Cheatsheets

Cheatsheets for CLI commands I use.

NOTE: The brackets are not literal, but the curly brackets are.

Remote Connection (ssh)

• ssh [user]@[host] ls -lNHha --color DIR: Remote ls
• ssh [user]@[host] "cat [file]" | diff - [local_file]: Remote diff
• ssh -Y -l [user] [host] -p [PORT]: Port Forwarding (X11)
• scp -pr [user]@[host]:[REMOTE_PATH] [LOCAL_PATH]: Download file(s) from server
• scp -pr [LOCAL_PATH] [user]@[host]:[REMOTE_PATH]: Upload file(s) to server
• Shift+Middle Click or Shift+Insert: Paste from clipboard to server

NOTE: [user]@[host] can be simplified by using aliased in $HOME/.ssh/config file

SGE (Sun Grid Engine)

• Submit Jobs:
  • qsub [script]: Submit a job that will execute the specified script
  • qsub [script] [arguments]: Submit a job that will execute the specified script with the specified arguments
  • qsub [script] [arguments]: Submit a job that will execute the specified script with the specified arguments
  • qsub -N [job_name] [script]: Submit a job that will execute the specified script with the specified job name
  • qsub -hold_jid [dependency_job] [script]: Submit a job that will execute the specified script but depends on the execution of another job
• Delete jobs:
  • qdel [job_id]: Delete the job with the specified job_id
  • qdel {[job_id_i]..[job_id_j]}: Delete jobs in the specified range (including both ends)
• View job statuses:
  • qstat -f: Display “full” information on all queues for all users
  • qstat -j [job_list]: Display information for the specified jobs (comma separated)
  • qstat -u [user_name]: Display information on all queues for the specified user
  • qstat -q [queue_name]: Display information on the specified queue
  • The options above can be combined, e.g.:
    • qstat -f -u [user_name] -q [queue_name]

SLURM

• Run Jobs
  • srun -u --pty --gres=gpu:1 bash -i: Allocate 1 GPU (--gres=gpu:1) and run bash interactively (bash -i)
  • srun -u --pty --gres=gpu:1 -t 2-0 bash -i: Allocate 1 GPU and run bash interactively for 2 days (-t 2-0)
  • srun -u --pty --gres=gpu:1 -t 200 bash -i: Allocate 1 GPU and run bash interactively for 2 and a half hours (-t 200)
  • srun -u --pty --gres=gpu:1 -C [constraint] bash -i: Allocate 1 GPU and run bash interactively when the constraint (e.g. TitanX) is met
  • srun -u --pty --gres=gpu:1 [script]: Allocate 1 GPU (--gres=gpu:1) and run the specified script
• Submit batch jobs
  • sbatch [script]: Submit a script job (using SBATCH commands in the script to specify options)
• View information about jobs:
  • squeue: View information about jobs from all users
  • squeue -u [user]: View information about jobs submitted from the specified user
• View job configuration:
  -scontrol show job: View configuration for all jobs
  -scontrol show job [job_id]: View configuration for the specified job

Tmux

• Prefix+Ctrl-s: Save tmux session that persists through reboots (requires tmux-resurrect)
• Prefix+Ctrl-r: Restore tmux session, even after reboot (requires tmux-resurrect)
• Prefix+?: Help
• Prefix+/: Search

Watch

• watch -t [command]: Execute command periodically every 2 seconds and display output without the command title (-t option)
• watch -t -n [seconds.deciseconds] [command]: Execute command periodically using the specified interval and display output
• watch -t -d [command]: Execute command periodically and display output, highlighting the differences