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algbio / ggcat

Compacted and colored de Bruijn graph construction and querying
MIT License
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Problem with GGCAT when using 32 threads #45

Open khodor14 opened 6 months ago

khodor14 commented 6 months ago

I was running ggcat on 72 human genomes (subset of human genomes used in ggcat paper and published on zenodo). I was executing it with 32 threads. After 24 hours it was still executing so I stopped it. Then I changed the number of threads to 20, it finished in 13 minutes. I tried to monitor both execution settings, in the first case (32 threads) phase eta was always 18446744073709551615 s, while for the 16 threads case it was 1290 s. I am not sure if this is the source of the problem?

Anyway, what could be the cause of such a problem? (it is supposed to be faster when using more threads).

Thank you in advance.

Guilucand commented 5 months ago

Hi, the problem could be some kind of race condition, does it always fail when using 32 threads or only sometimes? On what subset of human genomes does it cause the problem? Can you attach the full log of the run that hangs?

Thanks, Andrea