All software is categorized by its usage or by the scientific field that uses it. Each software package contains a link to documentation, its availability, and a short description. Availability is broken down into 3 categories:
- Open Source
- Free, open source software
- Site License
- Sitewide license available to all users
- Group License
- License paid for by one or more groups
Open Source and Site License software can be used by all users. Group License software is only available to groups that pay for it. If you are a member of a group that pays for a particular software license and would like access to it, ask your PI to email us at firstname.lastname@example.org asking us to add you to the group.
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|CUDA||Open Source||CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU).|
|G95||Open Source||G95 is a stable, production Fortran 95 compiler available for multiple cpu architectures and operating systems. Innovations and optimizations continue to be worked on. Parts of the F2003 standard have been implemented in g95.|
|GCC||Open Source||The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages.|
|Intel||Site License||The Intel® compiler suites offer C, C++ and Fortran compilers with optimization features and multithreading capabilities, highly optimized performance libraries, and error-checking, security, and profiling tools.|
|Java||Open Source||JDK (Java SE Development Kit). For Java Developers. Includes a complete JRE plus tools for developing, debugging, and monitoring Java applications.|
|NAG||Site License||The NAG Fortran Compiler provides support for Fortran 2008 (partial), Fortran 2003 (almost complete), Fortran 95 and OpenMP 3.1.|
|NASM||Open Source||The Netwide Assembler, NASM, is an 80×86 and x86-64 assembler designed for portability and modularity.|
|PGI||Site License||PGI compilers offer world-class performance and features including auto-parallelization for multicore, OpenMP directive-based parallelization, and support for the PGI Unified Binary™ technology. The PGI Unified Binary streamlines cross-platform support by combining into a single executable file code optimized for multiple x64 processors.|
MPI and Communications
Message Passing Interface (MPI)
Software Availability Description MPICH Open Source MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard. MVAPICH2 Open Source The MVAPICH2 software, based on MPI 3.1 standard, delivers the best performance, scalability and fault tolerance for high-end computing systems and servers using InfiniBand, Omni-Path, Ethernet/iWARP, and RoCE networking technologies. OpenMPI Open Source The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.
Software Availability Description Hydra Open Source Hydra is a process management system for starting parallel jobs. Hydra is designed to natively work with existing launcher daemons (such as ssh, rsh, fork), as well as natively integrate with resource management systems (such as slurm, pbs, sge).
Software Availability Description Global Arrays Open Source Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model. It provides primitives for one-sided communication (Get, Put, Accumulate) and Atomic Operations (read increment). It supports blocking and non-blocking primtives, and supports location consistency.
Software Availability Description bbFTP Open Source bbFTP is a file transfer software. It implements its own transfer protocol, which is optimized for large files (larger than 2GB) and secure as it does not read the password in a file and encrypts the connection information. Globus Toolkit Open Source The Globus® Toolkit is an open source software toolkit used for building grids. It is being developed by the Globus Alliance and many others all over the world. A growing number of projects and companies are using the Globus Toolkit to unlock the potential of grids for their cause.
Due to the increasing amount of python packages we switched to Anaconda python distribution for python package management.
Anaconda modules that we provide include common set of packages: pip, numpy, scipy, matplotlib, mpi4py, etc.
Use anaconda/4.4.0 module if you need python 2 and use anaconda3/5.0.0 or anaconda3/5.2.0 if you need python 3.
If the anaconda module does not have python package that you need already installed you can create anaconda environment inside your home directory and install needed packages there.
To create a new environment:
Load the anaconda module that you need:
$ module load anaconda/version
To list the installed packages run:
$ conda list
The following command will create anaconda environment in your home directory:
$ conda create -n environment_name
To activate that environment run:
$ source activate environment_name
Now you are ready to installed the package:
$ conda install package_name
The instructions on how to use anaconda are at https://conda.io/docs/index.html
If the packages are not provided with pip or anaconda and the procedure for installation is very complex feel free to email to email@example.com
Math Libraries and Languages
BLAS/LAPACK and FFT
Software Availability Description ATLAS Open Source ATLAS (Automatically Tuned Linear Algebra Software) provides highly optimized Linear Algebra kernels for arbitrary cache-based architectures. ATLAS provides ANSI C and Fortran77 interfaces for the entire BLAS API, and a small portion of the LAPACK API. FFTW Open Source FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). MKL Site License The Intel® Math Kernel Library (Intel® MKL) features highly optimized, threaded and vectorized functions to maximize performance on each processor family. It utilizes de facto standard C and Fortran APIs for compatibility with BLAS, LAPACK and FFTW functions from other math libraries. OpenBLAS Open Source OpenBLAS is an optimized BLAS library.
Software Availability Description polymake Open Source polymake is open source software for research in polyhedral geometry. It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, graphs, tropical hypersurfaces, and other objects.
Software Availability Description IDL Site License IDL (Interactive Data Language) is a programming language used for data analysis. It is popular in particular areas of science, such as astronomy, atmospheric physics and medical imaging. MATLAB Site License MATLAB (MATrix LABoratory) is a multi-paradigm numerical computing environment and fourth-generation programming language. A proprietary programming language developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, Fortran and Python. Octave Open Source GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable. R Open Source R is a language and environment for statistical computing and graphics.
Other Math Libraries
Software Availability Description Armadillo Open Source Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use. Eigen Open Source Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. GSL Open Source The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. METIS Open Source METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. MPFR Open Source The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. PETSc Open Source PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It supports MPI, and GPUs through CUDA or OpenCL, as well as hybrid MPI-GPU parallelism. SUNDIALS Open Source SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers) Wannier90 Open Source Calculates maximally-localised Wannier functions (MLWFs).
Version Control Systems (VCS)
Software Availability Description Git Open Source Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Mercurial Open Source Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. Subversion Open Source Apache Subversion – an open source version control system.
Software Availability Description Automake Open Source Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards. Autoconf Open Source Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. CMake Open Source CMake is an open-source, cross-platform family of tools designed to build, test and package software. libtool Open Source GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. Make Open Source GNU Make is a tool which controls the generation of executables and other non-source files of a program from the program’s source files. Makedepf90 Open Source Makedepf90 is a program for automatic creation of Makefile dependency lists for Fortran source code. SCons Open Source SCons is an Open Source software construction tool—that is, a next-generation build tool. Think of SCons as an improved, cross-platform substitute for the classic Make utility with integrated functionality similar to autoconf/automake and compiler caches such as ccache. In short, SCons is an easier, more reliable and faster way to build software.
Software Availability Description Docutils Open Source Docutils is an open-source text processing system for processing plaintext documentation into useful formats, such as HTML, LaTeX, man-pages, open-document or XML. It includes reStructuredText, the easy to read, easy to use, what-you-see-is-what-you-get plaintext markup language. Sphinx Open Source Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. It was originally created for the new Python documentation, and it has excellent facilities for the documentation of Python projects, but C/C++ is already supported as well, and it is planned to add special support for other languages as well.
File Storage and Compression
Common Data Format (CDF)
Software Availability Description HDF4 Open Source HDF4 (also known as HDF) is a library and multi-object file format for storing and managing data between machines. HDF5 Open Source HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format. NCO Open Source The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. NetCDF Open Source NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. PnetCDF Open Source PnetCDF is a library providing high-performance parallel I/O while still maintaining file-format compatibility with Unidata’s NetCDF
Software Availability Description pigz Open Source A parallel implementation of gzip for modern multi-processor, multi-core machines. Szip Open Source An implementation of the extended-Rice lossless compression algorithm. It provides lossless compression of scientific data, and is provided with HDF software products.
Graphics and Visualization
Graphics, Audio, and Video
Software Availability Description FFmpeg Open Source A complete, cross-platform solution to record, convert and stream audio and video. ImageMagick Open Source ImageMagick is a software suite used to create, edit, compose, or convert bitmap images. JasPer Open Source The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard (i.e., ISO/IEC 15444-1).
Software Availability Description gnuplot Open Source Gnuplot is a portable command-line driven graphing utility. It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. GTK+ Open Source GTK+, or the GIMP Toolkit, is a multi-platform toolkit for creating graphical user interfaces. Offering a complete set of widgets, GTK+ is suitable for projects ranging from small one-off tools to complete application suites. h5utils Open Source h5utils is a set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format. Jmol Open Source Jmol: an open-source Java viewer for chemical structures in 3D. NCL Open Source The NCAR Command Language (NCL), a product of the Computational & Information Systems Laboratory at the National Center for Atmospheric Research (NCAR) and sponsored by the National Science Foundation, is a free interpreted language designed specifically for scientific data processing and visualization. Ncview Open Source Ncview is a visual browser for netCDF format files. ParaView Open Source ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities. Qt Open Source Qt is a comprehensive cross-platform C++ application framework. tkdiff Open Source tkdiff is a graphical front end to the diff program. It provides a side-by-side view of the differences between two files, along with several innovative features such as diff bookmarks and a graphical map of differences for quick navigation. VisIt Open Source VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. VMD Open Source VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VTK Open Source The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing, and visualization.
Debuggers and Performance
|Allinea Forge||Site License||Allinea Forge is the complete toolsuite for software development – with everything needed to debug, profile, optimize, edit and build C, C++ and Fortran applications on Linux for high performance – from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA. Includes DDT and MAP.|
|Allinea Reports||Site License||Allinea Performance Reports are the most effective way to characterize and understand the performance of HPC application runs. One single-page HTML report elegantly answers a range of vital questions for any HPC site.|
|HPCToolkit||Open Source||HPCToolkit is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to the nation’s largest supercomputers.|
|Intel VTune Amplifier||Site License||Intel VTune Amplifier performance profiler is a commercial application for software performance analysis of 32 and 64-bit x86 based machines. It has both a GUI (graphical user interface) and command line tools. To use this on Bebop: SSH into Bebop with X forwarding enabled and then do a module load <module name> where <module name> is any of the intel-parallel-studio modules we have available (you can get a list of options with module avail intel-parallel-studio). To start the application, run amplxe-gui.|
|PAPI||Open Source||PAPI (Performance Application Programming Interface) provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors.|
|TAU||Open Source||TAU (Tuning and Analysis Utilities) Performance System® is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, UPC, Java, Python.|
|TotalView||Site License||Faster fault isolation, improved memory optimization, and dynamic visualization for your high performance computing apps. TotalView for HPC is a scalable and intuitive debugger for parallel applications written in C, C++, and Fortran that simplifies and shortens the process of developing, debugging, and optimizing complex applications. Purpose-built for multicore and parallel computing, TotalView for HPC delivers a set of tools providing unprecedented control over processes and thread execution, along with deep visibility into program states and data.|
|Valgrind||Open Source||Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail.|
|BLAST||Open Source||BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.|
|HMMER||Open Source||HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).|
|MG-RAST||Open Source||MG-RAST (the Metagenomics RAST) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data.|
|mpiBLAST||Open Source||mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors.|
Chemistry and Materials
|ABINIT||Open Source||ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.|
|ASE||Open Source||The Atomic Simulation Environment (ASE) is a set of tools and Python modules for atomistic simulations.|
|Cantera||Open Source||Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes.|
|CP2K||Open Source||CP2K can perform atomistic simulations of solid state, liquid, molecular, and biological systems.|
|CPMD||Group License||CPMD is a plane wave/pseudopotential Density Functional Theory (DFT) code , designed for ab-initio molecular dynamics.|
|CRYSTAL||Group License||The CRYSTAL program computes the electronic structure of periodic systems (Hartree Fock or DFT) with Gaussian basis sets.|
|Elk||Open Source||An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features.|
|GAMESS||Site License||The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.|
|Gaussian||Group License||Gaussian provides state-of-the-art capabilities for electronic structure modeling.|
|GPAW||Open Source||GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).|
|HOOMD-blue||Open Source||HOOMD-blue is a general-purpose particle simulation toolkit.|
|LAMMPS||Open Source||LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state.|
|Libxc||Open Source||Libxc is a library of exchange-correlation functionals for density-functional theory.|
|Molpro||Group License||Molpro is a comprehensive system of ab initio programs for advanced molecular electronic structure calculations. It comprises efficient and well parallelized programs for standard computational chemistry applications, such as DFT with a large choice of functionals, as well as state-of-the art high-level coupled-cluster and multi-reference wave function methods.|
|NAMD||Open Source||NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.|
|NWChem||Open Source||NWChem provides tools that can treat computational chemistry problems efficiently on parallel computing resources.|
|OpenKIM||Open Source||OpenKIM (Knowledgebase of Interatomic Models) is an online suite of open source tools for molecular simulation of materials.|
|ORCA||Open Source||An ab initio, DFT and semiempirical SCF-MO package.|
|PSI4||Open Source||PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties.|
|PWGUI||Open Source||PWgui is a GUI for PWscf based programs from Quantum-ESPRESSO integrated suite of codes for electronic structure calculations and materials modeling at the nanoscale.|
|PWTK||Open Source||PWTK (PWscf ToolKit)is a Tcl scripting interface to PWscf set of programs contained in the Quantum Espresso distribution.|
|Qbox||Open Source||Qbox is a First-Principles Molecular Dynamics code.|
|Quantum ESPRESSO||Open Source||Quantum ESPRESSO is a suite of software for DFT electronic-structure calculations, with plane waves and pseudopotentials.|
|SIESTA||Site License||SIESTA is a computer program to perform efficient linear scaling electronic structure calculations.|
|VASP||Group License||VASP performs ab initio quantum mechanical molecular dynamics with DFT, pseudopotentials and a plane wave basis set.|
In addition to the software listed below, climate modeling software often relies on HDF and NetCDF. These packages can be found under the general category of “File Storage and Compression”.
|CDAT||Open Source||CDAT (Climate Data Analysis Tool) makes use of an open-source, object-oriented, easy-to-learn scripting language (Python) to link together separate software subsystems and packages to form an integrated environment for data analysis.|
|GrADS||Open Source||The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data.|
Engineering and Physics
|ASTRA||Open Source||A Space Charge Tracking Algorithm.|
|CLHEP||Open Source||CLHEP (Class Library for High Energy Physics) is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra.|
|Geant4||Open Source||Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.|
|Libctl||Open Source||libctl is a free Guile-based library implementing flexible control files for scientific simulations.|
|MCNP||Open Source||MCNP is a general-purpose Monte Carlo N-Particle code that can be used for neutron, photon, electron, or coupled neutron/photon/electron transport. The code treats an arbitrary three-dimensional configuration of materials in geometric cells bounded by first- and second-degree surfaces and fourth-degree elliptical tori.|
|Meep||Open Source||Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.|
|MOOSE||Open Source||The Multiphysics Object-Oriented Simulation Environment (MOOSE) is a finite-element, multiphysics framework primarily developed by Idaho National Laboratory.|
|OPAL||Open Source||OPAL (Object Oriented Particle Accelerator Library) is an open source C++ framework for general particle accelerator simulations including 3D space charge, short range wake fields and particle matter interaction.|
|VizGlow||Group License||VizGlow software tool is used for high-fidelity multi-dimensional modeling of non-equilibrium plasma discharges.|
Fluid Dynamics (CFD)
|CONVERGE||Group License||CONVERGE is a revolutionary computational fluid dynamics (CFD) program that eliminates the grid generation bottleneck from the simulation process. CONVERGE was developed by engine simulation experts and is straightforward to use for both engine and non-engine simulations. Unlike many CFD programs, CONVERGE automatically generates a perfectly orthogonal, structured grid at runtime based on simple, user-defined grid control parameters. This grid generation method completely eliminates the need to manually generate a grid. In addition, CONVERGE offers many other features to expedite the setup process and to ensure that your simulations are as computationally efficient as possible.|
|FOAM-extend||Open Source||The foam-extend project is a fork of the OpenFOAM open source library for Computational Fluid Dynamics (CFD).|
|Nek5000||Open Source||Nek5000 is an open source, highly scalable and portable spectral element code designed to simulate unsteady Stokes, unsteady incompressible Navier-Stokes, low Mach-number flows, heat transfer and species transport, and incompressible magnetohydrodynamics (MHD).|
|OpenFOAM||Open Source||OpenFOAM (Open source Field Operation and Manipulation) is a free, open source computational fluid dynamics (CFD) software package released by the OpenFOAM Foundation.|
|STAR-CCM+||Site License||STAR-CCM+ (STAR Computational Continuum Mechanics) CFD solver.|
|STAR-CD||Site License||Legacy CFD solver.|
|Singularity||Open Source||Singularity is a container technology designed for HPC|