[Treebase-devel] Fwd: treebase file download issues

[Mattison W. <mat...@ne...>]

---------- Forwarded message ----------
From: Michael Jones <mjo...@gm...>
Date: Tue, Jun 19, 2012 at 4:30 PM
Subject: Re: [Treebase-devel] treebase file download issues
To: Mattison Ward <mat...@ne...>


P.S.
I sent an email to Hilmar asking if TreeBASE was down for maintenance
at 1:28. I had tried to download something, realized it was taking a
really long time, reloaded, and then reattempted downloading. Then I
got a site unavailable error.
Cheers,
Micael

On Tue, Jun 19, 2012 at 4:27 PM, Michael Jones <mjo...@gm...> wrote:
> Hi Mattison,
> I'm not sure how much traffic there is on TreeBASE, but I was using
> the production site when it crashed (under the username jonesmcc). I
> can't remember specifically, but I was definitely working on one of my
> "In Progress" submissions and think I was attempting to diagnose some
> taxa labeling issues while interconverting between nex and NeXML
> formats.
> Let me know if you would like any further information.
> Cheers,
> Michael
>
> On Tue, Jun 19, 2012 at 4:03 PM, Mattison Ward
> <mat...@ne...> wrote:
>> Sorry for the repeat message to some folks, but I wanted to send this
>> to the whole list.
>>
>> Occasionally the tomcat process on the production or development site
>> will go through the roof for cpu usage and stop responding until
>> killed and restarted.  I have searched through the error logs, but
>> haven't found anything obvious to me.  I am starting to suspect that
>> trying to download certain studies in nexml format precipitates the
>> problem.  If several of these nexml files in a row start to pile up,
>> memory usage by the JVM keeps increasing and the server stops
>> responding.
>>
>> You can see this yourself if you try to download the nexml file from
>> http://treebase-dev.nescent.org/treebase-web/search/study/summary.html?id=12742
>>
>> The nexus file for that study downloads almost immediately.
>>
>> You can see in the screenshot one that I left running for over 10
>> minutes.  It maybe if I left these running long enough they would
>> complete, but in practice these requests can overwhelm the server if
>> they are not serial (like in my test).
>>
>> Other "problem" study ids between 12800 and 11753
>> 12201 killed after 10 minutes (killed nexus download after 10
>> minutes,but database was busy rather than java/tomcat)
>> 12156 killed after 10 minutes (5 seconds for nexus)
>> 12064 = 5 minutes (3 seconds for nexus)
>> 12032 = 4 minutes (1 second for nexus)
>> 11872 = 10 minutes (52 seconds for nexus)
>> 11811 killed after 10 minutes (35 seconds for nexus)
>>
>> Note that I turned Apache caching off for these tests and will leave
>> it off for anyone else to test.
>>
>> Could timeouts for uploading and downloading files be implemented so
>> too many concurrent downloads don't disable the site?
>>
>> Maybe some studies are too large to be converted to nexml in a
>> workable amount of time?
>>
>> Is treebase written in such a way that we could deploy many tomcat
>> instances pointed to a common database so that if one client requested
>> many downloads, it would only tie up one tomcat instance while the
>> other 7 would keep serving requests happily?
>>
>> --
>> Mattison
>>
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-- 
Mattison Ward
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