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Advanced HPC Topics

These topics require the knowledge of using the HPC or the beginner courses. They cover advanced topics including System Administration.

  • 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
            Last modified: 2025-05-27 06:59:41
            • Instructor Lead
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            • 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?
              • 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
                • Mathematics
                • 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
              • Compilers
                • Workflow compiler
                • Hybrid Jobs
                • Linking the MKL version of fftw3
                • MPI and OpenMP
                • Workflow Intel MPI
                • Workflow OpenMP
                • Workflow OpenMPI
              • Spack
                • Spack FAQs
              • Storage Systems
                • Data Stores
                  • HOME
                  • Project
                  • SCRATCH/WORK
                  • 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
              • 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
                    • Anaconda (conda) and Mamba
                    • antlr
                    • Arm DDT
                    • Charm++
                    • Intel oneAPI Compiler Suite
                    • Intel oneAPI MPI
                    • Intel oneAPI Performance Tools
                      • VTune Profiler
                      • VTune Profiler (extended workshop version)
                    • Julia
                    • LIKWID Performance Tool Suite
                    • OpenMPI
                    • Patchelf
                    • Python
                    • 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
                      • ParaView
                      • pyfesom2
                    • Wannier90
              • Applications
                • Ansys Suite
                  • CFX
                  • Fluent
                  • LS-DYNA
                  • Mechanical
                • Ferret (Apptainer)
                • Foam-extend
                • Gaussian
                • Likwid
                • MATLAB
                • OpenFOAM
                • TURBOMOLE
              • Compilers and Interpreters
                • AMD Optimizing Compilers (AOCC)
                • Conda & Python
                  • Tensorflow
                • CPython
                • GCC
                • Go
                • Intel Compilers
                • Julia
                • LLVM (Clang, etc.)
                • MATLAB PARALLEL SERVER ON THE SCC
                • Nvidia HPC Compilers
                • R
                • rustc
              • Parallelization
                • MPI
                  • OpenMPI
                  • Intel MPI
                • OpenACC
                • OpenCL
                  • Nvidia Driver
                  • PoCL
                • OpenMP
                • Apache Spark
            • 4. Services
              • Arcana/RAG
                • AI Transparency Statement
                • Datenschutzhinweis
                • Terms of use
                • 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
              • 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
            • 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
            • 7. Support
              • Known issues
            • Citing us

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