HLRN Modules (hlrn-tmod)

The default stack on the NHR cluster except on the Emmy Phase 3 nodes. This software stack dates back to HLRN and was built in collaboration with ZIB (Zuse Institute Berlin) with their Lise cluster (another NHR center). For the purposes of setting the desired software stack (see Software Stacks), its short name is hlrn-tmod.

This stack uses Environment Modules (Tmod) as its module system, which is also known as Tmod. You can learn more about how to use the module system at Module Basics.

Adding Your Own Modules

See Using Your Own Module Files.

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)
• 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.
• 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

• AEC library — Adaptive Entropy Coding library
• CDO — The Climate Data Operators
• ECCODES — ECMWF application programming interface
• HDF5 Libraries and 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
• NCO — The NetCdf Operators
• netCDF — Network Common Data Form
• Octave — Add short Excerpt. This will be included in the Software list
• 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

• 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
• 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 — 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).
• Foam-extend — The Open Source CFD Toolbox
• How to bring your own license
• OpenFOAM — An object-oriented Computational Fluid Dynamics(CFD) toolkit
• STAR-CCM+ — A Package for Computational Fluid Dynamics Simulations
• ParaView — An interactive data analysis and visualisation tool with 3D rendering capability

Miscellaneous

• libcurl — curl - a tool for transferring data from or to a server
• libz — A Massively Spiffy Yet Delicately Unobtrusive Compression Library
• nocache — nocache - minimize caching effects in lustre filesystems
• Singularity — enables users to have full control of their environment
• 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.

Visualization

• 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