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HPC user config

My dotfiles for HPC clusters. They make navigating around in a terminal via ssh a lot more comfortable. Used in the following competitions:

Feel free to copy and adapt them to your own needs.

Cheat sheets

System monitoring

htop CPU & RAM usage

watch -n 0.5 nvidia-smi htop for GPUs, alternative: nvidia-smi --loop=1

PBS cheat sheet

Job scheduling

qsub <script.sh> Submit script

qdel <job_id> Cancel submitted job

Job management

qstat -q List all queues

qstat -fQ <queue> List full information about queue

qstat -u $USER Show all current jobs from your user in all queues

qpeek <job_id> Display current contents of stdout for this job

qpeek -f <job_id> Display end of stdout for this job and keep listening (terminate with Ctrl+C)

Interactive session

qsub -I -N stdin -l nodes=1:ppn=16 -l walltime=1:00:00

Slurm cheat sheet

Job scheduling

sbatch <script.sh> Submit script

scancel <job_id> Cancel submitted job

Job management

sinfo -a List all queues

squeue List all jobs

squeue -u $USER Show jobs for your users

Interactive session

srun --pty bash

salloc --nodes=3 --bell The terminal bell will notify you once allocation has been granted. Note that you need to manually connect to that allocation using srun --jobid=<job_id> --pty /bin/bash

Spack cheat sheet

spack find --loaded Find loaded packages

spack install <pkg>%[email protected] +openmp Install package, compile it with gcc 9.2.0 and enable the openmp feature

To update spack: git pull in the spack directory

ToDo

  • Add Slurm sample submission script
  • Add vim/neovim configuration
  • Write bash script that automatically sets up this configuration
  • Add aliases for slurm / other useful things
  • Add references in the README for easier navigation
  • Add explanation for tmux shortcuts
  • Explain .zshrc, add p10k & oh-my-zsh configurations