Using Lab Resources

Using the lab servers

  1. http://grad.biology.ualberta.ca/mlewis/computing/ or http://www.math.ualberta.ca/~mduller/LRG-IT/index.html
  2. We have 4 servers, LRG1 and LRG2 (more powerful), and deneb and gilford (less cores, less memory)
  3. The servers run in Unix but you can use them to run Python, R, and Matlab code
  4. Getting started on the servers
    1. Use PuTTY or MobaXTerm to run commands on the server
    2. Use WinSCP to send files to the server’s file system, and retrieve files created by your server commands
  5. Use “top” to see what’s running, “q” to exit
  6. Tips on how to increase your effectiveness on the server
    1. Using “screen”, or alternatively, “tmux”
      1. screen -S giveitaname
        1. To detach: Ctl-a d
        2. To attach: screen -d -r name
      2. Tmux new -t giveitaname
        1. To detach: ctrl-b d
        2. To attach: tmux attach -t name
    2. Running code in parallel
  7. Tips on how to cooperate with others on the server
    1. “nice” command – if your code isn’t super high priority, you can tab it to run after higher priority commands
      1. Lower number is higher priority (example: nice -n 9 commandname)
      2. Can do renice command.
  8. Shell script example
    1. #!/bin/bash
    2. nice -n 9 Rscript server_example_20201123.R
    3. mail -s “Testing the server’s capability” pt1@ualberta.ca <<< ‘Done’
    4. Need to set the execution flag on the file, can use winscp file properties or use command line (chmod 700 filename)