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Problem with /usr/local/cpanel/scripts/update_db_cache

ITGabs
Hi, I am getting the 5th or 6th email with the following error from cron daemon 30 */4 * * * /usr/bin/test -x /usr/local/cpanel/scripts/update_db_cache && /usr/local/cpanel/scripts/update_db_cache Error while connecting to MySQL: Cpanel::DBI::Mysql connect('','root',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2) at /usr/local/cpanel/Cpanel/Mysql.pm line 140
This is a cpanel bug?? I am just a bit intrigued about security implications with root and /tmp/mysql.sock ...the activity of Mysql seems normal version: CENTOS 6.5 x86_64 vmware WHM 11.44.0 (build 16)

Comments

21 comments

Date Votes
  • cPanelMichael
    Hello :) Is MySQL running well on your system? If so, try updating the MySQL root password via: "WHM Home " SQL Services " MySQL Root Password" Then, check to see if the issue persists by running that command manually: /usr/local/cpanel/scripts/update_db_cache
    Thank you.
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  • ITGabs
    Hi Michael, MySql is working without any issue. MYSQL version mysql Ver 14.14 Distrib 5.5.37, for Linux (x86_64) using readline 5.1 I created a new password for root, I tried force an update, reboot the server too. mysql --host= --user=root --password='rootpass' mysql connect without problems and any other user connect without problems, cpanel whm phpmyadmin are ok, the problems are just with the /scripts/* that connect with mysql wwwacct killacct etc I tried to read the line 140 with vim but update_db_cache is a binary, Probably the password it's ok but need the 'localhost' in Cpanel::DBI::Mysql connect('HERE','root',...) More info: I did chmod 770 temporally and comment my settings in all '[.]my.cnf' in the server. I checked the logs and the other files, everything looks ok except that /tmp/mysql.sock not exist in the logs of mysql the sock is on /var/lib/mysql/mysql.sock... I tested changing the socket to /tmp/mysql.sock in /root/.my.cnf and in /etc/my.cnf and the error change with socket=/tmp/mysql.sock #/usr/local/cpanel/scripts/update_db_cache [QUOTE]/usr/bin/mysqladmin: connect to server at 'localhost' failed error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)' Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists! warn [update_db_cache] local mysql server is not running
    I checked in the logs and the problem start here with [auto-adjust-mysql-limits] this was exactly after an update Another thing are the errors of cpses_ the cpses_tool give me time out [QUOTE] [COLOR="#B22222">[2014-06-19 01:00:02 -0700] info [cpbackup] Started at Thu Jun 19 01:00:02 2014 [2014-06-19 01:53:44 -0700] warn [updatenow] program "/scripts/predovecotup" is not executable at /usr/local/cpanel/Cpanel/Hooks.pm line 213 Cpanel::Hooks::exec_script('main', HASH(0x4323820), HASH(0x42c4e90), undef) called at /usr/local/cpanel/Cpanel/Hooks.pm line 126 Cpanel::Hooks::exec_hook('main', HASH(0x4323820), HASH(0x42c4e90), undef) called at /usr/local/cpanel/Cpanel/Hooks.pm line 60 eval {...} called at /usr/local/cpanel/Cpanel/Hooks.pm line 55 Cpanel::Hooks::hook(HASH(0x42c4e90)) called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 28448 eval {...} called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 28439 Cpanel::RPM::Versions::File::commit_changes(Cpanel::RPM::Versions::File=HASH(0x2f7ace0)) called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 875 eval {...} called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 875 Cpanel::Update::Now::install_files(Cpanel::Update::Now=HASH(0x9ff448)) called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 405 Cpanel::Update::Now::run(Cpanel::Update::Now=HASH(0x9ff448)) called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 39348 eval {...} called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 39348 [2014-06-19 01:53:44 -0700] warn [updatenow] program "/scripts/premysqlup" is not executable at /usr/local/cpanel/Cpanel/Hooks.pm line 213 Cpanel::Hooks::exec_script('main', HASH(0x42c39e0), HASH(0x42c4e90), undef) called at /usr/local/cpanel/Cpanel/Hooks.pm line 126 Cpanel::Hooks::exec_hook('main', HASH(0x42c39e0), HASH(0x42c4e90), undef) called at /usr/local/cpanel/Cpanel/Hooks.pm line 60 eval {...} called at /usr/local/cpanel/Cpanel/Hooks.pm line 55 Cpanel::Hooks::hook(HASH(0x42c4e90)) called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 28448 eval {...} called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 28439 Cpanel::RPM::Versions::File::commit_changes(Cpanel::RPM::Versions::File=HASH(0x2f7ace0)) called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 875 eval {...} called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 875 Cpanel::Update::Now::install_files(Cpanel::Update::Now=HASH(0x9ff448)) called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 405 Cpanel::Update::Now::run(Cpanel::Update::Now=HASH(0x9ff448)) called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 39348 eval {...} called at /usr/local/cpanel/scripts/updatenow.static-cpanelsync line 39348 [2014-06-19 01:53:54 -0700] info [smtpmailgidonly] cpanel.config Notification =>*********** via EMAIL [level => 3] [2014-06-19 01:53:54 -0700] info [smtpmailgidonly] cpanel.config Notification => ************ via PAGER [level => 3] [06/19/2014:08:53:55 -0000] info [cpsrvd] reloading config based on -HUP signal [COLOR="#B22222">[2014-06-19 01:54:33 -0700] warn [auto-adjust-mysql-limits] Cpanel::DBI::Mysql connect('','root',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2) at /usr/local/cpanel/Cpanel/MysqlUtils/Connect.pm line 42 at /usr/local/cpanel/Cpanel/MysqlUtils/MyCnf/Adjust.pm line 61 Cpanel::MysqlUtils::MyCnf::Adjust::catch {...} (__CPANEL_HIDDEN__) called at /usr/local/cpanel/Cpanel/CPAN/Try/Tiny.pm line 162 Cpanel::CPAN::Try::Tiny::try(CODE(0x82b810), Try::Tiny::Catch=REF(0xf40818)) called at /usr/local/cpanel/Cpanel/MysqlUtils/MyCnf/Adjust.pm line 62 Cpanel::MysqlUtils::MyCnf::Adjust::__ANON__() called at /usr/local/cpanel/Cpanel/MysqlUtils/MyCnf/Adjust.pm line 150 Cpanel::MysqlUtils::MyCnf::Adjust::auto_adjust(HASH(0x818fe0)) called at /usr/local/cpanel/scripts/auto-adjust-mysql-limits line 33 scripts::auto_adjust_mysql_limits::run('--no-restart') called at /usr/local/cpanel/scripts/auto-adjust-mysql-limits line 14 [06/19/2014:08:54:57 -0000] info [cpsrvd] reloading config based on -HUP signal [2014-06-19 01:55:07 -0700] warn [updatenow] program "/scripts/postdovecotup" is not executable at /usr/local/cpanel/Cpanel/Hooks.pm line 213 Cpanel::Hooks::exec_script('main', HASH(0x42d21a0), HASH(0x44483f8), undef) called at /usr/local/cpanel/Cpanel/Hooks.pm line 126
    Edit2: Finally I fixed the problem in a dirty way creating a symlink # ln -s /var/lib/mysql/mysql.sock /tmp/mysql.sock # service mysql restart For what I read the problem should be in some set vars in that /usr/local/cpanel/Cpanel/Mysql.pm (line 140) The solution should be something like this but I can't see the source code MYSQL_UNIX_ADDR=/var/lib/mysql/mysql.sock MYSQL_UNIX_PORT=/var/lib/mysql/mysql.sock MYSQL_SOCKET=/var/lib/mysql/mysql.sock
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  • cPanelMichael
    [quote="ITGabs, post: 1671771">Finally I fixed the problem in a dirty way creating a symlink # ln -s /var/lib/mysql/mysql.sock /tmp/mysql.sock # service mysql restart
    I am happy to see you were able to resolve the issue. Note we do have an internal case open (#101989) to address this issue throughout cPanel. Thank you.
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  • ITGabs
    [quote="cPanelMichael, post: 1672381">I am happy to see you were able to resolve the issue. Note we do have an internal case open (#101989) to address this issue throughout cPanel. Thank you.
    It's possible to add a note in the internal case open (#101989) to update this thread when it's patched or fixed?
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  • Venomous21
    Please, forgive me if I should have included this in its own thread but it seemed similar. Would like to know your thoughts. Received a Cron email from one of my servers this morning: Cron /usr/bin/test -x /usr/local/cpanel/scripts/update_db_cache && /usr/local/cpanel/scripts/update_db_cache body: /bin/sh: line 1: 24104 Killed /usr/local/cpanel/scripts/update_db_cache I checked /var/lib/mysql error log & at the same time, I saw: 140625 08:32:50 mysqld_safe Number of processes running now: 0 140625 08:32:50 mysqld_safe mysqld restarted 140625 8:32:50 [Warning] /usr/sbin/mysqld: Option '--set-variable' is deprecated. Use --variable-name=value instead. 140625 8:32:50 [Warning] '--log_slow_queries' is deprecated and will be removed in a future release. Please use ''--slow_query_log'/'--slow_query_log_file'' instead. 140625 8:32:50 [Warning] '--safe-show-database' is deprecated and will be removed in a future release. Please use 'GRANT SHOW DATABASES' instead. 140625 8:32:50 [Note] Plugin 'FEDERATED' is disabled. 140625 8:32:51 InnoDB: Initializing buffer pool, size = 8.0M 140625 8:32:51 InnoDB: Completed initialization of buffer pool InnoDB: The log sequence number in ibdata files does not match InnoDB: the log sequence number in the ib_logfiles! 140625 8:32:51 InnoDB: Database was not shut down normally! InnoDB: Starting crash recovery. InnoDB: Reading tablespace information from the .ibd files... InnoDB: Restoring possible half-written data pages from the doublewrite InnoDB: buffer... 140625 8:33:04 InnoDB: Started; log sequence number 0 4072497396 140625 8:33:06 [Note] Event Scheduler: Loaded 0 events 140625 8:33:06 [Note] /usr/sbin/mysqld: ready for connections. Version: '5.1.73-cll' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPLv2) A developer was apparently working on a test site around this same time. I will let the developer know and the server has been stable since this incident from this morning. Do you recommend investigating further? Thank you.
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  • ITGabs
    Try to create a new account in WHM, if you get an error, it's the same bug the work around is this symlink ln -s /var/lib/mysql/mysql.sock /tmp/mysql.sock service mysql restart and again try to create a new account in WHM... if you still get an error means is another thing, better to revert (delete) the symlink in that case EDIT: I got the error again and was my tmpwatch that delete the symlink just to avoid more complications... [QUOTE]crontab -e 0 * * * * /usr/sbin/tmpwatch --mtime --all 12 /tmp && ln -s /var/lib/mysql/mysql.sock /tmp/mysql.sock 2>/dev/null
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  • cPanelMichael
    [quote="ITGabs, post: 1672781">It's possible to add a note in the internal case open (#101989) to update this thread when it's patched or fixed?
    Yes, I will update this thread when a resolution has been pushed out. Thank you.
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  • Webuser2014
    [quote="cPanelMichael, post: 1674302">Yes, I will update this thread when a resolution has been pushed out. Thank you.
    Ok I am getting this error while running the Cpanel EasyApache as shown below. Any ideas on what to do? Thank you. -- Begin step 'Updating rule id(s) and directive names in modsec conf file(s)' -- !! Include directives in all configuration files: '/usr/local/apache/conf/httpd.conf /usr/local/apache/conf/extra/proxy-html.conf /usr/local/apache/conf/modsec2.user.conf /usr/local/apache/conf/mod_ruid2.conf /usr/local/apache/conf/modsec2.conf' !! !! Updated '/usr/local/apache/conf/modsec2.conf' with action id(s): '[1234123456] ' !! !! Made a backup '/usr/local/apache/conf/modsec2.conf.cpbackup2' before updating '/usr/local/apache/conf/modsec2.conf' !! -- End step 'Updating rule id(s) and directive names in modsec conf file(s)' -- -- Begin step 'Setting up parser' -- -- End step 'Setting up parser' -- -- Begin step 'Setting up database' -- !! sub-step '1' !! !! sub-step '2' !! Cpanel::DBI::Mysql connect('','root',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2) at /usr/local/cpanel/Cpanel/MysqlUtils/Connect.pm line 42
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  • cPanelMichael
    Have you tried the solution referenced in the previous posts (ln -s /var/lib/mysql/mysql.sock /tmp/mysql.sock)? Thank you.
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  • Webuser2014
    I am confused as to when is the right time to do the sym link. The upgrade seems to be stuck on the sql connection error. I did ssh in and do that command but it still looks stuck.
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  • simonas
    you should re-run the update quit, and launch it again
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  • Webuser2014
    ok seems to have gone through ok.... Thank you!
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  • PPNSteve
    OK I'm now ALSO having an issue with this.. Went to update MySQL to latest cP version and it stopped as noted above by Webuser2014 Cpanel::DBI::Mysql connect('','root',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2) at /usr/local/cpanel/Cpanel/MysqlUtils/Connect.pm line 135
    Now MySQL won't restart, build apache is stuck.. and restart the upgrade cause it says an easyapache process is still running (there isn't one running) NOW WHAT?
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  • cPanelMichael
    Please ensure you run the following command: ln -s /var/lib/mysql/mysql.sock /tmp/mysql.sock
    Then, kill off any existing update processes and start it again. Thank you.
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  • cPanelMichael
    Note that internal case number 101989 was included with cPanel version 11.44.0.22: Fixed case 101989: Improve MySQL socket handling for localhost. Thank you.
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  • ITGabs
    Hi Michael, Thanks for add the info, My servers are in 11.44.1.x but I had a problem again with the socket. How this was fixed? Apparently still need the symlink in /tmp ? Please confirm, I am having problems right now.
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  • cPanelMichael
    Could you elaborate on the specific problem you had with the MySQL socket? Thank you.
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  • ITGabs
    Well everything started with problems with Exim 4 hours ago "451 Temporary local problem - please try later" I checked the logs and I found a lot of problems... [2014-09-10 07:07:50 -0700] warn [cpanellogd] RRDs Error: /var/cpanel/bandwidth/obrcozat-all-peak.rrd: DBD::mysql::db do failed: Out of resources when opening file './eximstats/smtp.MYD' (Errcode: 24) Cpanel::Exception::create_raw('Database::Error', 'DBD::mysql::db do failed: Out of resources when opening file ...', 'HASH(0x332c588)') called at /usr/local/cpanel/Cpanel/DBI.pm line 79 Cpanel::DBI::_create_exception('Cpanel::DBI::Mysql::db=HASH(0x308e738)', 'DBD::mysql::db do failed: Out of resources when opening file ...', undef) called at /usr/local/cpanel/Cpanel/DBI.pm line 70 Cpanel::DBI::_error_handler('DBD::mysql::db do failed: Out of resources when opening file ...', 'Cpanel::DBI::Mysql::db=HASH(0x308e738)', undef) called at /usr/local/cpanel/Cpanel/Logd.pm line 1379 Cpanel::DBI::Mysql connect('','leechprotect',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2) at /usr/local/cpanel/Cpanel/MysqlUtils/Connect.pm line 136 ... Ensuring services are online.../usr/bin/mysqladmin: connect to server at 'localhost' failed error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (11)' Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists! .... a cron fail /usr/bin/mysqladmin: connect to server at 'localhost' failed error: 'Lost connection to MySQL server at 'waiting for initial communication packet', system error: 95' DBD::mysql::st execute failed: Can't read dir of '.' (errno: 24) at /usr/local/cpanel/Cpanel/Exception.pm line 96 Cpanel::Exception::new('Cpanel::Exception::Database::Error', 'Cpanel::ExceptionMessage::Raw=SCALAR(0x1359180)', 'HASH(0x274ac00)') called at /usr/local/cpanel/Cpanel/Exception.pm line 47 Cpanel::Exception::create('Database::Error', 'Cpanel::ExceptionMessage::Raw=SCALAR(0x1359180)', 'HASH(0x274ac00)') called at /usr/local/cpanel/Cpanel/Exception.pm line 55 Cpanel::Exception::create_raw('Database::Error', 'DBD::mysql::st execute failed: Can\'t read dir of \'.\' (errno: ...', 'HASH(0x274ac00)') called at /usr/local/cpanel/Cpanel/DBI.pm line 79 Cpanel::DBI::_create_exception('Cpanel::DBI::Mysql::st=HASH(0x2735a70)', 'DBD::mysql::st execute failed: Can\'t read dir of \'.\' (errno: ...', undef) called at /usr/local/cpanel/Cpanel/DBI.pm line 70 Cpanel::DBI::_error_handler('DBD::mysql::st execute failed: Can\'t read dir of \'.\' (errno: ...', 'Cpanel::DBI::Mysql::st=HASH(0x2735a70)', undef) called at bin/update_db_cache line 322 Script::Update::DB::Cache::can_get_mysql_usage('HASH(0x1332cb0)', 'HASH(0x13fe430)', 'Cpanel::DB::Map::Collection::Index=HASH(0x2733e60)') called at bin/update_db_cache line 57 Script::Update::DB::Cache::script('Script::Update::DB::Cache') called at bin/update_db_cache line 32
    and finally I tried to create a new account (wwwacct) and I got a similar error than before Ensuring services are online.../usr/bin/mysqladmin: connect to server at 'localhost' failed error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (11)' Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!
    Mysql was working in all the sites but apparently something happen (36 or 24 hours ago) after I deleted the symlink, few minutes ago I rebooted the server and checked the /tmp folder and now without symlink everything it's working fine. Probably after I deleted the symlink from the tmpwatch cron I should running it manually first and later restart mysql not 100% sure. crontab -e 0 * * * * /usr/sbin/tmpwatch --mtime --all 24 /tmp && ln -s /var/lib/mysql/mysql.sock /tmp/mysql.sock 2>/dev/null to 0 * * * * /usr/sbin/tmpwatch --mtime --all 24 /tmp 2>/dev/null
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  • cPanelMichael
    I am happy to see the issue is now resolved. Could you clarify what issue lead you to manually deleting the symbolic link? Thank you.
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  • ITGabs
    I thought that the symlink was not necessary after the "Fixed case 101989: Improve MySQL socket handling for localhost." But I am having a new problem with the /usr/local/cpanel/scripts/update_db_cache from cron Subject: /usr/bin/test -x /usr/local/cpanel/scripts/update_db_cache && /usr/local/cpanel/scripts/update_db_cache /usr/bin/mysqladmin: connect to server at 'localhost' failed error: 'Lost connection to MySQL server at 'waiting for initial communication packet', system error: 95' DBD::mysql::st execute failed: Can't read dir of '.' (errno: 24) at /usr/local/cpanel/Cpanel/Exception.pm line 96 Cpanel::Exception::new('Cpanel::Exception::Database::Error', 'Cpanel::ExceptionMessage::Raw=SCALAR(0x1359180)', 'HASH(0x2dfa390)') called at /usr/local/cpanel/Cpanel/Exception.pm line 47 Cpanel::Exception::create('Database::Error', 'Cpanel::ExceptionMessage::Raw=SCALAR(0x1359180)', 'HASH(0x2dfa390)') called at /usr/local/cpanel/Cpanel/Exception.pm line 55 Cpanel::Exception::create_raw('Database::Error', 'DBD::mysql::st execute failed: Can\'t read dir of \'.\' (errno: ...', 'HASH(0x2dfa390)') called at /usr/local/cpanel/Cpanel/DBI.pm line 79 Cpanel::DBI::_create_exception('Cpanel::DBI::Mysql::st=HASH(0x2de60e0)', 'DBD::mysql::st execute failed: Can\'t read dir of \'.\' (errno: ...', undef) called at /usr/local/cpanel/Cpanel/DBI.pm line 70 Cpanel::DBI::_error_handler('DBD::mysql::st execute failed: Can\'t read dir of \'.\' (errno: ...', 'Cpanel::DBI::Mysql::st=HASH(0x2de60e0)', undef) called at bin/update_db_cache line 322 Script::Update::DB::Cache::can_get_mysql_usage('HASH(0x1332cb0)', 'HASH(0x13fe430)', 'Cpanel::DB::Map::Collection::Index=HASH(0x2be7720)') called at bin/update_db_cache line 57 Script::Update::DB::Cache::script('Script::Update::DB::Cache') called at bin/update_db_cache line 32
    I am checking right now, MySQL was unresponsive I manually restarted MySQL and I am checking the logs.
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  • cPanelMichael
    Feel free to open a support ticket if the issue persists 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.
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