I had the exact same problem the day I did the upgrade. Please post your
/opt/zimbra/conf/my.cnf
or compare your with the following:
Code:
[mysqld]
slow_query_log = 1
plugin-load = innodb=ha_innodb_plugin.so;innodb_trx=ha_innodb_plugin.so;innodb_locks=ha_innodb_plugin.so;innodb_lock_waits=ha_innodb_plugin.so;innodb_cmp=ha_innodb_plugin.so;innodb_cmp_reset=ha_innodb_plugin.so;innodb_cmpmem=ha_innodb_plugin.so;innodb_cmpmem_reset=ha_innodb_plugin.so
ignore-builtin-innodb
innodb=FORCE
innodb_flush_log_at_trx_commit = 0
tmpdir = /opt/zimbra/data/tmp
basedir = /opt/zimbra/mysql
datadir = /opt/zimbra/db/data
socket = /opt/zimbra/db/mysql.sock
pid-file = /opt/zimbra/db/mysql.pid
bind-address = localhost
port = 7306
user = zimbra
external-locking
#log-slow-queries = /opt/zimbra/log/myslow.log
slow_query_log_file = /opt/zimbra/log/myslow.log
long-query-time = 1
log-queries-not-using-indexes
thread_cache_size = 110
max_connections = 110
# We do a lot of writes, query cache turns out to be not useful.
query_cache_type = 0
sort_buffer_size = 1048576
read_buffer_size = 1048576
# Increase the size of the table cache, since each mailbox has its
# own set of tables
table_cache = 1200
innodb_buffer_pool_size = 238806834
innodb_log_file_size = 104857600
innodb_log_buffer_size = 8388608
innodb_file_per_table
innodb_open_files = 2710
innodb_max_dirty_pages_pct = 10
innodb_flush_method = O_DIRECT
[mysqld_safe]
pid-file = /opt/zimbra/db/mysql.pid
err-log = /opt/zimbra/log/mysqld.log
This should be standard for single machine Zimbra installation.
But also check if your zimbra mysql version, should be:
Code:
/opt/zimbra/mysql-standard-5.1.52-pc-linux-gnu-i686-glibc23
If the above config fix this issue, you should run upgrade again and this time should go all the way to normal completion.
Another thing to check is the linux user zimbra is able to sudo (/etc/sudoer) and ssh (/etc/ssh/sshd_config). I am using Debian here, RedHaat may be a bit different.
Bugzilla
Wiki
Source
Upgrade Problem from Zimbra 6.0.8 to Zimbra 7 
Linear Mode
