Hello,

I picked up some weird MySQL behaviour when querying my local mart.
Basically, there would be entries left in the MySQL process list which
resemble process zombies on the operating system level.

For example, 'show processlist;' would display the following information:
 Id, db, Command, Time, State, Info
 16538, NULL, Query, 0, NULL, show processlist
 16543, ensembl_mart_56, Sleep, 471, , NULL
 17100, biomart, Sleep, 10, , NULL
 17101, ensembl_mart_56, Query, 10, Sending data, SELECT
main.stable_id_1023, ...

Apparently, the thread 17100 is started at the same time as the query
with the thread id 17101, but the former has a strange signature.
Basically, I do not know what it does. The older thread 16543 looks
very much the same as 17100, but whilst its associated query has
successfully terminated, the thread 16543 lingers on. I have not yet
found a reproducible procedure to create these zombie queries, but
they do appear every now and then.

Perhaps related, I have also noticed that not all MartView queries
would necessarily generate an SQL query. In those cases, the little
spinning and the text 'Loading...' would stay there forever.

Since the marts of www.biomart.org seem to work perfectly well, I am
wondering whether I am using old Perl code or an unpatched version of
BioMart. Does anyone else experience these problems I am having?

Thanks,
Joachim

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Faculty of Life Sciences
The University of Manchester
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United Kingdom

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