CSE-745 – Parallel and High Performance Computing
McMaster University
2025 Winter Semester

 

Instructor: Dr. Sergey Mashchenko
 

Course outline: HTML
 

Important notes:

  • If you do not have an Alliance (former Compute Canada) account, consider applying for one (it's free, and will be very helpful for your home assignments). Instructions. If your supevisor doesn't have an Alliance account, s/he will have to apply first.
  • Instructions for using Alliance national systems for home assignments:
    • Use MobaXterm (Windows) or any other ssh client to login to the cluster using your Alliance login name and password, e.g.
      ssh login_name@narval.alliancecan.ca
    • Reserve an interactive node with 32 cpu cores for up to 3 hours using salloc command:
      salloc --time=0-03:00 -c 32 -A def-user --mem=0 (For OpenMP excercises.)
      salloc --time=0-03:00 -N 1 -n 32 -A def-user --mem-per-cpu=3G (For MPI excercises.)
      Replace "def-user" with your default account name (which is likely your supervisor's account). To find out the name, execute command id on the cluster, and look for "def-***" string in the output.
    • When the resource becomes available, you will be taken automatically to the compute node. When you are done, execute "exit" to release the resource. After 3 hours the resource will be released automatically.
    • Our clusters have dynamic CPU clocks - the more load you give to a core, the faster the clock rate becomes. This makes scalability tests a bit tricky. The following strategy seems to work pretty well. Execute the code (both serial and parallel ones) in a continuous loop multiple time (>10), and choose the best timing for both, e.g.
      for ((i=0; i<20; i++)); do ./your_code | grep "time:"; done > out ; sort -gr out
  • Instructions for accessing Alliance clusters by Windows users:
    • Download and install a free Windows program Mobaxterm (Home Edition).
    • In the main (black) window, type "ssh user_name@narval.alliancecan.ca" to login to our cluster Narval, where user_name is your Alliance user name.
    • After you login to a cluster, in the left window you can access the remote file system browser.
    • Mobaxterm has a pretty decent built-in text editor, which can be used to edit remote files (simply double-click on a file name). To create a new remote file, click on the button "Create new file" on top of the file browser window.
    • In the same spot, the buttons "Download selected files" and "Upload to current folder" can be used to copy data from the cluster to you machine, and vice versa.

    Lecture notes (in PDF format):

    • Jan. 6, Lecture 1 (notes): Introduction to HPC computing
    • Jan. 13, Lecture 2 (notes): Introduction to HPC computing (continued)

    Home work

     

    To read PDF files on this page you will need the free Acrobat PDF Reader.