[Gmod-help] Re: [Gmod-gbrowse] Gbrowse does not display detail tracks when running in a proxy

[Scott Cain]

Hi Christian,

I guess the thing that is not clear to me about the segfaults is where
they are happening.  If it is actually on the proxy server and not on
the server that is running GBrowse, I don't see how this could be
GBrowse's fault.  Are other things accessible through the proxy?

Scott


On Mon, Feb 16, 2009 at 4:31 PM, Dave Clements, GMOD Help Desk
<gmodhelp at googlemail.com> wrote:
> Hi Christian,
>
> The line 587 errors are, as you expected, harmless.  They are from a
> leftover debugging statement that made it into the 1.69 release (and
> is now gone from the code).
>
> On the real problem, the seg faults, I am much less (OK, entirely)
> unsure.  I haven't worked with Apache proxies in years, but it looks
> to me like this is an Apache problem.  My memory of proxies is they
> just pass things through.  If the problem were with GBrowse, the seg
> fault would be happening on the server running GBrowse (and you'd have
> to be running it under something like mod_perl).
>
> You can try stuff like what is described on
> http://httpd.apache.org/dev/debugging.html.  That may tell you what
> Apache Module it is crashing in.  You could also try searching the web
> for combinations of the seg fault error message and Apache module
> names.  Focus on the apache modules installed on your proxy, that
> aren't installed on the GBrowse server.
>
> Anyone else have suggestions?
>
> Dave C.
>
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
>
>
> On Sun, Feb 15, 2009 at 5:43 AM, Christian M. Probst
> <cmacprobst at gmail.com> wrote:
>> Hi, all.
>>
>> I have a reverse proxy configured in Apache that redirects connections to
>> two internal servers.
>>
>> One of the servers is configured with Gbrowse 1.68 and I can see the details
>> page when connecting to the internal server through the redirection address.
>> The other one is configured with Gbrowse 1.69 and I cannot see the details
>> page. It renders the overview, but only if the element size is larger than
>> 500 kb.
>> Attached, there are the links for the examples.
>>
>> The Apache error log in the internal server (running the Gbrowse 1.69) has:
>>
>> [Sun Feb 15 00:30:06 2009] [error] [client 10.0.1.1]
>> Bio::Graphics::BrowserConfig=HASH(0x8c1fc1c) at
>> /opt/coolstack/lib/perl5/site_perl/5.8.8/i86pc-solaris/Bio/Graphics/Browser.pm
>> line 587., referer:
>> http://200.183.132.14:3124/notch/cgi-bin/gbrowse/KinetoDB/?name=NC_009276
>> [Sun Feb 15 00:30:07 2009] [error] [client 10.0.1.1]
>> Bio::Graphics::BrowserConfig=HASH(0x8c1fc1c) at
>> /opt/coolstack/lib/perl5/site_perl/5.8.8/i86pc-solaris/Bio/Graphics/Browser.pm
>> line 587., referer:
>> http://200.183.132.14:3124/notch/cgi-bin/gbrowse/KinetoDB/?name=NC_009276
>> [Sun Feb 15 00:30:07 2009] [error] [client 10.0.1.1]
>> Bio::Graphics::BrowserConfig=HASH(0x8c1fc1c) at
>> /opt/coolstack/lib/perl5/site_perl/5.8.8/i86pc-solaris/Bio/Graphics/Browser.pm
>> line 587., referer:
>> http://200.183.132.14:3124/notch/cgi-bin/gbrowse/KinetoDB/?name=NC_009276
>> [Sun Feb 15 00:30:07 2009] [error] [client 10.0.1.1]
>> Bio::Graphics::BrowserConfig=HASH(0x8c1fc1c) at
>> /opt/coolstack/lib/perl5/site_perl/5.8.8/i86pc-solaris/Bio/Graphics/Browser.pm
>> line 587., referer:
>> http://200.183.132.14:3124/notch/cgi-bin/gbrowse/KinetoDB/?name=NC_009276
>>
>> This  seems a common error, that occurs also when I access the Gbrowse 1.69
>> in the localhost, where the details part is rendered normaly.  Probably is a
>> harmless (or so) error.
>>
>> The Apache error log in the remote proxy is:
>>
>> [Sun Feb 15 05:56:20 2009] [notice] child pid 1383 exit signal Segmentation
>> fault (11)
>> [Sun Feb 15 05:56:28 2009] [notice] child pid 1385 exit signal Segmentation
>> fault (11)
>> [Sun Feb 15 05:56:35 2009] [notice] child pid 1386 exit signal Segmentation
>> fault (11)
>> [Sun Feb 15 06:01:41 2009] [notice] child pid 1387 exit signal Segmentation
>> fault (11)
>>
>> I don't know where I can obtain more information to understand why is
>> happening this segmentation fault.
>>
>> As both internal servers are accessible through the reverse proxy, and the
>> different GBrowse versions are related to different outcomes, I am
>> suspicious about Gbrowse 1.69.
>>
>> Any help is largely appreciated.
>>
>> Christian
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>
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research