HPC Day 2 morning session

  1. Let’s continue with the questions we did not finish on Tuesday.
Question 14

Suggest a computational problem to parallelize. Which of the parallel tools mentioned in the videos would you use, and why?

If you are not sure about the right tool, suggest a problem, and we can brainstorm the approach together.

 
Question 15

If you use Python or R in your work, try running a Python or R script in the terminal.

If this script depends on packages, try installing them in your own directory with virtualenv. Probably, only a few of you should do this on the training cluster at the same time.

 
Question 16 Any remaining questions? Type your question into the chat, ask via audio (unmute), or raise your hand in Zoom.
 
  1. Review the program for this morning: you have 1h15m of videos to watch until 11:30am Pacific.

By mid-day you should be familiar with:

  • how jobs are scheduled in Slurm
  • submitting …
    • serial, shared-memory, distributed-memory and hybrid jobs
    • array jobs
    • interactive jobs, and switching between interactive and batch jobs for the same task
  • how to estimate memory requirements of a completed Slurm job

Some of the hands-on exercises we will do in the mid-day Zoom session:

  • Using a serial job, time optimized (-O2) vs. unoptimized C code.
  • Using a serial job, time a C code vs. a Python code.
  • Submit an array job for different number of terms in the summation of \pi.
  • Try scaling an MPI job with 1 -> 2 -> 4 -> 8 cores and measuring the speedup.
  • Test a code inside an interactive job.