fix: handle benmark bug that arise with singularity #1671
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running snakemake with singularity results in invalid benchmark statistics, since snakemake doesn't have read access to all pids.
johanneskoester
requested changes
May 19, 2022
johanneskoester
requested changes
May 31, 2022
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Kudos, SonarCloud Quality Gate passed!
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johanneskoester
requested changes
Jul 19, 2022
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Kudos, SonarCloud Quality Gate passed!
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@johanneskoester I have updated the commit with more handling for events when no benchmark can be collected. When debbuing is turned on and if any process cannot be processed information about which process that can and cannot be processed will be printed. |
johanneskoester
approved these changes
Aug 25, 2022
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Description
Running snakemake with singularity results in (nearly) empty benchmark statistics. benchmark tries to read a process with name "starter-suid" which raise a AccessDenied event, resulting in that the other processes belonging to the snakemake process aren't read. Wrapping the proc.memory_full_info() in a try-statement that fires a continue event enables the other processes to be parsed.
This should help solve issue: #1267
QC
docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).