FinisTerrae III User Guide

• Overview
  • Node groups description
• First steps
  • Creating an account
  • Connecting with CESGA
• HPC Glossary
• How to connect
  • Installation and configuration of Checkpoint on Windows
  • Installation and configuration of Checkpoint on MacOS
  • Installation and configuration of Checkpoint on Linux
  • Installation and configuration of Checkpoint on Android or iPhone mobile
  • FinisTerrae III fingerprints
• System use
• Remote desktops and visualization tools
  • Remote desktops
  • Desktops CLI
  • Jupyter notebook
• Data transfer
  • MobaXterm
  • SCP and SFTP clients
  • DTN nodes
• Permanent storage
  • Filesystem Quotas
    • Quota exceeded: locate directories that take up the most space and number of files
• Temporary storage (Scratch)
• Parallelization
  • Single-node parallelism (OpenMP)
  • Multi-node parallelism (MPI)
  • Hybrid MPI/OpenMP
• Batch system: Submitting jobs with SLURM
  • Memory and time
  • Partitions
  • QOS
    • User Account Limits
    • Assoc-Group Limits
  • Basic commands
    • sbatch
    • srun
    • sinfo
    • squeue
    • scancel
    • scontrol
    • sacct
    • seff
    • sqstat
  • Sample Job Scripts
    • Using srun
    • Using sbatch
    • Using sbatch and GPUs
    • OpenMP job submission
    • MPI job submission
    • Hybrid MPI/OpenMP programs
  • Job array
  • Multiple tasks on a job
    • Running multiple programs with --multi-prog option
    • Running multistep programs and -r, –relative=<n>
    • Running multiple programs within a job using GNU Parallel and srun
  • Tasks on specific cores
    • 1. Task level affinity (Pure MPI)
    • 2. Thread level affinity (OpenMP and MPI/OpenMP jobs)
  • Job states
  • Output files
  • Email notifications
• Binding: tasks on specific cores
• Redundant cron
• Job signals
  • Clean-up function
• Job Requeue
  • Summary and Generalization
  • Use case
• Applications, compilers and development tools
• EESSI
• Environment modules (Lmod)
  • Conda environments
  • Module command use
• High Memory nodes (fat nodes)
• AI nodes (GPU nodes)
  • NVIDIA A100
  • Tesla T4
• High Troughput nodes
  • Intel Cascade Lake nodes
  • AMD EPYC nodes
• F.A.Q.
  • Connection
    • Workaround for Windows SSH and VS Code Users
    • How can I connect to FinisTerrae III?
    • I cannot access to any CESGA server
    • What are the credentials used for authentication in Checkpoint?
  • Use of FinisTerrae III
    • How can FinisTerrae III be used?
    • How to know which applications and modules are installed? How do I load a module?
    • Is it possible to connect to the nodes where I have a job running?
    • Why do I get errors or warnings when I try to launch a job?
    • Why is my job not running? How much time will I have to wait? What can I do to reduce the waiting times?
    • How can I know how much memory are using my jobs? or How can I adjust the memory request for job submission?
    • I can’t list or load modules using “module” or “module spider”
  • Storage
    • How much storage space is being used?
    • How to locate directories that take up the most space or number of files?
    • Which are the differences between $HOME, $STORE and $LUSTRE directories? What is the function of each of them?
    • How to restore a deleted file or directory?
  • Remote Desktops
    • I can’t create any Remote Desktops from User Portal or command line
• Dissemination and publicity
• Further assistance