Why do I get too many open files error?

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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.