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

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Thu Nov 30 19:56:02 EST 2006

Chris & Chris,

I've run the maintenance scripts for MediaWiki (just in case they 
weren't run in the upgrade to 1.8.2), restarted Apache (with no 
significant changes on website response), then rebooted the machine 
(seems like MySQL restart didn't do the trick) and apparently its 
behaving much better. Please check if the reported error still happens.


Chris Dagdigian wrote:
> 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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>> Root-l at lists.open-bio.org
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arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM

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