I've been having consistent problems(last 4 upgrades) where during the final stage of the upgrade, the mailbox service does not start because of the java heap memory percent being allocated too large. I have to manually go into the zmmailboxdctl file in /opt/zimbra/bin and hard code a jm=1300 size which sets the mailboxd_java_heap_memory_percent to 46 instead of letting the system calculate it on it's own. I am running 4GB of memory at FC7. Bug 21348 seems to be the orignal problem but it was closed as fixed but I still have the issue. I have seen tuning notes about the default max user space being 2GB in a 32 bit environment but it seems like the install scripts calculates over that amount. Any help would be appreciated.
One fallout is this in the log:
Upgrading Document templates...
Sat Dec 13 22:01:04 2008 *** Running as zimbra user: /opt/zimbra/bin/zmprov ut -h zimbra.acme.com /opt/zimbra/wiki/Template
ERROR: zclient.IO_ERROR (invoke Connection refused, server: localhost) (cause: java.net.ConnectException Connection refused)
Sat Dec 13 22:01:05 2008 failed.
Sat Dec 13 22:01:05 2008 Restarting mailboxd...
Sat Dec 13 22:01:05 2008 *** Running as zimbra user: /opt/zimbra/bin/zmmailboxdctl restart
Stopping mailboxd...mailboxd is not running