When debugging a threaded program with TotalView (http://www.etnus.com/), killing the program from the debugger after threads have been created creates zombie processes. This does not happen on the FC2 2.6.8 kernels. It also happens on the 2.6.9 FC2 kernel, so is not specific to FC3. This seems to not happen when debugging with GDB. I'm guessing that this could be due to some ptrace changes in the 2.6.9 kernel.
This has happened on two similar machines, one running FC2 and one FC3. These are old dual P3@1GHz Dell rack machines. Kernels tested with the bug: kernel-smp-2.6.9-1.667 (FC3) kernel-smp-2.6.9-1.681_FC3 kernel-smp-2.6.9-1.6_FC2 Kernels without the bug: kernel-smp-2.6.8-1.521 (FC2) I'll try the working 2.6.8 kernel on the FC3 machine.
With the 2.6.8 FC2 kernel on the FC3 machine, the problem is gone.
fixed in the 2.6.10 updates ?
With kernel-smp-2.6.10-1.741_FC3, TotalView is still unable to kill the process properly (they end up as zombies), but exiting TotalView now removes the zombies (which is an improvement). So, better, but still not good -- you can't restart the program in the debugger.
Recent TotalView versions have a work-around for this problem.
An update has been released for Fedora Core 3 (kernel-2.6.12-1.1372_FC3) which may contain a fix for your problem. Please update to this new kernel, and report whether or not it fixes your problem. If you have updated to Fedora Core 4 since this bug was opened, and the problem still occurs with the latest updates for that release, please change the version field of this bug to 'fc4'. Thank you.
The first computer I tried this on would not boot (unable to mount the root filesystem). Will try on another later, and report back.
With mkinitrd fixed (mkinitrd-4.1.18.1-1), 2.6.12 now boots, and seems to have fixed the issue.