# Software

Here you can find a list of the installed software. It is possible that in the meantime new software packages are installed, that have not yet been added to this list. To get an exact overview of all available modules and their versions, you can query a list via the command:

```
module avail
```

For software requests please contact us: phoenix-support@tu-bs.de.

#### **Chemistry** 

- <div class="li">[Gromacs](http://www.gromacs.org/ "http://www.gromacs.org") - A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.   
    </div>
- <div class="li">[NAMD](https://www.ks.uiuc.edu/Research/namd/ "https://www.ks.uiuc.edu/Research/namd/") - A parallel, object-oriented molecular dynamics code designed for high-performance simulations of large biomolecular systems using force fields.   
    </div>
- <div class="li">[LAMMPS](https://www.lammps.org/ "https://www.lammps.org/") - A parallel, classical potential molecular dynamics code for solid-state materials, soft matter and coarse-grained or mesoscopic systems.   
    </div>
- <div class="li">[LIGGGHTS](https://www.cfdem.com/liggghts-open-source-discrete-element-method-particle-simulation-code "https://www.cfdem.com/liggghts-open-source-discrete-element-method-particle-simulation-code") - An Open Source Discrete Element Method Particle Simulation Software.  
    </div>
- <div class="li">[DL\_POLY Classic](https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx "https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx") - A general purpose classical molecular dynamics (MD) simulation software.  
    </div>
- <div class="li">[Gaussian](https://gaussian.com/ "https://gaussian.com/") - A general purpose computational chemistry software package.  
    </div>
- <div class="li">[GOMC](https://gomc.eng.wayne.edu/ "https://gomc.eng.wayne.edu/") - A software for simulating molecular systems using the Metropolis Monte Carlo algorithm.  
    </div>
- <div class="li">[Towhee](http://towhee.sourceforge.net/ "http://towhee.sourceforge.net/") - A Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields.  
    </div>

#### **Biology** 

- <div class="li">[Bowtie](http://bowtie-bio.sourceforge.net/index.shtml "http://bowtie-bio.sourceforge.net/index.shtml") - A fast and memory-efficient short read aligner that aligns short DNA sequences to the human genome.  
    </div>
- <div class="li">[BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi "https://blast.ncbi.nlm.nih.gov/Blast.cgi") - A basic local alignment search tool that finds regions of local similarity between protein or nucleotide sequences.  
    </div>
- <div class="li">[Exonerate](https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate") - A generic tool for pairwise sequence comparison with many alignment models, either exhaustive dynamic programming or a variety of heuristics.  
    </div>
- <div class="li">[ANTs](https://github.com/ANTsX/ANTs "https://github.com/ANTsX/ANTs") - A tool for high-dimensional mappings to capture the statistics of brain structure and function.  
    </div>
- <div class="li">[SAMtools](https://github.com/samtools/ "https://github.com/samtools/") - A Sequence Alignment/Map format for storing large nucleotide sequence alignments.  
    </div>
- <div class="li">[trimAl](http://trimal.cgenomics.org/ "http://trimal.cgenomics.org/") - A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.  
    </div>

#### **Engineering** 

- <div class="li">[ABAQUS](https://doku.rz.tu-bs.de/doku.php?id=hlr:phoenix:nutzeranleitung#starting_abaqus_jobs "https://doku.rz.tu-bs.de/doku.php?id=hlr:phoenix:nutzeranleitung#starting_abaqus_jobs") - A Finite Element Analysis Package for Engineering Application.  
    </div>
- <div class="li">[ANSYS CFX](https://doku.rz.tu-bs.de/doku.php?id=hlr:phoenix:nutzeranleitung#starting_ansys_jobs "https://doku.rz.tu-bs.de/doku.php?id=hlr:phoenix:nutzeranleitung#starting_ansys_jobs") - A computational fluid dynamics solver focused on turbo-machinery (vertex-centered FVM).  
    </div>
- <div class="li">[ANSYS Fluent](https://doku.rz.tu-bs.de/doku.php?id=hlr:phoenix:nutzeranleitung#starting_ansys_jobs "https://doku.rz.tu-bs.de/doku.php?id=hlr:phoenix:nutzeranleitung#starting_ansys_jobs") - A general computational fluid dynamics solver (cell-centered FVM).  
    </div>
- <div class="li">[ANSYS Mechanical](https://doku.rz.tu-bs.de/doku.php?id=hlr:phoenix:nutzeranleitung#starting_ansys_jobs "https://doku.rz.tu-bs.de/doku.php?id=hlr:phoenix:nutzeranleitung#starting_ansys_jobs") - A Package for Coupled Physics Simulations.  
    </div>
- <div class="li">[LS-DYNA](https://www.dynamore.de/en/products/dyna/Introduction?set_language=en "https://www.dynamore.de/en/products/dyna/Introduction?set_language=en") - One of the most advanced simulation tools for nonlinear structural analysis, its core-competency lies in highly nonlinear transient dynamic finite element analysis (FEA).  
    </div>
- <div class="li">[OpenFOAM](https://de.wikipedia.org/wiki/OpenFOAM "https://de.wikipedia.org/wiki/OpenFOAM") - An object-oriented Computational Fluid Dynamics (CFD) toolkit.  
    </div>
- <div class="li">[ParaView](https://www.paraview.org/ "https://www.paraview.org") - An interactive data analysis and visualisation tool with 3D rendering capability.  
    </div>
- <div class="li">[FDS](https://pages.nist.gov/fds-smv/ "https://pages.nist.gov/fds-smv/") - A large-eddy simulation code for low-speed flows, with an emphasis on smoke and heat transport from fires.  
    </div>
- <div class="li">[HyperWorks](https://www.altair.de/hyperworks/ "https://www.altair.de/hyperworks/") - A CAE program that enables finite element analysis, modeling, and simulation.  
    </div>
- <div class="li">[LS-DYNA](https://www.lstc.com/products/ls-dyna "https://www.lstc.com/products/ls-dyna") - An advanced general-purpose multiphysics simulation software package, corecompetency is highly nonlinear transient dynamic finite element analysis (FEA) using explicit time integration.   
    </div>
- <div class="li">[PAM-CRASH](https://www.esi-group.com/pam-crash "https://www.esi-group.com/pam-crash") - A software package used for crash simulation and the design of occupant safety systems, primarily in the automotive industry.  
    </div>
- <div class="li">[SU2](https://github.com/su2code/SU2 "https://github.com/su2code/SU2") - An open-source suite for multiphysics simulation and design.  
    </div>

#### **Numerics** 

- <div class="li">[OpenBLAS](http://www.openblas.net/ "http://www.openblas.net") - BLAS (Basic Linear Algebra Subprograms).   
    </div>
- <div class="li">[FFTW3](https://www.fftw.org/ "https://www.fftw.org/") - A C-subroutine library for computing discrete Fourier transforms.  
    </div>
- <div class="li">[GSL](https://www.gnu.org/software/gsl/ "https://www.gnu.org/software/gsl/") - The GNU Scientific Library (GSL)- a numerical library for C and C++ programmers.  
    </div>
- <div class="li">[Scotch](https://gitlab.inria.fr/scotch/scotch "https://gitlab.inria.fr/scotch/scotch") - Software package and libraries for sequential and parallel graph partitioning, static mapping, sparse matrix block ordering, and sequential mesh and hypergraph partitioning.  
    </div>
- <div class="li">[METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview") - A set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices.  
    </div>
- <div class="li">[Octave](https://www.gnu.org/software/octave/index "https://www.gnu.org/software/octave/index") - A software featuring a high-level programming language, primarily intended for numerical computations, data analysis and visualisation.  
    </div>
- <div class="li">[Eigen](https://eigen.tuxfamily.org/index.php?title=Main_Page "https://eigen.tuxfamily.org/index.php?title=Main_Page") - A C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.  
    </div>
- <div class="li">[Matlab](https://www.mathworks.com/products/matlab.html "https://www.mathworks.com/products/matlab.html") - A proprietary multi-paradigm programming language and numeric computing environment that allows matrix manipulations, plotting of functions and data, among other things.  
    </div>
- <div class="li">[PETSc](https://petsc.org/release/ "https://petsc.org/release/") - A suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.  
    </div>

#### **Data manipulation, tools and libraries** 

- <div class="li">[HDF5](https://www.hdfgroup.org/solutions/hdf5/ "https://www.hdfgroup.org/solutions/hdf5/") - A hierarchical data format.  
    </div>
- <div class="li">[NCO](http://nco.sourceforge.net/ "http://nco.sourceforge.net/") - A toolkit to manipulate and analyze data stored in NetCDF-accessible formats.  
    </div>
- <div class="li">[NetCDF](https://www.unidata.ucar.edu/software/netcdf/ "https://www.unidata.ucar.edu/software/netcdf/") - Network Common Data Format, a set of software libraries and machine-independent data formats.  
    </div>
- <div class="li">[boost](https://www.boost.org/ "https://www.boost.org/") - Boost C++ libraries that provides support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing.  
    </div>
- <div class="li">[CGAL](https://www.cgal.org/ "https://www.cgal.org/") - A computational geometry algorithms library.  
    </div>
- <div class="li">[CGNS](https://cgns.github.io/WhatIsCGNS.html "https://cgns.github.io/WhatIsCGNS.html") - A general, portable, and extensible standard for the storage and retrieval of computational fluid dynamics (CFD) analysis data.   
    </div>
- <div class="li">[curl](https://curl.se/ "https://curl.se/") - A command line tool and library for transerring data with URLs.  
    </div>
- <div class="li">[OpenSSL](https://curl.se/ "https://curl.se/") - A software library for applications that secure communications over computer networks against eavesdropping or need to identify the party at the other end.  
    </div>

#### **Development tools, compilers, translators, languages, performance analysis** 

- <div class="li">[Charm++](https://charmplusplus.org/ "https://charmplusplus.org/") - A parallel object-oriented programming framework.  
    </div>
- <div class="li">[Patchelf](https://github.com/NixOS/patchelf "https://github.com/NixOS/patchelf") - A simple utility for modifying existing ELF executables and libraries.  
    </div>
- <div class="li">[Python](https://www.python.org/ "https://www.python.org/") - A high-level, general-purpose programming language.  
    </div>
- <div class="li">[CMake](https://cmake.org/ "https://cmake.org/") - A cross-platform family of tools designed to build, test and package software.  
    </div>
- <div class="li">[GCC](https://gcc.gnu.org/ "https://gcc.gnu.org/") - A GNU Compiler Collection for C, C++, Fortran, Go, Objc, Objc++ and Lto.  
    </div>
- <div class="li">[Make](https://www.gnu.org/software/make/ "https://www.gnu.org/software/make/") - A GNU tool which controls the generation of executables and other non-source files of a program from the program's source files.  
    </div>
- <div class="li">[OpenMPI](https://www.open-mpi.org/ "https://www.open-mpi.org/") - An open source Message Passing Interface (MPI) implementation.  
    </div>
- <div class="li">[MPICH](https://www.mpich.org/ "https://www.mpich.org/") - A high performance and widely portable implementation of MPI.  
    </div>
- <div class="li">[Intel MPI](https://www.intel.com/content/www/us/en/developer/tools/oneapi/mpi-library.html#gs.sjnaqv "https://www.intel.com/content/www/us/en/developer/tools/oneapi/mpi-library.html#gs.sjnaqv") - A MPI implementation of Intel with two compiler wrappers (for GCC and for Intel compilers).  
    </div>
- <div class="li">[MVAPICH](https://mvapich.cse.ohio-state.edu/ "https://mvapich.cse.ohio-state.edu/") - A MPI implementation, that particularly performs good on computing systems using InfiniBand and Omni-Path.  
    </div>
- <div class="li">[Threading Building Blocks (TBB)](https://github.com/oneapi-src/oneTBB "https://github.com/oneapi-src/oneTBB") - A C++ template library developed by Intel for parallel programming on multi-core processors.  
    </div>
- <div class="li">[Binutils](https://www.gnu.org/software/binutils/ "https://www.gnu.org/software/binutils/") - A collection of binary tools, e.g. GNU linker, GNU assembler.  
    </div>
- <div class="li">[MPC](https://lists.gnu.org/archive/html/info-gnu/2018-01/msg00005.html "https://lists.gnu.org/archive/html/info-gnu/2018-01/msg00005.html") - A GNU C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result.  
    </div>
- <div class="li">[MPFR](https://www.mpfr.org/ "https://www.mpfr.org/") - A GNU C library for multiple-precision floating-point computations with correct rounding.  
    </div>
- <div class="li">[GMP](https://gmplib.org/ "https://gmplib.org/") - A GNU library for arbitrary precision arithmetic.  
    </div>
- <div class="li">[LLVM](https://llvm.org/ "https://llvm.org/") - A set of compiler and toolchain technologies, which can be used to develop a front end for any programming language and a back end for any instruction set architecture.  
    </div>
- <div class="li">[Ccache](https://ccache.dev/ "https://ccache.dev/") - A compiler cache that speeds up recompilation.  
    </div>
- <div class="li">[Clang](https://clang.llvm.org/ "https://clang.llvm.org/") - A compiler front end for languages in the C language family, as well as the OpenMP, OpenCL, RenderScript, CUDA, and HIP frameworks.  
    </div>
- <div class="li">[Intel System Studio](https://software.intel.com/en-us/system-studio/2017 "https://software.intel.com/en-us/system-studio/2017") - An all-in-one, cross-platform tool suite, purpose-built to simplify system bring-up and improve system performance on Intel platforms.  
    </div>
- <div class="li">[Intel Advisor](https://www.intel.com/content/www/us/en/developer/tools/oneapi/advisor.html#gs.sjzmpg "https://www.intel.com/content/www/us/en/developer/tools/oneapi/advisor.html#gs.sjzmpg") - A design and analysis tool for SIMD vectorization, threading, memory use and GPU offload optimization.  
    </div>
- <div class="li">[Julia](https://julialang.org/ "https://julialang.org/") - A general-purpose, high-level, high-performance, dynamic programming language. Many features are well suited for numerical analysis and computational science.  
    </div>
- <div class="li">[Lua](https://www.lua.org/ "https://www.lua.org/") - A powerful, efficient, lightweight, embeddable scripting language. It supports procedural programming, object-oriented programming, functional programming, data-driven programming, and data description.  
    </div>
- <div class="li">[DejaGnu](https://www.gnu.org/software/dejagnu/ "https://www.gnu.org/software/dejagnu/") - A framework for testing other programs. Its purpose is to provide a single front end for all tests.  
    </div>
- <div class="li">[GNU Debugger (GDB)](https://www.sourceware.org/gdb/ "https://www.sourceware.org/gdb/") - A portable debugger that works for many programming languages.  
    </div>
- <div class="li">[Bison](https://www.gnu.org/software/bison/ "https://www.gnu.org/software/bison/") - A general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.  
    </div>
- <div class="li">[Flex](https://github.com/westes/flex "https://github.com/westes/flex") - A fast lexical analyzer generator to recognize lexical patterns in text.  
    </div>
- <div class="li">[GNU C Library (glibc)](https://www.gnu.org/software/libc/ "https://www.gnu.org/software/libc/") - A library that provides the core libraries for the GNU system.  
    </div>
- <div class="li">[CUDA](https://developer.nvidia.com/cuda-zone "https://developer.nvidia.com/cuda-zone") - A parallel computing platform and programming model developed by NVIDIA for general computing on graphical processing units (GPUs).  
    </div>

#### **Computer Graphics** 

- <div class="li">[NVIDIA OptiX](https://developer.nvidia.com/rtx/ray-tracing/optix "https://developer.nvidia.com/rtx/ray-tracing/optix") - An application framework for achieving optimal ray tracing performance on the GPU.  
    </div>
- <div class="li">[OpenCV](https://opencv.org/ "https://opencv.org") - A library of programming functions for image processing and computer vision.   
    </div>
- <div class="li">[Embree](https://github.com/embree/embree "https://github.com/embree/embree") - A collection of high-performance ray tracing kernels, developed at Intel.   
    </div>

#### **Visualisation** 

- <div class="li">[ParaView](https://www.paraview.org/ "https://www.paraview.org") - An interactive data analysis and visualisation tool with 3D rendering capability.  
    </div>
- <div class="li">[VisIt](https://visit-dav.github.io/visit-website/index.html "https://visit-dav.github.io/visit-website/index.html") - An interactive parallel visualization and graphical analysis tool for viewing scientific data.  
    </div>
- <div class="li">[VTK](https://vtk.org/ "https://vtk.org/") - A visualization toolkit for manipulating and displaying scientific data.  
    </div>

#### **Miscellaneous** 

- <div class="li">[Singularity](https://en.wikipedia.org/wiki/Singularity_(software) "https://en.wikipedia.org/wiki/Singularity_(software)") - Enables users to have full control of their environment.  
    </div>
- <div class="li">[Texinfo](https://www.gnu.org/software/texinfo/ "https://www.gnu.org/software/texinfo/") - A typesetting syntax used for generating documentation in both on-line and printed form (creating filetypes as dvi, html, pdf, etc., and its own hypertext format, info) with a single source file.  
    </div>
- <div class="li">[Git](https://git-scm.com/ "https://git-scm.com/") - A fast, scalable, distributed revision control system.</div>