[ensembl-dev] EFG Array Mapping inconsistent performance

Nathan Johnson njohnson at ebi.ac.uk
Wed Sep 15 10:58:37 BST 2010


Hi Gavin

For v60 we have now set the cigar_line field to a VARCHAR with a sensible field length of 50. The current largest cigar_line in human is around 30 characters long.

This should remove the issue of tmp tables being created on disk.

Nath



On 25 Aug 2010, at 10:12, Oliver, Gavin wrote:

> Hi all,
>  
> I’ve been running some tests on our server, annotating a test batch of around 50 Affy probesets (25-mer probes, 11 probes per set).
>  
> Running the same batch of probesets has completed in anywhere from 30 mins to just over 2 hours!
>  
> The load on the server does not seem to be the issue.  I have run a number of mysql tuners to optimize things and the only complaint I am seeing is that 50% of our temporary tables are being created on disk rather than in memory.  Apparently this is a major cause of inconsistent mySQL performance.  I have increased all relevant variables but it does not seem to affect the % of temp tables being created on disk.  I know that BLOB and TEXT fields cannot be stored in memory and must be created on disk so I’m beginning to think this may be the problem.  Has anyone else experienced similar problems or does anyone have any ideas on how the BLOB and TEXT fields could be redefined to enable in-memory storage?
>  
>  
> Best,
>  
> Gavin
>  
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Nathan Johnson
Scientific Programmer
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
Email: njohnson at ebi.ac.uk
TelNo: (+44)1223 492629





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