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 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.
|
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 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/1.8.13Both 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/sharedWe 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.
|
|
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 . ~/.bashrc
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:
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 /)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.
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.
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/2013bAlthough 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.
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. Note that all packages, much less all versions of all packages, are not necessarily available on all clusters, so please verify that te package and/or version of the package you need is available on the cluster you intend to use.
This section list all installed research software, unsorted by field of research/category/etc.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| abaqus | Abaqus: Finite-element analysis/Computer-aided engineering software | x86_64 | |
| adios2 | adios2: The Adapatble Input/Output System, version 2 | zen, zen2 | |
| amdblis | amdblis: AMD Optimized BLAS libraries | zen2 | |
| amdfftw | amdfftw: AMD Discrete Fourier Transform library | zen2 | Yes |
| amdlibflame | amdlibflame: AMD Optimized BLAS libraries | zen2 | |
| amdlibm | amdlibm: AMD Optimized BLAS libraries | zen2 | |
| amdscalapack | amdscalapack: AMD Optimized Scalable linear algebra package | zen2 | 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 | |
| aocc | aocc: AMD Optimizing Compiler Suite | x86_64 | |
| aocl-sparse | aocl-sparse: Suite of Sparse Matrix algorithms | zen2 | |
| armadillo | armadillo: Linear algebra library for C++ | zen2 | |
| arpack-ng | arpack-ng: Fortran77 subroutines designed to solve large scale eigenvalue problems | x86_64, zen, zen2 | Yes |
| bamtools | BamTools: Command line toolkit for dealing with BAM files | zen, zen2 | |
| bcftools | bcftools: BCFtools is a set of utilities that manipulate variant calls | zen2 | Yes |
| bedtools2 | bedtools2: swiss-army knife of genomics analysis tasks | zen2 | |
| blast-plus | blast-plus: Basic Local Alignment Search Tool | zen, zen2 | |
| bml | bml: Basic Matrix Library | zen, zen2 | Yes |
| boost | boost: free, portable C++ source libraries | zen, zen2 | Yes |
| bowtie | bowtie: ultrafast sequence aligner | zen2 | |
| bowtie2 | bowtie2: ultrafast sequence aligner | zen2 | |
| bwa | bwa: Burrows-Wheeler Aligner | zen2 | |
| bzip2 | bzip2: patent-free high quality data compression libraries | x86_64, zen, zen2 | |
| c-blosc | c-blosc: A blocking, shuffling, and loss-less compression library | zen, zen2 | |
| caffe | caffe: Deep learning framework | zen, zen2 | |
| cdo | cdo: Climate Data Operators | zen2 | Yes |
| cfitsio | CFITSIO: Libraries for Flexible Image Transport System (FITS) data format | zen, zen2 | |
| cfour | cfour: Software for quantum chemical modeling | x86_64 | |
| cgal | cgal: Computations Geometry Algorithms Library | zen, zen2 | Yes |
| cgns | cgns: CFD General notation system | x86_64, zen, zen2 | Yes |
| charm4py | Charm4py: distributed/parallel programing framework for Python | zen, zen2 | Yes |
| charmm | charmm: Chemistry at HARvard Macromolecular Mechanics. | zen2 | Yes |
| charmpp | Charm++: parallel programming framework in C++ | x86_64, zen, zen2 | |
| cmake | cmake: cross-platform, open-source build system | x86_64, zen, zen2 | |
| cmdstan | CmdStan: command line interface to Stan | zen2 | Yes |
| cminpack | cminpack: Library for solving nonlinear equations and nonlinear least squares problems | zen, zen2 | |
| comsol | Comsol: General-purpose simulation software | x86_64 | |
| cosma | COSMA: Distributed Communication-Optimal Matrix-Matrix Multiplication Library | zen2 | Yes |
| cp2k | CP2K: quantum chemistry and solid state physics package | zen2 | |
| cuda | cuda: parallel computing platform/programming model for NVIDIA GPUs | x86_64, zen, zen2 | |
| cudnn | cudnn: Library of deep learning/neural network primitives for GPUs | x86_64, zen, zen2 | Yes |
| curl | curl: command line tool for transferring data | x86_64, zen, zen2 | |
| cython | cython: Compiler for writing C extensions for Python | zen, zen2 | |
| deepthought2 | deepthought2: Default env setting for the Deepthought2 (DT2) cluster | x86_64 | |
| dmtcp | dmtcp: Distributed Multithreaded Checkpointing | zen, zen2 | |
| dplr | dplr: Hypersonic Continuum CFD Code | skylake_avx512, x86_64 | |
| dyninst | dyninst: API for dynamic binary instrumentation | zen, zen2 | Yes |
| eccodes | eccodes: Libraries for encoding/decoding weather related data formats | zen, zen2 | Yes |
| eigen | eigen: C++ template library for matrix and vector operations, | zen, zen2 | |
| elpa | elpa: Eigenvalue solvers for Petaflop Applications | zen2 | |
| 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 | zen, zen2 | Yes |
| exonerate | Exonerate: generic tool for pairwise sequence comparison | zen2 | |
| fastqc | fastqc: quality control tool for high throughput sequence data. | zen2 | |
| fds | FDS: Fire Dynamics Simulator | x86_64 | |
| ffmpeg | FFmpeg: | zen, zen2 | |
| fftw | fftw: Discrete Fourier Transform library | x86_64, zen, zen2 | Yes |
| fribidi | FriBidi: Unicode Bidirectional Algorithm implementation | zen, zen2 | |
| fun3d | fun3d: FUN3d (Fully Unstructured Navier-Stokes) CFD suite | skylake_avx512 | |
| gaussian | Gaussian: Software for electronic structure modeling | x86_64 | |
| gcc | gcc: GNU Compiler Suite | x86_64, zen2 | Yes |
| gdal | gdal: Geospatial Data Abstraction Library | zen2 | Yes |
| gdb | gdb: GNU Project Debugger | skylake_avx512, x86_64 | |
| geos | geos: C++ Geometry Engine Open Source | zen, zen2 | |
| git-lfs | git-lfs: command line tool for managing cloud storage | zen2 | |
| gloo | gloo: Gloo collective communications package | skylake_avx512, x86_64, zen, zen2 | |
| gmp | gmp: GNU Multiple Precision Arithmetic Library | x86_64, zen, zen2 | |
| gnuplot | gnuplot: command-line driven graphing utility | zen, zen2 | |
| go | go: Go programming language | zen2 | |
| grads | grads: Grid Analysis and Display System | zen2 | |
| gromacs | gromacs: Chemical simulation/Molecular dynamics package | zen, zen2 | Yes |
| gsl | gsl: GNU Scientific Library | x86_64, zen, zen2 | |
| gssha | GSSHA: Gridded Surface/Subsurface Hydrologic Analysis | x86_64 | |
| gurobi | gurobi: Gurobi Optimizer for numerical programming | x86_64 | |
| h5utils | h5utils: Utilities for visualization/conversion of HDF5 data | zen2 | Yes |
| harfbuzz | HarfBuzz: Text shaping library | zen, zen2 | |
| hdf-eos2 | HDF-EOS2: HDF for Earth Observing System (hdf4) | zen, zen2 | |
| hdf-eos5 | HDF-EOS5: HDF for Earth Observing System (hdf5) | zen2 | Yes |
| hdf4 | hdf4: Libraries for Hierarchical Data Format v4 | x86_64, zen, zen2 | |
| hdf5 | hdf5: Libraries for Hierarchical Data Format v5 | x86_64, zen, zen2 | Yes |
| hello-umd | hello-umd: Simple Hello world binary | x86_64, zen, zen2 | Yes |
| hmmer | hmmer: biosequence analyser using profile hidden Markov models | x86_64, zen, zen2 | Yes |
| hpcc | hpcc: Default env setting for the various clusters | x86_64 | |
| hpctoolkit | hpctoolkit: toolkit for performance measurement and analysis | zen2 | Yes |
| hpl | hpl: High Performance Computing Linpack Benchmark | zen2 | Yes |
| hpx | hpx: C++ runtime for parallel and distributed applications | zen, zen2 | |
| hypre | HPYRE: Scalable Linear Solvers and Multigrid Methods | x86_64, zen2 | Yes |
| igv | igv: Integrative Genomics Viewer | zen2 | |
| impute2 | IMPUTE2: genotype imputatin and haplotype phasing tool | zen2 | |
| intel | Intel: Intel OneAPI Classic compilers | x86_64 | |
| intel-advisor | intel-advisor: Intel advisor performance analysis tool | zen2 | |
| intel-dal | intel-dal: Intel Data Analytics Library (DAL) | zen2 | |
| intel-dnn | intel-dnn: Intel Deep Neural Network Library | zen2 | |
| intel-dpl | intel-dpl: Intel Data Parallel C++ Library (DPL) | zen2 | |
| intel-inspector | intel-inspector: Intel Inspector memory, thread checking and debugging tool | zen2 | |
| intel-ipp | intel-ipp: Intel Integrated Performance Primitives (IPP) | zen2 | |
| intel-ippcp | intel-ippcp: Intel Integrated Performance Primitives Cryptography (IPP Crypto) | zen2 | |
| intel-mkl | intel-mkl: Intel Math Kernel Library (MKL/oneMKL) | zen2 | |
| intel-mpi | intel-mpi: Intel Message Passing Interface (MPI) Library | zen2 | |
| intel-tbb | intel-tbb: Intel Threaded Building Blocks | zen, zen2 | |
| intel-vpl | intel-vpl: Intel Video Processing Library (oneVPL) | zen2 | |
| intel-vtune | intel-vtune: Intel oneAPI VTune Profiler | zen2 | |
| ior | ior: Parallel IO benchmark | x86_64, zen2 | Yes |
| jasper | jasper: Library for manipulating JPEG-2000 images | zen2 | |
| jasper.test | jasper.test: Library for manipulating JPEG-2000 images | zen2 | |
| jellyfish | jellyfish: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. | zen, zen2 | |
| jn | jn: Default env setting for the Juggernaut (JN) cluster | x86_64 | |
| json-c | JSON-C: JSON library implemented in C | zen, zen2 | |
| jsoncpp | JsonCpp: JSON library implemented in C++ | zen, zen2 | |
| julia | julia: Julia programming language: A fresh approach to technical computing | zen2 | Yes |
| jupyter | jupyter: The Jupyter Notebook application | zen, zen2 | |
| kahip | kahip: Karlsruhe High Quality Graph Partitioning Framework | zen, zen2 | Yes |
| kallisto | kallisto: Program for RNA-sequence quantification | zen2 | |
| lammps | lammps: LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator | zen, zen2 | Yes |
| latte | latte: Open source density functional tight binding molecular dynamics. | zen, zen2 | Yes |
| libint | libint: library to evaluate molecular integrals | zen, zen2 | Yes |
| libpng | libpng: libpng is the official PNG reference library | zen, zen2 | |
| libvdwxc | Libvdwxc: library for vdW-DF exchange-correlation functionals | x86_64, zen, zen2 | Yes |
| libxsmm | LIBXSMM: library for specialized dense and sparse matrix operations | zen, zen2 | |
| libzmq | libzmq: ZeroMQ networking/concurrency library and core API | zen, zen2 | |
| lz4 | lz4: Lossless compression utility and library | x86_64, zen, zen2 | |
| magics | magics: meteorological plotting software | zen2 | Yes |
| magma | magma: Matrix Algebra on GPU and Multicore Architectures | zen2 | Yes |
| mathematica | Mathematica: Mathematica symbolic and computational mathematics package. | x86_64 | |
| matio | matio: MATLAB MAT file I/O library | zen, zen2 | Yes |
| matlab | matlab: Matlab numerical computing environment | x86_64 | |
| matplotlib | matplotlib: Open-source software library for creating visualizations in Python | zen, zen2 | Yes |
| mercurial | mercurial: Mercurial source control management system | zen2 | |
| metis | metis: Metis unstructured graph partitioner | x86_64, zen, zen2 | |
| mgridgen | mgridgen: Multilevel Serial & Parallel Coarse Grid Construction Library | x86_64, zen, zen2 | Yes |
| mt-metis | mt-metis: Metis unstructured graph partitioner | zen, zen2 | |
| mumps | mumps: MUltifrontal Massively Parallel sparse direct Solver | zen, zen2 | Yes |
| namd | NAMD: Nanoscale Molecular Dynamics | zen, zen2 | Yes |
| ncl | NCL: NCAR Command Language | zen2 | Yes |
| nco | nco: Toolkits for manipulating data in NetCDF formats | zen, zen2 | Yes |
| ncview | ncview: Viewer for NetCDF files | zen2 | Yes |
| netcdf | netcdf: C Libraries for NetCDF data format | x86_64, zen, zen2 | Yes |
| netcdf-cxx | netcdf-cxx: C++ Libraries for NetCDF data format | x86_64, zen, zen2 | Yes |
| netcdf-fortran | netcdf-fortran: Fortran Libraries for NetCDF data format | 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 | |
| oneapi | Intel: Intel OneAPI new compilers | x86_64 | |
| openblas | openblas: Optimized BLAS libraries | x86_64, zen, zen2 | |
| opencv | opencv: Open-source Computer Vision Library | zen2 | |
| openfoam | openfoam: Opensource C++ CFD toolbox | zen, zen2 | Yes |
| openjdk | openjdk: Open-source implementation of Java | x86_64, zen, zen2 | |
| openmm | openmm: A high-performance toolkit for molecular simulation. | zen2 | Yes |
| openmpi | openmpi: OpenMPI implementation of Message Passing Interface | x86_64, zen, zen2 | Yes |
| orca | ORCA: Ab initio quantum chemistry package | x86_64 | |
| osu-micro-benchmarks | osu-micro-benchmarks: Microbenchmarks for MPI | x86_64, zen, zen2 | |
| parallel-netcdf | parallel-netcdf: Parallel I/O library for NetCDF file format | x86_64, zen, zen2 | Yes |
| paraview | paraview: data analysis and visualization application | zen, zen2 | |
| paraview-headless | paraview-headless: data analysis and visualization application (headless version) | zen, zen2 | |
| pari-gp | pari-gp: computer algebra system for computations in number theory | zen2 | Yes |
| parmetis | parmetis: Parallel Metis | x86_64, zen, zen2 | Yes |
| parmgridgen | ParMGridGen: Multilevel Serial & Parallel Coarse Grid Construction Library | x86_64, zen, zen2 | Yes |
| perl | perl: Perl scripting language | x86_64, zen, zen2 | |
| petsc | PETSc: PETSc (Portable, Extensible Toolkit for Scientific Computation) | zen2 | |
| pexsi | PEXSI: electronic structure calculation based on Kohn-Sham density functional theory | x86_64, zen, zen2 | Yes |
| pfft | pfft: Parallel Fast Fourier Transform library | x86_64, zen, zen2 | Yes |
| pgplot | pgplot: PGPLOT Graphics Subroutine Library | zen2 | |
| plink | PLINK: genome association analysis toolset | zen2 | |
| plplot | plplot: Cross-platform software for creating scientific plots | zen2 | |
| plumed | PLUMED: plugin for molecular dynamics | zen, zen2 | Yes |
| pointwise | pointwise: Pointwise mesh generation software for CFD | x86_64 | |
| popoolation2 | popoolation2: PoPoolation2 allows to compare allele frequencies for single-nucleotide polymorphisms. | zen2 | |
| povray | POV-Ray: Persistence of Vision Ray tracer | zen, zen2 | |
| proj | proj: Generic Coordinate Transformation package | zen, zen2 | |
| python | python: Python scripting language | zen, zen2 | |
| pytorch | pytorch: Open-source machine learning library | zen2 | Yes |
| qmd-progress | qmd-progress: PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver | zen, zen2 | Yes |
| qnnpack | qnnpack: Quantized Neural Networks PACKage | skylake_avx512, x86_64 | |
| quantum-espresso | quantum-espresso: Electronic-structure calculations at the nanoscale. | zen2 | Yes |
| r | r: R statistical computing scripting language | zen2 | |
| rclone | Rclone: command line tool for managing cloud storage | zen2 | |
| rust | rust: Rust programming language | zen, zen2 | |
| samtools | samtools: SAM (Sequence/Alignment Mapping) Tools | zen, zen2 | |
| scalapack | scalapack: Scalable linear algebra package | x86_64, zen, zen2 | Yes |
| scons | SCons: SCons open-source software construction tool | zen2 | |
| scorep | scorep: suite for profiling, event tracing, and analysis of HPC applications | zen2 | Yes |
| scotch | scotch: Package for graph and mesh partitioning, graph clustering, and sparse matrix ordering | x86_64, zen, zen2 | Yes |
| shapeit4 | SHAPEIT4: estimation of haplotypes for sequencing data. | zen2 | |
| silo | silo: libraries for reading/writing a variety of scientific data | x86_64, zen, zen2 | Yes |
| singularity | singularity: Singularity container utilities | x86_64 | |
| sirius | SIRIUS: domain specific library for electronic structure calculations | zen, zen2 | |
| slepc | SLEPc: Scalable Library for Eigenvalue Problem Computations | zen2 | |
| smokeview | Smokeview: Visualization tool for FDS and CFAST output | x86_64 | |
| spfft | SpFFT: 3D FFT library for sparse frequency domain data | x86_64, zen, zen2 | |
| spglib | spglib: C library for finding and handling crystal symmetries | zen, zen2 | |
| suite-sparse | suite-sparse: Suite of Sparse Matrix algorithms | zen, zen2 | |
| superlu | superlu: Sparse Linear system solver (sequential) | zen, zen2 | |
| superlu-dist | superlu-dist: Sparse Linear system solver (distributed mem/MPI) | x86_64, zen, zen2 | |
| superlu-mt | superlu-mt: Sparse Linear system solver (multithreaded) | zen, zen2 | |
| swig | swig: compiler to interface C/C++ libraries to Perl, Python, etc | zen, zen2 | |
| sz | sz: Error-bounded Lossy Compressor for HPC Data | zen, zen2 | Yes |
| tecplot360 | Tecplot360: CFD visualization software | x86_64 | |
| tensorflow | tensorflow: Open-source software library for machine intelligence | zen, zen2 | Yes |
| tensorflowORIG | tensorflowORIG: Open-source software library for machine intelligence | zen, zen2 | |
| toolchain | toolchain: Compiler/library toolkits | x86_64 | |
| tophat | tophat: Spliced read mapper for RNA-Seq | x86_64 | |
| trilinos | Trilinos: Solvers collection including linear, non-linear, optimization, and transient solvers | zen2 | |
| us3d | us3d: Aeordynamic and Aerothermodynamic Simulations Software | skylake_avx512, x86_64 | |
| vasp | vasp: VASP: Vienna Ab-initio Simulation Package | zen2 | |
| virtualgl | virtualgl: Toolkit to allow remote display to run OpenGL applications with full hardware acceleration | zen, zen2 | |
| 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 | zen, zen2 | |
| vtk | vtk: 3D computer graphics, image processing and visualization library | zen, zen2 | Yes |
| wannier90 | Wannier90: tool to calculate maximally-localized Wannier functions | x86_64, zen, zen2 | Yes |
| xerces-c | xerces-c: validating XML parser in C++ | zen, zen2 | |
| xssp | xssp: Secondary structure assignments for entries in the Protein Data Bank | zen, zen2 | Yes |
| xz | xz: Lossless compression utility and library | x86_64, zen, zen2 | |
| zfp | zfp: Library for lossy compression of multidimensional arrays | zen, zen2 | |
| zlib | zlib: General purpose, patent-free compression ibrary | x86_64, zen, zen2 | |
| zoltan | zoltan: Toolkit for parallel combinatorial algorithms | x86_64, zen, zen2 | Yes |
| zstd | zstd: Fast, lossless compression algorithm | x86_64, zen, zen2 |
This section lists various software packages related to Aeronautics, Aviation, Aerospace Sciences and related fields (Astronautics, Hypersonics, Aerothermodynamics, etc.)
| 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 |
This section lists various software packages related to Astronomy and related fields.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| cfitsio | CFITSIO: Libraries for Flexible Image Transport System (FITS) data format | zen, zen2 |
This section lists various software packages related to Computational Fluid Dynamics (CFD).
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| cgns | cgns: CFD General notation system | x86_64, zen, zen2 | Yes |
| dplr | dplr: Hypersonic Continuum CFD Code | skylake_avx512, x86_64 | |
| fds | FDS: Fire Dynamics Simulator | x86_64 | |
| fun3d | fun3d: FUN3d (Fully Unstructured Navier-Stokes) CFD suite | skylake_avx512 | |
| openfoam | openfoam: Opensource C++ CFD toolbox | zen, zen2 | Yes |
| pointwise | pointwise: Pointwise mesh generation software for CFD | x86_64 | |
| smokeview | Smokeview: Visualization tool for FDS and CFAST output | x86_64 | |
| tecplot360 | Tecplot360: CFD visualization software | x86_64 |
This section lists various software packages related to Chemistry, Computational Chemistry, Quantum Chemistry, etc. See also MolecularDynamics and MaterialScience.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| cfour | cfour: Software for quantum chemical modeling | x86_64 | |
| charmm | charmm: Chemistry at HARvard Macromolecular Mechanics. | zen2 | Yes |
| cp2k | CP2K: quantum chemistry and solid state physics package | zen2 | |
| gaussian | Gaussian: Software for electronic structure modeling | x86_64 | |
| gromacs | gromacs: Chemical simulation/Molecular dynamics package | zen, zen2 | Yes |
| lammps | lammps: LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator | zen, zen2 | Yes |
| libint | libint: library to evaluate molecular integrals | zen, zen2 | Yes |
| namd | NAMD: Nanoscale Molecular Dynamics | zen, zen2 | Yes |
| openmm | openmm: A high-performance toolkit for molecular simulation. | zen2 | Yes |
| orca | ORCA: Ab initio quantum chemistry package | x86_64 | |
| plumed | PLUMED: plugin for molecular dynamics | zen, zen2 | Yes |
| qmd-progress | qmd-progress: PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver | zen, zen2 | Yes |
| sirius | SIRIUS: domain specific library for electronic structure calculations | zen, zen2 | |
| vasp | vasp: VASP: Vienna Ab-initio Simulation Package | zen2 | |
| vmd | VMD: Visual Molecular Dynamics | x86_64 |
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.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| caffe | caffe: Deep learning framework | zen, zen2 | |
| opencv | opencv: Open-source Computer Vision Library | zen2 | |
| pytorch | pytorch: Open-source machine learning library | zen2 | Yes |
| tensorflow | tensorflow: Open-source software library for machine intelligence | zen, zen2 | Yes |
| tensorflowORIG | tensorflowORIG: Open-source software library for machine intelligence | zen, zen2 |
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.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| bzip2 | bzip2: patent-free high quality data compression libraries | x86_64, zen, zen2 | |
| c-blosc | c-blosc: A blocking, shuffling, and loss-less compression library | zen, zen2 | |
| lz4 | lz4: Lossless compression utility and library | x86_64, zen, zen2 | |
| sz | sz: Error-bounded Lossy Compressor for HPC Data | zen, zen2 | Yes |
| xerces-c | xerces-c: validating XML parser in C++ | zen, zen2 | |
| xz | xz: Lossless compression utility and library | x86_64, zen, zen2 | |
| zfp | zfp: Library for lossy compression of multidimensional arrays | zen, zen2 | |
| zlib | zlib: General purpose, patent-free compression ibrary | x86_64, zen, zen2 | |
| zstd | zstd: Fast, lossless compression algorithm | x86_64, zen, zen2 |
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.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| adios2 | adios2: The Adapatble Input/Output System, version 2 | zen, zen2 | |
| bamtools | BamTools: Command line toolkit for dealing with BAM files | zen, zen2 | |
| cdo | cdo: Climate Data Operators | zen2 | Yes |
| cfitsio | CFITSIO: Libraries for Flexible Image Transport System (FITS) data format | zen, zen2 | |
| eccodes | eccodes: Libraries for encoding/decoding weather related data formats | zen, zen2 | Yes |
| h5utils | h5utils: Utilities for visualization/conversion of HDF5 data | zen2 | Yes |
| hdf-eos2 | HDF-EOS2: HDF for Earth Observing System (hdf4) | zen, zen2 | |
| hdf-eos5 | HDF-EOS5: HDF for Earth Observing System (hdf5) | zen2 | Yes |
| hdf4 | hdf4: Libraries for Hierarchical Data Format v4 | x86_64, zen, zen2 | |
| hdf5 | hdf5: Libraries for Hierarchical Data Format v5 | x86_64, zen, zen2 | Yes |
| matio | matio: MATLAB MAT file I/O library | zen, zen2 | Yes |
| nco | nco: Toolkits for manipulating data in NetCDF formats | zen, zen2 | Yes |
| ncview | ncview: Viewer for NetCDF files | zen2 | Yes |
| netcdf | netcdf: C Libraries for NetCDF data format | x86_64, zen, zen2 | Yes |
| netcdf-cxx | netcdf-cxx: C++ Libraries for NetCDF data format | x86_64, zen, zen2 | Yes |
| netcdf-fortran | netcdf-fortran: Fortran Libraries for NetCDF data format | x86_64, zen, zen2 | Yes |
| parallel-netcdf | parallel-netcdf: Parallel I/O library for NetCDF file format | x86_64, zen, zen2 | Yes |
| silo | silo: libraries for reading/writing a variety of scientific data | x86_64, zen, zen2 | Yes |
This section lists various software packages related to various Earth sciences. See also Meteorology.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| esmf | esmf: The Earth System Modeling Framework | zen, zen2 | Yes |
| gdal | gdal: Geospatial Data Abstraction Library | zen2 | Yes |
| geos | geos: C++ Geometry Engine Open Source | zen, zen2 | |
| grads | grads: Grid Analysis and Display System | zen2 | |
| gssha | GSSHA: Gridded Surface/Subsurface Hydrologic Analysis | x86_64 | |
| hdf-eos2 | HDF-EOS2: HDF for Earth Observing System (hdf4) | zen, zen2 | |
| hdf-eos5 | HDF-EOS5: HDF for Earth Observing System (hdf5) | zen2 | Yes |
| proj | proj: Generic Coordinate Transformation package | zen, zen2 |
This section lists various software packages related to various Engineering fields.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| abaqus | Abaqus: Finite-element analysis/Computer-aided engineering software | x86_64 | |
| 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 | |
| comsol | Comsol: General-purpose simulation software | x86_64 | |
| petsc | PETSc: PETSc (Portable, Extensible Toolkit for Scientific Computation) | zen2 | |
| trilinos | Trilinos: Solvers collection including linear, non-linear, optimization, and transient solvers | zen2 |
This section lists various software packages related to Genomics, Genetics, and related fields.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| bamtools | BamTools: Command line toolkit for dealing with BAM files | zen, zen2 | |
| bcftools | bcftools: BCFtools is a set of utilities that manipulate variant calls | zen2 | Yes |
| bedtools2 | bedtools2: swiss-army knife of genomics analysis tasks | zen2 | |
| blast-plus | blast-plus: Basic Local Alignment Search Tool | zen, zen2 | |
| bowtie | bowtie: ultrafast sequence aligner | zen2 | |
| bowtie2 | bowtie2: ultrafast sequence aligner | zen2 | |
| bwa | bwa: Burrows-Wheeler Aligner | zen2 | |
| exonerate | Exonerate: generic tool for pairwise sequence comparison | zen2 | |
| fastqc | fastqc: quality control tool for high throughput sequence data. | zen2 | |
| hmmer | hmmer: biosequence analyser using profile hidden Markov models | x86_64, zen, zen2 | Yes |
| igv | igv: Integrative Genomics Viewer | zen2 | |
| impute2 | IMPUTE2: genotype imputatin and haplotype phasing tool | zen2 | |
| jellyfish | jellyfish: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. | zen, zen2 | |
| kallisto | kallisto: Program for RNA-sequence quantification | zen2 | |
| plink | PLINK: genome association analysis toolset | zen2 | |
| popoolation2 | popoolation2: PoPoolation2 allows to compare allele frequencies for single-nucleotide polymorphisms. | zen2 | |
| samtools | samtools: SAM (Sequence/Alignment Mapping) Tools | zen, zen2 | |
| shapeit4 | SHAPEIT4: estimation of haplotypes for sequencing data. | zen2 | |
| tophat | tophat: Spliced read mapper for RNA-Seq | x86_64 |
This section lists various software packages related to the processing/editting/manipulation/etc of image or video files.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| embree | Embree: High performance ray tracing kernels | x86_64 | |
| ffmpeg | FFmpeg: | zen, zen2 | |
| jasper | jasper: Library for manipulating JPEG-2000 images | zen2 | |
| jasper.test | jasper.test: Library for manipulating JPEG-2000 images | zen2 | |
| libpng | libpng: libpng is the official PNG reference library | zen, zen2 |
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
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| caffe | caffe: Deep learning framework | zen, zen2 | |
| cudnn | cudnn: Library of deep learning/neural network primitives for GPUs | x86_64, zen, zen2 | Yes |
| gloo | gloo: Gloo collective communications package | skylake_avx512, x86_64, zen, zen2 | |
| libxsmm | LIBXSMM: library for specialized dense and sparse matrix operations | zen, zen2 | |
| opencv | opencv: Open-source Computer Vision Library | zen2 | |
| pytorch | pytorch: Open-source machine learning library | zen2 | Yes |
| qnnpack | qnnpack: Quantized Neural Networks PACKage | skylake_avx512, x86_64 | |
| tensorflow | tensorflow: Open-source software library for machine intelligence | zen, zen2 | Yes |
| tensorflowORIG | tensorflowORIG: Open-source software library for machine intelligence | zen, zen2 |
This section lists various software packages related to Material Science and related fields. See also Chemistry and SolidStatePhysics.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| cp2k | CP2K: quantum chemistry and solid state physics package | zen2 | |
| spglib | spglib: C library for finding and handling crystal symmetries | zen, zen2 | |
| vasp | vasp: VASP: Vienna Ab-initio Simulation Package | zen2 |
This section lists various software packages related to Meteorology, Weather, Atmospheric and Oceanographic Sciences and related fields. See also Earth Sciences
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| cdo | cdo: Climate Data Operators | zen2 | Yes |
| eccodes | eccodes: Libraries for encoding/decoding weather related data formats | zen, zen2 | Yes |
| magics | magics: meteorological plotting software | zen2 | Yes |
Miscellaneous packages. Libraries and other stuff which we need a modulefile for but do not belong anywhere else and do not merit there own category.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| fribidi | FriBidi: Unicode Bidirectional Algorithm implementation | zen, zen2 | |
| harfbuzz | HarfBuzz: Text shaping library | zen, zen2 |
This section lists various software packages related to Molecular Dynamics and related fields. See also Chemistry and Material Science.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| charmm | charmm: Chemistry at HARvard Macromolecular Mechanics. | zen2 | Yes |
| gromacs | gromacs: Chemical simulation/Molecular dynamics package | zen, zen2 | Yes |
| lammps | lammps: LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator | zen, zen2 | Yes |
| latte | latte: Open source density functional tight binding molecular dynamics. | zen, zen2 | Yes |
| libint | libint: library to evaluate molecular integrals | zen, zen2 | Yes |
| libvdwxc | Libvdwxc: library for vdW-DF exchange-correlation functionals | x86_64, zen, zen2 | Yes |
| namd | NAMD: Nanoscale Molecular Dynamics | zen, zen2 | Yes |
| openmm | openmm: A high-performance toolkit for molecular simulation. | zen2 | Yes |
| plumed | PLUMED: plugin for molecular dynamics | zen, zen2 | Yes |
| qmd-progress | qmd-progress: PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver | zen, zen2 | Yes |
| quantum-espresso | quantum-espresso: Electronic-structure calculations at the nanoscale. | zen2 | Yes |
| sirius | SIRIUS: domain specific library for electronic structure calculations | zen, zen2 | |
| spglib | spglib: C library for finding and handling crystal symmetries | zen, zen2 | |
| vmd | VMD: Visual Molecular Dynamics | x86_64 | |
| wannier90 | Wannier90: tool to calculate maximally-localized Wannier functions | x86_64, zen, zen2 | Yes |
| xssp | xssp: Secondary structure assignments for entries in the Protein Data Bank | zen, zen2 | Yes |
This section lists various software packages related to Multiphysics.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| petsc | PETSc: PETSc (Portable, Extensible Toolkit for Scientific Computation) | zen2 | |
| trilinos | Trilinos: Solvers collection including linear, non-linear, optimization, and transient solvers | zen2 |
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.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| amdblis | amdblis: AMD Optimized BLAS libraries | zen2 | |
| amdfftw | amdfftw: AMD Discrete Fourier Transform library | zen2 | Yes |
| amdlibflame | amdlibflame: AMD Optimized BLAS libraries | zen2 | |
| amdlibm | amdlibm: AMD Optimized BLAS libraries | zen2 | |
| amdscalapack | amdscalapack: AMD Optimized Scalable linear algebra package | zen2 | Yes |
| aocl-sparse | aocl-sparse: Suite of Sparse Matrix algorithms | zen2 | |
| arpack-ng | arpack-ng: Fortran77 subroutines designed to solve large scale eigenvalue problems | x86_64, zen, zen2 | Yes |
| bml | bml: Basic Matrix Library | zen, zen2 | Yes |
| cgal | cgal: Computations Geometry Algorithms Library | zen, zen2 | Yes |
| cminpack | cminpack: Library for solving nonlinear equations and nonlinear least squares problems | zen, zen2 | |
| cosma | COSMA: Distributed Communication-Optimal Matrix-Matrix Multiplication Library | zen2 | Yes |
| eigen | eigen: C++ template library for matrix and vector operations, | zen, zen2 | |
| elpa | elpa: Eigenvalue solvers for Petaflop Applications | zen2 | |
| envi | ENVI: ENVI software for processing and analyzing geospatial data | x86_64 | |
| fftw | fftw: Discrete Fourier Transform library | x86_64, zen, zen2 | Yes |
| gmp | gmp: GNU Multiple Precision Arithmetic Library | x86_64, zen, zen2 | |
| gsl | gsl: GNU Scientific Library | x86_64, zen, zen2 | |
| gurobi | gurobi: Gurobi Optimizer for numerical programming | x86_64 | |
| hypre | HPYRE: Scalable Linear Solvers and Multigrid Methods | x86_64, zen2 | Yes |
| kahip | kahip: Karlsruhe High Quality Graph Partitioning Framework | zen, zen2 | Yes |
| magma | magma: Matrix Algebra on GPU and Multicore Architectures | zen2 | Yes |
| mathematica | Mathematica: Mathematica symbolic and computational mathematics package. | x86_64 | |
| matio | matio: MATLAB MAT file I/O library | zen, zen2 | Yes |
| matlab | matlab: Matlab numerical computing environment | x86_64 | |
| metis | metis: Metis unstructured graph partitioner | x86_64, zen, zen2 | |
| mgridgen | mgridgen: Multilevel Serial & Parallel Coarse Grid Construction Library | x86_64, zen, zen2 | Yes |
| mt-metis | mt-metis: Metis unstructured graph partitioner | zen, zen2 | |
| mumps | mumps: MUltifrontal Massively Parallel sparse direct Solver | zen, zen2 | Yes |
| ncl | NCL: NCAR Command Language | zen2 | Yes |
| openblas | openblas: Optimized BLAS libraries | x86_64, zen, zen2 | |
| pari-gp | pari-gp: computer algebra system for computations in number theory | zen2 | Yes |
| parmetis | parmetis: Parallel Metis | x86_64, zen, zen2 | Yes |
| parmgridgen | ParMGridGen: Multilevel Serial & Parallel Coarse Grid Construction Library | x86_64, zen, zen2 | Yes |
| pexsi | PEXSI: electronic structure calculation based on Kohn-Sham density functional theory | x86_64, zen, zen2 | Yes |
| pfft | pfft: Parallel Fast Fourier Transform library | x86_64, zen, zen2 | Yes |
| pytorch | pytorch: Open-source machine learning library | zen2 | Yes |
| scalapack | scalapack: Scalable linear algebra package | x86_64, zen, zen2 | Yes |
| scotch | scotch: Package for graph and mesh partitioning, graph clustering, and sparse matrix ordering | x86_64, zen, zen2 | Yes |
| slepc | SLEPc: Scalable Library for Eigenvalue Problem Computations | zen2 | |
| spfft | SpFFT: 3D FFT library for sparse frequency domain data | x86_64, zen, zen2 | |
| suite-sparse | suite-sparse: Suite of Sparse Matrix algorithms | zen, zen2 | |
| superlu | superlu: Sparse Linear system solver (sequential) | zen, zen2 | |
| superlu-dist | superlu-dist: Sparse Linear system solver (distributed mem/MPI) | x86_64, zen, zen2 | |
| superlu-mt | superlu-mt: Sparse Linear system solver (multithreaded) | zen, zen2 | |
| tensorflow | tensorflow: Open-source software library for machine intelligence | zen, zen2 | Yes |
| tensorflowORIG | tensorflowORIG: Open-source software library for machine intelligence | zen, zen2 | |
| voropp | Voro++: library for 3D computations of the Voronoi tessellation | zen, zen2 | |
| zoltan | zoltan: Toolkit for parallel combinatorial algorithms | x86_64, zen, zen2 | Yes |
This section lists various software packages containing python modules which can be imported in your python code, after the corresponding environmental module is loaded.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| charm4py | Charm4py: distributed/parallel programing framework for Python | zen, zen2 | Yes |
| charmm | charmm: Chemistry at HARvard Macromolecular Mechanics. | zen2 | Yes |
| cython | cython: Compiler for writing C extensions for Python | zen, zen2 | |
| jupyter | jupyter: The Jupyter Notebook application | zen, zen2 | |
| magics | magics: meteorological plotting software | zen2 | Yes |
| matplotlib | matplotlib: Open-source software library for creating visualizations in Python | zen, zen2 | Yes |
| openmm | openmm: A high-performance toolkit for molecular simulation. | zen2 | Yes |
| pytorch | pytorch: Open-source machine learning library | zen2 | Yes |
| tensorflow | tensorflow: Open-source software library for machine intelligence | zen, zen2 | Yes |
| tensorflowORIG | tensorflowORIG: Open-source software library for machine intelligence | zen, zen2 | |
| trilinos | Trilinos: Solvers collection including linear, non-linear, optimization, and transient solvers | zen2 |
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.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| amdblis | amdblis: AMD Optimized BLAS libraries | zen2 | |
| amdfftw | amdfftw: AMD Discrete Fourier Transform library | zen2 | Yes |
| amdlibflame | amdlibflame: AMD Optimized BLAS libraries | zen2 | |
| amdlibm | amdlibm: AMD Optimized BLAS libraries | zen2 | |
| amdscalapack | amdscalapack: AMD Optimized Scalable linear algebra package | zen2 | Yes |
| aocc | aocc: AMD Optimizing Compiler Suite | x86_64 | |
| aocl-sparse | aocl-sparse: Suite of Sparse Matrix algorithms | zen2 | |
| armadillo | armadillo: Linear algebra library for C++ | zen2 | |
| bml | bml: Basic Matrix Library | zen, zen2 | Yes |
| boost | boost: free, portable C++ source libraries | zen, zen2 | Yes |
| cgal | cgal: Computations Geometry Algorithms Library | zen, zen2 | Yes |
| charm4py | Charm4py: distributed/parallel programing framework for Python | zen, zen2 | Yes |
| charmpp | Charm++: parallel programming framework in C++ | x86_64, zen, zen2 | |
| cmake | cmake: cross-platform, open-source build system | x86_64, zen, zen2 | |
| cmdstan | CmdStan: command line interface to Stan | zen2 | Yes |
| cminpack | cminpack: Library for solving nonlinear equations and nonlinear least squares problems | zen, zen2 | |
| cosma | COSMA: Distributed Communication-Optimal Matrix-Matrix Multiplication Library | zen2 | Yes |
| cuda | cuda: parallel computing platform/programming model for NVIDIA GPUs | x86_64, zen, zen2 | |
| cudnn | cudnn: Library of deep learning/neural network primitives for GPUs | x86_64, zen, zen2 | Yes |
| cython | cython: Compiler for writing C extensions for Python | zen, zen2 | |
| dmtcp | dmtcp: Distributed Multithreaded Checkpointing | zen, zen2 | |
| dyninst | dyninst: API for dynamic binary instrumentation | zen, zen2 | Yes |
| eccodes | eccodes: Libraries for encoding/decoding weather related data formats | zen, zen2 | Yes |
| eigen | eigen: C++ template library for matrix and vector operations, | zen, zen2 | |
| elpa | elpa: Eigenvalue solvers for Petaflop Applications | zen2 | |
| envi | ENVI: ENVI software for processing and analyzing geospatial data | x86_64 | |
| esmf | esmf: The Earth System Modeling Framework | zen, zen2 | Yes |
| ffmpeg | FFmpeg: | zen, zen2 | |
| fftw | fftw: Discrete Fourier Transform library | x86_64, zen, zen2 | Yes |
| gcc | gcc: GNU Compiler Suite | x86_64, zen2 | Yes |
| gdal | gdal: Geospatial Data Abstraction Library | zen2 | Yes |
| gdb | gdb: GNU Project Debugger | skylake_avx512, x86_64 | |
| geos | geos: C++ Geometry Engine Open Source | zen, zen2 | |
| gloo | gloo: Gloo collective communications package | skylake_avx512, x86_64, zen, zen2 | |
| go | go: Go programming language | zen2 | |
| gsl | gsl: GNU Scientific Library | x86_64, zen, zen2 | |
| gurobi | gurobi: Gurobi Optimizer for numerical programming | x86_64 | |
| hdf4 | hdf4: Libraries for Hierarchical Data Format v4 | x86_64, zen, zen2 | |
| hdf5 | hdf5: Libraries for Hierarchical Data Format v5 | x86_64, zen, zen2 | Yes |
| hello-umd | hello-umd: Simple Hello world binary | x86_64, zen, zen2 | Yes |
| hpctoolkit | hpctoolkit: toolkit for performance measurement and analysis | zen2 | Yes |
| hpl | hpl: High Performance Computing Linpack Benchmark | zen2 | Yes |
| hpx | hpx: C++ runtime for parallel and distributed applications | zen, zen2 | |
| hypre | HPYRE: Scalable Linear Solvers and Multigrid Methods | x86_64, zen2 | Yes |
| intel | Intel: Intel OneAPI Classic compilers | x86_64 | |
| intel-advisor | intel-advisor: Intel advisor performance analysis tool | zen2 | |
| intel-dal | intel-dal: Intel Data Analytics Library (DAL) | zen2 | |
| intel-dnn | intel-dnn: Intel Deep Neural Network Library | zen2 | |
| intel-dpl | intel-dpl: Intel Data Parallel C++ Library (DPL) | zen2 | |
| intel-inspector | intel-inspector: Intel Inspector memory, thread checking and debugging tool | zen2 | |
| intel-ipp | intel-ipp: Intel Integrated Performance Primitives (IPP) | zen2 | |
| intel-ippcp | intel-ippcp: Intel Integrated Performance Primitives Cryptography (IPP Crypto) | zen2 | |
| intel-mkl | intel-mkl: Intel Math Kernel Library (MKL/oneMKL) | zen2 | |
| intel-mpi | intel-mpi: Intel Message Passing Interface (MPI) Library | zen2 | |
| intel-tbb | intel-tbb: Intel Threaded Building Blocks | zen, zen2 | |
| intel-vpl | intel-vpl: Intel Video Processing Library (oneVPL) | zen2 | |
| intel-vtune | intel-vtune: Intel oneAPI VTune Profiler | zen2 | |
| ior | ior: Parallel IO benchmark | x86_64, zen2 | Yes |
| jasper | jasper: Library for manipulating JPEG-2000 images | zen2 | |
| jasper.test | jasper.test: Library for manipulating JPEG-2000 images | zen2 | |
| json-c | JSON-C: JSON library implemented in C | zen, zen2 | |
| jsoncpp | JsonCpp: JSON library implemented in C++ | zen, zen2 | |
| julia | julia: Julia programming language: A fresh approach to technical computing | zen2 | Yes |
| kahip | kahip: Karlsruhe High Quality Graph Partitioning Framework | zen, zen2 | Yes |
| libpng | libpng: libpng is the official PNG reference library | zen, zen2 | |
| libxsmm | LIBXSMM: library for specialized dense and sparse matrix operations | zen, zen2 | |
| libzmq | libzmq: ZeroMQ networking/concurrency library and core API | zen, zen2 | |
| magma | magma: Matrix Algebra on GPU and Multicore Architectures | zen2 | Yes |
| mathematica | Mathematica: Mathematica symbolic and computational mathematics package. | x86_64 | |
| matio | matio: MATLAB MAT file I/O library | zen, zen2 | Yes |
| matlab | matlab: Matlab numerical computing environment | x86_64 | |
| metis | metis: Metis unstructured graph partitioner | x86_64, zen, zen2 | |
| mgridgen | mgridgen: Multilevel Serial & Parallel Coarse Grid Construction Library | x86_64, zen, zen2 | Yes |
| mt-metis | mt-metis: Metis unstructured graph partitioner | zen, zen2 | |
| mumps | mumps: MUltifrontal Massively Parallel sparse direct Solver | zen, zen2 | Yes |
| ncl | NCL: NCAR Command Language | zen2 | Yes |
| nco | nco: Toolkits for manipulating data in NetCDF formats | zen, zen2 | Yes |
| netcdf | netcdf: C Libraries for NetCDF data format | x86_64, zen, zen2 | Yes |
| netcdf-cxx | netcdf-cxx: C++ Libraries for NetCDF data format | x86_64, zen, zen2 | Yes |
| netcdf-fortran | netcdf-fortran: Fortran Libraries for NetCDF data format | 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 | |
| oneapi | Intel: Intel OneAPI new compilers | x86_64 | |
| openblas | openblas: Optimized BLAS libraries | x86_64, zen, zen2 | |
| opencv | opencv: Open-source Computer Vision Library | zen2 | |
| openjdk | openjdk: Open-source implementation of Java | x86_64, zen, zen2 | |
| openmpi | openmpi: OpenMPI implementation of Message Passing Interface | x86_64, zen, zen2 | Yes |
| osu-micro-benchmarks | osu-micro-benchmarks: Microbenchmarks for MPI | x86_64, zen, zen2 | |
| parallel-netcdf | parallel-netcdf: Parallel I/O library for NetCDF file format | x86_64, zen, zen2 | Yes |
| parmetis | parmetis: Parallel Metis | x86_64, zen, zen2 | Yes |
| perl | perl: Perl scripting language | x86_64, zen, zen2 | |
| pfft | pfft: Parallel Fast Fourier Transform library | x86_64, zen, zen2 | Yes |
| python | python: Python scripting language | zen, zen2 | |
| qnnpack | qnnpack: Quantized Neural Networks PACKage | skylake_avx512, x86_64 | |
| r | r: R statistical computing scripting language | zen2 | |
| rust | rust: Rust programming language | zen, zen2 | |
| scalapack | scalapack: Scalable linear algebra package | x86_64, zen, zen2 | Yes |
| scons | SCons: SCons open-source software construction tool | zen2 | |
| scorep | scorep: suite for profiling, event tracing, and analysis of HPC applications | zen2 | Yes |
| scotch | scotch: Package for graph and mesh partitioning, graph clustering, and sparse matrix ordering | x86_64, zen, zen2 | Yes |
| silo | silo: libraries for reading/writing a variety of scientific data | x86_64, zen, zen2 | Yes |
| singularity | singularity: Singularity container utilities | x86_64 | |
| suite-sparse | suite-sparse: Suite of Sparse Matrix algorithms | zen, zen2 | |
| superlu | superlu: Sparse Linear system solver (sequential) | zen, zen2 | |
| superlu-dist | superlu-dist: Sparse Linear system solver (distributed mem/MPI) | x86_64, zen, zen2 | |
| superlu-mt | superlu-mt: Sparse Linear system solver (multithreaded) | zen, zen2 | |
| swig | swig: compiler to interface C/C++ libraries to Perl, Python, etc | zen, zen2 | |
| toolchain | toolchain: Compiler/library toolkits | x86_64 | |
| zlib | zlib: General purpose, patent-free compression ibrary | x86_64, zen, zen2 | |
| zoltan | zoltan: Toolkit for parallel combinatorial algorithms | x86_64, zen, zen2 | Yes |
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.
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| curl | curl: command line tool for transferring data | x86_64, zen, zen2 | |
| deepthought2 | deepthought2: Default env setting for the Deepthought2 (DT2) cluster | x86_64 | |
| dmtcp | dmtcp: Distributed Multithreaded Checkpointing | zen, zen2 | |
| git-lfs | git-lfs: command line tool for managing cloud storage | zen2 | |
| 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 | zen, zen2 | |
| mercurial | mercurial: Mercurial source control management system | zen2 | |
| rclone | Rclone: command line tool for managing cloud storage | zen2 | |
| singularity | singularity: Singularity container utilities | x86_64 |
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.
| 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 | zen, zen2 | |
| grads | grads: Grid Analysis and Display System | zen2 | |
| magics | magics: meteorological plotting software | zen2 | Yes |
| ncl | NCL: NCAR Command Language | zen2 | Yes |
| paraview | paraview: data analysis and visualization application | zen, zen2 | |
| paraview-headless | paraview-headless: data analysis and visualization application (headless version) | zen, zen2 | |
| pgplot | pgplot: PGPLOT Graphics Subroutine Library | zen2 | |
| plplot | plplot: Cross-platform software for creating scientific plots | zen2 | |
| povray | POV-Ray: Persistence of Vision Ray tracer | zen, zen2 | |
| virtualgl | virtualgl: Toolkit to allow remote display to run OpenGL applications with full hardware acceleration | zen, zen2 | |
| 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 | zen, zen2 | Yes |
This section lists all software packages available on the Zaratan cluster
| Package Name | Description | Supported CPUs | GPU ready? |
|---|---|---|---|
| abaqus | Abaqus: Finite-element analysis/Computer-aided engineering software | x86_64 | |
| adios2 | adios2: The Adapatble Input/Output System, version 2 | zen, zen2 | |
| amdblis | amdblis: AMD Optimized BLAS libraries | zen2 | |
| amdfftw | amdfftw: AMD Discrete Fourier Transform library | zen2 | Yes |
| amdlibflame | amdlibflame: AMD Optimized BLAS libraries | zen2 | |
| amdlibm | amdlibm: AMD Optimized BLAS libraries | zen2 | |
| amdscalapack | amdscalapack: AMD Optimized Scalable linear algebra package | zen2 | 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 | |
| aocc | aocc: AMD Optimizing Compiler Suite | x86_64 | |
| aocl-sparse | aocl-sparse: Suite of Sparse Matrix algorithms | zen2 | |
| armadillo | armadillo: Linear algebra library for C++ | zen2 | |
| arpack-ng | arpack-ng: Fortran77 subroutines designed to solve large scale eigenvalue problems | x86_64, zen, zen2 | Yes |
| bamtools | BamTools: Command line toolkit for dealing with BAM files | zen, zen2 | |
| bcftools | bcftools: BCFtools is a set of utilities that manipulate variant calls | zen2 | Yes |
| bedtools2 | bedtools2: swiss-army knife of genomics analysis tasks | zen2 | |
| blast-plus | blast-plus: Basic Local Alignment Search Tool | zen, zen2 | |
| bml | bml: Basic Matrix Library | zen, zen2 | Yes |
| boost | boost: free, portable C++ source libraries | zen, zen2 | Yes |
| bowtie | bowtie: ultrafast sequence aligner | zen2 | |
| bowtie2 | bowtie2: ultrafast sequence aligner | zen2 | |
| bwa | bwa: Burrows-Wheeler Aligner | zen2 | |
| bzip2 | bzip2: patent-free high quality data compression libraries | x86_64, zen, zen2 | |
| c-blosc | c-blosc: A blocking, shuffling, and loss-less compression library | zen, zen2 | |
| caffe | caffe: Deep learning framework | zen, zen2 | |
| cdo | cdo: Climate Data Operators | zen2 | Yes |
| cfitsio | CFITSIO: Libraries for Flexible Image Transport System (FITS) data format | zen, zen2 | |
| cfour | cfour: Software for quantum chemical modeling | x86_64 | |
| cgal | cgal: Computations Geometry Algorithms Library | zen, zen2 | Yes |
| cgns | cgns: CFD General notation system | x86_64, zen, zen2 | Yes |
| charm4py | Charm4py: distributed/parallel programing framework for Python | zen, zen2 | Yes |
| charmm | charmm: Chemistry at HARvard Macromolecular Mechanics. | zen2 | Yes |
| charmpp | Charm++: parallel programming framework in C++ | x86_64, zen, zen2 | |
| cmake | cmake: cross-platform, open-source build system | x86_64, zen, zen2 | |
| cmdstan | CmdStan: command line interface to Stan | zen2 | Yes |
| cminpack | cminpack: Library for solving nonlinear equations and nonlinear least squares problems | zen, zen2 | |
| comsol | Comsol: General-purpose simulation software | x86_64 | |
| cosma | COSMA: Distributed Communication-Optimal Matrix-Matrix Multiplication Library | zen2 | Yes |
| cp2k | CP2K: quantum chemistry and solid state physics package | zen2 | |
| cuda | cuda: parallel computing platform/programming model for NVIDIA GPUs | x86_64, zen, zen2 | |
| cudnn | cudnn: Library of deep learning/neural network primitives for GPUs | x86_64, zen, zen2 | Yes |
| curl | curl: command line tool for transferring data | x86_64, zen, zen2 | |
| cython | cython: Compiler for writing C extensions for Python | zen, zen2 | |
| dmtcp | dmtcp: Distributed Multithreaded Checkpointing | zen, zen2 | |
| dplr | dplr: Hypersonic Continuum CFD Code | skylake_avx512, x86_64 | |
| dyninst | dyninst: API for dynamic binary instrumentation | zen, zen2 | Yes |
| eccodes | eccodes: Libraries for encoding/decoding weather related data formats | zen, zen2 | Yes |
| eigen | eigen: C++ template library for matrix and vector operations, | zen, zen2 | |
| elpa | elpa: Eigenvalue solvers for Petaflop Applications | zen2 | |
| 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 | zen, zen2 | Yes |
| exonerate | Exonerate: generic tool for pairwise sequence comparison | zen2 | |
| fastqc | fastqc: quality control tool for high throughput sequence data. | zen2 | |
| fds | FDS: Fire Dynamics Simulator | x86_64 | |
| ffmpeg | FFmpeg: | zen, zen2 | |
| fftw | fftw: Discrete Fourier Transform library | x86_64, zen, zen2 | Yes |
| fribidi | FriBidi: Unicode Bidirectional Algorithm implementation | zen, zen2 | |
| fun3d | fun3d: FUN3d (Fully Unstructured Navier-Stokes) CFD suite | skylake_avx512 | |
| gaussian | Gaussian: Software for electronic structure modeling | x86_64 | |
| gcc | gcc: GNU Compiler Suite | x86_64, zen2 | Yes |
| gdal | gdal: Geospatial Data Abstraction Library | zen2 | Yes |
| geos | geos: C++ Geometry Engine Open Source | zen, zen2 | |
| git-lfs | git-lfs: command line tool for managing cloud storage | zen2 | |
| gmp | gmp: GNU Multiple Precision Arithmetic Library | x86_64, zen, zen2 | |
| gnuplot | gnuplot: command-line driven graphing utility | zen, zen2 | |
| go | go: Go programming language | zen2 | |
| grads | grads: Grid Analysis and Display System | zen2 | |
| gromacs | gromacs: Chemical simulation/Molecular dynamics package | zen, zen2 | Yes |
| gsl | gsl: GNU Scientific Library | x86_64, zen, zen2 | |
| gssha | GSSHA: Gridded Surface/Subsurface Hydrologic Analysis | x86_64 | |
| gurobi | gurobi: Gurobi Optimizer for numerical programming | x86_64 | |
| h5utils | h5utils: Utilities for visualization/conversion of HDF5 data | zen2 | Yes |
| harfbuzz | HarfBuzz: Text shaping library | zen, zen2 | |
| hdf-eos2 | HDF-EOS2: HDF for Earth Observing System (hdf4) | zen, zen2 | |
| hdf-eos5 | HDF-EOS5: HDF for Earth Observing System (hdf5) | zen2 | Yes |
| hdf4 | hdf4: Libraries for Hierarchical Data Format v4 | x86_64, zen, zen2 | |
| hdf5 | hdf5: Libraries for Hierarchical Data Format v5 | x86_64, zen, zen2 | Yes |
| hello-umd | hello-umd: Simple Hello world binary | x86_64, zen, zen2 | Yes |
| hmmer | hmmer: biosequence analyser using profile hidden Markov models | x86_64, zen, zen2 | Yes |
| hpcc | hpcc: Default env setting for the various clusters | x86_64 | |
| hpctoolkit | hpctoolkit: toolkit for performance measurement and analysis | zen2 | Yes |
| hpl | hpl: High Performance Computing Linpack Benchmark | zen2 | Yes |
| hpx | hpx: C++ runtime for parallel and distributed applications | zen, zen2 | |
| hypre | HPYRE: Scalable Linear Solvers and Multigrid Methods | x86_64, zen2 | Yes |
| igv | igv: Integrative Genomics Viewer | zen2 | |
| impute2 | IMPUTE2: genotype imputatin and haplotype phasing tool | zen2 | |
| intel | Intel: Intel OneAPI Classic compilers | x86_64 | |
| intel-advisor | intel-advisor: Intel advisor performance analysis tool | zen2 | |
| intel-dal | intel-dal: Intel Data Analytics Library (DAL) | zen2 | |
| intel-dnn | intel-dnn: Intel Deep Neural Network Library | zen2 | |
| intel-dpl | intel-dpl: Intel Data Parallel C++ Library (DPL) | zen2 | |
| intel-inspector | intel-inspector: Intel Inspector memory, thread checking and debugging tool | zen2 | |
| intel-ipp | intel-ipp: Intel Integrated Performance Primitives (IPP) | zen2 | |
| intel-ippcp | intel-ippcp: Intel Integrated Performance Primitives Cryptography (IPP Crypto) | zen2 | |
| intel-mkl | intel-mkl: Intel Math Kernel Library (MKL/oneMKL) | zen2 | |
| intel-mpi | intel-mpi: Intel Message Passing Interface (MPI) Library | zen2 | |
| intel-tbb | intel-tbb: Intel Threaded Building Blocks | zen, zen2 | |
| intel-vpl | intel-vpl: Intel Video Processing Library (oneVPL) | zen2 | |
| intel-vtune | intel-vtune: Intel oneAPI VTune Profiler | zen2 | |
| ior | ior: Parallel IO benchmark | x86_64, zen2 | Yes |
| jasper | jasper: Library for manipulating JPEG-2000 images | zen2 | |
| jasper.test | jasper.test: Library for manipulating JPEG-2000 images | zen2 | |
| jellyfish | jellyfish: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. | zen, zen2 | |
| json-c | JSON-C: JSON library implemented in C | zen, zen2 | |
| jsoncpp | JsonCpp: JSON library implemented in C++ | zen, zen2 | |
| julia | julia: Julia programming language: A fresh approach to technical computing | zen2 | Yes |
| jupyter | jupyter: The Jupyter Notebook application | zen, zen2 | |
| kahip | kahip: Karlsruhe High Quality Graph Partitioning Framework | zen, zen2 | Yes |
| kallisto | kallisto: Program for RNA-sequence quantification | zen2 | |
| lammps | lammps: LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator | zen, zen2 | Yes |
| latte | latte: Open source density functional tight binding molecular dynamics. | zen, zen2 | Yes |
| libint | libint: library to evaluate molecular integrals | zen, zen2 | Yes |
| libpng | libpng: libpng is the official PNG reference library | zen, zen2 | |
| libvdwxc | Libvdwxc: library for vdW-DF exchange-correlation functionals | x86_64, zen, zen2 | Yes |
| libxsmm | LIBXSMM: library for specialized dense and sparse matrix operations | zen, zen2 | |
| libzmq | libzmq: ZeroMQ networking/concurrency library and core API | zen, zen2 | |
| lz4 | lz4: Lossless compression utility and library | x86_64, zen, zen2 | |
| magics | magics: meteorological plotting software | zen2 | Yes |
| magma | magma: Matrix Algebra on GPU and Multicore Architectures | zen2 | Yes |
| mathematica | Mathematica: Mathematica symbolic and computational mathematics package. | x86_64 | |
| matio | matio: MATLAB MAT file I/O library | zen, zen2 | Yes |
| matlab | matlab: Matlab numerical computing environment | x86_64 | |
| matplotlib | matplotlib: Open-source software library for creating visualizations in Python | zen, zen2 | Yes |
| mercurial | mercurial: Mercurial source control management system | zen2 | |
| metis | metis: Metis unstructured graph partitioner | x86_64, zen, zen2 | |
| mgridgen | mgridgen: Multilevel Serial & Parallel Coarse Grid Construction Library | x86_64, zen, zen2 | Yes |
| mt-metis | mt-metis: Metis unstructured graph partitioner | zen, zen2 | |
| mumps | mumps: MUltifrontal Massively Parallel sparse direct Solver | zen, zen2 | Yes |
| namd | NAMD: Nanoscale Molecular Dynamics | zen, zen2 | Yes |
| ncl | NCL: NCAR Command Language | zen2 | Yes |
| nco | nco: Toolkits for manipulating data in NetCDF formats | zen, zen2 | Yes |
| ncview | ncview: Viewer for NetCDF files | zen2 | Yes |
| netcdf | netcdf: C Libraries for NetCDF data format | x86_64, zen, zen2 | Yes |
| netcdf-cxx | netcdf-cxx: C++ Libraries for NetCDF data format | x86_64, zen, zen2 | Yes |
| netcdf-fortran | netcdf-fortran: Fortran Libraries for NetCDF data format | 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 | |
| oneapi | Intel: Intel OneAPI new compilers | x86_64 | |
| openblas | openblas: Optimized BLAS libraries | x86_64, zen, zen2 | |
| opencv | opencv: Open-source Computer Vision Library | zen2 | |
| openfoam | openfoam: Opensource C++ CFD toolbox | zen, zen2 | Yes |
| openjdk | openjdk: Open-source implementation of Java | x86_64, zen, zen2 | |
| openmm | openmm: A high-performance toolkit for molecular simulation. | zen2 | Yes |
| openmpi | openmpi: OpenMPI implementation of Message Passing Interface | x86_64, zen, zen2 | Yes |
| orca | ORCA: Ab initio quantum chemistry package | x86_64 | |
| osu-micro-benchmarks | osu-micro-benchmarks: Microbenchmarks for MPI | x86_64, zen, zen2 | |
| parallel-netcdf | parallel-netcdf: Parallel I/O library for NetCDF file format | x86_64, zen, zen2 | Yes |
| paraview | paraview: data analysis and visualization application | zen, zen2 | |
| paraview-headless | paraview-headless: data analysis and visualization application (headless version) | zen, zen2 | |
| pari-gp | pari-gp: computer algebra system for computations in number theory | zen2 | Yes |
| parmetis | parmetis: Parallel Metis | x86_64, zen, zen2 | Yes |
| parmgridgen | ParMGridGen: Multilevel Serial & Parallel Coarse Grid Construction Library | x86_64, zen, zen2 | Yes |
| perl | perl: Perl scripting language | x86_64, zen, zen2 | |
| petsc | PETSc: PETSc (Portable, Extensible Toolkit for Scientific Computation) | zen2 | |
| pexsi | PEXSI: electronic structure calculation based on Kohn-Sham density functional theory | x86_64, zen, zen2 | Yes |
| pfft | pfft: Parallel Fast Fourier Transform library | x86_64, zen, zen2 | Yes |
| pgplot | pgplot: PGPLOT Graphics Subroutine Library | zen2 | |
| plink | PLINK: genome association analysis toolset | zen2 | |
| plplot | plplot: Cross-platform software for creating scientific plots | zen2 | |
| plumed | PLUMED: plugin for molecular dynamics | zen, zen2 | Yes |
| popoolation2 | popoolation2: PoPoolation2 allows to compare allele frequencies for single-nucleotide polymorphisms. | zen2 | |
| povray | POV-Ray: Persistence of Vision Ray tracer | zen, zen2 | |
| proj | proj: Generic Coordinate Transformation package | zen, zen2 | |
| python | python: Python scripting language | zen, zen2 | |
| pytorch | pytorch: Open-source machine learning library | zen2 | Yes |
| qmd-progress | qmd-progress: PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver | zen, zen2 | Yes |
| quantum-espresso | quantum-espresso: Electronic-structure calculations at the nanoscale. | zen2 | Yes |
| r | r: R statistical computing scripting language | zen2 | |
| rclone | Rclone: command line tool for managing cloud storage | zen2 | |
| rust | rust: Rust programming language | zen, zen2 | |
| samtools | samtools: SAM (Sequence/Alignment Mapping) Tools | zen, zen2 | |
| scalapack | scalapack: Scalable linear algebra package | x86_64, zen, zen2 | Yes |
| scons | SCons: SCons open-source software construction tool | zen2 | |
| scorep | scorep: suite for profiling, event tracing, and analysis of HPC applications | zen2 | Yes |
| scotch | scotch: Package for graph and mesh partitioning, graph clustering, and sparse matrix ordering | x86_64, zen, zen2 | Yes |
| shapeit4 | SHAPEIT4: estimation of haplotypes for sequencing data. | zen2 | |
| silo | silo: libraries for reading/writing a variety of scientific data | x86_64, zen, zen2 | Yes |
| singularity | singularity: Singularity container utilities | x86_64 | |
| sirius | SIRIUS: domain specific library for electronic structure calculations | zen, zen2 | |
| slepc | SLEPc: Scalable Library for Eigenvalue Problem Computations | zen2 | |
| smokeview | Smokeview: Visualization tool for FDS and CFAST output | x86_64 | |
| spfft | SpFFT: 3D FFT library for sparse frequency domain data | x86_64, zen, zen2 | |
| spglib | spglib: C library for finding and handling crystal symmetries | zen, zen2 | |
| suite-sparse | suite-sparse: Suite of Sparse Matrix algorithms | zen, zen2 | |
| superlu | superlu: Sparse Linear system solver (sequential) | zen, zen2 | |
| superlu-dist | superlu-dist: Sparse Linear system solver (distributed mem/MPI) | x86_64, zen, zen2 | |
| superlu-mt | superlu-mt: Sparse Linear system solver (multithreaded) | zen, zen2 | |
| swig | swig: compiler to interface C/C++ libraries to Perl, Python, etc | zen, zen2 | |
| sz | sz: Error-bounded Lossy Compressor for HPC Data | zen, zen2 | Yes |
| tecplot360 | Tecplot360: CFD visualization software | x86_64 | |
| tensorflow | tensorflow: Open-source software library for machine intelligence | zen, zen2 | Yes |
| tensorflowORIG | tensorflowORIG: Open-source software library for machine intelligence | zen, zen2 | |
| toolchain | toolchain: Compiler/library toolkits | x86_64 | |
| aocc | aocc: AOCC Compiler Toolchains | x86_64 | |
| gcc | gcc: GNU Compiler Toolchains | x86_64 | |
| intel | intel: Intel Classic Compiler Toolchains | x86_64 | |
| tophat | tophat: Spliced read mapper for RNA-Seq | x86_64 | |
| trilinos | Trilinos: Solvers collection including linear, non-linear, optimization, and transient solvers | zen2 | |
| hello-umd | hello-umd: Simple Hello world binary | x86_64, zen, zen2 | Yes |
| us3d | us3d: Aeordynamic and Aerothermodynamic Simulations Software | skylake_avx512, x86_64 | |
| vasp | vasp: VASP: Vienna Ab-initio Simulation Package | zen2 | |
| virtualgl | virtualgl: Toolkit to allow remote display to run OpenGL applications with full hardware acceleration | zen, zen2 | |
| 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 | zen, zen2 | |
| vtk | vtk: 3D computer graphics, image processing and visualization library | zen, zen2 | Yes |
| wannier90 | Wannier90: tool to calculate maximally-localized Wannier functions | x86_64, zen, zen2 | Yes |
| xerces-c | xerces-c: validating XML parser in C++ | zen, zen2 | |
| xssp | xssp: Secondary structure assignments for entries in the Protein Data Bank | zen, zen2 | Yes |
| xz | xz: Lossless compression utility and library | x86_64, zen, zen2 | |
| zfp | zfp: Library for lossy compression of multidimensional arrays | zen, zen2 | |
| zlib | zlib: General purpose, patent-free compression ibrary | x86_64, zen, zen2 | |
| zoltan | zoltan: Toolkit for parallel combinatorial algorithms | x86_64, zen, zen2 | Yes |
| zstd | zstd: Fast, lossless compression algorithm | x86_64, zen, zen2 |
This section lists all software 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 |
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.
|
|
These sections are still under development. We hope to have it more
accurate in the near future.
|
| Extension name | Version |
|---|---|
| absl-py | 0.13.0 |
| aiohttp | 3.8.1 |
| aiosignal | 1.2.0 |
| appdirs | 1.4.4 |
| argon2-cffi-bindings | 21.2.0 |
| argon2-cffi | 21.3.0 |
| asdf | 2.4.2 |
| astropy | 4.0.1.post1 |
| async-timeout | 4.0.2 |
| attrs | 21.4.0 |
| audioread | 2.1.8 |
| automat | 20.2.0 |
| babel | 2.9.1 |
| backcall | 0.2.0 |
| beautifulsoup4 | 4.10.0 |
| bintrees | 2.0.7 |
| biopython | 1.78 |
| bleach | 4.1.0 |
| blinker | 1.4 |
| bottleneck | 1.3.2 |
| cachetools | 4.2.4 |
| certifi | 2021.10.8 |
| cffi | 1.15.0 |
| cftime | 1.0.3.4 |
| charset-normalizer | 2.0.12 |
| cmyt | 1.1.2 |
| colorspacious | 1.1.2 |
| constantly | 15.1.0 |
| contourpy | 1.0.5 |
| cryptography | 35.0.0 |
| cssselect | 1.1.0 |
| cycler | 0.11.0 |
| cython | 0.29.24 |
| debugpy | 1.5.1 |
| decorator | 5.1.1 |
| defusedxml | 0.7.1 |
| docutils | 0.18 |
| entrypoints | 0.4 |
| envmodules | 0.1 |
| fastjsonschema | 2.15.1 |
| flake8 | 4.0.1 |
| flatbuffers | 2.0 |
| frozenlist | 1.3.0 |
| fsspec | 2021.7.0 |
| future | 0.18.2 |
| gast | 0.4.0 |
| gevent | 1.5.0 |
| gmpy2 | 2.1.2 |
| google-auth | 1.6.3 |
| greenlet | 1.1.2 |
| griddataformats | 0.5.0 |
| gsd | 1.9.3 |
| h5py | 3.6.0 |
| html5lib | 1.1 |
| hyperlink | 21.0.0 |
| idna | 3.3 |
| imageio | 2.10.3 |
| importlib-metadata | 4.11.1 |
| importlib-resources | 5.3.0 |
| incremental | 21.3.0 |
| iniconfig | 1.1.1 |
| ipykernel | 6.4.1 |
| ipython-genutils | 0.2.0 |
| ipython | 7.23.1 |
| ipywidgets | 7.7.0 |
| jax | 0.2.25 |
| jaxlib | 0.1.74 |
| jedi | 0.18.1 |
| jinja2 | 3.0.3 |
| jmespath | 0.10.0 |
| joblib | 1.1.0 |
| jplephem | 2.9 |
| jsonschema | 4.4.0 |
| jupyter-client | 7.0.6 |
| jupyter-core | 4.7.1 |
| jupyterlab-pygments | 0.1.2 |
| jupyterlab-widgets | 1.1.0 |
| kiwisolver | 1.3.2 |
| kwant | 1.4.2 |
| labmath | 2.2.0 |
| librosa | 0.9.1 |
| llvmlite | 0.37.0 |
| lxml | 4.8.0 |
| m2r | 0.2.1 |
| mako | 1.1.6 |
| markdown | 3.3.4 |
| markupsafe | 2.0.1 |
| matplotlib-inline | 0.1.3 |
| matplotlib | 3.4.3 |
| mccabe | 0.6.1 |
| mistune | 0.8.4 |
| mmtf-python | 1.1.2 |
| mock | 4.0.3 |
| more-itertools | 8.12.0 |
| mpi4py | 3.1.2 |
| mpmath | 1.2.1 |
| msgpack | 1.0.2 |
| multidict | 6.0.2 |
| nbclient | 0.5.5 |
| nbconvert | 6.5.0 |
| nbformat | 5.4.0 |
| nest-asyncio | 1.5.4 |
| netcdf4 | 1.5.3 |
| networkx | 2.7.1 |
| nibabel | 3.2.1 |
| notebook | 6.4.11 |
| numba | 0.54.0 |
| numexpr | 2.7.3 |
| numpy | 1.19.5 |
| oauthlib | 3.1.1 |
| opt-einsum | 3.3.0 |
| optax | 0.1.4 |
| packaging | 21.0 |
| pandas | 1.3.4 |
| pandocfilters | 1.5.0 |
| parso | 0.8.2 |
| patsy | 0.5.1 |
| pexpect | 4.8.0 |
| pickleshare | 0.7.5 |
| pillow | 8.4.0 |
| pluggy | 1.0.0 |
| pooch | 1.5.2 |
| prometheus-client | 0.12.0 |
| prompt-toolkit | 3.0.29 |
| protobuf | 3.17.3 |
| psutil | 5.8.0 |
| ptyprocess | 0.7.0 |
| py | 1.11.0 |
| pyaml | 21.8.3 |
| pyasn1-modules | 0.2.8 |
| pyasn1 | 0.4.8 |
| pybind11 | 2.6.2 |
| pycodestyle | 2.8.0 |
| pycparser | 2.20 |
| pycuda | 2021.1 |
| pydeprecate | 0.3.1 |
| pyflakes | 2.4.0 |
| pygments | 2.10.0 |
| pyjwt | 2.1.0 |
| pymumps | 0.3.2 |
| pyparsing | 2.4.7 |
| pyrsistent | 0.18.0 |
| pysocks | 1.7.1 |
| pytest | 6.2.5 |
| python-dateutil | 2.8.2 |
| pytools | 2021.2.9 |
| pytz | 2021.3 |
| pywavelets | 1.1.1 |
| pyyaml | 6.0 |
| pyzmq | 22.3.0 |
| regex | 2020.11.13 |
| requests | 2.26.0 |
| resampy | 0.2.2 |
| rsa | 4.7.2 |
| scikit-image | 0.18.3 |
| scikit-learn | 1.0.1 |
| scipy | 1.7.1 |
| semantic-version | 2.8.2 |
| send2trash | 1.8.0 |
| setuptools-rust | 0.12.1 |
| setuptools | 62.3.2 |
| sip | 4.19.21 |
| six | 1.16.0 |
| snowballstemmer | 2.0.0 |
| sortedcontainers | 2.1.0 |
| soundfile | 0.11.0 |
| soupsieve | 2.2.1 |
| spams | 2.6.2.5 |
| statsmodels | 0.12.2 |
| sympy | 1.8 |
| tables | 3.6.1 |
| tensorboardx | 2.5.1 |
| terminado | 0.12.1 |
| threadpoolctl | 3.0.0 |
| tifffile | 2021.11.2 |
| tinyarray | 1.2.3 |
| tinycss2 | 1.1.1 |
| toml | 0.10.2 |
| tomli-w | 1.0.0 |
| tomli | 1.2.1 |
| tornado | 6.1 |
| tqdm | 4.62.3 |
| traitlets | 5.1.1 |
| twisted | 21.7.0 |
| typing-extensions | 4.1.1 |
| unyt | 2.9.2 |
| urllib3 | 1.26.6 |
| voluptuous | 0.11.7 |
| wcwidth | 0.2.5 |
| webencodings | 0.5.1 |
| werkzeug | 2.0.2 |
| widgetsnbextension | 3.6.0 |
| yarl | 1.7.2 |
| yt | 4.1.2 |
| zipp | 3.6.0 |
| zope-interface | 5.4.0 |
| Extension name | Version |
|---|---|
| absl-py | 0.13.0 |
| asn1crypto | 1.4.0 |
| attrs | 21.4.0 |
| azure-common | 1.1.25 |
| azure-core | 1.21.1 |
| azure-storage-blob | 12.9.0 |
| biopython | 1.78 |
| bleach | 4.1.0 |
| blinker | 1.4 |
| bottleneck | 1.3.2 |
| cachetools | 4.2.4 |
| certifi | 2021.10.8 |
| cffi | 1.15.0 |
| cftime | 1.0.3.4 |
| charm4py | 1.0 |
| charset-normalizer | 2.0.12 |
| click | 8.0.3 |
| cryptography | 2.7 |
| entrypoints | 0.3 |
| envmodules | 0.1 |
| fastjsonschema | 2.15.1 |
| flake8 | 3.7.8 |
| future | 0.17.1 |
| gast | 0.3.3 |
| google-auth | 1.6.3 |
| google-pasta | 0.2.0 |
| greenlet | 1.1.2 |
| griddataformats | 0.5.0 |
| idna | 3.3 |
| importlib-metadata | 1.7.0 |
| importlib-resources | 5.3.0 |
| isodate | 0.6.1 |
| joblib | 1.1.0 |
| jsonschema | 4.4.0 |
| jupyter-client | 7.0.6 |
| jupyter-core | 4.7.1 |
| keras-preprocessing | 1.1.0 |
| llvmlite | 0.37.0 |
| markdown | 3.3.4 |
| markupsafe | 2.0.1 |
| mccabe | 0.6.1 |
| mock | 4.0.3 |
| mpi4py | 3.0.3 |
| mpmath | 1.2.1 |
| msgpack | 0.6.2 |
| msrest | 0.6.21 |
| nbclient | 0.5.5 |
| nbconvert | 6.0.1 |
| nbformat | 5.4.0 |
| netcdf4 | 1.5.3 |
| networkx | 2.6.3 |
| numba | 0.54.0 |
| numexpr | 2.7.3 |
| numpy | 1.18.4 |
| oauthlib | 3.1.0 |
| packaging | 21.0 |
| pandas | 1.0.3 |
| patsy | 0.5.1 |
| protobuf | 3.12.2 |
| pyasn1-modules | 0.2.8 |
| pyasn1 | 0.4.8 |
| pybind11 | 2.5.0 |
| pycodestyle | 2.5.0 |
| pycparser | 2.20 |
| pyflakes | 2.1.1 |
| pyjwt | 1.7.1 |
| pyopenssl | 19.0.0 |
| pyparsing | 2.4.7 |
| pyrsistent | 0.18.0 |
| pysocks | 1.7.1 |
| python-dateutil | 2.8.2 |
| pytz | 2021.3 |
| pyyaml | 5.3.1 |
| regex | 2019.11.1 |
| requests-oauthlib | 1.3.0 |
| requests | 2.26.0 |
| rsa | 4.7.2 |
| scikit-learn | 0.23.0 |
| scipy | 1.4.1 |
| setuptools | 58.2.0 |
| sip | 4.19.21 |
| six | 1.16.0 |
| snowballstemmer | 2.0.0 |
| statsmodels | 0.10.2 |
| sympy | 1.4 |
| tables | 3.6.1 |
| threadpoolctl | 3.0.0 |
| tinyarray | 1.2.3 |
| toml | 0.10.2 |
| tomli-w | 1.0.0 |
| tomli | 1.2.1 |
| tomlkit | 0.7.2 |
| tornado | 6.1 |
| traitlets | 5.1.1 |
| typing-extensions | 3.10.0.2 |
| urllib3 | 1.25.6 |
| webencodings | 0.5.1 |
| werkzeug | 2.0.2 |
| wheel | 0.37.0 |
| zipp | 3.6.0 |
| 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 |
| Extension name | Version |
|---|---|
| abind | 1.4-5 |
| amap | 0.8-18 |
| annotate | 1.68.0 |
| annotationdbi | 1.52.0 |
| ape | 5.4-1 |
| argparse | 2.0.3 |
| askpass | 1.1 |
| assertthat | 0.2.1 |
| backports | 1.2.1 |
| base64enc | 0.1-3 |
| bayesm | 3.1-4 |
| bessel | 0.6-0 |
| bh | 1.72.0-3 |
| biasedurn | 1.07 |
| biobase | 2.50.0 |
| biocfilecache | 1.14.0 |
| biocgenerics | 0.36.0 |
| biocio | 1.6.0 |
| biocparallel | 1.24.1 |
| biomart | 2.46.2 |
| biostrings | 2.58.0 |
| bit64 | 4.0.5 |
| bit | 4.0.4 |
| bitops | 1.0-6 |
| blob | 1.2.1 |
| boot | 1.3-28 |
| brew | 1.0-7 |
| brio | 1.1.0 |
| broom | 0.8.0 |
| bslib | 0.3.1 |
| cachem | 1.0.6 |
| callr | 3.7.0 |
| catools | 1.18.2 |
| cellranger | 1.1.0 |
| checkmate | 2.0.0 |
| cli | 3.0.1 |
| clipr | 0.7.1 |
| cluster | 2.1.0 |
| cmdstanr | 0.5.1 |
| codetools | 0.2-18 |
| colorspace | 2.0-0 |
| commonmark | 1.8.0 |
| covr | 3.5.1 |
| cowplot | 1.1.1 |
| cpp11 | 0.4.0 |
| crayon | 1.4.1 |
| credentials | 1.3.2 |
| crosstalk | 1.2.0 |
| ctc | 1.64.0 |
| ctmm | 1.0.0 |
| curl | 4.3.2 |
| data-table | 1.14.2 |
| dbi | 1.1.0 |
| dbplyr | 2.1.1 |
| delayedarray | 0.16.1 |
| deldir | 1.0-6 |
| deoptimr | 1.0-11 |
| desc | 1.2.0 |
| deseq2 | 1.30.0 |
| devtools | 2.3.2 |
| diffobj | 0.3.3 |
| digest | 0.6.28 |
| distributional | 0.3.0 |
| doparallel | 1.0.17 |
| dosnow | 1.0.20 |
| dotcall64 | 1.0-1 |
| dplyr | 1.0.7 |
| dqrng | 0.3.0 |
| dt | 0.23 |
| dtplyr | 1.2.1 |
| dynamictreecut | 1.63-1 |
| edger | 3.32.1 |
| ellipsis | 0.3.2 |
| evaluate | 0.14 |
| expm | 0.999-6 |
| fansi | 0.5.0 |
| farver | 2.1.0 |
| fastcluster | 1.1.25 |
| fastmap | 1.1.0 |
| fasttime | 1.1-0 |
| fields | 13.3 |
| findpython | 1.0.7 |
| fitdistrplus | 1.1-8 |
| fnn | 1.1.3.1 |
| forcats | 0.5.1 |
| foreach | 1.5.2 |
| foreign | 0.8-81 |
| formatr | 1.7 |
| formula | 1.2-4 |
| fs | 1.5.0 |
| futile-logger | 1.4.3 |
| futile-options | 1.0.1 |
| future-apply | 1.9.0 |
| future | 1.26.1 |
| genefilter | 1.72.1 |
| geneplotter | 1.68.0 |
| generics | 0.1.1 |
| genomeinfodb | 1.26.2 |
| genomeinfodbdata | 1.2.1 |
| genomicranges | 1.42.0 |
| geomorph | 4.0.3 |
| geosphere | 1.5-14 |
| gert | 1.6.0 |
| ggdendro | 0.1.23 |
| ggplot2 | 3.3.5 |
| ggrepel | 0.9.1 |
| ggridges | 0.5.3 |
| gh | 1.3.0 |
| gitcreds | 0.1.1 |
| glimma | 2.0.0 |
| globals | 0.15.0 |
| glue | 1.4.2 |
| gmedian | 1.2.7 |
| gmp | 0.6-5 |
| go-db | 3.12.1 |
| goftest | 1.2-3 |
| goplot | 1.0.2 |
| gplots | 3.1.1 |
| gridextra | 2.3 |
| gsl | 2.1-6 |
| gstat | 2.0-9 |
| gtable | 0.3.0 |
| gtools | 3.9.2.1 |
| haven | 2.5.0 |
| here | 1.0.1 |
| highr | 0.9 |
| hmisc | 4.4-2 |
| hms | 1.1.1 |
| htmltable | 2.1.0 |
| htmltools | 0.5.1.1 |
| htmlwidgets | 1.5.3 |
| httpuv | 1.6.5 |
| httr | 1.4.2 |
| hwriter | 1.3.2.1 |
| ica | 1.0-2 |
| igraph | 1.2.6 |
| impute | 1.70.0 |
| ini | 0.3.1 |
| intervals | 0.15.2 |
| iranges | 2.24.1 |
| irdisplay | 1.1 |
| irkernel | 1.3 |
| irlba | 2.3.5 |
| isoband | 0.2.3 |
| iterators | 1.0.14 |
| jpeg | 0.1-8.1 |
| jquerylib | 0.1.4 |
| jsonlite | 1.7.2 |
| kernlab | 0.9-30 |
| kernsmooth | 2.23-18 |
| knitr | 1.33 |
| ks | 1.13.5 |
| labeling | 0.4.2 |
| lambda-r | 1.2.4 |
| later | 1.3.0 |
| lattice | 0.20-44 |
| latticeextra | 0.6-29 |
| lazyeval | 0.2.2 |
| leiden | 0.3.9 |
| lifecycle | 1.0.1 |
| limma | 3.52.1 |
| listenv | 0.8.0 |
| lme4 | 1.1-29 |
| lmtest | 0.9-40 |
| locfit | 1.5-9.4 |
| lubridate | 1.8.0 |
| magrittr | 2.0.1 |
| manipulate | 1.0.1 |
| manipulatewidget | 0.11.1 |
| maps | 3.3.0 |
| markdown | 1.1 |
| mass | 7.3-54 |
| matrix | 1.3-4 |
| matrixgenerics | 1.2.1 |
| matrixstats | 0.61.0 |
| mclust | 5.4.10 |
| memoise | 1.1.0 |
| mgcv | 1.8-38 |
| mime | 0.11 |
| miniui | 0.1.1.1 |
| minqa | 1.2.4 |
| misc3d | 0.9-1 |
| modelr | 0.1.8 |
| multicool | 0.1-12 |
| munsell | 0.5.0 |
| mvtnorm | 1.1-3 |
| ncdf4 | 1.17 |
| nlme | 3.1-153 |
| nloptr | 2.0.3 |
| nnet | 7.3-14 |
| numderiv | 2016.8-1.1 |
| openssl | 1.4.5 |
| parallelly | 1.31.1 |
| patchwork | 1.1.1 |
| pbapply | 1.5-0 |
| pbdzmq | 0.3-7 |
| pbivnorm | 0.6.0 |
| pbkrtest | 0.5.1 |
| pillar | 1.6.4 |
| pkgbuild | 1.2.0 |
| pkgconfig | 2.0.3 |
| pkgload | 1.1.0 |
| plogr | 0.2.0 |
| plot3d | 1.4 |
| plotly | 4.10.0 |
| plyr | 1.8.6 |
| png | 0.1-7 |
| polyclip | 1.10-0 |
| posterior | 1.2.1 |
| pracma | 2.3.8 |
| praise | 1.0.0 |
| preprocesscore | 1.58.0 |
| prettyunits | 1.1.1 |
| processx | 3.5.2 |
| progress | 1.2.2 |
| promises | 1.2.0.1 |
| ps | 1.5.0 |
| purrr | 0.3.4 |
| quadprog | 1.5-8 |
| quantmod | 0.4.20 |
| qvalue | 2.22.0 |
| r-methodss3 | 1.8.1 |
| r-oo | 1.24.0 |
| r-utils | 2.10.1 |
| r6 | 2.5.0 |
| randomforest | 4.6-14 |
| rann | 2.6.1 |
| rappdirs | 0.3.3 |
| raster | 3.5-15 |
| rcmdcheck | 1.4.0 |
| rcolorbrewer | 1.1-2 |
| rcpp | 1.0.7 |
| rcppannoy | 0.0.19 |
| rcpparmadillo | 0.10.1.2.2 |
| rcppeigen | 0.3.3.9.1 |
| rcppparallel | 5.0.2 |
| rcppprogress | 0.4.2 |
| rcpptoml | 0.1.7 |
| rcurl | 1.98-1.2 |
| readr | 2.1.2 |
| readxl | 1.3.1 |
| rematch2 | 2.1.2 |
| rematch | 1.0.1 |
| remotes | 2.4.2 |
| repr | 1.1.4 |
| reprex | 2.0.1 |
| reshape2 | 1.4.3 |
| restfulr | 0.0.13 |
| reticulate | 1.25 |
| rex | 1.2.1 |
| rgdal | 1.5-32 |
| rgl | 0.104.16 |
| rhtslib | 1.99.5 |
| rjson | 0.2.21 |
| rlang | 0.4.12 |
| rmarkdown | 2.11 |
| rmpfr | 0.8-9 |
| rmpi | 0.6-9 |
| robustbase | 0.95-0 |
| rocr | 1.0-11 |
| rots | 1.18.0 |
| roxygen2 | 7.1.2 |
| rpart | 4.1-15 |
| rprojroot | 2.0.2 |
| rrpp | 1.2.3 |
| rspectra | 0.16-1 |
| rsqlite | 2.2.2 |
| rstudioapi | 0.13 |
| rsvd | 1.0.5 |
| rtsne | 0.16 |
| rversions | 2.1.1 |
| rvest | 1.0.2 |
| s4vectors | 0.28.1 |
| sass | 0.4.1 |
| scales | 1.1.1 |
| scattermore | 0.8 |
| sctransform | 0.3.3 |
| selectr | 0.4-2 |
| sessioninfo | 1.1.1 |
| seurat | 3.2.3 |
| shape | 1.4.6 |
| shiny | 1.5.0 |
| shinyjs | 2.1.0 |
| sitmo | 2.0.2 |
| sm | 2.2-5.6 |
| snow | 0.4-3 |
| sourcetools | 0.1.7 |
| sp | 1.4-7 |
| spacetime | 1.2-6 |
| spam | 2.8-0 |
| spatstat-data | 2.2-0 |
| spatstat-utils | 2.3-1 |
| spatstat | 1.64-1 |
| squarem | 2021.1 |
| statmod | 1.4.36 |
| stringi | 1.6.2 |
| stringr | 1.4.0 |
| summarizedexperiment | 1.20.0 |
| survival | 3.2-7 |
| sys | 3.4 |
| tensor | 1.5 |
| tensora | 0.36.2 |
| terra | 1.5-21 |
| testthat | 3.0.1 |
| tibble | 3.1.5 |
| tidyr | 1.1.4 |
| tidyselect | 1.1.1 |
| tidyverse | 1.3.0 |
| tinytex | 0.39 |
| tseries | 0.10-48 |
| ttr | 0.24.3 |
| tximport | 1.24.0 |
| tximportdata | 1.24.0 |
| tzdb | 0.2.0 |
| usethis | 2.0.0 |
| utf8 | 1.1.4 |
| uuid | 1.1-0 |
| uwot | 0.1.11 |
| vctrs | 0.3.8 |
| viridis | 0.5.1 |
| viridislite | 0.3.0 |
| vroom | 1.5.7 |
| waldo | 0.2.3 |
| webshot | 0.5.3 |
| wgcna | 1.69 |
| whisker | 0.4 |
| withr | 2.4.2 |
| xfun | 0.31 |
| xgboost | 1.3.2.1 |
| xml2 | 1.3.2 |
| xml | 3.99-0.5 |
| xopen | 1.0.0 |
| xtable | 1.8-4 |
| xts | 0.12.1 |
| xvector | 0.30.0 |
| yaml | 2.2.1 |
| zip | 2.2.0 |
| zlibbioc | 1.36.0 |
| zoo | 1.8-10 |