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MSU HPCC User Documentation

MSU-ICER-User-Documentation

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OS Upgrade Summer 2024
OS Upgrade Summer 2024
- Overview
- Migrating to the new operating system
- Accessing nodes running Ubuntu
- Changelog and known issues
- Backwards compatibility scripts
- Migration specifics
  Migration specifics
Access the HPCC
Access the HPCC
HPCC resources
HPCC resources
- HPCC layout
- Cluster resources
- GPU resources
- Development nodes
- The Data Machine
  The Data Machine
  - Data Machine overview
  - Using the Data Machine
- NVIDIA Grace nodes
- Classroom support
Computing environment
Computing environment
- Linux shells
- Editing text with nano
- File permissions
- Managing file permissions
- Change primary group
- Virtual Terminals
- Basics of parallel computing
- AMD Hardware
  AMD Hardware
  - AMD CPU architecture
  - Optimizing for AMD CPUs
File systems
File systems
File transfer
File transfer
- File transfer
- Large file transfer (Globus)
  Large file transfer (Globus)
- Cloud storage file transfer
- Mapping drives
  Mapping drives
  - Mapping drives using Samba
  - Mapping drives using SSHFS
Software module system
Software module system
Powertools
Powertools
Job submission by SLURM
Job submission by SLURM
- Overview
- SLURM commands
- Requesting Resources & Submitting Jobs
  Requesting Resources & Submitting Jobs
- Managing Jobs
  Managing Jobs
- Job policies
- Buy-in and account management
- Understanding the Scheduler
  Understanding the Scheduler
- Checkpointing
  Checkpointing
- Connections to compute nodes
- Migrating from Torque
Software tutorials
Software tutorials
- AlphaFold
  AlphaFold
  - AlphaFold on HPCC
  - AlphaFold via Singularity
- ANSYS
- Bioinformatics software
  Bioinformatics software
- BLAS and FlexiBLAS
- Command line and shell scripting
  Command line and shell scripting
- Compiling code
  Compiling code
  - Compilers and Libraries
  - Compiling for GPUs
- COMSOL
- Containers: Singularity and Docker
  Containers: Singularity and Docker
- Data Display Debugger
- Gaussian
  Gaussian
- Installing software: EasyBuild
  Installing software: EasyBuild
  - EasyBuild tutorial
  - EasyBuild reference
- make
- Matlab
- OnDemand Apps
  OnDemand Apps
  - Quick start - Open OnDemand
- Perl
  Perl
  - Installing Local Perl Modules with CPAN
- Python
  Python
- R
  R
- Stata
- TensorFlow
  TensorFlow
Training material
Training material
- Workshop materials
- Exercises and Solution
  Exercises and Solution
- External Resources
- Others
  Others
  - Targeting Cluster Architectures
FAQ
Glossary
Lab Notebooks
Help desk access
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March 12, 2024 March 12, 2024

rajshash

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