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Category :: Life Science

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  • Life Science and Bioinformatics
    Home > Start Here > Science Domains
  • Home
  • 1. Start Here
    • Getting An Account
    • Cluster Overview
    • Types of User Accounts
    • Connecting (SSH)
      • Installing SSH Clients
      • Generating SSH Keys
      • Uploading SSH Keys
      • Configuring SSH
      • Logging In
      • SSH Troubleshooting
        • "Corrupted MAC" errors on Windows
        • Error: "permission denied"
        • Warning: unprotected key file
      • SSH FAQ
        • Is password authentication supported?
        • What 2FA methods are available?
        • What type of user account do I have?
        • Why are only ed25519, ed25519-sk, and 4096-bit rsa keys recommended?
    • Using AI Services
      • Institutional Access to AI Services
    • NHR Application Process
      • Apply for a Compute Project
      • Proposal Format
      • JARDS - Guide to filling out
    • KISSKI Application Process
    • Accounting Core-h
    • Science Domains
      • AI
      • Chemistry
      • Data Science
      • Digital Humanities
      • Earth Science
      • Engineering
      • Forest
      • Life Science and Bioinformatics
      • Mathematics
      • Physics
      • Quantum Computing
  • 2. How to use...
    • Slurm
      • Multiple programs and multiple data
      • GPU Usage
      • Interactive Jobs
      • Job arrays
      • Job runtimes and QoS
      • Multiple concurrent programs on a single node
      • Resource monitoring and Reports
      • Self-Resubmitting jobs
    • Compute Partitions
      • CPU Partitions
      • GPU Partitions
    • Spack
      • Spack FAQs
    • Storage Systems
      • Data Stores
        • HOME
        • Project
        • SCRATCH/WORK
        • Workspaces
        • COLD
        • ARCHIVE/PERM
        • Requestable Storage
      • Cluster Storage Map
      • Quota
        • Checking Usage And Quotas
        • Fixing Quota Issues
        • Increasing Quota
      • Temporary Storage
      • Project Map
      • Optimizing IO Performance
    • Data Transfers
    • Data Sharing
    • Terminal multiplexer
    • SSH
  • 3. Software Stacks
    • Module Basics
    • Software Licensing
    • Spack
    • Available modules
      • Apptainer (formerly Singularity)
      • GWDG Modules (gwdg-lmod)
        • Software Revision 25.04
          • Emmy Core Modules
          • Emmy GCC11 Modules
          • Emmy GCC14 Modules
          • Emmy Intel Modules
          • Grete Core Modules
          • Grete GCC13 Modules
      • NHR Modules (nhr-lmod)
        • Software Revision 24.05
          • Emmy Core Modules (24.05)
          • Emmy Intel Modules (24.05)
          • Grete Core Modules (24.05)
      • SCC Modules (scc-lmod)
      • HLRN Modules (hlrn-tmod)
        • Devtools Compiler Debugger
          • antlr
          • Arm DDT
          • Charm++
          • Intel oneAPI Performance Tools
            • VTune Profiler
            • VTune Profiler (extended workshop version)
          • Julia
          • LIKWID Performance Tool Suite
          • Patchelf
          • Valgrind instrumentation framework
          • VS Code
        • Legacy Applications
          • Abaqus
          • AEC library
            • Install AEC GNU
            • Install AEC Intel
          • BLAS
          • CDO
          • Chemistry
            • CP2K
            • Exciting
            • GPAW
            • GROMACS
            • NAMD
            • Octopus
            • Quantum ESPRESSO
            • RELION
            • VASP
            • Wannier90
          • CP2K
          • Data Manipulation
            • AEC library
              • Install AEC GNU
              • Install AEC Intel
            • CDO
            • ECCODES
              • Installing ECCODES
                • Install ecCodes with intel compilers
                • Install ecCodes with gcc
            • HDF5 Libraries and Binaries
              • HDF5 Installation
                • Enable autotools
                • HDF5 1.12.2 configuration
                • HDF5 1.12.2 parallel (impi) installation
                • HDF5 1.12.2 parallel (ompi) installation
                • Libaec Installation
            • Libtiff
            • NCO
            • netCDF
              • Install netCDF
              • Linking with the netcdf library
                • Example netcdf program
            • Octave
            • pigz
            • PROJ
            • R
              • Installing R and R-packages
            • Szip
            • UDUNITS2
          • ECCODES
            • Installing ECCODES
              • Install ecCodes with intel compilers
              • Install ecCodes with gcc
          • Engineering
            • Abaqus
            • How to bring your own license
            • STAR-CCM+
          • Exciting
          • FFTW3
            • The Fftw3-Installation at HLRN
          • GPAW
          • GROMACS
          • GSL
            • Configure and make GSL
          • HDF5 Libraries and Binaries
            • HDF5 Installation
              • Enable autotools
              • HDF5 1.12.2 configuration
              • HDF5 1.12.2 parallel (impi) installation
              • HDF5 1.12.2 parallel (ompi) installation
              • Libaec Installation
          • How to bring your own license
          • libcurl
          • Libtiff
          • libz
          • Miscellaneous
            • libcurl
            • libz
            • nocache
          • MUMPS
          • NAMD
          • NCO
          • netCDF
            • Install netCDF
            • Linking with the netcdf library
              • Example netcdf program
          • NFFT
            • Building NFFT
          • nocache
          • Numerics
            • BLAS
            • FFTW3
              • The Fftw3-Installation at HLRN
            • GSL
              • Configure and make GSL
            • MUMPS
            • NFFT
              • Building NFFT
            • ScaLAPACK
            • Scotch
          • Octave
          • Octopus
          • pigz
          • PROJ
          • Quantum ESPRESSO
          • R
            • Installing R and R-packages
          • RELION
          • ScaLAPACK
          • Scotch
          • STAR-CCM+
          • Szip
          • UDUNITS2
          • VASP
          • Visualization tools
            • GraDS
            • NCL
            • NcView
            • pyfesom2
          • Wannier90
    • Applications
      • Ansys Suite
        • CFX
        • Fluent
        • LS-DYNA
        • Mechanical
      • Ferret (Apptainer)
      • Foam-extend
      • Gaussian
      • Likwid
      • Mathematica
      • MATLAB
      • OpenFOAM
      • ParaView
      • preCICE
      • Tensorflow
      • TURBOMOLE
    • Compilers and Interpreters
      • AMD Optimizing Compilers (AOCC)
      • GCC
      • Go
      • Intel Compilers
      • Julia
      • LLVM (Clang, etc.)
      • MATLAB PARALLEL SERVER ON THE SCC
      • Nvidia HPC Compilers
      • Python
      • R
      • rustc
    • Parallelization
      • Hybrid MPI + OpenMP
      • MPI
        • OpenMPI
        • Intel MPI
      • OpenACC
      • OpenCL
        • Nvidia Driver
        • PoCL
      • OpenMP
      • Apache Spark
    • Numeric Libraries
      • Intel MKL
  • 4. Services
    • Arcana/RAG
      • AI Transparency Statement
      • Datenschutzhinweis
      • Terms of use
      • Migration Guide
      • Setting up an Arcana
      • How to use Arcana
      • Docling process
      • Public Arcana links
      • RAG Service
      • Support and FAQ
    • Chat AI
      • Available Models
      • Chat AI FAQ
      • Personas
      • Data Privacy Notice
      • Datenschutzhinweis
      • Terms of use
    • CoCo AI
    • Data Pool
      • Validator
    • GöDL - Data Catalog
    • Graphcore
    • Image AI
      • Image-AI FAQ
      • Data Privacy Notice
      • Datenschutzhinweis
      • Terms of use(English)
      • Terms of use(German)
    • JupyterHub
      • Creating your own JuypterHPC container
    • Neuromorphic Computing
      • Neuromorphic Computing Tools and Libraries
      • SpiNNaker
    • Protein-AI
      • Protein-AI FAQ
      • Terms of use
    • Quantum Computing Simulators
      • QC Simulators FAQ
      • Qibo
      • Qiskit
      • Qsim and Cirq
      • Qulacs
      • QuTip
    • RStudio-JupyterHub
    • SAIA
    • Secure HPC
      • Getting Started
      • Success stories
      • User Guide
    • Software Performance Engineering
    • Voice-AI
      • Voice-AI FAQ
      • Data Privacy Notice
      • Datenschutzhinweis
      • Terms of use
  • 5. Project Management
    • Project Portal
    • User Perspective
    • Managing a Project
    • Applying for projects on the SCC
    • Data Migration Guide
    • NHR/HLRN Project Migration
    • Project Structure
    • Export Control
  • 6. Training
    • Community Events
      • NHR Roadshow
    • GWDG Academy
      • HPC Beginners Courses
        • Getting started with Linux Bash
        • How to KISSKI
        • Supercomputing for Every Scientist
        • Using the GWDG Scientific Compute Cluster
      • General HPC usage
        • Deep Dive into Containers
        • Practical Course in High-Performance Computing
        • Secure HPC - Parallel Computing with Highest Security
        • Using Jupyter Notebooks on HPC
      • Advanced HPC Topics
        • High Performance Data Analytics: Big Data meets HPC
        • Monitoring HPC Systems in the GWDG
        • Practical: High-Performance Computing System Administration
        • Quantum Computing with Simulators on HPC
        • System, User and Developer Perspectives on Parallel I/O
      • Performance Engineering
        • Introduction to Performance Engineering
        • Parallel Programming with MPI
        • Performance Analysis of AI and HPC Workloads
      • Artificial Intelligence / GPU Programming
        • Deep Learning Bootcamp: Building and Deploying AI Models
        • Deep Learning with GPU Cores
        • Effectively Utilize AI Tools in Research
        • Fundamentals of Accelerated Computing with CUDA Python
        • GPU Programming with CUDA
        • KI in der Verwaltung: Eine Einführung in die Nutzung für alle Mitarbeiter*innen
      • Data Management in HPC
        • Data Management Concepts for Efficient and User-Friendly HPC
        • Using the GöDL Data Catalog for Semantic Data Access on the GWDG HPC Systems
        • Using the GWDG Data Pools for Scientific Data Sharing
      • Application Science / Science Domains
        • Ansys on Cluster and Post-Processing of Simulation Results
        • Debugging Scientific Applications - Illustration on OpenFOAM
        • Introduction to AlphaFold
        • Introduction to Research Software Development with MATLAB
        • Parallel Computing with MATLAB Part I: Parallelize on your local machine
        • Parallel Computing with MATLAB Part II: Scaling up to the GWDG Scientific Compute Cluster
        • Snakemake for HPC Workflows
    • HPC Workshops
    • Self Paced tutorials
      • Linux bash tutorial
      • Slurm tutorial
      • AI Competence Training
      • Effectively Utilize AI Tools in Research
      • KI in der Verwaltung
      • KI Kompetenz Training
  • 7. Support
    • Known issues
  • Citing us
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