[ensembl-dev] EFG Array Mapping inconsistent performance

[Oliver, Gavin]

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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