Question: Gbrowse2 & Mod_Fcgid
gravatar for Gregor Rot
8.8 years ago by
Gregor Rot450
Zurich, Switzerland
Gregor Rot450 wrote:


i am trying to run gbrowse2 with apache2 mod_fcgid. I get this error in the error.log:

[notice] mod_fcgid: process /usr/lib/cgi-bin/gb2/gbrowse(8313)
exit(communication error), terminated by calling exit()
return code: 0

Can anybody suggest where the problem could be? Or at least give an idea of how to debug the problem?

If i run "sudo -u www-data /usr/lib/cgi-bin/gb2/gbrowse" (running this process as www-data, the user apache is running under) i just get this info:

Status: 302 Found
Location: /yeast/

Thank you, Gregor

ADD COMMENTlink modified 8.8 years ago by Neilfws49k • written 8.8 years ago by Gregor Rot450
gravatar for Scott Cain
8.8 years ago by
Scott Cain750
Scott Cain750 wrote:

Hello Gregor,

I don't know off the top of my head, but the GBrowse mailing list is probably a better place to ask this question, as I know there are people on that list that run GBrowse under fastCGI:

When you write the list, please be sure to include what version of GBrowse you are running.


ADD COMMENTlink modified 16 months ago by _r_am32k • written 8.8 years ago by Scott Cain750
gravatar for Michael Dondrup
8.8 years ago by
Bergen, Norway
Michael Dondrup48k wrote:

Hi, maybe this is not an option for you because it is a different module, but I am using mod_fastcgi sucessfully with the following configuration stanza in httpd.conf, I tried all modules mod_perl (worked for me), mod_fastcgi (worked, feels faster that mod_perl) and mod_fcgid but had some problems making mod_fcgid work at all on mac(ports). So here is the alternative:

LoadModule fastcgi_module modules/
<IfModule mod_fastcgi.c>
  Alias /fgb2 "/opt/local/apache2/cgi-bin/gb2"
  <Location /fgb2>
    SetHandler   fastcgi-script
    Options      ExecCGI
  # Note: you may need to increase -idle-timeout if file uploads are timing out and returning server
  # errors.
  FastCgiConfig -idle-timeout 600 -maxClassProcesses 40  -initial-env GBROWSE_CONF=/opt/local/apache2/conf/gbrowse2
ADD COMMENTlink written 8.8 years ago by Michael Dondrup48k
gravatar for Neilfws
8.8 years ago by
Sydney, Australia
Neilfws49k wrote:

Google search for the error brought up this page, which suggests that mod_fcgid is timing out for some reason. The author writes: "We found this mostly happens if the script runs too long waiting for external IO (i.e. database or ldap)."

You may be able to increase the value of IPCCommTimeout in your Apache config to see if that helps.

ADD COMMENTlink written 8.8 years ago by Neilfws49k

Tnx, but its probably not a timeout issue since the process is terminated immediatelly (<1 second).

ADD REPLYlink written 8.8 years ago by Gregor Rot450
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