Failed to validate my.cnf file for version 5.6

Kent Brockman

Well-Known Member
PartnerNOC
Jan 20, 2008
1,272
63
178
Buenos Aires, Argentina
cPanel Access Level
Root Administrator
Hello guys! I'm interested in upgrading and old server to MariaDB 10.1 but the starting point is MySQL 5.5. When trying to upgrade to 5.6, this warning comes up:

Code:
System Specific Warnings
Severity: Critical
Message: The system detected issues with the current “/etc/my.cnf” file. These issues may interfere with the upgrade to MySQL 5.6:

Failed to validate my.cnf file for version 5.6:
160830  2:58:27 [ERROR] Fatal error: Please read "Security" section of the manual to find out how to run mysqld as root!
160830  2:58:27 [ERROR] Aborting
What does this mean? The my.cnf does contain nothing weird. In fact is the same configuration as in other servers where it worked just fine. Even if I rename my.cnf to something else, the error is the same. And I didn't found anything like this by googling.

Any ideas?
Thanks in advance
 

rpvw

Well-Known Member
Jul 18, 2013
1,101
462
113
UK
cPanel Access Level
Root Administrator
MySQL / MariaDB reads the my.cnf configuration files in a preset order. See the SQL docs for full details

As well as an /etc/my.cnf , I found a /usr/my.cnf file that is read after the /etc/my.cnf

You might want to search for any additional my.cnf files your system has :) perhaps your issue lies there.
 

Kent Brockman

Well-Known Member
PartnerNOC
Jan 20, 2008
1,272
63
178
Buenos Aires, Argentina
cPanel Access Level
Root Administrator
@Infopro: nope! Since this message happens at prerequisites checkpoint, I didn't thought a restart would be necessary.
I can test that of course, but late in the night, because this server have huge sites in production actually.
 

Kent Brockman

Well-Known Member
PartnerNOC
Jan 20, 2008
1,272
63
178
Buenos Aires, Argentina
cPanel Access Level
Root Administrator
@rpvw:
Please read my originally quoted code, it states that the conflict originate on “/etc/my.cnf”.

Just for the curious, this is the content of my /etc/my.cnf:

Code:
[myisamchk]
ft_min_word_len=2
key_buffer_size=64M
sort_buffer_size=64M
read_buffer=2M
write_buffer=2M

[mysqld]
bind-address=127.0.0.1
tmp_table_size=120M
max_heap_table_size=120M

sort_buffer_size=6M
read_buffer_size=2M
read_rnd_buffer_size=2M
default-storage-engine=INNODB

query_cache_type=1
query_cache_size=128M
query_cache_limit=1M

ft_min_word_len=2
key_buffer_size=64M
long_query_time=5
max_allowed_packet=268435456
max_connections=200
myisam_sort_buffer_size=8M
net_buffer_length=16K
open_files_limit=50000
table_cache=6000
table_definition_cache=6000
table_open_cache=6000
thread_cache_size=16
innodb_file_per_table=1

innodb_buffer_pool_size=61865984
[mysqldump]
max_allowed_packet=16M
quick

[mysqlhotcopy]
interactive-timeout
Anything you can criticize? Let me know please.
 

cPanelMichael

Administrator
Staff member
Apr 11, 2011
47,909
2,228
463
Hi @Kent Brockman,

The specific reason for the failed validation should appear in /usr/local/cpanel/logs/error_log when this happens. Do you notice any additional output in this log that's not in the UI?

Thanks.
 

cPanelMichael

Administrator
Staff member
Apr 11, 2011
47,909
2,228
463
Please post the output from the following command:

Code:
mysql --version
Thank you.
 

cPanelMichael

Administrator
Staff member
Apr 11, 2011
47,909
2,228
463
The only time I've seen this happen in the past is when a third-party installation of Percona was installed, but that doesn't look to be the case here. Would you mind opening a support ticket so we can take a closer look? You can post the ticket number here so we can update this thread with the outcome.

Thank you.
 

Kent Brockman

Well-Known Member
PartnerNOC
Jan 20, 2008
1,272
63
178
Buenos Aires, Argentina
cPanel Access Level
Root Administrator
The only time I've seen this happen in the past is when a third-party installation of Percona was installed, but that doesn't look to be the case here. Would you mind opening a support ticket so we can take a closer look? You can post the ticket number here so we can update this thread with the outcome.

Thank you.
You're almost there pal. Yes, this is a VPS which originally came with Percona and I asked the hosting provider to switch it back to native MySQL. It was almost 2 years ago. Maybe some Percona debris may remain? And if so, will the tech ops in a ticket be able to cleanse it? I cannot move the sites hosted right now and at the same time wanted to at least upgrade to MySQL 5.6 to improve performance (the target of the switch is arrive to MariaDB 10 and PHP 7)
 

cPanelMichael

Administrator
Staff member
Apr 11, 2011
47,909
2,228
463
It's possible some leftover configuration data from the Percona installation is causing this problems. We can help to determine if that's the case in the support ticket, yes.

Thank you.