JUSUF user documentation

This documentation explains various aspects of using the JUSUF system at Jülich Supercomputing Centre. It contains both introductory and advanced material.

First time users might want to start at the beginning and work through the first few chapters, skipping those sub-chapters that contain advanced material. This way, you will learn how to log in to JUSUF, familiarize yourself with the environment, find pre-installed software, compile your own programs, and run them on JUSUF.

Advanced users can peruse the table of contents below to find out about particular topics they are interested in.

Contents:

• Access
  • Prerequisites
  • SSH Login
  • MFA with TOTP
  • Login Nodes
  • Alternative Login Methods
• Configuration
  • Hardware Configuration
  • Software Overview
• Environment
  • Shell
  • Active project
  • Available file systems
  • Machine identification file
  • Transferring files with scp, rsync, etc.
  • Using Git on JUSUF
• Software Modules
  • Basic module usage
  • Available compilers
  • MPI runtimes
  • GPUs and modules
  • Finding software packages
  • Stages
  • Stages Changelog
  • Scientific software at JSC
  • Requesting new software
  • Installing your own software with EasyBuild
• Building Software
  • Compiled Languages
  • Interpreted Languages
  • Pre-Compiled Binaries
• Batch system
  • Slurm Partitions
  • Internet Access
  • Allocations, Jobs and Job Steps
  • Writing a Batch Script
  • Generic Resources, Features and Topology-aware Allocations
  • Job Steps
  • Dependency Chains
  • Interactive Sessions
  • Hold and Release Batch Jobs
  • Slurm commands
  • Summary of sbatch and srun Options
  • CPU Limiting Options
• Processor Affinity
  • Slurm options
  • Affinity visualization tool
  • Affinity examples
• MPMD: Multiple Program Multiple Data Execution Model
• GPU Computing
  • JUSUF GPU Nodes
  • GPU Visibility/Affinity
  • Setting GPU Clock Rates
  • NVIDIA Profiling Tools and Clock Speed
  • CUDA MPS: Multiple MPI Ranks per GPU
  • Job Script Examples
• GPFS File Systems in the Jülich Environment
  • Best practice notes
• Data Transfer to and from JUSUF
• Known Issues on JUSUF
  • Open Issues
  • Recently Resolved and Closed Issues
• FAQ
  • General FAQ
  • FAQ about Data Management
• Maintenance
• Heterogeneous and Cross-Module Jobs
  • Heterogeneous Jobs
  • Loading Software in a Heterogeneous Environment
• Accounting
  • Accounting Mode
  • Command description
• JSC Tools
  • JuDoor
  • Status Page
  • LLview Job Reporting
  • Pinning Tool
  • JUBE Benchmarking Environment
  • User tool jutil
  • UNICORE access
  • BLABLADOR documentation
• Container Runtime on JUSUF
  • What Containers Provide
  • Getting Access
  • Apptainer on JUSUF
  • Container Build System
  • Apptainer image building
• Jacamar CI Runners
  • Getting Access
  • Runners Tags on JUSUF
  • Jacamar Example .gitlab-ci.yml File
• Parallel Debugging and Performance Analysis
  • Debugging with TotalView on JUSUF
  • Using TotalView
  • Memory Debugging with TotalView
• Support