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Introduction to Linux File Systems and Job Submission in HPC Environments

This workshop provides an essential introduction to using Linux file systems, shell environments, and job submission processes in High Performance Computing (HPC). Participants will become familiar with basic file system structures, including the $HOME and $WORK directories, and learn how to navigate the BASH shell. The workshop covers queuing systems such as PBS and SLURM, detailing how to submit serial and MPI parallel jobs. Additional useful SLURM commands for checking job details and available partitions will also be discussed, setting a strong foundation for effective HPC usage.

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Introduction to Linux File Systems and Job Submission in HPC Environments

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  1. HPC at HCCJun Wang hcc.unl.edu Outline of Workshop2 Familiar with Linux file system Familiar with Shell environment Familiar with module command Familiar with queuing system How to submit a serial job How to submit a MPI parallel job

  2. HPC at HCCJun Wang hcc.unl.edu Familiar with Linux file system Basic File System Structure Basic File System Partitions On tusker and sandhills: $HOME (/home) is read-only on computing nodes, 10 GB space/group, daily backup $WORK (/work) is writable on all nodes, 50 TB space/group, no backup

  3. HPC at HCCJun Wang hcc.unl.edu Familiar with BASH Shell environment

  4. HPC at HCCJun Wang hcc.unl.edu Familiar with module command

  5. HPC at HCCJun Wang hcc.unl.edu Familiar with module command

  6. HPC at HCCJun Wang hcc.unl.edu Familiar with queuing system-PBS

  7. HPC at HCCJun Wang hcc.unl.edu Familiar with queuing system-SLURM

  8. HPC at HCCJun Wang hcc.unl.edu How to submit a serial job

  9. HPC at HCCJun Wang hcc.unl.edu How to submit a serial job

  10. HPC at HCCJun Wang hcc.unl.edu How to submit a MPI parallel job

  11. HPC at HCCJun Wang hcc.unl.edu How to submit a MPI parallel job

  12. HPC at HCCJun Wang hcc.unl.edu More useful SLURM commands “sinfo” : Check available partitions and their status

  13. HPC at HCCJun Wang hcc.unl.edu More useful SLURM commands “scontrol show job YourJobID”: Check details of a specific job

  14. HPC at HCCJun Wang hcc.unl.edu Thank You! To be continued: How to run Gaussian09 How to compile and run GAMESS How to compile and run GROMACS

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