Posts Tagged ‘mysqld’

How to Set MySQL MariaDB server root user to be able to connect from any host on the Internet / Solution to ‘ ERROR 1045 (28000): Access denied for user ‘root’@’localhost’ (using password: YES) ‘

Tuesday, September 3rd, 2019

Reading Time: 5minutes


In this small article, I'll shortly explain on how I setup a Standard default package MariaDB Database server on Debian 10 Buster Linux and how I configured it to be accessible from any hostname on the Internet in order to make connection from remote Developer PC with MySQL GUI SQL administration tools such as MySQL WorkBench / HeidiSQL / Navicat / dbForge  as well as the few set-backs experienced in the process (e.g. what was the reason for ' ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) '  error and its solution.

Setting new or changing old MariaDB (MySQL) root server password


I've setup a brand new MariaDB database (The new free OpenSource software fork of MySQL) mariadb-server-10.3 on a Debian 10, right after the OS was installed with the usual apt command:

# apt install mariadb-server

Next tep was to change the root access password which was set to empty pass by default, e.g. connected with mysql CLI locally while logged via SSH on server and run:

MariaDB [(none)]> mysql -u root -p

use mysql;
update user set authentication_string=PASSWORD("MyChosenNewPassword") where User='root';

There was requirement by the customer, that MySQL server is not only accessed locally but be accessed from any IP address from anywhere on the Internet, so next step was to do so.

Allowing access to MySQL server from Anywhere

Allowing access from any host to MariaDB SQL server  is a bad security practice but as the customer is the King I've fulfilled this weird wish too, by changing the listener for MariaDB (MySQL) on Debian 10 codenamed Buster
changingthe defaultlistener
to be not the default (localhost) but any listener is done by modifying the bind-address directive in conf /etc/mysql/mariadb.conf.d/50-server.cnf:

root@linux:~# vim /etc/mysql/mariadb.conf.d/50-server.cnf

Then comment out

bind-address  =

and  add instead (any listener)


bind-address  =
root@linux:/etc/mysql/mariadb.conf.d# grep -i bind-address 50-server.cnf
##bind-address            =
bind-address    =

Then to make the new change effective restart MariaDB (luckily still using the old systemV init script even though systemd is working.

root@linux:~# /etc/init.d/mysql restart
[ ok ] Restarting mysql (via systemctl): mysql.service.

To make sure it is properly listening on MySQL defaults TCP port 3306, then as usual used netcat.

root@pritchi:~# netstat -etna |grep -i 3306
tcp        0      0  *               LISTEN      109        1479917  


By the way the exact mariadb.cnf used on this middle-sized front-backend server is here – the serveris planned to be a Apache Web server + Database host with MySQL DB of a middle range to be able to serve few thousand of simultaneous unique customers.

To make sure no firewall is preventing MariaDB to be accessed, I've checked for any reject rules iptables and ipset definitions, e.g.:

root@linux:~# iptables -L |gre -i rej

root@linux:~# ipset list


Then to double make sure the MySQL is allowed to access from anywhere, used simple telnet from my Desktop Laptop PC (that also runs Debian Linux) towards the server .

hipo@jeremiah:~$ telnet 3306
Connected to
Escape character is '^]'.
Connection closed by foreign host.


As telnet is not supporting the data encryption after TCP proto connect, in a few seconds time, remote server connection is terminated.


Setting MySQL user to be able to connect to local server MySQL from any remote hostname

I've connected locally to MariaDB server with mysql -u root -p and issued following set of SQL commands to make MySQL root user be able to connect from anywhere:


CREATE USER 'root'@'%' IDENTIFIED BY 'my-secret-pass';
GRANT ALL ON *.* TO 'root'@'localhost';
GRANT ALL ON *.* TO 'root'@'%';


Next step, I've took was to try logging in with root (admin) MariaDB superuser from MySQL CLI (Command Line Interface) on my desktop just to find out, I'm facing a nasty error.

hipo@jeremiah:~$ mysql -u root -H -p
Enter password:
ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES)

My first guess was something is wrong with my root user created in MySQL's mysql.user table (In MySQL this is the privileges table that stores, how MySQL user credentials are handled by mysqld local OS running process.


Changing the MySQL root (admin) password no longer possible on Debian 10 Buster?


The standard way ot change the MySQL root password well known via a simple dpkg-reconfigure (provided by Debian's debconf is no longer working so below command produces empty output instead of triggering the good old Ncurses text based interface well-known over the years …


root@linux:~# /usr/sbin/dpkg-reconfigure mariadb-server-10.3



Viewing MariaDB (MySQL) username / password set-up from the CLI


To list how this set-privileges looked like I've used following command:


MariaDB [mysql]> select * from mysql.user where User = 'root';
| Host      | User | Password                                  | Select_priv | Insert_priv | Update_priv | Delete_priv | Create_priv | Drop_priv | Reload_priv | Shutdown_priv | Process_priv | File_priv | Grant_priv | References_priv | Index_priv | Alter_priv | Show_db_priv | Super_priv | Create_tmp_table_priv | Lock_tables_priv | Execute_priv | Repl_slave_priv | Repl_client_priv | Create_view_priv | Show_view_priv | Create_routine_priv | Alter_routine_priv | Create_user_priv | Event_priv | Trigger_priv | Create_tablespace_priv | Delete_history_priv | ssl_type | ssl_cipher | x509_issuer | x509_subject | max_questions | max_updates | max_connections | max_user_connections | plugin                | authentication_string | password_expired | is_role | default_role | max_statement_time |
| localhost | root | *E6D338325F50177F2F6A15EDZE932D68C88B8C4F | Y           | Y           | Y           | Y           | Y           | Y         | Y           | Y             | Y            | Y         | Y          | Y               | Y          | Y          | Y            | Y          | Y                     | Y                | Y            | Y               | Y                | Y                | Y              | Y                   | Y                  | Y                | Y          | Y            | Y                      | Y                   |          |            |             |              |             0 |           0 |               0 |                    0 | mysql_native_password |                       | N                | N       |              |           0.000000 |
| %         | root | *E6D338325F50177F2F6A15EDZE932D68C88B8C4F | Y           | Y           | Y           | Y           | Y           | Y         | Y           | Y             | Y            | Y         | N          | Y               | Y          | Y          | Y            | Y          | Y                     | Y                | Y            | Y               | Y                | Y                | Y              | Y                   | Y                  | Y                | Y          | Y            | Y                      | Y                   |          |            |             |              |             0 |           0 |               0 |                    0 |                       |                       | N                | N       |              |           0.000000 |


The hashed (encrypted) password string is being changed from the one on the server, so please don't try to hack me (decrypt it) 🙂
As it is visible from below output the Host field for root has the '%' string which means, any hostname is authorized to be able to connect and login to the MySQL server, so this was not the problem.

After quite some time on reading on what causes
' ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES)
I've spend some time reading various forum discussions online on the err such as the one on StackOverflow here's  how to fix access denied for user 'root'@'localhost' and one on's – ERROR 1045(28000) : Access denied for user 'root@localhost' (using password: no ) and after a while finally got it, thanks to a cool IRC.FREENODE.NET guy nicknamed, hedenface who pointed me I'm that, I'm trying to use the -H flag (Prodice HTML) instead of -h (host_name), it seems somehow I ended up with the wrong memory that the -H stands for hostname, by simply using -h I could again login Hooray!!!


root@linux:~$ mysql -u root -h -p
Enter password:
Welcome to the MariaDB monitor.  Commands end with ; or \g.
Your MariaDB connection id is 14
Server version: 10.3.15-MariaDB-1 Debian 10


Copyright (c) 2000, 2018, Oracle, MariaDB Corporation Ab and others.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

I've further asked the customer to confirm, he can connect also from his Microsoft Windows 10 PC situated on a different LAN network and got his confirmation. Few notes to make here is I've also installed phpmyadmin on the server using phpmyadmin php source code latest version, as in Debian 10 it seems the good old PHP is no longer available (as this crazy developers again made a mess and there is no phpmyadmin .deb package in Debian Buster – but that's a different story I'll perhaps try to document in some small article in future.

Why du and df reporting different on a filesystem / How to fix inconsistency between used space on FS and disk showing full strangeness

Wednesday, July 24th, 2019

Reading Time: 6minutes


If you're a sysadmin on a large server environment such as a couple of hundred of Virtual Machines running Linux OS on either physical host or OpenXen / VmWare hosted guest Virtual Machine, you might end up sometimes at an odd case where some mounted partition mount point reportsits file use different when checked with
cmd than when checked with du command, like for example:

root@sqlserver:~# df -hT /var/lib/mysql
Filesystem   Type  Size Used Avail Use% Mounted On
/dev/sdb5      ext4    19G  3,4G    14G  20% /var/lib/mysql

Here the '-T' argument is used to show us the filesystem.

root@sqlserver:~# du -hsc /var/lib/mysql
0K    /var/lib/mysql/
0K    total


1. Simple debug on what might be the root cause for df / du inconsistency reporting


Of course the basic thing to do when in that weird situation is to be totally shocked how this is possible and to investigate a bit what is the biggest first level sub-directories that eat up the space on the mounted location, with du:


# du -hkx –max-depth=1 /var/lib/mysql/|uniq|sort -n
4       /var/lib/mysql/test
8       /var/lib/mysql/ezmlm
8       /var/lib/mysql/micropcfreak
8       /var/lib/mysql/performance_schema
12      /var/lib/mysql/mysqltmp
24      /var/lib/mysql/speedtest
64      /var/lib/mysql/yourls
144     /var/lib/mysql/narf
320     /var/lib/mysql/webchat_plus
424     /var/lib/mysql/goodfaithair
528     /var/lib/mysql/moonman
648     /var/lib/mysql/daniel
852     /var/lib/mysql/lessn
1292    /var/lib/mysql/gallery

The given output is in Kilobytes so it is a little bit hard to read, if you're used to Mbytes instead, do


 # du -hmx –max-depth=1 /var/lib/mysql/|uniq|sort -n|less


I've also investigated on the complete /var directory contents sorted by size with:


 # du -akx ./ | sort -n
5152564    ./cache/rsnapshot/hourly.2/localhost
5255788    ./cache/rsnapshot/hourly.2
5287912    ./cache/rsnapshot
7192152    ./cache

Even after finding out the bottleneck dirs and trying to clear up a bit, continued facing that inconsistently shown in two commands and if you're likely to be stunned like me and try … to move some files to a different filesystem to free up space or assigned inodes with a hope that shown inconsitency output will be fixed as it might be caused  due to some kernel / FS caching ?? and this will eventually make the mounted FS to refresh …

But unfortunately, if you try it you'll figure out clearing up a couple of Megas or Gigas will make no difference in cmd output.

In my exact case /var/lib/mysql is a separate mounted ext4 filesystem, however same issue was present also on a Network Filesystem (NFS) and thus, my first thought that this is caused by a network failure problem or NFS bug turned to be wrong.

After further short investigation on the inodes on the Filesystem, it was clear enough inodes are available:

# df -i /var/lib/mysql
Filesystem       Inodes  IUsed   IFree IUse% Mounted on
/dev/sdb5      1221600  2562 1219038   1% /var/lib/mysql


So the filled inodes count assumed issue also has been rejected.
P.S. (if you're not well familiar with them read manual, i.e. – man 7 inode).

– Remounting the mounted filesystem

To make sure the filesystem shown inconsistency between du and df is not due to some hanging network mount or bug, first logical thing I did is to remount the filesytem showing different in size, in my case this was done with:

# mount -o remount,rw -t ext4 /var/lib/mysql

For machines with NFS remote mounted storage locations, used:

# mount -o remount,rw -t nfs /var/www

FS remount did not solved it so I continued to ponder what oddity and of course I thought of a workaround (in case if this issues are caused by kernel bug or OS lib issue) reboot might be the solution, however unfortunately restarting the VMs was not a wanted easy to do solution, thus I continued investigating what is wrong …

Next check of course was to check, what kind of network connections are opened to the affected hosts with:

# netstat -tupanl

Did not found anything that might point me to the reported different Megabytes issue, so next step was to check what is the situation with currently opened files by running processes on the weird df / du reported systems with lsof, and boom there I observed oddity such as multiple files


# lsof -nP | grep '(deleted)'

mysqld   2588  mysql    4u   REG 253,17      52     0  1495 /var/lib/mysql/tmp/ibY0cXCd (deleted)
mysqld   2588  mysql    5u   REG 253,17    1048     0  1496 /var/lib/mysql/tmp/ibOrELhG (deleted)
mysqld   2588  mysql    6u   REG 253,17       777884290     0  1497 /var/lib/mysql/tmp/ibmDFAW8 (deleted)
mysqld   2588  mysql    7u   REG 253,17       123667875     0 11387 /var/lib/mysql/tmp/ib2CSACB (deleted)
mysqld   2588  mysql   11u   REG 253,17       123852406     0 11388 /var/lib/mysql/tmp/ibQpoZ94 (deleted)


Notice that There were plenty of '(deleted)' STATE files shown in memory an overall of 438:


# lsof -nP | grep '(deleted)' |wc -l

As I've learned a bit online about the problem, I found it is also possible to find deleted unlinked files only without any greps (to list all deleted files in memory files with lsof args only):


# lsof +L1|less

The SIZE field (fourth column)  shows a number of files that are really hard in size and that are kept in open on filesystem and in memory, totally messing up with the filesystem. In my case this is temp files created by MYSQLD daemon but depending on the server provided service this might be apache's www-data, some custom perl / bash script executed via a cron job, stalled rsync jobs etc.

2. Check all the list open files with the mysql / root user as part of the the server filesystem inconsistency debugging with:


– Grep opened files on server by user

# lsof |grep mysql
mysqld    1312                       mysql  cwd       DIR               8,21       4096          2 /var/lib/mysql
mysqld    1312                       mysql  rtd       DIR                8,1       4096          2 /
mysqld    1312                       mysql  txt       REG                8,1   20336792   23805048 /usr/sbin/mysqld
mysqld    1312                       mysql  mem       REG               8,21      24576         20 /var/lib/mysql/tc.log
mysqld    1312                       mysql  DEL       REG               0,16                 29467 /[aio]
mysqld    1312                       mysql  mem       REG                8,1      55792   14886933 /lib/x86_64-linux-gnu/


# lsof | grep root
COMMAND    PID   TID TASKCMD          USER   FD      TYPE             DEVICE   SIZE/OFF       NODE NAME
systemd      1                        root  cwd       DIR                8,1       4096          2 /
systemd      1                        root  rtd       DIR                8,1       4096          2 /
systemd      1                        root  txt       REG                8,1    1489208   14928891 /lib/systemd/systemd
systemd      1                        root  mem       REG                8,1    1579448   14886924 /lib/x86_64-linux-gnu/

Other command that helped to track the discrepancy between df and du different file usage on FS is:

# du -hxa  / | egrep '^[[:digit:]]{1,1}G[[:space:]]*'


3. Fixing large files kept in memory filesystem problem

What is the real reason for ending up with this file handlers opened by running backgrounded programs on the Linux OS?
It could be multiple  but most likely it is due to exceeded server / client interactions or breaking up RAM or HDD drive with writing plenty of logs on the FS without ending keeping space occupied or Programming library bugs used by hanged service leaving the FH opened on storage.

What is the solution to file system files left in memory problem?

The best solution is to first fix custom script or hanged service and then if possible to simply restart the server to make the kernel / services reload or if this is not possible just restart the problem creation processes.

Once the process is identified like in my case this was MySQL on systemd enabled newer OS distros, just do:



# systemctl restart mysqld.service

or on older init.d system V ones:

# /etc/init.d/service restart

For custom hanged scripts being listed in ps axuwef you can grep the pid and do a kill -HUP (if the script is written in a good way to recognize -HUP and restart the sub-running process properly – BE EXTRA CAREFUL IF YOU'RE RESTARTING BROKEN SCRIPTS as this might cause your running service disruptions …).

# pgrep -l

# kill -HUP PID


Now finally this should either mitigate or at best case completely solve the reported disagreement between df and du, after which the calculated / reported disk space should be back to normal and show up approximately the same (note that size changes a bit as mysql service is writting data) constantly extending the size between the two checks.


# df -hk /var/lib/mysql; du -hskc /var/lib/mysql
Filesystem       Inodes  IUsed   IFree IUse% Mounted on
/dev/sdb5        19097172 3472744 14631296  20% /var/lib/mysql
3427772    /var/lib/mysql
3427772    total


What we learned?

What I've explained in this article is why and how it comes that 'zoombie' files reside on a filesystem
appearing to be eating disk space on a mounted local or network partition, giving strange inconsistent
reports, leading to system service disruptions and impossibility to have correctly shown information on used
disk space on mounted drive.

I went through with some standard logic on debugging service / filesystem / inode issues up explainat, that led me to the finding about deleted files being kept in filesystem and producing the filesystem strange sized / showing not correct / filled even after it was extended with tune2fs and was supposed to have extra 50GBs.

Finally it was explained shortly how to HUP / restart hanging script / service to fix it.

Some few good readings that helped to fix the issue:

What to do when du and df report different usage is here
df in linux not showing correct free space after file removal is here
Why do “df” and “du” commands show different disk usage?

‘host-name’ is blocked because of many connection errors; unblock with ‘mysqladmin flush-hosts’

Sunday, May 20th, 2012

Reading Time: 3minutes

My home run machine MySQL server was suddenly down as I tried to check my blog and other sites today, the error I saw while trying to open, this blog as well as other hosted sites using the MySQL was:

Error establishing a database connection

The topology, where this error occured is simple, I have two hosts:

1. Apache version 2.0.64 compiled support externally PHP scripts interpretation via libphp – the host runs on (FreeBSD)

2. A Debian GNU / Linux squeeze running MySQL server version 5.1.61

The Apache host is assigned a local IP address and the SQL server is running on a host with IP

To diagnose the error I've logged in to and weirdly the mysql-server was appearing to run just fine:

debian:~# ps ax |grep -i mysql
31781 pts/0 S 0:00 /bin/sh /usr/bin/mysqld_safe
31940 pts/0 Sl 12:08 /usr/sbin/mysqld –basedir=/usr –datadir=/var/lib/mysql –user=mysql –pid-file=/var/run/mysqld/ –socket=/var/run/mysqld/mysqld.sock –port=3306
31941 pts/0 S 0:00 logger -t mysqld -p daemon.error
32292 pts/0 S+ 0:00 grep -i mysql

Moreover I could connect to the localhost SQL server with mysql -u root -p and it seemed to run fine. The error Error establishing a database connection meant that either something is messed up with the database or Mysql port 3306 is not properly accessible.

My first guess was something is wrong due to some firewall rules, so I tried to connect from to with telnet:

freebsd# telnet 3306
Connected to jericho.
Escape character is '^]'.
Host 'webserver' is blocked because of many connection errors; unblock with 'mysqladmin flush-hosts'
Connection closed by foreign host.

Right after the telnet was initiated as I show in the above output the connection was immediately closed with the error:

Host 'webserver' is blocked because of many connection errors; unblock with 'mysqladmin flush-hosts'Connection closed by foreign host.

In the error 'webserver' is my Apache machine set hostname. The error clearly states the problems with the 'webserver' apache host unable to connect to the SQL database are due to 'many connection errors' and a fix i suggested with mysqladmin flush-hosts

To temporary solve the error and restore my normal connectivity between the Apache and the SQL servers I logged I had to issue on the SQL host:

mysqladmin -u root -p flush-hostsEnter password:

Thogh this temporar fix restored accessibility to the databases and hence the websites errors were resolved, this doesn't guarantee that in the future I wouldn't end up in the same situation and therefore I looked for a permanent fix to the issues once and for all.

The permanent fix consists in changing the default value set for max_connect_error in /etc/mysql/my.cnf, which by default is not too high. Therefore to raise up the variable value, added in my.cnf in conf section [mysqld]:

debian:~# vim /etc/mysql/my.cnf

and afterwards restarted MYSQL:

debian:~# /etc/init.d/mysql restart
Stopping MySQL database server: mysqld.
Starting MySQL database server: mysqld.
Checking for corrupt, not cleanly closed and upgrade needing tables..

To make sure the assigned max_connect_errors=4294967295 is never reached due to Apache to SQL connection errors, I've also added as a cronjob.

debian:~# crontab -u root -e
00 03 * * * mysqladmin flush-hosts

In the cron I have omitted the mysqladmin -u root -p (user/pass) input options because for convenience I have already stored the mysql root password in /root/.my.cnf

Here is how /root/.my.cnf looks like:

debian:~# cat /root/.my.cnf

Now hopefully, this would permanently solve SQL's 'failure to accept connections' due to too many connection errors for future.

How to check Apache Webserver and MySQL server uptime – Check uptime of a running daemon with PS (process) command

Tuesday, March 10th, 2015

Reading Time: 2minutes


Something very useful that most Apache LAMP (Linux Apache MySQL PHP) admins should know is how to check Apache Webserver uptime and MySQL server running (uptime).
Checking Apache / MySQL uptime is primary useful for scripting purposes – creating auto Apache / MySQL service restart scripts, or just as a quick console way to check what is the status and uptime of Webserver / SQL.

My experience as a sysadmin shows that lack of Periodic Apache and MySQL restart every week or every month often creates sys-admin a lot of a headaches cause (Apache / NGINX / SQL  server) starts eating too much memory or under some circumstances leads to service or system crashes. Periodic system main services restart is especially helpful in case if Website's backend programming code is writetn in a bad and buggy uneffient way by unprofessional (novice) programmers.
While I was still working as Senior SysAdmin in Design.BG, I've encountered many such Crappy Web applications developed by dozen of different programmers (because company's programmers changed too frequently and many of the hired Web Developers ,were still learning to program, I guess same is true also for other Start-UP Web / IT Company where crappy programming code is developed you will certainly need to keep an eye on Apache / MYSQL uptime.  If that's the case below 2 quick one liners with PS command will help you keep an eye on Apache / MYSQL uptime


ps -eo "%U %c %t"| grep apache2 | grep -v grep|grep root
root     apache2            02:30:05

Note that above example is Debian specific on RPM based distributions you will have to grep for httpd instead of apache2

ps -eo "%U %c %t"| grep http| grep -v grep|grep root

root     apache2            10:30:05

To check MySQL uptine:

ps -eo "%U %c %t"| grep mysqld
root     mysqld_safe        20:42:53
mysql    mysqld             20:42:53

Though example is for mysql and Apache you can easily use ps cmd in same way to check any other Linux service uptime such as Java / Qmail / PostgreSQL / Postfix etc.

ps -eo "%U %c %t"|grep qmail
qmails   qmail-send      19-01:10:48
qmaill   multilog        19-01:10:48
qmaill   multilog        19-01:10:48
qmaill   multilog        19-01:10:48
root     qmail-lspawn    19-01:10:48
qmailr   qmail-rspawn    19-01:10:48
qmailq   qmail-clean     19-01:10:48
qmails   qmail-todo      19-01:10:48
qmailq   qmail-clean     19-01:10:48
qmaill   multilog        40-18:02:53


 ps -eo "%U %c %t"|grep -i nginx|grep -v root|uniq
nobody   nginx           55-01:22:44


ps -eo "%U %c %t"|grep -i java|grep -v root |uniq
hipo   java            27-22:02:07


How to determine which processes make most writes on the hard drive in GNU / Linux using kernel variable

Thursday, November 13th, 2014

Reading Time: 2minutes

In Linux there are plenty of tools to measure input / ouput – read / write server bottlenecks. Just to mention a few such are, the native part of all Linux distributions IOSTAT – which is a great tool to measure hard disk bottlenecks. However as iostat requires certain sysadmin skills for novice sys-admins, there is also ofcourse more interactive tools such as DSTAT or even betterGLANCE which monitors not only disk writes but memory use, CPU load and Network use.

This tools can help you measure which processes are writting most (a lot) to hard disk drive but there is another quick and efficient way to track disk i/o by directly using the Linux kernel this is done via kernel parameter :


To enable block_dump kernel logging:

echo 1 > /proc/sys/vm/block_dump

To later track in real time output from kernel interactively on which running process calling the kernel is writing to server hard drive

tail -f /var/log/syslog

The output  looks like so:

Nov 13 12:25:51 pcfreak kernel: [1075037.701056] kjournald(297): WRITE block 482293496 on sda1
Nov 13 12:25:51 pcfreak kernel: [1075037.701059] kjournald(297): WRITE block 482293504 on sda1
Nov 13 12:25:51 pcfreak kernel: [1075037.701062] kjournald(297): WRITE block 482293512 on sda1
Nov 13 12:25:51 pcfreak kernel: [1075037.701066] kjournald(297): WRITE block 482293520 on sda1
Nov 13 12:25:51 pcfreak kernel: [1075037.701069] kjournald(297): WRITE block 482293528 on sda1
Nov 13 12:25:51 pcfreak kernel: [1075037.701072] kjournald(297): WRITE block 482293536 on sda1
Nov 13 12:25:51 pcfreak kernel: [1075037.702824] kjournald(297): WRITE block 482293544 on sda1
Nov 13 12:25:52 pcfreak kernel: [1075039.219288] apache2(3377): dirtied inode 3571740 (_index.html.old) on sda1
Nov 13 12:25:52 pcfreak kernel: [1075039.436133] mysqld(22945): dirtied inode 21546676 (#sql_c0a_0.MYI) on sda1
Nov 13 12:25:52 pcfreak kernel: [1075039.436826] mysqld(22945): dirtied inode 21546677 (#sql_c0a_0.MYD) on sda1
Nov 13 12:25:53 pcfreak kernel: [1075039.662832] mysqld(22945): dirtied inode 21546676 (#sql_c0a_0.MYI) on sda1
Nov 13 12:25:53 pcfreak kernel: [1075039.663297] mysqld(22945): dirtied inode 21546677 (#sql_c0a_0.MYD) on sda1
Nov 13 12:25:53 pcfreak kernel: [1075039.817120] apache2(3377): dirtied inode 3571754 (_index.html) on sda1
Nov 13 12:25:53 pcfreak kernel: [1075039.819968] apache2(3377): dirtied inode 3571740 (_index.html_gzip) on sda1
Nov 13 12:25:53 pcfreak kernel: [1075039.820016] apache2(3377): dirtied inode 3571730 (?) on sda1
Nov 13 12:25:53 pcfreak kernel: [1075040.491378] mysqld(22931): dirtied inode 21546676 (#sql_c0a_0.MYI) on sda1
Nov 13 12:25:53 pcfreak kernel: [1075040.492309] mysqld(22931): dirtied inode 21546677 (#sql_c0a_0.MYD) on sda1
Nov 13 12:25:54 pcfreak kernel: [1075041.551513] apache2(3377): dirtied inode 1474706 (_index.html_gzip.old) on sda1
Nov 13 12:25:54 pcfreak kernel: [1075041.551566] apache2(3377): dirtied inode 1474712 (_index.html.old) on sda1
Nov 13 12:25:55 pcfreak kernel: [1075041.769036] mysqld(22941): dirtied inode 21546676 (#sql_c0a_0.MYI) on sda1
Nov 13 12:25:55 pcfreak kernel: [1075041.769804] mysqld(22941): dirtied inode 21546677 (#sql_c0a_0.MYD) on sda1
Nov 13 12:25:55 pcfreak kernel: [1075041.985857] apache2(3282): dirtied inode 4063282 (data_9d97a7f62d54bc5fd791fba3245ba591-SMF-modSettings.php) on sda1
Nov 13 12:25:55 pcfreak kernel: [1075041.987460] apache2(3282): dirtied inode 29010186 (data_9d97a7f62d54bc5fd791fba3245ba591-SMF-permissions–1.php) on sda1
Nov 13 12:25:55 pcfreak kernel: [1075041.988357] flush-8:0(289): WRITE block 51350632 on sda1

Using the kernel method to see which processes are stoning your server is great way especially for servers without connectivity to the Internet where you have no possibility to install sysstat package (contaning iostat),  dstat or glance.
Thanks to Marto's blog for  this nice hack.

swap_pager_getswapspace: failed, MySQL troubles on FreeBSD 7.2 cause and solution

Tuesday, May 3rd, 2011

Reading Time: 2minutes
Every now and then my FreeBSD router dmesg ( /var/log/ ) logs, gets filled with error messages like:

pid 86369 (httpd), uid 80, was killed: out of swap space
swap_pager_getswapspace(14): failed
swap_pager_getswapspace(16): failed
swap_pager_getswapspace(11): failed
swap_pager_getswapspace(12): failed
swap_pager_getswapspace(16): failed
swap_pager_getswapspace(16): failed
swap_pager_getswapspace(16): failed
swap_pager_getswapspace(16): failed
swap_pager_getswapspace(14): failed
swap_pager_getswapspace(16): failed
swap_pager_getswapspace(8): failed

Using swapinfo during the swap_pager_getswapspace(16): failed messages were logged in, I figured out that definitely the swap memory over-use is the bottleneck for the troubles, to find this I used the command:

freebsd# swapinfo
Device 1K-blocks Used Avail Capacity Type
/dev/ad0s1b 49712 45920 3792 92% Interleaved

After some investigation, I’ve figured out that the MySQL server is causing the kernel exceeded swap troubles.

My current MySQL server version is installed from the ports tree, whether I’m using the bsd port /usr/ports/databases/mysql51-server/ and it appears to work just fine.

However I have noticed that the mysql-server is missing a my.cnf file!, which means the mysql server is running under a mode with some kind of default configurations.

Strangely in the system process list it appeared it is using a default my.cnf file located in /var/db/mysql/my.cnf

Below you see the paste from the ps command:

ps axuww freebsd# ps axuww | grep -i my.cnf | grep -v grep
mysql 7557 0.0 0.1 3464 1268 p1 I 12:03PM 0:00.01 /bin/sh /usr/local/bin/mysqld_safe --defaults-extra-file=/var/db/mysql/my.cnf --user=mysql --datadir=/var/db/mysql --pid-file=/var/db/mysql/pcfreak.pidmysql 7589 0.0 5.1 93284 52852 p1 I 12:03PM 0:59.01 /usr/local/libexec/mysqld --defaults-extra-file=/var/db/mysql/my.cnf --basedir=/usr/local --datadir=/var/db/mysql --user=mysql --pid-file=/var/db/mysql/ --port=3306 --socket=/tmp/mysql.sock

Nevertheless it appeared the sql server is running the file /var/db/mysql/my.cnf conf was not existing! This was really weird for me as I’m used to have the default my.cnf from my previous experience with Linux servers!

Thus the next logical thing I did was to create my.cnf conf file in order to be able to have a proper limiting configuration for the sql server.

The FreeBSD my.cnf skele files are found in /usr/local/share/mysql/, here are the 4 files one can use as a starting basis for further configuration of the mysql-server.

freebsd# ls -al /usr/local/share/mysql/my-*.cnf
-r--r--r-- 1 root wheel 4948 Aug 12 2009 /usr/local/share/mysql/my-huge.cnf
-r--r--r-- 1 root wheel 20949 Aug 12 2009 /usr/local/share/mysql/my-innodb-heavy-4G.cnf
-r--r--r-- 1 root wheel 4924 Aug 12 2009 /usr/local/share/mysql/my-large.cnf
-r--r--r-- 1 root wheel 4931 Aug 12 2009 /usr/local/share/mysql/my-medium.cnf
-r--r--r-- 1 root wheel 2502 Aug 12 2009 /usr/local/share/mysql/my-small.cnf

I have chosen to use the my-medium.cnf as a skele to tune up, as my server is not high iron one e.g. the host I run the mysql is a (simple dual core 1.2Ghz system).

Further on I copied the /usr/local/share/mysql/my-medium.cnf to /var/db/mysql/my.cnf e.g.:

freebsd# cp -rpf /usr/local/share/mysql/my-medium.cnf /var/db/mysql/my.cnf

As a next step to properly tune up the default values of the newly copied my.cnf to my specific server I used the Tuning-Primer MySQL tuning script

Using is really easy as all I did is download, launch it and follow the script suggestions to correct some of the values already in my.cnf

I have finally ended up with the following my.cnf after using to optimize mysql server to work with my bsd host

Now I really hope the shitty swap_pager_getswapspace: failed errors would not haunt me once again by crashing my server and causing mem overheads.

Still I wonder why the port developer Alex Dupre – choose not to provide the default mysql51-server conf with some kind of my.cnf file? I hope he had a good reason.

How to check and repair broken MySQL ISAM tables

Monday, July 11th, 2011

Reading Time: < 1minute
MySQL repair artistic picture

If you are stuffed with errors in /var/log/mysqld.log similar to:

110711 11:00:48 [ERROR] /usr/libexec/mysqld: Incorrect information in file: './anyboots_moncler_spaccio/zen_seo_cache.frm'
110711 11:00:48 [ERROR] /usr/libexec/mysqld: Incorrect information in file: './anyboots_moncler_spaccio/zen_sessions.frm'

This is a sure sign something terrible has happened with your mysql database tables that lead to corruption.
Having corrupt table in mysql installation can severely lead to data loss as well as significantly reduce the speed and performance of a MySQL server in this awful times mysqlcheck is the best friend of the administrator, here is how you can check and repair broken tables in MySQL server:

mysql-server:~# mysqlcheck --all-databases -u root -p
chillor_hjbgl.vn_users OK
chillor_lul.mybb_adminlog OK
chillor_lul.mybb_adminoptions OK
chillor_lul.mybb_adminsessions OK
chillor_lul.mybb_adminviews OK
chillor_lul.mybb_announcements OK

You will notice the corrupt sql tables will be reported as corrupt by the tool and mysqlcheck will try it’s best to recover the corrupt tables.

In most cases this should be enough to recover corrupt tables.

How to tune MySQL Server to increase MySQL performance using and

Tuesday, August 9th, 2011

Reading Time: 7minutesMySQL Easy performance tuning with and scripts

Improving MySQL performance is crucial for improving a website responce times, reduce server load and improve overall work efficiency of a mysql database server.

I’ve seen however many Linux System administrators who does belittle or completely miss the significance of tuning a newly installed MySQL server installation.
The reason behind that is probably caused by fact that many people think MySQL config variables, would not significantly improve performance and does not pay back for optimization efforts. Moreover there are a bunch of system admins who has to take care for numerous services so they don’t have time to get good knowledge to optimize MySQL servers.
Thus many admins and webmasters nowdays, think optimizations depend mostly on the side of the website programmers.
It’s also sometimes falsely believed that optimizing a MySQL server could reduce the overall server stability.

With the boom of Internet website building and internet marketing, many webmasters emerged and almost anybody with almost no knowledge on GNU/Linux or minimal or no knowledge on PHP can start his Online store, open a blog or create a website powered by some CMS like joomla.
Thus nowdays many servers even doesn’t have a hired system administrators but are managed by people whose knowledge on *Nix is almost next to zero, this is another reason why dozens of MySQL installations online are a default ones and are not taking a good advantage of the server hardware.

The incrase of website visitors leads people servers expectations for hardware also to grow, thus many companies simply buy a new hardware instead of taking the few time to investigate on how current server hardware can be utilized better.
In that manner of thought I though it will be a good idea to write this small article on Tuning mysql servers with two scripts and
The scripts are ultra easy to use and does not require only a minimal knowledge on MySQL, Linux or (*BSD *nix if sql is running on BSD). and are therefore suitable for a quick MySQL server optimizations to even people who are no computer experts.

I use this two scripts for MySQL server optimizations on almost every new configured GNU/Linux with a MySQL backend.
Use of the script comes to simply download with wget, lynx, curl or some other web client and execute it on the server host which is already running the MySQL server.

Here is an example of how simple it is to run the scripts to Optimize MySQL:

debian:~# perl
>> MySQLTuner 1.2.0 - Major Hayden ><
>> Bug reports, feature requests, and downloads at
>> Run with '--help' for additional options and output filtering

——– General Statistics ————————————————–
[–] Skipped version check for MySQLTuner script
[OK] Currently running supported MySQL version 5.1.49-3
[OK] Operating on 64-bit architecture

——– Storage Engine Statistics ——————————————-
[–] Status: +Archive -BDB -Federated +InnoDB -ISAM -NDBCluster
[–] Data in MyISAM tables: 6G (Tables: 952)
[!!] InnoDB is enabled but isn’t being used
[!!] Total fragmented tables: 12

——– Security Recommendations ——————————————-
[OK] All database users have passwords assigned

——– Performance Metrics ————————————————-
[–] Up for: 1d 2h 3m 35s (68M q [732.193 qps], 610K conn, TX: 49B, RX: 11B)
[–] Reads / Writes: 76% / 24%
[–] Total buffers: 512.0M global + 2.8M per thread (2000 max threads)
[OK] Maximum possible memory usage: 6.0G (25% of installed RAM)
[OK] Slow queries: 0% (3K/68M)
[OK] Highest usage of available connections: 7% (159/2000)
[OK] Key buffer size / total MyISAM indexes: 230.0M/1.7G
[OK] Key buffer hit rate: 97.8% (11B cached / 257M reads)
[OK] Query cache efficiency: 76.6% (46M cached / 61M selects)
[!!] Query cache prunes per day: 1822075
[OK] Sorts requiring temporary tables: 0% (1K temp sorts / 2M sorts)
[!!] Joins performed without indexes: 63635
[OK] Temporary tables created on disk: 1% (26K on disk / 2M total)
[OK] Thread cache hit rate: 99% (159 created / 610K connections)
[!!] Table cache hit rate: 4% (1K open / 43K opened)
[OK] Open file limit used: 17% (2K/16K)
[OK] Table locks acquired immediately: 99% (36M immediate / 36M locks)

——– Recommendations —————————————————–
General recommendations:
Add skip-innodb to MySQL configuration to disable InnoDB
Run OPTIMIZE TABLE to defragment tables for better performance
Enable the slow query log to troubleshoot bad queries
Increasing the query_cache size over 128M may reduce performance
Adjust your join queries to always utilize indexes
Increase table_cache gradually to avoid file descriptor limits
Variables to adjust:
query_cache_size (> 256M) [see warning above] join_buffer_size (> 256.0K, or always use indexes with joins) table_cache (> 7200)

You see there are plenty of things, the script reports, for the unexperienced most of the information can be happily skipped without need to know the cryptic output, the section of importance here is Recommendations for some clarity, I’ve made this section to show up bold.

The most imporant things from the Recommendations script output is actually the lines who give suggestions for incrase of certain variables for MySQL.In this example case this are the last three variables:
join_buffer_size and

All of these variables are tuned from /etc/mysql/my.cnf (on Debian) and derivatives distros and from /etc/my.cnf on RHEL, CentOS, Fedora and the other RPM based Linux distributions.

On some custom server installs my.cnf is also located in /usr/local/mysql/etc/ or some other a bit more unstandard location 😉

Anyways now having the Recommendation from the script, it’s necessery to edit my.cnf and try to double the values for the suggested variables.

First, I check if all the suggested variables are existent in my config with grep , if they’re not then I’ll simply add the variable with doubled size of the suggested values.
P.S: One note here is sometimes some values which are configured, are the default value for the MySQL server and does not have a record in my.cnf

debian:~# grep -E 'query_cache_size|join_buffer_size|table_cache' /etc/mysql/my.cnf table_cache = 7200
query_cache_size = 256M
join_buffer_size = 262144

All of my variables are in the config so, now edit my.cnf and set values to:
table_cache = 14400
query_cache_size = 512M
join_buffer_size = 524288

I always, however preserve the old variable’s value, because sometimes raising the value might create problem and the MySql server might be unable to restart properly.
Thus before going with adding the new values make sure the old ones are commented with # , e.g.:
#table_cache = 7200
#query_cache_size = 256M
#join_buffer_size = 262144

I would recommend vim as editor of choice while editing my.cnf as vim completely rox 😉 If you’re not acquainted to vim use nano or mcedit or your editor of choice 😉 :

debian:~# vim /etc/mysql/my.cnf

Assuming that the changes are made, it’s time to restart MySQL to make sure the new values are read by the SQL server.

debian:~# /etc/init.d/mysql restart
* Stopping MySQL database server mysqld [ OK ]
* Starting MySQL database server mysqld [ OK ]
Checking for tables which need an upgrade, are corrupt or were not closed cleanly.

If mysql server fails, however to restart, make sure immediately you reverse back the changed variables to the commented values and restart once again via mysql init script to make server load.

Afterwards start adding the values one by one until find out which one is causing the mysqld to fail.

Now the second script ( is also really nice for MySQL performance optimizations are necessery. However it’s less portable (as it’s written in bash scripting language).
Consider running this script among different GNU/Linux distributious (especially the newer ones) might produce errors. requires some minor code changes to be able to run on FreeBSD, NetBSD and OpenBSD *nices.

The way works is precisely like , one runs it it gives some info about current running MySQL server and based on certain factors gives suggestions on how increasing or decresing certain my.cnf variables could reduce sql query bottlenecks, solve table locking issues as well as generally improve INSERT, UPDATE query times.

Here is an example output from run on another server:

server:~# wget
server:~# sh
- By: Matthew Montgomery -

MySQL Version 5.0.51a-24+lenny5 x86_64

Uptime = 8 days 10 hrs 19 min 8 sec
Avg. qps = 179
Total Questions = 130851322
Threads Connected = 1

Server has been running for over 48hrs.
It should be safe to follow these recommendations

To find out more information on how each of these
runtime variables effects performance visit:

Current long_query_time = 1 sec.
You have 16498 out of 130851322 that take longer than 1 sec. to complete
The slow query log is NOT enabled.
Your long_query_time seems to be fine

Current max_connections = 2000
Current threads_connected = 1
Historic max_used_connections = 85
The number of used connections is 4% of the configured maximum.
Your max_connections variable seems to be fine.

Current thread_cache_size = 128
Current threads_cached = 84
Current threads_per_sec = 0
Historic threads_per_sec = 0
Your thread_cache_size is fine

MEMORY USAGE line 994: let: expression expected
Max Memory Ever Allocated : 741 M
Configured Max Memory Limit : 5049 M
Total System Memory : 23640 M

Current MyISAM index space = 1646 M
Current key_buffer_size = 476 M
Key cache miss rate is 1 / 56
Key buffer fill ratio = 90.00 %
You could increase key_buffer_size
It is safe to raise this up to 1/4 of total system memory;
assuming this is a dedicated database server.

Query cache is enabled
Current query_cache_size = 64 M
Current query_cache_used = 38 M
Current Query cache fill ratio = 59.90 %

Current sort_buffer_size = 2 M
Current record/read_rnd_buffer_size = 256.00 K
Sort buffer seems to be fine

Current join_buffer_size = 128.00 K
You have had 111560 queries where a join could not use an index properly
You have had 91 joins without keys that check for key usage after each row
You should enable “log-queries-not-using-indexes”
Then look for non indexed joins in the slow query log.
If you are unable to optimize your queries you may want to increase your
join_buffer_size to accommodate larger joins in one pass.

Current table_cache value = 3600 tables
You have a total of 798 tables
You have 1904 open tables.
The table_cache value seems to be fine

Current tmp_table_size = 128 M
1% of tmp tables created were disk based
Created disk tmp tables ratio seems fine

Current read_buffer_size = 128.00 K
Current table scan ratio = 797 : 1
read_buffer_size seems to be fine

Current Lock Wait ratio = 1 : 1782
You may benefit from selective use of InnoDB.

As seen from script output, there are certain variables which might be increased a bit for better SQL performance, one such variable as suggested is key_buffer_size(You could increase key_buffer_size)

Now the steps to make the tunings to my.cnf are precisely the same as with, e.g.:
1. Preserve old config variables which will be changed by commenting them
2. Double value of current variables in my.cnf suggested by script
3. Restart Mysql server via /etc/init.d/mysql restart cmd.
4. If mysql runs fine monitor mysql performance with mtop or mytop for at least 15 mins / half an hour.

if all is fine run once again the tuning scripts to see if there are no further improvement suggestions, if there are more follow the 4 steps described procedure once again.

It’s also a good idea that these scripts are periodically re-run on the server like once per few months as changes in SQL queries amounts and types will require changes in MySQL operational variables.
The authors of these nice scripts has done great job and have saved us a tons of nerves time, downtimes and money spend on meaningless hardware. So big thanks for the awesome scripts guys 😉
Finally after hopefully succesful deployment of changes, enjoy the incresed SQL server performance 😉

How to solve “Incorrect key file for table ‘/tmp/#sql_9315.MYI’; try to repair it” mysql start up error

Saturday, April 28th, 2012

Reading Time: 2minutes

When a server hard disk scape gets filled its common that Apache returns empty (no content) pages…
This just happened in one server I administer. To restore the normal server operation I freed some space by deleting old obsolete backups.
Actually the whole reasons for this mess was an enormous backup files, which on the last monthly backup overfilled the disk empty space.

Though, I freed about 400GB of space on the the root filesystem and on a first glimpse the system had plenty of free hard drive space, still restarting the MySQL server refused to start up properly and spit error:

Incorrect key file for table '/tmp/#sql_9315.MYI'; try to repair it" mysql start up error

Besides that there have been corrupted (crashed) tables, which reported next to above error.
Checking in /tmp/#sql_9315.MYI, I couldn't see any MYI – (MyISAM) format file. A quick google look up revealed that this error is caused by not enough disk space. This was puzzling as I can see both /var and / partitions had plenty of space so this shouldn't be a problem. Also manally creating the file /tmp/#sql_9315.MYI with:

server:~# touch /tmp/#sql_9315.MYI

Didn't help it, though the file created fine. Anyways a bit of a closer examination I've noticed a /tmp filesystem mounted besides with the other file system mounts ????
You can guess my great amazement to find this 1 Megabyte only /tmp filesystem hanging on the server mounted on the server.

I didn't mounted this 1 Megabyte filesystem, so it was either an intruder or some kind of "weird" bug…
I digged in Googling to see, if I can find more on the error and found actually the whole mess with this 1 mb mounted /tmp partition is caused by, just recently introduced Debian init script /etc/init.d/mountoverflowtmp.
It seems this script was introduced in Debian newer releases. mountoverflowtmp is some kind of emergency script, which is triggered in case if the root filesystem/ space gets filled.
The script has only two options:

# /etc/init.d/mountoverflowtmp
Usage: mountoverflowtmp [start|stop]

Once started what it does it remounts the /tmp to be 1 megabyte in size and stops its execution like it never run. Well maybe, the developers had something in mind with introducing this script I will not argue. What I should complain though is the script design is completely broken. Once the script gets "activated" and does its job. This 1MB mount stays like this, even if hard disk space is freed on the root partition – / ….

Hence to cope with this unhandy situation, once I had freed disk space on the root partition for some reason mountoverflowtmp stop option was not working,
So I had to initiate "hard" unmount:

server:~# mount -l /tmp

Also as I had a bunch of crashed tables and to fix them, also issued on each of the broken tables reported on /etc/init.d/mysql start start-up.

server:~# mysql -u root -p
mysql> use Database_Name;
mysql> repair table Table_Name extended;

Then to finally solve the stupid Incorrect key file for table '/tmp/#sql_XXYYZZ33444.MYI'; try to repair it error, I had to restart once again the SQL server:

Stopping MySQL database server: mysqld.
Starting MySQL database server: mysqld.
Checking for corrupt, not cleanly closed and upgrade needing tables..

Tadadadadam!, SQL now loads and works back as before!