[GMOD-devel] Any solutions to the GBrowse memory leak problem?

[Jayaraman, P. <pja...@mc...>]

RUN(): POST: http://test.rgd.mcw.edu/fgb2/gbrowse/rgd_904/
action=retrieve_multiple;track_ids

=HumanSyntenyBlock;track_ids=RatSyntenyBlock;track_ids=dbSNP_Track;tk_Hu
manSyntenyBlock=26117e647b7417d62fcfd434df39df4b;tk_RatSyntenyBlock=9b2c
1f8a09b0e005fd06638a9645eb78;tk_db

SNP_Track=a653ea6516e414ecf2af259e986b2442;_= at
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/
Browser2/Render.pm line 201., referer: http://test.rgd.mc

w.edu/fgb2/gbrowse/rgd_904/

[Tue Apr 19 11:56:46 2011] [warn] [client 141.106.161.52] mod_fcgid:
stderr: [11552] add_user_tracks() at
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-, referer: http://test.rgd

.mcw.edu/fgb2/gbrowse/rgd_904/

[Tue Apr 19 11:56:46 2011] [warn] [client 141.106.161.52] mod_fcgid:
stderr: thread-multi/Bio/Graphics/Browser2/Render.pm line 209., referer:
http://test.rgd.mcw.edu/fgb2/gbrowse

/rgd_904/

[Tue Apr 19 11:56:46 2011] [warn] [client 141.106.161.52] mod_fcgid:
stderr: [11552] testing for asynchronous event() at
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult

i/Bio/Graphics/Browser2/Render.pm line 214., referer:
http://test.rgd.mcw.edu/fgb2/gbrowse/rgd_904/

[Tue Apr 19 11:56:46 2011] [warn] [client 141.106.161.52] mod_fcgid:
stderr: [11552] asynchronous exit at
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/

Browser2/Render.pm line 216., referer:
http://test.rgd.mcw.edu/fgb2/gbrowse/rgd_904/

[Tue Apr 19 11:57:44 2011] [warn] [client 141.106.161.52] mod_fcgid:
read data timeout in 40 seconds, referer:
http://test.rgd.mcw.edu/fgb2/gbrowse/rgd_904/

[Tue Apr 19 11:57:44 2011] [error] [client 141.106.161.52] Premature end
of script headers: gbrowse, referer:
http://test.rgd.mcw.edu/fgb2/gbrowse/rgd_904/

[Tue Apr 19 11:57:53 2011] [warn] [client 141.106.161.52] mod_fcgid:
read data timeout in 40 seconds, referer:
http://test.rgd.mcw.edu/fgb2/gbrowse/rgd_904/

[Tue Apr 19 11:57:53 2011] [error] [client 141.106.161.52] Premature end
of script headers: gbrowse_img, referer:
http://test.rgd.mcw.edu/fgb2/gbrowse/rgd_904/

 

I see these errors in my error logs.. I see a "read data timeout" .. how
do I counter that?

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pja...@mc...

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:pja...@mc...] 
Sent: Tuesday, April 19, 2011 11:34 AM
To: gmo...@li...; gmo...@li...
Subject: [Gmod-gbrowse] Any colutions to the GBrowse memory leak
problem?

 

Hello, 

I am referring to this particular issue that we seem to be experiencing
as well... 

http://comments.gmane.org/gmane.science.biology.gmod.gbrowse/7572

 

Our Gbrowse process simply hangs even if we have just three tracks open
for a range of 1MB. Reloading the page seems to make it okay and
everything renders quickly.. 

Our Gbrowse process is 2.15. 

 

The issue ( follow link) reports that it is some sort of memory leak in
gbrowse.. 

 

Would you guys out there know any solution to this problem.. or a fix
that we might have to integrate?

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pja...@mc...

Work: 414-955-2229

www.rgd.mcw.edu