Review the lesson content

[cdkharris]

Definition of Done / Acceptance Criteria

We recently made a big merge with the upstream repo which includes new content and significant changes to lessons. The new material needs to be checked over to make sure we can use it as-presented on Myriad. The other lessons should also be read, for completeness and my own peace of mind.

Index

Tick off all of these as read; comb more carefully where noted.

• [x] 10
• [x] 11
• [x] 12
• [x] 13
• [x] 14 env variables Read and test this and make a patch so that the lesson doesn't use my name
• [x] 15 modules read and perhaps update this
• [x] 16 transferring files Read and test this
• [x] 17 parallel Read and test this
• [x] 18
• [x] 19

Testing

No response

Documentation

No response

Dependencies

No response

Comments

No response

[cdkharris]

11

• double check host vs system config vars. "For systems like login12.myriad.ucl.ac.uk" should be Myriad
  • (i feel like there was another phrase typo somewhere)
• for us: putty isn't on the "new" d@ua by default. it can be loaded from the ucl application store. this also brings in the accessory apps. then it's in the apps list. exceed is only available on the legacy d@ua.
• typo "the ssh-agent command creates opens a connection" should be either creates or opens or probably just manages.

[cdkharris]

12

• update nodetypes output
• update qhost in "Explore..." so it queries a valid node

[cdkharris]

13

• correct the second version of example-job.sh. the time req as stated will not work with sge

[cdkharris]

18

• "Although we covered requesting resources from the scheduler earlier with the π code" is the "pi code" still a relevant reference?
• this text is not quite accurate for jobhist, which doesn't report memory usage. I don't think there's anything tidy to do about this.
• correct this solution: should be #$ -l h_rt=00:02:00

[cdkharris]

19

• we have a lot of specific resources which could be explained here, but those may have been left off intentionally- i think we rarely make it to this part of the lesson and it mostly re-iterates points that have already been made earlier.

[cdkharris]

15 Modules

• thunder slightly stolen because we have stumbled out of the dark ages and now python3 is just available on the system when you log in.
  • it would work mostly as-written with julia, but then that disturbs the subsequent examples
  • i can make most of the same points with python --version
• ansys works with no trouble now. lol.
  • R is ok to sub here
• can happily remove some notes since we updated modules:
  • Some HPC systems will automatically load dependencies like this, but at the time of writing (June 2020) UCL’s Myriad does not.
  • (On some systems, this will also unload the modules it depends on. Currently this is not the case with Myriad.)
• again, matlab default just works now; can do this with R
• fix the format of the time directive for sge

[cdkharris]

17 Parallel

• The python install instructions are a good moment to explain about python modules. should be something like

  module load python/recommended
  module unload compilers mpi
  module load compilers/gnu/4.9.2 mpi4py
  cd amdahl
  python3 -m pip install --user .

  • check that amdahl winds up on the path
• check that the scripts run
• and replace the output with smth suitable

[cdkharris]

14

• Correct the SGE env variables
• Correct the job script

the name thing is sort of ok... doesn't turn up in more than a few lines.