[Bioperl-l] Fwd: [Gmod-gbrowse] sleeping mysql processes w/Bio::DB::SeqFeature::Store

[Jason Stajich]

Another reason to make sure this module is its own package so Lincoln can release it more rapidly than BioPerl. Hope new branch can fix that. 

Sent from my iPhone-please excuse typos

--
Jason Stajich

Begin forwarded message:

> From: Lincoln Stein <lincoln.stein at gmail.com>
> Date: July 10, 2013, 7:58:05 PDT
> To: Martin Mokrejs <mmokrejs at fold.natur.cuni.cz>
> Cc: Jim Hu <jimhu at tamu.edu>, GMOD GBrowse List <gmod-gbrowse at lists.sourceforge.net>
> Subject: Re: [Gmod-gbrowse] sleeping mysql processes w/Bio::DB::SeqFeature::Store
> 
> I have just uploaded GBrowse version 2.55 to CPAN. It contains a bioperl
> patch that fixes slow loading of multiple GFF3 files, and changes the
> timeout values for mod_fastcgi and mod_fcgid. I have also noticed that
> mod_fastcgi now seems to be faster than mod_fcgid when the timeout issue is
> fixed.
> 
> I don't think that the FastCGI issues are related to the sleeping mysql
> process issue, actually, because this was first reported in the context of
> running GBrowse in CGI mode. I am starting work on CGI mode now.
> 
> Lincoln
> 
> 
> On Tue, Jul 9, 2013 at 6:49 PM, Martin Mokrejs
> <mmokrejs at fold.natur.cuni.cz>wrote:
> 
>> Hi,
>> 
>> Lincoln Stein wrote:
>>> Hi Folks,
>>> 
>>> With respect to the FastCGI errors, I have tracked the problem down to
>> the following sequence of events:
>>> 
>>> 1. The FastCGI executive module launches a fresh gbrowse instance.
>>> 2. GBrowse tries to load its default database into memory.
>>> 3. If the default database takes more than 3s to load, then FastCGI
>> times it out.
>>> 4. FastCGI launches a new instance of GBrowse.
>>> 5. GBrowse tries to load its default database into memory.
>>> 6. FastCGI times the new instance out.
>>> 7. Repeat 4-6 indefinitely.
>>> 
>>> Note that this only happens for databases that are slow to load,
>> typically in-memory databases. For example, the full tutorial database
>> takes ~8s to load on my machine (unreasonably slow for reasons that are
>> unclear to me: I am going to start debugging bioperl next). Once the
>> database is loaded, however, all subsequent accesses are fast.
>>> 
>>> Here's what to do to fix the problem:
>>> 
>>>  * for mod_fcgid, add the following directive to
>> /etc/apache2/conf.d/gbrowse2 (in the same section as *FcgidIOTimeout*)
>>>      o   *FcgidConnectTimeout 30*
>>>  * for mod_fastcgi, change *FastCGIConfig* to
>>>      o *FastCGIConfig *-startDelay 30 -appConnTimeout 30 -idle-timeout
>> 600 -maxClassProcesses 20  -initial-env GBROWSE_CONF=/etc/gbrowse2
>> 
>> Hmm, I would call this a workaround instead. Why isn't there something
>> like a lock
>> in Gbrowse so that multiple connections to mysql wouldn't be established?
>> This
>> will definitely trick again some user or sysadmin. At least if gbrowse
>> would test
>> for a timeout value and complain and exit if it would be too short.
>> 
>> In my eyes gbrowse is full of such tricks and reading this lists only
>> ensures me that
>> the code should be more careful about what user has configured, what is
>> and what is not
>> available, and ... provide helpful error messages. I don't have the time
>> to contribute
>> some code in this regard but anything leading to perl unitialized values
>> should be
>> fixed. At least, I could fish some emails from the archives and emphasize
>> the worst
>> examples. Or the other way around, jsut take a working setup and start to
>> screw file/dir
>> permission, place bad filenames/dbnames/dirnames into config, set screw
>> variable names.
>> It will all generate all kinds of funny messages to apache logs and that
>> should fairly
>> doable to put a couple of roadblocks along the way.
>> 
>> This would only be helpful to everybody asking here on this list for help
>> with some weird
>> messages in apache logs.
>> 
>> Just my 2cents, ;-)
>> Martin
> 
> 
> 
> -- 
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> ------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
> Start your free trial of AppDynamics Pro today!
> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse