Software
Content
Note: You can get a complete overview of the installed software with the command module available
.
(Read more)
AI Frameworks and Tools
The compute partitions available for NHR@ZIB contain several popular artificial intelligence (AI) frameworks and tools for use with both CPU and GPU resources. These packages can be accessed through the custom anaconda3/2023.09
module and its system-wide Python distribution. For a list of installed Python packages, one may call conda list
after the module is loaded. The full list of anaconda packages can be found here.
Chemistry
- CP2K — A package for atomistic simulations of solid state, liquid, molecular, and biological systems offering a wide range of computational methods with the mixed Gaussian and plane waves approaches.
- exciting — a full-potential all-electron code, employing linearized augmented planewaves (LAPW) plus local orbitals (lo) as basis set.
- Gaussian — a computational chemistry application provided by Gaussian Inc https://gaussian.com/.
- GPAW — a density functional theory Python code based on the projector-augmented wave method.
- GROMACS — a versatile package to perform molecular dynamics for systems with hundreds to millions of particles.
- NAMD — a parallel, object-oriented molecular dynamics code designed for high-performance simulations of large biomolecular systems using force fields.
- Octopus — a software package for density-functional theory (DFT), and time-dependent density functional theory (TDDFT)
- Quantum ESPRESSO — an integrated suite of codes for electronic structure calculations and materials modeling at the nanoscale, based on DFT, plane waves, and pseudopotentials.
- RELION — REgularised LIkelihood OptimisatioN is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy(cryo-EM)
- SIESTA — “both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.” SIESTA project https://siesta-project.org/siesta/About/overview.html
- TURBOMOLE — TURBOMOLE is a computational chemistry program that implements various quantum chemistry methods (ab initio methods). It was initially developed at the University of Karlsruhe.
- VASP — a first-principles code for electronic structure calculations and molecular dynamics simulations in materials science and engineering.
- Wannier90 — A program that calculates maximally-localised Wannier functions.
- Abinit
- ASE – The Atomic Simulation Environment – a set of tools and Python modules for setting up, manipulating, running, visualizing, and analyzing atomistic simulations.
- LAMMPS – A parallel, classical potential molecular dynamics code for solid-state materials, soft matter and coarse-grained or mesoscopic systems.
- TURBOMOLE – A program package for ab initio electronic structure calculations. (see "module avail turbomole" on the SMP cluster)
- NWChem – A general computational chemistry code with capabilities from classical molecular dynamics to highly correlated electronic structure methods, designed to run on massively parallel machines.
- MOLPRO – A comprehensive system of ab initio programs for advanced molecular electronic structure calculations.
- PLUMED – A tool for trajectory analysis and plugin for molecular dynamics codes for free energy calculations in molecular systems
- CPMD – A plane wave / pseudopotential implementation of DFT, designed for massively parallel ab-initio molecular dynamics.
- BandUP – Band unfolding for plane wave based electronic structure calculations.
Data manipulation, tools and libraries
Add new Data Manipulation Software
- AEC library — Adaptive Entropy Coding library
- CDO — The Climate Data Operators
- ECCODES — ECMWF application programming interface
- HDF5 libraries / binaries — HDF5 - hierarchical data format
- libtiff — A software package containing a library for reading and writing _Tag Image File Format_(TIFF), and a small collection of tools for simple manipulations of TIFF images
- libz — A Massively Spiffy Yet Delicately Unobtrusive Compression Library
- NCO — The NetCdf Operators
- netCDF — Network Common Data Form
- pigz — A parallel implementation of gzip for modern multi-processor, multi-core machine
- PROJ — Cartographic Projections Library
- R — R - statistical computing and graphics
- Szip — Szip, fast and lossless compression of scientific data
- UDUNITS2 — Unidata UDUNITS2 Package, Conversion and manipulation of units
- Boost – Boost C++ libraries
- CGAL – The Computational Geometry Algorithms Library
Development tools, compilers, translators, languages, performance analysis
Add new Development/Debugging Tool or Compiler
- Anaconda (conda) and Mamba — Anaconda package manager (predominantly Python) and mambaforge
- antlr — Another Tool for Language Recognition
- Arm DDT — Parallel debugger, including MPI/OpenMP programs.
- Charm++ — Parallel Programming Framework
- Intel oneAPI Compiler Suite — Intel new and classic compilers for C/C++, Fortran, DPC++/SYCL
- Intel oneAPI MPI — Intel´s implementation of the MPI standard
- Intel oneAPI Performance Tools — VTune, APS, Advisor, Inspector, Trace Analyzer and Collector
- Julia — A high-level, high-performance, dynamic programming language
- LIKWID Performance Tool Suite — Performance tools and library for GNU Linux operating system.
- OpenMPI — High Performance Message Passing Library
- Patchelf — a simple utility for modifying existing ELF executables and libraries.
- Python — An Overview over the different Python Versions available on our System
- SYCL — An open industry and cross-platform programming standard for C++ in a data-parallel and explicit fashion.
- Valgrind instrumentation framework — an instrumentation framework for building dynamic analysis tools
- VS Code — VS Code is an IDE that while not provided on the clusters, many users use on their own machines and connect into the clusters with.
- CMake – CMake build environment
- GCC – GNU Compiler Collection for C, C++, Fortran, Go, Objc, Objc++ and Lto
- Intel oneAPI Performance Libraries – Integrated Performance Primitives (IPP), Collective Communications Library (CCL), Data Analytics Library (DAL), Deep Neural Network Library (DNNL), DPC++ Library (DPL), Math Kernel Library (MKL), Threading Building Blocks (TBB), Video Processing Library (VPL)
(included in "intel
" environment modules)
Engineering
- Abaqus - only with own license — a Finite Element Analysis Package for Engineering Application
- Ansys Suite — The full Ansys Academic Multiphysics Campus Solution is available, e.g. Mechanical, CFX, Fluent, LS-Dyna, Electronic, SCADE (but not Lumerical, GRANTA).
- MATLAB - only with own license — a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks
- OpenFOAM — an object-oriented open source CFD toolkit
- STAR-CCM+ — a Package for Computational Fluid Dynamics Simulations
- Bring your own license — of any software from you own license server
- HDF5 libraries / binaries
- ParaView — An interactive data analysis and visualisation tool with 3D rendering capability
Miscellaneous
Add new Miscellaneous Software
- libcurl — curl - a tool for transferring data from or to a server
- nocache — nocache - minimize caching effects in lustre filesystems
- texlive – LaTeX distribution, typesetting system
- git – A fast, scalable, distributed revision control system
Numerics
- BLAS — BLAS (Basic Linear Algebra Subprograms)
- FFTW3 — A C-subroutine library for computing discrete Fourier transforms
- GSL — The GNU Scientific Library (GSL)- a numerical library for C and C++ programmers
- MUMPS — MUltifrontal Massively Parallel sparse direct Solver.
- NFFT — Discrete Fourier transform (DFT) in one or more dimensions
- ScaLAPACK — Scalable LAPACK
- Scotch — Software package and libraries for sequential and parallel graph partitioning, static mapping, sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
- METIS – A set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices.
- ParMETIS – An MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
- PETSc – Portable, Extensible Toolkit for Scientific Computation: widely used parallel numerical software library for partial differential equations and sparse matrix computations.
Visualisation
Add new Visualisation Software
- Ferret - Data Visualization and Analysis — your ferret in large and complex gridded data sets.
- GraDS — An interactive desktop tool for easy access, manipulation, and visualization of earth science data
- NCL
- NcView — Ncview - a visual browser for netCDF formated files.
- ParaView — An interactive data analysis and visualisation tool with 3D rendering capability
- pyfesom2 — Python library and tools for handling of FESOM2 ocean model output