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Why is mblast slower than ncbi and legacy blast? #112

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Foxcapades opened this issue Mar 7, 2022 · 4 comments
Open

Why is mblast slower than ncbi and legacy blast? #112

Foxcapades opened this issue Mar 7, 2022 · 4 comments
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Foxcapades commented Mar 7, 2022 •
edited by aurreco-uga
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Why is job 8712B1497978065E708AD3433906A4A8 so slow?
This job was running subjobs > 50minutes in runtime before being manually killed. Why are these jobs so slow?

Additionally this full job broke NCBI's blast

slow_query.txt
@Foxcapades Foxcapades added the todo New feature or request label Mar 7, 2022
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An individual query that was taking 45+ minutes before it was killed ran in under 2 minutes on NCBI.

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We are going to test on the non-active production server tomorrow to reproduce.

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Additional performance difference between mblast and the old blast is that the old blast is allowed to use at least 4 cores to execute where mblast is using a single core per blast process.

@aurreco-uga aurreco-uga changed the title Why is job 8712B1497978065E708AD3433906A4A8 so slow? Why is mblast slower than ncbi and legacy blast? Mar 31, 2022
@aurreco-uga aurreco-uga reopened this Mar 31, 2022
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Foxcapades commented Mar 31, 2022 •
edited by aurreco-uga
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ask bob for access to dev blast container and run the command from the above job id with the same query using n cores.
test faster (4 cores) first to not use caching

@aurreco-uga aurreco-uga self-assigned this Mar 31, 2022
@Foxcapades Foxcapades removed the todo New feature or request label Jul 12, 2022
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