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.

• PyTorch

• TensorFlow

• JAX

• XGBoost

Add new Chemistry Software

• 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 — A program package for ab initio and DFT electronic structure calculations.
• 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. 
• 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. 
  
• 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. 

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

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.
• Perforce TotalView — A parallel debugger with a Replay Engine feature
• 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)

Add Engineering Software

• Abaqus - only with own license — a Finite Element Analysis Package for Engineering Application
• Ansys Suite — All Ansys components are installed e.g. Fluent, CFX, LS-Dyna, Mechanical, Lumerical, Electronic, SCADE.
• 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

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 

Add new Numerics Software

• 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.  

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