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User Manual
User Manual
Results will update as you type.
  • Application Guide
  • Status of System
  • Usage Guide
    • SSH Login
    • Data Transfer
    • File Systems
    • MPI, OpenMP build and run workflows
    • Slurm usage
  • Compute partitions
  • Software
  • FAQ
  • NHR Community
  • Contact
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    Usage Guide

    Usage Guide

    Okt. 08, 2025

    Usage Guide intro (this page)

    All Usage Guide sections

    Related sections:

    • Application Guide
    • Compute Project
    • Compute partitions
    • Software

    Partitions on system Lise

    Compute system Lise at NHR@ZIB contains different Compute partitions for CPUs and GPUs. Your choice for the partition affects

    • Login nodes,
    • slurm partition (Compute partitions and Accounting), and
    • Software.

    Login nodes

    To login to system Lise, please

    • choose a login node associated to your Compute partitions and
    • use authentication via SSH Login.

    Software and environment modules

    The webpage Software gives you information about available software on the NHR systems.

    NHR provides a number of compilers and software packages for parallel computing and (serial) pre- and postprocessing:

    • Compilers: Intel, GNU
    • Libraries: NetCDF, LAPACK, ScaLAPACK, BLAS, FFTW, ...
    • Debuggers: Allinea DDT, Roguewave TotalView...
    • Tools: octave, python, R ...
    • Visualisation: mostly tools to investigate gridded data sets from earth-system modelling
    • Application software: mostly for engineering and chemistry (molecular dynamics)

    Environment Modules are used to manage the access to software/libraries. The module command offers the following functionality.

    1. Show lists of available software
    2. Enables access to software in different versions


    Example: Show the currently available software and access the Intel compiles
    blogin1:~ $ module avail
...
blogin1:~ $ module load intel
Module for Intel Parallel Studio XE Composer Edition (version 2019 Update 5) loaded.
blogin1:~ $ module list
Currently Loaded Modulefiles:
 1) sw.skl   2) slurm   3) HLRNenv   4) intel/19.0.5(default)

    To avoid conflicts between different compilers and compiler versions, builds of most important libraries are provided for all compilers and major release numbers.

    File systems

    Each complex has the following file systems available. More information about Quota, usage, and best pratices are available on System Quota. Hints for data transfer are given here.

    • Home file system containing $HOME directories /home/${USER}/
    • Scratch parallel file system with 20 PiByte capacity containing
      • $WORK directories /scratch/usr/${USER}/
      • project data directories /scratch/projects/<projectID>/ (not yet available)
    • Tape archive (accessible on the login nodes, only)
    , multiple selections available,
    {"serverDuration": 10, "requestCorrelationId": "eaa73238088e4917927ad4008c96d9ba"}