparse: Suite of Sparse Matrix algorithms ivybridge, x86_64, zen Yes
superlu superlu: Sparse Linear system solver (sequential) ivybridge, x86_64, zen
superlu-dist superlu-dist: Sparse Linear system solver (distributed mem/MPI) ivybridge, x86_64 Yes
superlu-mt superlu-mt: Sparse Linear system solver (multithreaded) ivybridge, x86_64, zen
swig swig: compiler to interface C/C++ libraries to Perl, Python, etc ivybridge, x86_64
sz sz: Error-bounded Lossy Compressor for HPC Data ivybridge, x86_64 Yes
tecplot360 Tecplot360: CFD visualization software x86_64
tensorflow tensorflow: Open-source software library for machine intelligence ivybridge, x86_64 Yes
tophat tophat: Spliced read mapper for RNA-Seq x86_64
trilinos Trilinos: Solvers collection including linear, non-linear, optimization, and transient solvers ivybridge Yes
trimmomatic trimmomatic: Trimming tool for Illumina NGS data. ivybridge
trinity trinity: trinity is a novel method to reconstruct transcriptomes for RNA-seq data. ivybridge Yes
hello-umd hello-umd: Simple Hello world binary ivybridge Yes
us3d us3d: Aeordynamic and Aerothermodynamic Simulations Software skylake_avx512, x86_64
vasp vasp: VASP: Vienna Ab-initio Simulation Package x86_64
virtualgl virtualgl: Toolkit to allow remote display to run OpenGL applications with full hardware acceleration ivybridge
visit visit: interactive, scalable, visualization, animation and analysis tool x86_64
vmd VMD: Visual Molecular Dynamics x86_64
voropp Voro++: library for 3D computations of the Voronoi tessellation ivybridge
vtk vtk: 3D computer graphics, image processing and visualization library ivybridge, x86_64 Yes
wannier90 Wannier90: tool to calculate maximally-localized Wannier functions ivybridge Yes
xerces-c xerces-c: validating XML parser in C++ ivybridge, x86_64
xssp xssp: Secondary structure assignments for entries in the Protein Data Bank ivybridge Yes
xz xz: Lossless compression utility and library ivybridge, x86_64, zen
zfp zfp: Library for lossy compression of multidimensional arrays ivybridge, x86_64, zen
zlib zlib: General purpose, patent-free compression ibrary ivybridge, sandybridge, x86_64, zen
zoltan zoltan: Toolkit for parallel combinatorial algorithms ivybridge, x86_64 Yes
zstd zstd: Fast, lossless compression algorithm ivybridge, x86_64, zen

All packages available on the Juggernaut cluster

This section lists all software packages available on the Juggernaut cluster

All packages available on the Juggernaut cluster
Package Name Description Supported CPUs GPU ready?
adios2 adios2: The Adapatble Input/Output System, version 2 skylake_avx512, x86_64, zen Yes
ansys ANSYS: Computer-aided engineering software x86_64
ansys-em ANSYSEM: Computer-aided engineering software for electromagnetic systems x86_64
ansys.old ANSYS: Computer-aided engineering software x86_64
arpack-ng arpack-ng: Fortran77 subroutines designed to solve large scale eigenvalue problems skylake_avx512, x86_64, zen, zen2 Yes
blast-plus blast-plus: Basic Local Alignment Search Tool skylake_avx512, x86_64, zen
bml bml: Basic Matrix Library skylake_avx512, x86_64, zen Yes
boost boost: free, portable C++ source libraries skylake_avx512, x86_64, zen, zen2 Yes
bzip2 bzip2: patent-free high quality data compression libraries skylake_avx512, x86_64, zen, zen2
c-blosc c-blosc: A blocking, shuffling, and loss-less compression library skylake_avx512, x86_64, zen, zen2
caffe caffe: Deep learning framework skylake_avx512, x86_64, zen
cfitsio cfitsio: Libraries for Flexible Image Transport System (FITS) data format skylake_avx512, x86_64, zen
cfour cfour: Software for quantum chemical modeling x86_64
cgal cgal: Computations Geometry Algorithms Library x86_64 Yes
cgns cgns: CFD General notation system skylake_avx512, x86_64, zen Yes
charm4py Charm4py: distributed/parallel programing framework for Python skylake_avx512, x86_64, zen Yes
charmpp Charm++: parallel programming framework in C++ skylake_avx512, x86_64, zen
cmake cmake: cross-platform, open-source build system skylake_avx512, x86_64, zen, zen2
cminpack cminpack: Library for solving nonlinear equations and nonlinear least squares problems skylake_avx512, x86_64, zen
cosma COSMA: Distributed Communication-Optimal Matrix-Matrix Multiplication Library x86_64 Yes
cuda cuda: parallel computing platform/programming model for NVIDIA GPUs skylake_avx512, x86_64, zen, zen2
cudnn cudnn: Library of deep learning/neural network primitives for GPUs skylake_avx512, x86_64, zen, zen2 Yes
curl curl: command line tool for transferring data skylake_avx512, x86_64, zen, zen2
dmtcp dmtcp: Distributed Multithreaded Checkpointing skylake_avx512, x86_64, zen, zen2
dplr dplr: Hypersonic Continuum CFD Code skylake_avx512, x86_64
dyninst dyninst: API for dynamic binary instrumentation skylake_avx512, x86_64, zen Yes
eccodes eccodes: Libraries for encoding/decoding weather related data formats skylake_avx512, x86_64, zen Yes
eigen eigen: C++ template library for matrix and vector operations, skylake_avx512, x86_64, zen
embree Embree: High performance ray tracing kernels x86_64
envi ENVI: ENVI software for processing and analyzing geospatial data x86_64
esmf esmf: The Earth System Modeling Framework skylake_avx512, x86_64, zen Yes
fastqc fastqc: quality control tool for high throughput sequence data. skylake_avx512
ffmpeg FFmpeg: skylake_avx512, x86_64, zen
fftw fftw: Discrete Fourier Transform library skylake_avx512, x86_64, zen Yes
fun3d fun3d: FUN3d (Fully Unstructured Navier-Stokes) CFD suite skylake_avx512
gcc gcc: GNU Compiler Suite x86_64 Yes
gdb gdb: GNU Project Debugger skylake_avx512, x86_64
geos geos: C++ Geometry Engine Open Source skylake_avx512, x86_64, zen
gloo gloo: Gloo collective communications package skylake_avx512, x86_64, zen, zen2
gnuplot gnuplot: command-line driven graphing utility skylake_avx512, x86_64, zen
go go: Go programming language skylake_avx512, x86_64, zen
gromacs gromacs: Chemical simulation/Molecular dynamics package x86_64 Yes
gsl gsl: GNU Scientific Library skylake_avx512, x86_64, zen, zen2
h5utils h5utils: Utilities for visualization/conversion of HDF5 data skylake_avx512, x86_64, zen, zen2
hdf-eos2 HDF-EOS2: HDF for Earth Observing System (hdf4) skylake_avx512, x86_64, zen, zen2
hdf-eos5 HDF-EOS5: HDF for Earth Observing System (hdf5) skylake_avx512, x86_64, zen Yes
hdf4 hdf4: Libraries for Hierarchical Data Format v4 skylake_avx512, x86_64, zen, zen2
hdf5 hdf5: Libraries for Hierarchical Data Format v5 skylake_avx512, x86_64, zen, zen2 Yes
hello-umd hello-umd: Simple Hello world binary skylake_avx512, x86_64, zen Yes
hmmer hmmer: biosequence analyser using profile hidden Markov models skylake_avx512, x86_64, zen Yes
hpcc hpcc: Default env setting for the various clusters x86_64
deepthought2 deepthought2: Default env setting for the Deepthought2 (DT2) cluster x86_64
jn jn: Default env setting for the Juggernaut (JN) cluster x86_64
hpctoolkit hpctoolkit: toolkit for performance measurement and analysis x86_64 Yes
hpx hpx: C++ runtime for parallel and distributed applications skylake_avx512, x86_64, zen Yes
hypre hypre: Scalable Linear Solvers and Multigrid Methods skylake_avx512, x86_64, zen
igv igv: Integrative Genomics Viewer skylake_avx512
intel Intel: Intel Parallel Studio collection (compilers, MPI, tools, etc) x86_64
intel-tbb intel-tbb: Intel Threaded Building Blocks skylake_avx512, x86_64, zen
jasper jasper: Library for manipulating JPEG-2000 images x86_64
jellyfish jellyfish: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. skylake_avx512, x86_64, zen
json-c JSON-C: JSON library implemented in C skylake_avx512, x86_64, zen
jsoncpp JsonCpp: JSON library implemented in C++ x86_64, zen
julia julia: Julia programming language: A fresh approach to technical computing skylake_avx512, x86_64, zen
jupyter jupyter: The Jupyter Notebook application x86_64
kahip kahip: Karlsruhe High Quality Graph Partitioning Framework skylake_avx512, x86_64, zen Yes
lammps lammps: LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator skylake_avx512, x86_64, zen
latte latte: Open source density functional tight binding molecular dynamics. skylake_avx512, x86_64, zen Yes
libint libint: library to evaluate molecular integrals skylake_avx512, x86_64, zen
libvdwxc Libvdwxc: library for vdW-DF exchange-correlation functionals skylake_avx512, x86_64, zen Yes
libxsmm LIBXSMM: library for specialized dense and sparse matrix operations skylake_avx512, x86_64, zen
libzmq libzmq: ZeroMQ networking/concurrency library and core API skylake_avx512, x86_64, zen
lz4 lz4: Lossless compression utility and library skylake_avx512, x86_64, zen, zen2
magics magics: meteorological plotting software skylake_avx512, x86_64, zen Yes
magma magma: Matrix Algebra on GPU and Multicore Architectures x86_64 Yes
matio matio: MATLAB MAT file I/O library skylake_avx512, x86_64, zen, zen2 Yes
matlab matlab: Matlab numerical computing environment x86_64
matplotlib matplotlib: Open-source software library for creating visualizations in Python x86_64
mercurial mercurial: Mercurial source control management system skylake_avx512, x86_64, zen
metis metis: Metis unstructured graph partitioner skylake_avx512, x86_64, zen, zen2
mgridgen mgridgen: Multilevel Serial & Parallel Coarse Grid Construction Library skylake_avx512, x86_64, zen Yes
mt-metis mt-metis: Metis unstructured graph partitioner skylake_avx512, x86_64, zen2
mumps mumps: MUltifrontal Massively Parallel sparse direct Solver skylake_avx512, x86_64, zen Yes
namd NAMD: Nanoscale Molecular Dynamics skylake_avx512, x86_64, zen
nco nco: Toolkits for manipulating data in NetCDF formats skylake_avx512, x86_64 Yes
netcdf netcdf: C Libraries for NetCDF data format skylake_avx512, x86_64, zen, zen2 Yes
netcdf-cxx netcdf-cxx: C++ Libraries for NetCDF data format skylake_avx512, x86_64, zen2
netcdf-fortran netcdf-fortran: Fortran Libraries for NetCDF data format skylake_avx512, x86_64, zen, zen2 Yes
nvhpc nvhpc: Nvidia HPC SDK Compiler suite x86_64
nvmpi nvmpi: MPI libraries from the Nvidia HPC SDK Compiler suite x86_64
openblas openblas: Optimized BLAS libraries skylake_avx512, x86_64, zen
openfoam openfoam: Opensource C++ CFD toolbox x86_64 Yes
openjdk openjdk: Open-source implementation of Java skylake_avx512, x86_64, zen
openmpi openmpi: OpenMPI implementation of Message Passing Interface skylake_avx512, x86_64, zen Yes
osu-micro-benchmarks osu-micro-benchmarks: Microbenchmarks for MPI skylake_avx512, x86_64, zen
parallel-netcdf parallel-netcdf: Parallel I/O library for NetCDF file format skylake_avx512, x86_64, zen Yes
paraview paraview: data analysis and visualization application x86_64
parmetis parmetis: Parallel Metis skylake_avx512, x86_64, zen Yes
parmgridgen ParMGridGen: Multilevel Serial & Parallel Coarse Grid Construction Library skylake_avx512, x86_64, zen Yes
perl perl: Perl scripting language skylake_avx512, x86_64, zen, zen2
petsc PETSc: PETSc (Portable, Extensible Toolkit for Scientific Computation) skylake_avx512, x86_64, zen Yes
pexsi PEXSI: electronic structure calculation based on Kohn-Sham density functional theory skylake_avx512, x86_64, zen Yes
pfft pfft: Parallel Fast Fourier Transform library skylake_avx512, x86_64, zen Yes
pointwise pointwise: Pointwise mesh generation software for CFD x86_64
povray POV-Ray: Persistence of Vision Ray tracer skylake_avx512, x86_64
python python: Python scripting language skylake_avx512, x86_64, zen
qmd-progress qmd-progress: PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver skylake_avx512, x86_64, zen Yes
qnnpack qnnpack: Quantized Neural Networks PACKage skylake_avx512, x86_64
rclone Rclone: command line tool for managing cloud storage x86_64
rust rust: Rust programming language skylake_avx512, x86_64, zen
samtools samtools: SAM (Sequence/Alignment Mapping) Tools skylake_avx512, x86_64, zen
scalapack scalapack: Scalable linear algebra package skylake_avx512, x86_64, zen Yes
scons SCons: SCons open-source software construction tool skylake_avx512, x86_64, zen
scotch scotch: Package for graph and mesh partitioning, graph clustering, and sparse matrix ordering skylake_avx512, x86_64, zen Yes
silo silo: libraries for reading/writing a variety of scientific data skylake_avx512, x86_64, zen, zen2 Yes
singularity singularity: Singularity container utilities skylake_avx512, x86_64, zen
sirius SIRIUS: domain specific library for electronic structure calculations x86_64
spfft SpFFT: 3D FFT library for sparse frequency domain data skylake_avx512, x86_64, zen
spglib spglib: C library for finding and handling crystal symmetries skylake_avx512, x86_64, zen2
suite-sparse suite-sparse: Suite of Sparse Matrix algorithms skylake_avx512, x86_64, zen Yes
superlu superlu: Sparse Linear system solver (sequential) skylake_avx512, x86_64
superlu-dist superlu-dist: Sparse Linear system solver (distributed mem/MPI) skylake_avx512, x86_64, zen
superlu-mt superlu-mt: Sparse Linear system solver (multithreaded) skylake_avx512, x86_64
swig swig: compiler to interface C/C++ libraries to Perl, Python, etc skylake_avx512, x86_64, zen
sz sz: Error-bounded Lossy Compressor for HPC Data skylake_avx512, x86_64, zen Yes
tecplot360 Tecplot360: CFD visualization software x86_64
tophat tophat: Spliced read mapper for RNA-Seq x86_64
trilinos Trilinos: Solvers collection including linear, non-linear, optimization, and transient solvers skylake_avx512, x86_64, zen Yes
hello-umd hello-umd: Simple Hello world binary skylake_avx512, x86_64, zen Yes
us3d us3d: Aeordynamic and Aerothermodynamic Simulations Software skylake_avx512, x86_64
vasp vasp: VASP: Vienna Ab-initio Simulation Package x86_64
virtualgl virtualgl: Toolkit to allow remote display to run OpenGL applications with full hardware acceleration x86_64
visit visit: interactive, scalable, visualization, animation and analysis tool x86_64
voropp Voro++: library for 3D computations of the Voronoi tessellation skylake_avx512, x86_64, zen
vtk vtk: 3D computer graphics, image processing and visualization library x86_64, zen Yes
wannier90 Wannier90: tool to calculate maximally-localized Wannier functions skylake_avx512, x86_64, zen Yes
xerces-c xerces-c: validating XML parser in C++ skylake_avx512, x86_64, zen
xssp xssp: Secondary structure assignments for entries in the Protein Data Bank skylake_avx512, x86_64, zen Yes
xz xz: Lossless compression utility and library skylake_avx512, x86_64, zen, zen2
zfp zfp: Library for lossy compression of multidimensional arrays skylake_avx512, x86_64, zen Yes
zlib zlib: General purpose, patent-free compression ibrary skylake_avx512, x86_64, zen, zen2
zoltan zoltan: Toolkit for parallel combinatorial algorithms skylake_avx512, x86_64, zen Yes
zstd zstd: Fast, lossless compression algorithm skylake_avx512, x86_64, zen, zen2

Packages installed for scripting languages

WARNING
Note: We are in the process of integrating the software documentation for the RHEL6 and RHEL8 environments on the Deepthought2 cluster and the RHEL7 environment on Juggernaut. This page mainly shows the RHEL7 and RHEL8 software, and we are in the process of migrating content from the old, RHEL6 software pages to the current pages. This process will be ongoing over fall of 2020. While this migration is underway, you might wish to check the old pages as well as the current pages.

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 most cases, the packages/modules are fairly lightweight, and we simply install them into the standard system directory location for the particular scripting language, upgrading them as needed. This means that they will just be found when you import/use/etc them; no additional work is needed on your part.

For a few cases, they are major packages in their own right, and we give them their own module. Those packages are included in the lists of software earlier in this document, and you will need to "module load" the appropriate package in order to use them.

This section is for the packages of the first type, and for the convenience of our users we provide a list of the packages/modules available for each install of a scripting language, by cluster and version. Note: that these lists do not include the standard library for the scripting language, i.e. those packages/modules that get included automatically in the installation of the scripting language, only those that need to be installed separately.

WARNING
These sections are still under development. We hope to have it more accurate in the near future.
  1. Modules/packages for Python
  2. Modules/packages for R
  3. Modules/packages for Perl

Packages/modules for Python by cluster, version

Extensions for Python version 3.7.7 (built for gcc@8.4.0 on Deepthought2

Available extensions for Python version 3.7.7 (built for gcc@8.4.0 on Deepthought2
Extension name Version
gdal 3.1.0
otf2 2.2
absl-py 0.7.1
alabaster 0.7.12
asn1crypto 0.24.0
astunparse 1.6.3
atomicwrites 1.3.0
attrs 19.3.0
babel 2.7.0
backcall 0.1.0
biopython 1.73
bleach 3.1.0
blinker 1.4
boto3 1.10.44
botocore 1.13.44
bottleneck 1.2.1
cached-property 1.5.1
cachetools 3.1.1
certifi 2019.9.11
cffi 1.13.0
cftime 1.0.3.4
chardet 3.0.4
click 7.0
cloudpickle 1.2.1
cmake 3.16.5
cryptography 2.7
cvxpy 1.0.25
cycler 0.10.0
cython 0.29.16
dargs 0.2.5
dask 2.16.0
decorator 4.4.2
deeptoolsintervals 0.1.9
defusedxml 0.6.0
dill 0.3.1
distributed 2.10.0
docutils 0.15.2
ecos 2.0.7.post1
entrypoints 0.3
envmodules 0.1
flake8 3.7.8
fsspec 0.7.3
funcsigs 1.0.2
fury 0.6.1
future 0.17.1
gast 0.3.3
google-auth-oauthlib 0.4.1
google-auth 1.6.3
google-pasta 0.1.8
greenlet 0.4.13
griddataformats 0.5.0
grpcio 1.27.2
gsd 1.9.3
h5py 2.10.0
heapdict 1.0.1
hypothesis 4.57.1
idna 2.8
imagesize 1.1.0
importlib-metadata 1.2.0
ipykernel 5.1.0
ipython-genutils 0.2.0
ipython 7.3.0
ipywidgets 7.5.1
jinja2 2.10.3
jmespath 0.9.4
joblib 0.14.0
jsonschema 3.0.1
jupyter-client 5.3.4
jupyter-console 6.1.0
jupyter-core 4.6.3
keras-preprocessing 1.1.0
kiwisolver 1.1.0
kwant 1.4.2
llvmlite 0.34.0
locket 0.2.0
m2r 0.2.1
mako 1.0.4
markdown 3.1.1
markupsafe 1.1.1
mccabe 0.6.1
mistune 0.8.4
mmtf-python 1.1.2
mock 3.0.5
monty 0.9.6
more-itertools 7.2.0
mpi4py 3.0.3
mpmath 1.1.0
msgpack 0.6.2
multiprocess 0.70.9
nbconvert 5.6.0
nbformat 4.4.0
netcdf4 1.5.3
networkx 2.4
nibabel 3.2.1
nltk 3.5
nose 1.3.7
notebook 6.0.3
numba 0.51.1
numexpr 2.7.0
numpy 1.18.4
numpydoc 0.6.0
oauthlib 3.1.0
opt-einsum 3.1.0
osqp 0.6.1
owslib 0.17.1
packaging 19.2
palettable 3.3.0
pandas 1.0.3
pandocfilters 1.4.2
partd 1.1.0
patsy 0.5.1
pexpect 4.7.0
pickleshare 0.7.5
pillow 7.0.0
pip 19.3
pkgconfig 1.5.1
plotly 2.2.0
pluggy 0.13.0
prometheus-client 0.7.1
prompt-toolkit 2.0.9
protobuf 3.11.2
psutil 5.6.3
ptyprocess 0.6.0
py2bit 0.2.1
py 1.8.0
pyasn1-modules 0.2.6
pyasn1 0.4.6
pybigwig 0.3.18
pybind11 2.5.0
pycodestyle 2.5.0
pycparser 2.19
pydicom 2.1.2
pydispatcher 2.0.5
pyepsg 0.3.2
pyfftw 0.12.0
pyflakes 2.1.1
pygments 2.4.2
pyjwt 1.7.1
pylibjpeg 1.1.1
pymumps 0.3.2
pyparsing 2.4.2
pyproj 2.6.0
pyrsistent 0.15.7
pyshp 2.1.0
pytest 5.2.1
python-dateutil 2.8.0
pytz 2019.3
pywavelets 0.5.2
pyyaml 5.3.1
pyzmq 18.1.0
regex 2019.11.1
requests-oauthlib 1.2.0
requests 2.22.0
rsa 4.0
s3transfer 0.2.1
scikit-build 0.10.0
scikit-learn 0.23.0
scipy 1.4.1
scs 2.1.1-2
send2trash 1.5.0
setuptools-scm 3.3.3
setuptools 46.1.3
shapely 1.7.0
simplegeneric 0.8.1
sip 4.19.24
six 1.14.0
snowballstemmer 2.0.0
sortedcontainers 2.1.0
spams 2.6.2.5
spglib 1.9.9.18
sphinx-rtd-theme 0.4.3
sphinx 3.0.0
sphinxcontrib-applehelp 1.0.1
sphinxcontrib-devhelp 1.0.1
sphinxcontrib-htmlhelp 1.0.2
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-programoutput 0.15
sphinxcontrib-qthelp 1.0.2
sphinxcontrib-serializinghtml 1.1.3
statsmodels 0.10.2
sympy 1.4
tables 3.6.1
tabulate 0.8.6
tblib 1.6.0
termcolor 1.1.0
terminado 0.8.2
testpath 0.4.2
threadpoolctl 2.0.0
tinyarray 1.2.3
toolz 0.9.0
tornado 6.0.3
tqdm 4.45.0
traitlets 4.3.3
transforms3d 0.3.1
twisted 15.4.0
urllib3 1.25.6
vermin 0.10.0
versioneer 0.18
voluptuous 0.11.7
wcwidth 0.1.7
webencodings 0.5.1
werkzeug 0.16.0
wheel 0.33.4
widgetsnbextension 3.5.1
wrapt 1.11.2
xarray 0.14.0
zict 1.0.0
zipp 0.6.0
scorep 6.0
vtk 8.1.2

Extensions for Python version 2.7.16 (built for gcc@8.4.0 on Deepthought2

Available extensions for Python version 2.7.16 (built for gcc@8.4.0 on Deepthought2
Extension name Version
backports-functools-lru-cache 1.5
cached-property 1.5.1
cycler 0.10.0
h5py 2.10.0
kiwisolver 1.1.0
mako 1.0.4
markupsafe 1.1.1
matplotlib 2.2.5
mpi4py 3.0.3
numpy 1.16.6
pillow 6.2.2
pyparsing 2.4.2
python-dateutil 2.8.0
pytz 2019.3
scipy 1.2.3
setuptools-scm 3.3.3
setuptools 44.1.0
six 1.14.0
subprocess32 3.5.4

Extensions for Python version 3.7.7 (built for gcc@8.4.0 on Juggernaut

Available extensions for Python version 3.7.7 (built for gcc@8.4.0 on Juggernaut
Extension name Version
alabaster 0.7.12
asn1crypto 0.24.0
babel 2.7.0
boto3 1.17.27
botocore 1.20.27
bottleneck 1.2.1
cached-property 1.5.2
cachetools 3.1.1
certifi 2020.6.20
cffi 1.14.3
cftime 1.0.3.4
chardet 3.0.4
cryptography 2.7
cython 0.29.22
decorator 4.4.2
docutils 0.15.2
ecos 2.0.7.post1
entrypoints 0.3
envmodules 0.1
flake8 3.7.8
future 0.17.1
gensim 3.8.3
google-api-core 1.14.2
google-auth 1.6.3
google-cloud-core 1.0.3
google-cloud-storage 1.18.0
google-resumable-media 0.3.2
googleapis-common-protos 1.6.0
greenlet 0.4.17
h5py 2.10.0
idna 2.8
imagesize 1.1.0
ipython-genutils 0.2.0
jedi 0.17.2
jinja2 2.10.3
jmespath 0.10.0
joblib 1.0.1
llvmlite 0.34.0
mako 1.0.4
markupsafe 1.1.1
mccabe 0.6.1
mpi4py 3.0.3
mpmath 1.1.0
netcdf4 1.5.3
numba 0.51.1
numexpr 2.7.2
numpy 1.18.4
packaging 19.2
pandas 1.0.3
parso 0.7.1
patsy 0.5.1
pexpect 4.7.0
pickleshare 0.7.5
pip 19.3
pkgconfig 1.5.1
prompt-toolkit 2.0.10
protobuf 3.11.2
ptyprocess 0.6.0
pyasn1-modules 0.2.6
pyasn1 0.4.6
pybind11 2.5.0
pycodestyle 2.5.0
pycparser 2.20
pyflakes 2.1.1
pygments 2.6.1
pymumps 0.3.2
pyopenssl 19.0.0
pyparsing 2.4.7
pysocks 1.7.1
pytest-runner 5.1
python-dateutil 2.8.1
pytz 2020.1
qsymm 1.2.7
requests 2.24.0
rsa 4.0
s3transfer 0.3.4
scikit-learn 0.23.0
scipy 1.4.1
setuptools-scm 4.1.2
setuptools 50.3.2
sip 4.19.21
six 1.15.0
smart-open 1.10.0
snowballstemmer 2.0.0
sphinx 3.0.0
sphinxcontrib-applehelp 1.0.1
sphinxcontrib-devhelp 1.0.1
sphinxcontrib-htmlhelp 1.0.2
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.2
sphinxcontrib-serializinghtml 1.1.3
statsmodels 0.10.2
sympy 1.4
tables 3.6.1
theano 1.0.4
threadpoolctl 2.0.0
tinyarray 1.2.3
toml 0.10.2
traitlets 5.0.4
urllib3 1.25.6
wcwidth 0.1.7

Packages/modules for R by cluster, version

Extensions for R version 3.6.3 (built for gcc@8.4.0 on Deepthought2

Available extensions for R version 3.6.3 (built for gcc@8.4.0 on Deepthought2
Extension name Version
acepack 1.4.1
amap 0.8-17
annotate 1.62.0
annotationdbi 1.46.1
ape 5.3
argparse 2.0.1
askpass 1.1
assertthat 0.2.1
backports 1.1.4
base64enc 0.1-3
bayesm 3.1-3
bh 1.72.0-2
biasedurn 1.07
biobase 2.44.0
biocgenerics 0.30.0
biocparallel 1.18.1
biomart 2.40.5
biostrings 2.52.0
bit64 0.9-7
bit 1.1-14
bitops 1.0-6
blob 1.2.0
boot 1.3-23
brew 1.0-6
broom 0.5.2
callr 3.4.3
catools 1.17.1.2
cellranger 1.1.0
checkmate 1.9.4
class 7.3-15
cli 2.0.2
clipr 0.7.0
clisymbols 1.2.0
cluster 2.1.0
codetools 0.2-16
colorspace 1.4-1
commonmark 1.7
crayon 1.3.4
crosstalk 1.0.0
ctc 1.58.0
curl 4.3
data-table 1.12.2
dbi 1.1.0
dbplyr 1.4.2
delayedarray 0.10.0
desc 1.2.0
deseq2 1.24.0
devtools 2.1.0
digest 0.6.25
dplyr 0.8.3
edger 3.26.8
ellipsis 0.3.0
evaluate 0.14
fansi 0.4.0
fastcluster 1.1.25
findpython 1.0.5
float 0.2-4
forcats 0.4.0
forecast 8.8
foreign 0.8-72
formatr 1.7
formula 1.2-3
fracdiff 1.4-2
fs 1.3.1
futile-logger 1.4.3
futile-options 1.0.1
gdata 2.18.0
genefilter 1.66.0
genelendatabase 1.20.0
geneplotter 1.62.0
generics 0.0.2
genomeinfodb 1.20.0
genomeinfodbdata 1.2.1
genomicalignments 1.20.1
genomicfeatures 1.36.4
genomicranges 1.36.1
getopt 1.20.3
ggdendro 0.1-20
ggplot2 3.2.0
gh 1.0.1
git2r 0.27.1
glimma 1.12.0
glue 1.4.0
go-db 3.4.1
goplot 1.0.2
goseq 1.36.0
gplots 3.0.1.1
gridextra 2.3
gsl 2.1-6
gtable 0.3.0
gtools 3.8.1
haven 2.1.1
highr 0.8
hmisc 4.2-0
hms 0.5.0
htmltable 1.13.1
htmltools 0.3.6
htmlwidgets 1.3
httpuv 1.5.1
httr 1.4.1
ini 0.3.1
iranges 2.18.3
irdisplay 0.7.0
irkernel master
jsonlite 1.6.1
kernsmooth 2.23-15
knitr 1.28
labeling 0.3
lambda-r 1.2.3
later 0.8.0
lattice 0.20-38
latticeextra 0.6-28
lazyeval 0.2.2
limma 3.40.6
lmtest 0.9-37
locfit 1.5-9.1
lubridate 1.7.4
magrittr 1.5
manipulatewidget 0.10.0
markdown 1.1
mass 7.3-51.5
matrix 1.2-17
matrixstats 0.55.0
memoise 1.1.0
metaskat 0.81
mgcv 1.8-28
mime 0.7
miniui 0.1.1.1
modelr 0.1.5
munsell 0.5.0
ncdf4 1.16.1
nlme 3.1-141
nnet 7.3-12
openssl 1.4.1
optparse 1.6.2
pbdbase 0.5-0
pbddmat 0.5-0
pbdml 0.1-1
pbdmpi 0.4-3
pbdslap 0.2-4
pbdxgb 0.90.0.2
pbdzmq 0.3-3
pillar 1.4.2
pkgbuild 1.0.8
pkgconfig 2.0.2
pkgload 1.0.2
plogr 0.2.0
plyr 1.8.4
praise 1.0.0
prettyunits 1.0.2
processx 3.4.1
progress 1.2.2
promises 1.0.1
ps 1.3.0
purrr 0.3.4
quadprog 1.5-7
quantmod 0.4-15
qvalue 2.16.0
r6 2.4.0
randomforest 4.6-14
rcmdcheck 1.3.3
rcolorbrewer 1.1-2
rcpp 1.0.4.6
rcpparmadillo 0.9.600.4.0
rcppeigen 0.3.3.5.0
rcppparallel 4.4.3
rcurl 1.98-1.2
readr 1.3.1
readxl 1.3.1
rematch 1.0.1
remotes 2.1.1
repr 1.0.1
reprex 0.3.0
reshape2 1.4.3
rgdal 1.4-4
rgl 0.100.26
rhtslib 1.18.1
rlang 0.4.6
rlecuyer 0.3-5
rmarkdown 1.14
rmpi 0.6-9
rots 1.12.0
roxygen2 7.1.0
rpart 4.1-15
rprojroot 1.3-2
rsamtools 2.2.1
rsqlite 2.1.2
rstudioapi 0.11
rth master
rtracklayer 1.44.4
rvest 0.3.4
s4vectors 0.22.1
scales 1.0.0
selectr 0.4-1
sessioninfo 1.1.1
shiny 1.3.2
skat 2.0.1
sm 2.2-5.6
snow 0.4-3
sourcetools 0.1.7
sp 1.3-1
spatest 3.1.2
squarem 2021.1
stringi 1.4.3
stringr 1.4.0
summarizedexperiment 1.14.1
survival 2.44-1.1
sys 3.2
testthat 2.3.2
tibble 2.1.3
tidyr 0.8.3
tidyselect 0.2.5
tidyverse 1.2.1
timedate 3043.102
tinytex 0.15
tseries 0.10-47
ttr 0.23-4
urca 1.3-0
usethis 1.5.1
utf8 1.1.4
uuid 0.1-2
vctrs 0.2.0
viridis 0.5.1
viridislite 0.3.0
webshot 0.5.1
whisker 0.3-2
withr 2.2.0
xfun 0.8
xgboost 0.90.0.2
xml2 1.3.2
xml 3.98-1.20
xopen 1.0.0
xtable 1.8-4
xts 0.11-2
xvector 0.24.0
yaml 2.2.0
zeallot 0.1.0
zlibbioc 1.30.0
zoo 1.8-6

Packages/modules for Perl by cluster, version

Extensions for Perl version 5.30.1 (built for gcc@8.4.0 on Deepthought2

Available extensions for Perl version 5.30.1 (built for gcc@8.4.0 on Deepthought2
Extension name Version
bioperl 1.7.6
db-file 1.840
encode-locale 1.05
extutils-config 0.008
extutils-helpers 0.026
extutils-installpaths 0.012
file-listing 6.04
html-parser 3.72
html-tagset 3.20
http-cookies 6.04
http-daemon 6.01
http-date 6.02
http-message 6.13
http-negotiate 6.01
io-html 1.001
io-tty 1.13_01
libwww-perl 6.33
lwp-mediatypes 6.02
module-build-tiny 0.039
module-build 0.4224
net-http 6.17
readonly 2.05
test-needs 0.002005
try-tiny 0.28
uri 1.72
www-robotrules 6.02
xml-dom-xpath 0.14
xml-parser 2.44
xml-xpathengine 0.14