Gbrowse2 & Mod_Fcgid

Question

[Gregor Rot]

Hello,

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

Answer 1

[Scott Cain]

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:

https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

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

Scott

Answer 2

[Michael]

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/mod_fastcgi.so
[...]
<IfModule mod_fastcgi.c>
  Alias /fgb2 "/opt/local/apache2/cgi-bin/gb2"
  <Location /fgb2>
    SetHandler   fastcgi-script
    Options      ExecCGI
  </Location>
  # 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
</IfModule>

Answer 3

[Neilfws]

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.

[Gregor Rot]

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