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hpc-carpentry / old-hpc-workflows

Scaling studies on high-performance clusters using Snakemake workflows
https://www.hpc-carpentry.org/old-hpc-workflows/
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Set cores #23

Closed bkmgit closed 1 year ago

bkmgit commented 2 years ago

Set number of cores to prevent an error

ocaisa commented 2 years ago

Out of curiosity, what was the error?

tkphd commented 2 years ago

Giving the --cores option has been mandatory since v5.11. It throws

Error: you need to specify the maximum number of CPU cores to be used at the same time with --cores.

This PR looks good, although we're introducing the flag (by necessity) without saying anything about it. Pedagogically, it would be good to run without --cores the first time, then at line 88, display the error and share the "fix."

After this first instance, it looks like short flags are given; for consistency, we can convert --cores 1 to -c 1.

bkmgit commented 2 years ago

Have used short flags after the first invocation.

Not including --cores 1 does not seem to have much pedagogical value as it is specific to this software package rather than something that is generally used. The time could be used for other activities. Have added an explanation for why --cores 1 is required.

bkmgit commented 2 years ago

@tkphd Can you take a look at this again. The changes can probably also be made to the original repository.

tobyhodges commented 2 years ago

Also, you should replace -j with -c in the keypoints in the YAML header of 07-resources.md (line 12).

bkmgit commented 1 year ago

@tkphd @tobyhodges Think this is ok now.