Backup errors MySQL and file permissions

[ospito]

Some of our backups produce errors:
Runtime error: The backup failed with errors!
Runtime error: The backup failed with errors!
Runtime error: The backup failed with errors!
Runtime error: The backup failed with errors!
Runtime error: The backup failed with errors!

Further investigation showed the domains with errors and the logs showed why:
DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
...

[root@server02 sessions]# grep "MySQL server has gone away at /usr/local/psa/PMM/" /usr/local/psa/PMM/sessions/2011-05-13*/stderr
/usr/local/psa/PMM/sessions/2011-05-13-002853.368/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-002853.368/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-002853.368/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-003416.994/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-003616.68/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-003616.68/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-004610.678/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-004610.678/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-005423.104/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-011919.249/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-011919.249/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-013627.461/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-013838.27/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-013838.27/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-015149.799/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-015614.544/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-015614.544/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-020319.505/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-021945.391/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-022716.259/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-023703.454/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-023703.454/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.
/usr/local/psa/PMM/sessions/2011-05-13-024609.408/stderr:DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/psa/PMM/agents/shared/Db/DbiBackend.pm line 66.

I don't know why MySQL is failing, because it's running for quiet long time (no restarts during backup):
mysqladmin status - Uptime: 688197
Only reason I can think of is slow response because of a high load during the backup schedule, it's raising to about 9.0. Maybe it's already done, but it could help if pleskbackup runs everything with a lower priority (nice -n 20 tar -czfp ...) and same for mysqldump, or similar.

We also get many errors about permissions of directories in subdomains:
/bin/tar: subdomains/<subdomain>/error_docs: Cannot savedir: Permission denied
/bin/tar: subdomains/<subdomain>/conf: Cannot savedir: Permission denied

Same stderr file:
/bin/tar: *: Cannot stat: No such file or directory
/bin/tar: Error exit delayed from previous errors
/bin/tar: *: Cannot stat: No such file or directory
/bin/tar: Error exit delayed from previous errors

These messages occur approximately the same times as subdomain failures above, but not exactly, there are more of these errors.

Permissions:
/var/www/vhosts/<vhost>/subdomains: 755: root: psaserv
/var/www/vhosts/<vhost>/subdomains/<subdomain>: 755: root: root
/var/www/vhosts/<vhost>/subdomains/<subdomain>/conf: 750: root: psaserv
/var/www/vhosts/<vhost>/subdomains/<subdomain>/error_docs: 750: root: psaserv

It might be no problem (didn't test it), but these directories aren't in the backup file, as obvious.

The last thing that worries me is:
/bin/tar: httpdocs/<subdir>/8268.jpg: Cannot open: Permission denied
/bin/tar: httpdocs/<subdir>/7938.jpg: Cannot open: Permission denied
/bin/tar: httpdocs/<subdir>/8245.jpg: Cannot open: Permission denied

[root@server02 sessions]# grep 'Cannot open: Permission denied' /usr/local/psa/PMM/sessions/2011-05-13-*/stderr | wc -l
1237

File permission and ownership of some of these files.
600 - apache: apache

I can imagine the cause of this, but the backup proces should backup everything, no matter the file permissions! After full restore a lot of files are missing, what do I need to tell my customer about these missing files?

How can all of this be solved?

 

[sistemis]

We have the same problem.
It seems that backup job keep an active mysql session while saving site file, session goes idle and mysqld close it.

Try setting wait_timeout into my.cf to a time large enough to complete your backup .