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Is your feature request related to a problem? Please describe.
The value for the "--cores" option has the unpleasant side effect of restricting the number of threads that can be used - even in a setting where the rules are submitted to cluster nodes. In such a setting a mechanism to ensure that the number of threads used in a rule is the same as specified in the submission statement for the rule would make sense. Of course, this can be achieved by using something like "-pe smp {threads}"; however, this is not enforced and left to the user. But it is enforced that the number of threads cannot be higher the number of cores provided.
What is really bad, is that there is no mention of the fact that the threads have been reduced because of the value provided to the "--cores" option in the SnakeMake output; just the reduced number of threads is reported. And, moreover, if "--cores 1" is provided as an option, then the value of threads is not reported at all.
Of course, one should not use --cores if jobs are submitted; but if one does - as I did - this can cause a bit of confusion.
Describe the solution you'd like
Make --cores a forbidden parameter if an executor is used
Describe alternatives you've considered
Leave everything as it is.
The text was updated successfully, but these errors were encountered:
sven0schuierer
changed the title
Remove --cores as a required parameter; in fact, make it a forbidden parameter if an executor is used.
Make --cores a forbidden parameter if an executor is used.
Apr 18, 2024
Is your feature request related to a problem? Please describe.
The value for the "--cores" option has the unpleasant side effect of restricting the number of threads that can be used - even in a setting where the rules are submitted to cluster nodes. In such a setting a mechanism to ensure that the number of threads used in a rule is the same as specified in the submission statement for the rule would make sense. Of course, this can be achieved by using something like "-pe smp {threads}"; however, this is not enforced and left to the user. But it is enforced that the number of threads cannot be higher the number of cores provided.
What is really bad, is that there is no mention of the fact that the threads have been reduced because of the value provided to the "--cores" option in the SnakeMake output; just the reduced number of threads is reported. And, moreover, if "--cores 1" is provided as an option, then the value of threads is not reported at all.
Of course, one should not use --cores if jobs are submitted; but if one does - as I did - this can cause a bit of confusion.
Describe the solution you'd like
Make --cores a forbidden parameter if an executor is used
Describe alternatives you've considered
Leave everything as it is.
The text was updated successfully, but these errors were encountered: