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Essential Workshop on Linux File Systems and Job Submission for HPC Users

Join our informative workshop led by Jun Wang at HPC at HCC, designed to familiarize participants with critical aspects of the Linux file system and shell environment. Learn about module commands, queuing systems (PBS and SLURM), and how to submit both serial and MPI parallel jobs. We will cover essential storage concepts on Tusker and Sandhills, including partition structures, and introduce useful SLURM commands for job management. This session is essential for anyone looking to enhance their HPC workflows and optimize computational tasks.

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Essential Workshop on Linux File Systems and Job Submission for HPC Users

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Presentation Transcript

  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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