I started zimbra as su or root and it seems to have broken a few things is there a way to mostly i get these errors now when i try to stop/start zimbra as the su zimbra user

[zimbra@shoemasters tmp]$ zmcontrol stop
Host shoemasters.com
Stopping antispam...Done
Stopping antivirus...Done
Stopping ldap...Done
Stopping logger...FAILED
Error: no pid in '/opt/zimbra/logger/db/mysql.pid'
/opt/zimbra/bin/zmlogswatchctl: line 52: kill: (20360) - No such process


Stopping mailbox...Done
Stopping mta...Done
Stopping snmp...Done
Stopping spell...Done
[zimbra@shoemasters tmp]$ zmcontrol start
Host shoemasters.com
Starting ldap...Done.
Starting antispam...Done.
Starting antivirus...Done.
Starting logger...Done.
Starting mailbox...Done.
Starting mta...Done.
Starting snmp...FAILED
chmod: changing permissions of `/tmp/swatch.out': Operation not permitted


Starting spell...Done.


I was working on a complete remote backup and need to shut down zimbra do back then restart zimbra. I think that bacula can do this but is there commands i can run a other than the one that requires u to be su zimbra

Also how do i fix what i have broken as starting and stopping zimbra as root can i just fix or erase the the tmp file ??

What are the correct mods and perms for these files i have changed them to owner and group zimbra like below

-r--r--r-- 1 root root 1136 Nov 29 04:44 crontab.zimbra
-rw-r--r-- 1 zimbra zimbra 181084 Dec 11 14:10 gengraphs.out
drwxr-xr-x 2 root root 4096 Dec 11 14:43 hsperfdata_root
drwxr-xr-x 2 zimbra zimbra 4096 Dec 11 14:43 hsperfdata_zimbra
-rw-r--r-- 1 zimbra zimbra 536 Dec 11 14:40 logprocess.out
-rwxrwxrwx 1 zimbra zimbra 82 Dec 11 14:43 logswatch.out
drwxrwxrwx 2 root root 4096 Nov 28 13:25 saveconfig.10256
drwxrwxrwx 2 root root 4096 Nov 29 04:07 saveconfig.11749
drwxrwxrwx 2 root root 4096 Nov 26 15:44 saveconfig.12254
drwxrwxrwx 2 root root 4096 Nov 29 04:39 saveconfig.20176
drwxrwxrwx 2 root root 4096 Nov 26 15:22 saveconfig.4022
drwxrwxrwx 2 root root 4096 Nov 28 11:25 saveconfig.4064
drwxrwxrwx 2 root root 4096 Nov 26 15:24 saveconfig.4069
drwxrwxrwx 2 root root 4096 Nov 28 12:38 saveconfig.4950
-rwxrwxrwx 1 zimbra zimbra 130 Dec 11 14:42 swatch.out
-rw-rw-r-- 1 zimbra zimbra 0 Dec 11 14:43 zmcontrol.out.23664

but i still get this error when stopping zimbra server but it seems to start ok

Error: no pid in '/opt/zimbra/logger/db/mysql.pid'
/opt/zimbra/bin/zmlogswatchctl: line 52: kill: (23866) - No such process

How do i fix this please help