[Bioperl-l] [Root-l] Intermittent MySQL problems on BioPerl wiki

Chris Dagdigian dag at sonsorol.org
Thu Nov 30 14:25:16 EST 2006


Reports like this need to go to support at helpdesk.open-bio.org so that  
they enter our RT helpdesk queue --  the main reason is that  
sometimes emails to the root-l at open-bio.org administrators mailing  
list can get lost in the shuffle.

I am going to bounce this message into RT and will restart mysql on  
the portal box. This is probably something we should be doing anyway  
to free up memory -- the wikis in particular seem to be pretty hard  
on mysql and free memory.

-Chris

On Nov 30, 2006, at 2:11 PM, Chris Fields wrote:

> I'm seeing some MySQL errors on the Bioperl wiki (using Firefox 2 and
> WinXP):
>
> Database error
>> From BioPerl
> Jump to: navigation, search
> A database query syntax error has occurred. This may indicate a bug  
> in the
> software. The last attempted database query was:
>
>     (SQL query hidden)
>
> from within function "MediaWikiBagOStuff::_doquery". MySQL returned  
> error
> "1205: Lock wait timeout exceeded; try restarting transaction  
> (localhost)".
>
>
> This occurs intermittently when editting pages, logging in, etc.   
> Also,
> pages loading to the browser seem much slower.
>
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
>
>
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