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Efficient jobs

Learning outcomes

  • Practice using the UPPMAX documentation
  • I can see the CPU and memory usage of jobs
  • I can read a jobstats plot
  • I can create a jobstats plot
  • I understand how to set up jobs efficiently
Want to see this session as a video?

Watch the YouTube video 'Intermediate Bianca workshop: efficient jobs'.

For teachers

Teaching goals are:

  • Learners have practiced using the UPPMAX documentation
  • Learners have seen the CPU and memory usage of jobs
  • Learners have read a jobstats plot
  • Learners have created a jobstats plot
  • Learners have discussed how to set up jobs efficiently

Lesson plan:

gantt
  title Efficient jobs
  dateFormat X
  axisFormat %s
  section First hour
  Course introduction: done, course_intro, 0, 10s
  Prior : intro, after course_intro, 5s
  Present: theory_1, after intro, 5s
  Challenge: crit, exercise_1, after theory_1, 40s
  Break: crit, milestone, after exercise_1
  section Second hour
  Challenge: crit, exercise_2, 0, 10s
  Feedback: feedback_2, after exercise_2, 10s
  SLURM: done, slurm, after feedback_2, 25s
  Break: done, milestone, after slurm

Prior questions:

  • How to schedule jobs efficiently?
  • What is the jobstats tool?

Present:

  • ?Show documentation

Why?

If everyone would use our computational resources effectively, there would be no queue.

From the UPPMAX documentation, original source unknown

Running efficient jobs allows you to run more jobs that start running faster.

Exercises

Exercise 1: reading a jobstats plot

Exercise 1.1: jobstats plot 1

See jobstats plot 1 below and answer these questions:

  • How much cores should this user book?
  • Why?

jobstats plot 1

jobstats plot 1

Answer

The user should have booked 1 core: the memory use will work fine with 1 core and this matches the CPU usage exactly.

It may be that the program is set up incorrectly and that it can use multiple cores if set up correctly.

Exercise 1.2: jobstats plot 2

See jobstats plot 2 below and answer these questions:

  • Did the job finish successfully?
  • How much cores should this user book?
  • Why?

jobstats plot 2

jobstats plot 2

Answer

The job did not finish successfully, the OUT_OF_MEMORY error indicites that.

How much cores the user should book is uncertain, we only know that it is more then currently used. One strategy is to double to amount of cores and finetune after a successful run.

Exercise 1.3: jobstats plot 3

  • See jobstats plot 3 below and answer these questions:
  • How much cores should this user book?
  • Why?

jobstats plot 3

jobstats plot 3

Answer

We don't know. The user uses all CPU power perfectly and there is enough memory available.

The user may benefit from more CPUs, as the program may be CPU limited.

It may be that the program used is designed to use 20 CPUs maximally, hence scheduling 20 cores is perfect!

It may be that using 20 cores is a strategy of the user: using multiple cores always brings computational overhead and hence wasted CPU resources.

Exercise 1.4: jobstats plot 4

See jobstats plot 4 below and answer these questions:

  • How much cores should this user book?
  • Why?

jobstats plot 4

jobstats plot 4

Answer

This seems to be the cleanest example of using the algorithm to use computational resources efficiently: the user needs 2 cores for memory and adds 1 for safely. The job is not clearly CPU limited.

Exercise 2: creating a jobstats plot

We are going to create a jobstats plot. For that, we need a job to plot. Here we first look for a job, after which we plot it.

  • Scan the UPPMAX finishedjobinfo documentation
  • Log in to your own Bianca project.
  • Find a job that has finished successfully that took longer than one hour (if there is none, use the job the ran longest)
Answer

Use any of the code snippets, for example How do I find jobs that have finished and took longer than an hour?:

finishedjobinfo | grep -E "runtime.([0-9]-)?[0-9][1-9]"

Press CTRL-C to stop the process: it will take very long to finish.

Answer 
jobstats --plot 12345678
Answer 
eog bianca-sens1234-sens1234-12345678.png
  • Was that a job that was set up well? If not, how should it be setup? Why?
  • Does the quote at the start of this sessions ('If everyone would use our computational resources effectively, there would be no queue') apply to your job?