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Why do I get too many open files error?

asked 2013-08-20 12:02:23 -0500

anonymous user

Anonymous

updated 2014-05-08 11:45:52 -0500

I just installed Pathway Tools and when I start up the application, I get an error "Too many open files". What does this mean and how do I fix it?

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answered 2013-08-20 12:17:56 -0500

ptools-admin gravatar image

updated 2014-05-19 20:02:48 -0500

Pathway Tools uses a database technology called acache that stores each organism via a file database. For large number of organisms, it requires access to a lot of these acache file databases. On most Unix based systems (including Mac OSX), there's a limit to the number of files a user process can access.

By default, most Linux systems has this set to 8k and Macs has this set to 256. Depending on which OS version or Linux distribution you're using, changing this setting will be different.

For Mac OSX, use launchctl to modify this setting: http://superuser.com/questions/302754/increase-the-maximum-number-of-open-file-descriptors-in-snow-leopard

 % sudo launchctl limit maxfiles 4096 8192

For Linux, you need to check both the system "hard" limits as well as the user limits: http://www.cyberciti.biz/faq/linux-increase-the-maximum-number-of-open-files/

  1. Check the hard limit setting usually in /etc/sysctl.conf via fs.file-max setting
  2. Change user limits via /etc/security/limits.conf via the "nofile" settings.

    Example:

     ptuser               soft    nofile          32768
     ptuser               hard    nofile          65535
    

NOTE: Location of files may differ between Debian and Redhat based distributions. After making the setting changes, you will need to either log out or reboot your system for the settings to take affect.

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Asked: 2013-08-20 12:02:23 -0500

Seen: 8,455 times

Last updated: May 19 '14