Not sure what causes the problem or how to fix it manually but a reboot cleared it up for me (same exact error message from terminal as original reporter). So after reboot it is working fine again. This is Ubuntu 16.04, btw.
-- You received this bug notification because you are a member of Desktop Packages, which is subscribed to gnome-system-monitor in Ubuntu. https://bugs.launchpad.net/bugs/1430068 Title: Unable to launch gnome-system-monitor Status in gnome-system-monitor package in Ubuntu: Confirmed Bug description: When you have too many open files, you can't launch gnome-system- monitor: $ gnome-system-monitor (gnome-system-monitor:23720): glibmm-CRITICAL **: unhandled exception (type Glib::Error) in signal handler: domain: g-io-error-quark code : 0 what : Unable to find default local directory monitor type (gnome-system-monitor:23720): Gtk-CRITICAL **: gtk_window_present_with_time: assertion 'GTK_IS_WINDOW (window)' failed ProblemType: Bug DistroRelease: Ubuntu 14.10 Package: gnome-system-monitor 3.8.2.1-2ubuntu4 ProcVersionSignature: Ubuntu 3.16.0-31.41-generic 3.16.7-ckt5 Uname: Linux 3.16.0-31-generic x86_64 ApportVersion: 2.14.7-0ubuntu8.2 Architecture: amd64 CurrentDesktop: Unity Date: Tue Mar 10 09:32:12 2015 InstallationDate: Installed on 2014-06-26 (255 days ago) InstallationMedia: Ubuntu 14.04 LTS "Trusty Tahr" - Release amd64 (20140417) SourcePackage: gnome-system-monitor UpgradeStatus: Upgraded to utopic on 2014-10-27 (133 days ago) To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/gnome-system-monitor/+bug/1430068/+subscriptions -- Mailing list: https://launchpad.net/~desktop-packages Post to : desktop-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~desktop-packages More help : https://help.launchpad.net/ListHelp