Changes between Version 5 and Version 6 of Ticket #7358, comment 3


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Timestamp:
Aug 2, 2022, 10:03:20 AM (3 years ago)
Author:
Tom Goddard

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  • Ticket #7358, comment 3

    v5 v6  
    99Next I am going to try the search of the 214 million sequence AlphaFold database on minsky and on crick.  Actually probably don't have enough disk space on minsky, index will take about 800 Gbytes and only have 700 Gbytes free because AlphaFold databases take up most of the 4 TB NVMe drive.  Could try reducing to 100 million sequences for test on minsky.
    1010
    11 On crick, 214 million sequence search took 810 seconds (13.5 minutes) on the first run. On second run took 568 seconds (9.5 minutes).  Sensitivity was 5.7.  Running with sensitivity 1 took 915 seconds first run, 597 seconds on second run. Strange that low sensitivity is slower.  Search on 100 million sequences with default sensitivity (5.7) took 315 seconds on first run, 304 seconds on second run.
     11On crick, 214 million sequences search took 810 seconds (13.5 minutes) on the first run. On second run took 568 seconds (9.5 minutes).  Sensitivity was 5.7.  Running with sensitivity 1 took 915 seconds first run, 597 seconds on second run. Strange that low sensitivity is slower.  Search on 100 million sequences with default sensitivity (5.7) took 315 seconds on first run, 304 seconds on second run.
     12
     13On Minsky with 100 million sequences search took 659 seconds (11 minutes) seconds on first run, 651 seconds (11 minutes) on second run, with default sensitivity.
     14
     15The index for the database is split across several files based on the amount of memory.  On crick with 376 GB of memory the 214 million sequence index is 6 files, with 4 of size 126 Mbytes, and for 100 million sequences have 5 files with two 118 Mbytes and one 52 MB.  On minsky the 100 million sequences has index with 11 files, 9  being 34 Mbytes and one at 52 Mbytes.