[Gmod-help] Session locks overwritten with mod_perl and fcgi

[joseph franklin]

I upgraded to 1.997.  Accessing the browser through mod_perl seems to  
be working fine now, with sessions locking as expected.  However, the  
default link (cgi-bin/gb2/gbrowse) comes up with an error, reported in  
the server log as:
[Thu Jul 30 14:19:44 2009] [error] [client xx] (13)Permission denied:  
exec of '/usr/lib/cgi-bin/gb2/gbrowse' failed
[Thu Jul 30 14:19:44 2009] [error] [client xx] Premature end of script  
headers: gbrowse

fast-cgi access also returns an error:
[Thu Jul 30 14:21:19 2009] [warn] (104)Connection reset by peer:  
mod_fcgid: read data from fastcgi server error.
[Thu Jul 30 14:21:19 2009] [error] [client xx] Premature end of script  
headers: gbrowse
[Thu Jul 30 14:21:22 2009] [notice] mod_fcgid: process /usr/lib/cgi- 
bin/gb2/gbrowse(23135) exit(communication error), terminated by  
calling exit(), return code: 255

Of course, those are superfluous now that mod_perl works.  I installed  
everything with root permission and to the default destinations, so  
I'm not sure what's causing those errors.

Thanks again,
Joe




On 30 Jul 2009, at 12:41, Lincoln Stein wrote:

> Hi Joseph,
>
> I believe I have fixed this bug. Please try version 1.997 that I  
> just uploaded to CPAN.
>
> Lincoln
>
> On Thu, Jul 30, 2009 at 10:10 AM, joseph franklin <joseph.franklin at yale.edu 
> > wrote:
> Lincoln,
> As far as I know, everything I'm doing related to session locking is  
> the default, except that I added the "session lock type = nfs" line  
> to try to make sure that it isn't using flock:
>
> # session settings
> session lock type = nfs
> session driver = driver:file;serializer:default
> session args   = Directory /var/tmp/gbrowse2/sessions
>
> Since this problem is limited to the mod_perl and fcgi modes, is  
> there something specific to those packages that needs to be  
> specified for proper session locking? (I know very little about  
> insides of those modules or apache2).
>
> Let me know if I can provide any more info.  Thanks-
> Joe
>
>
> On 29 Jul 2009, at 16:10, Lincoln Stein wrote:
>
>> This is unpleasant news; I thought the session locking was pretty  
>> well tested. Can you describe how to reproduce this bug?
>>
>> Lincoln
>>
>> On Tue, Jul 28, 2009 at 12:26 PM, joseph franklin <joseph.franklin at yale.edu 
>> > wrote:
>> (Now that I've recovered the browser installation, I'll post my  
>> original question)
>>
>> When I use either ModPerl or Fast-CGI in Gbrowse2 (1.996), track  
>> loading and refresh are both nicely accelerated.  However, in  
>> either of these modes, it seems like the session locks get  
>> overwritten, rather than created, when a new user accesses the  
>> browser (the landmarks, tracks, etc. are lost for the first user).   
>> The default installation (localhost/cgi-bin/gb2/) appears to be  
>> locking sessions normally.
>>
>> Realizing that GBrowse 2 is pre-release, I'd love to hear if anyone  
>> has any easy suggestions (or perhaps this is a bug).
>>
>> I'm running this on Ubuntu 9.04 (webserver: Apache/2.2.11 (Ubuntu)  
>> PHP/5.2.6-3ubuntu4.1 with Suhosin-Patch mod_perl/2.0.4 Perl/v5.10.0  
>> Server).
>>
>> Here is my GBrowse.conf session settings stanza:
>> # session settings
>> session driver = driver:file;serializer:default
>> session args   = Directory /var/tmp/gbrowse2/sessions
>>
>>
>> /var/tmp/gbrowse2/sessions and /var/tmp/gbrowse2/locks are both  
>> writable to the server, and indeed written to when any new session  
>> is started (except in the mod_perl or fcgi cases, when relevant  
>> session/lock files are overwritten).
>>
>>
>> Thanks,
>> joe
>>
>>
>>
>> ________________________________
>> Joe Franklin
>> Department of Cell Biology
>> Yale University School of Medicine
>> 295 Congress Ave, BCMM 137
>> New Haven, CT 06519
>> USA
>>
>> joseph.franklin at yale.edu
>> 407 341 3263 (cell)
>> 203 654 7494 (google voice)
>>
>>
>>
>>
>> -- 
>> 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>
>
> ________________________________
> Joe Franklin
> Department of Cell Biology
> Yale University School of Medicine
> 295 Congress Ave, BCMM 137
> New Haven, CT 06519
> USA
>
> joseph.franklin at yale.edu
> 407 341 3263 (cell)
> 203 654 7494 (google voice)
>
>
>
>
> -- 
> 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>
]
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