Upgraded to 4.5.11; mysqld Now Consuming 99.9% CPU

[L. Mark Stone]

Hi,
We upgraded our SuSE ES9 32-bit NE installation from 4.5.6 to 4.5.11 and have noticed that the mysqld process is now frequently consuming 99.9% of CPU as reported by top.
Our hardware has 6GB of RAM and Zimbra support previously set the memory allocation for Tomcat and MySQL to 20% back when we were running 4.0.3.
Now that we are at 4.5.11 I am wondering if some tweaking is called for. This particular server hardware is an HP DL360 G4p with 2 x 3.00GHz 2MB CPUs and 2 x 146GB 15K disks in a RAID1 array.
I noticed in the my.cnf file that since the upgrade the last line declaring the pid file is listed twice. I also attach yesterdays MySQL slow log file.
Any tips would be greatly appreciated!
Thanks!

Mark
my.cnf.txt
myslow.log.1.txt

[jholder]

can you grab the /opt/zimbra/log/zmmailboxd.out from the same time? Also, a crontabl -l -u zimbra would help.

[bobby]

Is it the mailbox mysqld or the logger mysqld that is consuming the cpu?

[L. Mark Stone]

[quote user="jholder"]can you grab the /opt/zimbra/log/zmmailboxd.out from the same time? Also, a crontabl -l -u zimbra would help.[/QUOTE]
Hi John,
Thanks for the reply.
There is no zmmailboxd.out:

zimbra@viognier:~> locate *.out

/etc/postfix.suse/makedefs.out

/opt/zimbra/apache-tomcat-5.5.15/logs/catalina.out

/opt/zimbra/log/convertd.out

/opt/zimbra/log/zmlogswatch.out

/opt/zimbra/postfix-2.2.9/conf/makedefs.out

/opt/zimbra/zmstat/zmstat.out
Attached though is the output from ps -ef | grep zimbra while the mysqld was pegged, along with the crontab you asked for.
All the best,

Mark
crontab_for_zimbra.txt
ps-ef.output.txt