Posts Tagged ‘cli’

Fix MySQL ibdata file size – ibdata1 file growing too large, preventing ibdata1 from eating all your server disk space

Thursday, April 2nd, 2015

fix-solve-mysql-ibdata-file-size-ibdata1-file-growing-too-large-and-preventing-ibdata1-from-eating-all-your-disk-space-innodb-vs-myisam

If you're a webhosting company hosting dozens of various websites that use MySQL with InnoDB  engine as a backend you've probably already experienced the annoying problem of MySQL's ibdata1 growing too large / eating all server's disk space and triggering disk space low alerts. The ibdata1 file, taking up hundreds of gigabytes is likely to be encountered on virtually all Linux distributions which run default MySQL server <= MySQL 5.6 (with default distro shipped my.cnf). The excremental ibdata1 raise appears usually due to a application software bug on how it queries the database. In theory there are no limitation for ibdata1 except maximum file size limitation set for the filesystem (and there is no limitation option set in my.cnf) meaning it is quite possible that under certain conditions ibdata1 grow over time can happily fill up your server LVM (Storage) drive partitions.

Unfortunately there is no way to shrink the ibdata1 file and only known work around (I found) is to set innodb_file_per_table option in my.cnf to force the MySQL server create separate *.ibd files under datadir (my.cnf variable) for each freshly created InnoDB table.
 

1. Checking size of ibdata1 file

On Debian / Ubuntu and other deb based Linux servers datadir is /var/lib/mysql/ibdata1

server:~# du -hsc /var/lib/mysql/ibdata1
45G     /var/lib/mysql/ibdata1
45G     total


2. Checking info about Databases and Innodb storage Engine

server:~# mysql -u root -p
password:

mysql> SHOW DATABASES;
+——————–+
| Database           |
+——————–+
| information_schema |
| bible              |
| blog               |
| blog-sezoni        |
| blogmonastery      |
| daniel             |
| ezmlm              |
| flash-games        |


Next step is to get some understanding about how many existing InnoDB tables are present within Database server:

mysql> SELECT COUNT(1) EngineCount,engine FROM information_schema.tables WHERE table_schema NOT IN ('information_schema','performance_schema','mysql') GROUP BY engine;
+————-+——–+
| EngineCount | engine |
+————-+——–+
|         131 | InnoDB |
|           5 | MEMORY |
|         584 | MyISAM |
+————-+——–+
3 rows in set (0.02 sec)

To get some more statistics related to InnoDb variables set on the SQL server:
 

mysqladmin -u root -p'Your-Server-Password' var | grep innodb


Here is also how to find which tables use InnoDb Engine

mysql> SELECT table_schema, table_name
    -> FROM INFORMATION_SCHEMA.TABLES
    -> WHERE engine = 'innodb';

+————–+————————–+
| table_schema | table_name               |
+————–+————————–+
| blog         | wp_blc_filters           |
| blog         | wp_blc_instances         |
| blog         | wp_blc_links             |
| blog         | wp_blc_synch             |
| blog         | wp_likes                 |
| blog         | wp_wpx_logs              |
| blog-sezoni  | wp_likes                 |
| icanga_web   | cronk                    |
| icanga_web   | cronk_category           |
| icanga_web   | cronk_category_cronk     |
| icanga_web   | cronk_principal_category |
| icanga_web   | cronk_principal_cronk    |


3. Check and Stop any Web / Mail / DNS service using MySQL

server:~# ps -efl |grep -E 'apache|nginx|dovecot|bind|radius|postfix'

Below cmd should return empty output, (e.g. Apache / Nginx / Postfix / Radius / Dovecot / DNS etc. services are properly stopped on server).

4. Create Backup dump all MySQL tables with mysqldump

Next step is to create full backup dump of all current MySQL databases (with mysqladmin):

server:~# mysqldump –opt –allow-keywords –add-drop-table –all-databases –events -u root -p > dump.sql
server:~# du -hsc /root/dump.sql
940M    dump.sql
940M    total

If you have free space on an external backup server or remotely mounted attached (NFS or SAN Storage) it is a good idea to make a full binary copy of MySQL data (just in case something wents wrong with above binary dump), copy respective directory depending on the Linux distro and install location of SQL binary files set (in my.cnf).
To check where are MySQL binary stored database data (check in my.cnf):

server:~# grep -i datadir /etc/mysql/my.cnf
datadir         = /var/lib/mysql

If server is CentOS / RHEL Fedora RPM based substitute in above grep cmd line /etc/mysql/my.cnf with /etc/my.cnf

if you're on Debian / Ubuntu:

server:~# /etc/init.d/mysql stop
server:~# cp -rpfv /var/lib/mysql /root/mysql-data-backup

Once above copy completes, DROP all all databases except, mysql, information_schema (which store MySQL existing user / passwords and Access Grants and Host Permissions)

5. Drop All databases except mysql and information_schema

server:~# mysql -u root -p
password:

mysql> SHOW DATABASES;

DROP DATABASE blog;
DROP DATABASE sessions;
DROP DATABASE wordpress;
DROP DATABASE micropcfreak;
DROP DATABASE statusnet;

          etc. etc.

ACHTUNG !!! DON'T execute!DROP database mysql; DROP database information_schema; !!! – cause this might damage your User permissions to databases

6. Stop MySQL server and add innodb_file_per_table and few more settings to prevent ibdata1 to grow infinitely in future

server:~# /etc/init.d/mysql stop

server:~# vim /etc/mysql/my.cnf
[mysqld]
innodb_file_per_table
innodb_flush_method=O_DIRECT
innodb_log_file_size=1G
innodb_buffer_pool_size=4G

Delete files taking up too much space – ibdata1 ib_logfile0 and ib_logfile1

server:~# cd /var/lib/mysql/
server:~#  rm -f ibdata1 ib_logfile0 ib_logfile1
server:~# /etc/init.d/mysql start
server:~# /etc/init.d/mysql stop
server:~# /etc/init.d/mysql start
server:~# ps ax |grep -i mysql

You should get no running MySQL instance (processes), so above ps command should return blank.
 

7. Re-Import previously dumped SQL databases with mysql cli client

server:~# cd /root/
server:~# mysql -u root -p < dump.sql

Hopefully import should went fine, and if no errors experienced new data should be in.

Altearnatively if your database is too big and you want to import it in less time to mitigate SQL downtime, instead import the database with:

server:~# mysql -u root -p
password:
mysql>  SET FOREIGN_KEY_CHECKS=0;
mysql> SOURCE /root/dump.sql;
mysql> SET FOREIGN_KEY_CHECKS=1;

If something goes wrong with the import for some reason, you can always copy over sql binary files from /root/mysql-data-backup/ to /var/lib/mysql/
 

8. Connect to mysql and check whether databases are listable and re-check ibdata file size

Once imported login with mysql cli and check whther databases are there with:

server:~# mysql -u root -p
SHOW DATABASES;

Next lets see what is currently the size of ibdata1, ib_logfile0 and ib_logfile1
 

server:~# du -hsc /var/lib/mysql/{ibdata1,ib_logfile0,ib_logfile1}
19M     /var/lib/mysql/ibdata1
1,1G    /var/lib/mysql/ib_logfile0
1,1G    /var/lib/mysql/ib_logfile1
2,1G    total

Now ibdata1 will grow, but only contain table metadata. Each InnoDB table will exist outside of ibdata1.
To better understand what I mean, lets say you have InnoDB table named blogdb.mytable.
If you go into /var/lib/mysql/blogdb, you will see two files
representing the table:

  •     mytable.frm (Storage Engine Header)
  •     mytable.ibd (Home of Table Data and Table Indexes for blogdb.mytable)

Now construction will be like that for each of MySQL stored databases instead of everything to go to ibdata1.
MySQL 5.6+ admins could relax as innodb_file_per_table is enabled by default in newer SQL releases.


Now to make sure your websites are working take few of the hosted websites URLs that use any of the imported databases and just browse.
In my case ibdata1 was 45GB after clearing it up I managed to save 43 GB of disk space!!!

Enjoy the disk saving! 🙂

MySQL: How to check user privileges and allowed hosts to connect with mysql cli

Wednesday, April 2nd, 2014

how-to-check-user-privileges-and-allowed-hosts-to-connect-with-mysql-cli

On a project there are some issues with root admin user unable to access the server from remote host and the most probable reason was there is no access to the server from that host thus it was necessary check mysql root user privilegse and allowed hosts to connect, here SQL query to do it:
 

mysql> select * from `user` where  user like '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 | ssl_type | ssl_cipher | x509_issuer | x509_subject | max_questions | max_updates | max_connections | max_user_connections |
+——————————–+——+——————————————-+————-+————-+————-+————-+————-+———–+————-+—————+————–+———–+————+—————–+————+————+————–+————+———————–+——————+————–+—————–+——————+——————+—————-+———————+——————–+——————+————+————–+———-+————+————-+————–+—————+————-+—————–+———————-+
| localhost                      | root | *5A07790DCF43AC89820F93CAF7B03DE3F43A10D9 | 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 |
| server737                        | root | *5A07790DCF43AC89820F93CAF7B03DE3F43A10D9 | 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 |
| 127.0.0.1                      | root | *5A07790DCF43AC89820F93CAF7B03DE3F43A10D9 | 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 |
| server737.server.myhost.net | root | *5A07790DCF43FC89820A93CAF7B03DE3F43A10D9 | 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 |
| server4586                        | root | *5A07790DCF43AC89820F93CAF7B03DE3F43A10D9 | N           | N           | N           | N           | N           | N         | N           | N             | N            | N         | N          | N               | N          | N          | N            | N          | N                     | N                | N            | N               | N                | N                | N              | N                   | N                  | N                | N          | N            |          |            |             |              |             0 |           0 |               0 |                    0 |
| server4586.myhost.net              | root | *5A07790DCF43AC89820F93CAF7B03DE3F43A10D9 | N           | N           | N           | N           | N           | N         | N           | N             | N            | N         | N          | N               | N          | N          | N            | N          | N                     | N                | N            | N               | N                | N                | N              | N                   | N                  | N                | N          | N            |          |            |             |              |             0 |           0 |               0 |                    0 |
+——————————–+——+——————————————-+————-+————-+————-+————-+————-+———–+————-+—————+————–+———–+————+—————–+————+————+————–+————+———————–+——————+————–+—————–+——————+——————+—————-+———————+——————–+——————+————+————–+———-+————+————-+————–+—————+————-+—————–+———————-+
6 rows in set (0.00 sec)

mysql> exit


Here is query explained:

select * from `user` where  user like 'root%'; query means:

select * – show all
from `user` – from user database
where user like 'root%' – where there is match in user column to any string starting with 'root*',
 

Mysql: How to disable single database without dropping or renaming it

Wednesday, January 22nd, 2014

mysql rename forbid disable database howto logo, how to disable single database without dropping it
A colleague of mine working on MySQL database asked me How it is possible to disable a MySQL database. He is in situation where the client has 2 databases and application and is not sure which of the two databases the application uses. Therefore the client asked one of the database is disabled and wait for few hours and see if something will break / stop working and in that way determine which of the two database is used by application.

My first guess was to backup both databases and drop one of them, then if it is the wrong one to restore from the SQL dump backup, however this wasn't acceptable solution. So second I though of RENAME of database to another one and then reverting the name, however as it is written in MySQL documentation RENAME database function was removed from MySQL (found to be dangerous) since version 5.1.23 onwards. Anyhow there is a quick hack to rename mysql database using a for loop shell script one below:

mysql -e "CREATE DATABASE \`new_database\`;"
for table in `mysql -B -N -e "SHOW TABLES;" old_database`
do
  mysql -e "RENAME TABLE \`old_database\`.\`$table\` to \`new_database\`.\`$table\`"
  done
  mysql -e "DROP DATABASE \`old_database\`;"

Other possible solution was to change permissions of Application used username, however this was also complicated from mysql cli, hence I thought of installing and using PHPMyAdmin to make modify of db user permissions easier but on this server there wasn't Apache installed and MySQL is behind a firewall and only accessible via java tomcat host.

Finally after some pondering what can be done I came with solution to request to disable mysql database using chmod in /var/lib/mysql/data/, i.e.:

sql-server:~# chmod 0 /var/lib/mysql/databasename

Where databasename is the same as the database is named listable via mysql cli.

After doing it that way with no need to restart MySQL server database stopped to appear in show databases; and client confirmed that disabled database is no longer needed so we proceeded dropping it.

Hope this little article will help someone out there. Cheers :

How to completely disable Replication in MySQL server 5.1.61 on Debian GNU / Linux

Monday, July 16th, 2012

Replication_mysql_disable

Some time ago on one of the Database MySQL servers, I've configured replication as it was required to test somethings. Eventually it turned out replication will be not used (for some reason) it was too slow and not fitting our company needs hence we needed to disable it.

It seemed logical to me that, simply removing any replication related directives from my.cnf and a restart of the SQL server will be enough to turn replication off on the Debian Linux host. Therefore I proceeded removed all replication configs from /etc/my/my.cnf and issued MySQL restart i. e.:

sql-server:~# /etc/init.d/mysql restart
....

This however didn't turned off replication,as I thought and in phpmyadminweb frontend interface, replication was still appearing to be active in the replication tab.

Something was still making the SQL server still act as an Replication Slave Host, so after a bit of pondering and trying to remember, the exact steps I took to make the replication work on the host I remembered that actually I issued:

mysql> START SLAVE;

Onwards I run:

mysql> SHOW SLAVE STATUS;
....

and found in the database the server was still running in Slave Replication mode

Hence to turn off the db host run as a Slave, I had to issue in mysql cli:

mysql> STOP SLAVE;
Query OK, 0 rows affected, 1 warning (0.01 sec)
mysql> RESET SLAVE;
Query OK, 0 rows affected, 1 warning (0.01 sec)

Then after a reload of SQL server in memory, the host finally stopped working as a Slave Replication host, e.g.

sql-server:~# /etc/init.d/mysql restart
....

After the restart, to re-assure myself the SQL server is no more set to run as MySQL replication Slave host:

mysql> SHOW SLAVE STATUS;
Empty set (0.00 sec)

Cheers 😉

Monitoring MySQL server queries and debunning performance (slow query) issues with native MySQL commands and with mtop, mytop

Thursday, May 10th, 2012

If you're a Linux server administrator running MySQL server, you need to troubleshoot performance and bottleneck issues with the SQL database every now and then. In this article, I will pinpoint few methods to debug basic issues with MySQL database servers.

1. Troubleshooting MySQL database queries with native SQL commands

a)One way to debug errors and get general statistics is by logging in with mysql cli and check the mysql server status:

# mysql -u root -p
mysql> SHOW STATUS;
+-----------------------------------+------------+
| Variable_name | Value |
+-----------------------------------+------------+
| Aborted_clients | 1132 |
| Aborted_connects | 58 |
| Binlog_cache_disk_use | 185 |
| Binlog_cache_use | 2542 |
| Bytes_received | 115 |
.....
.....
| Com_xa_start | 0 |
| Compression | OFF |
| Connections | 150000 |
| Created_tmp_disk_tables | 0 |
| Created_tmp_files | 221 |
| Created_tmp_tables | 1 |
| Delayed_errors | 0 |
| Delayed_insert_threads | 0 |
| Delayed_writes | 0 |
| Flush_commands | 1 |
.....
.....
| Handler_write | 132 |
| Innodb_page_size | 16384 |
| Innodb_pages_created | 6204 |
| Innodb_pages_read | 8859 |
| Innodb_pages_written | 21931 |
.....
.....
| Slave_running | OFF |
| Slow_launch_threads | 0 |
| Slow_queries | 0 |
| Sort_merge_passes | 0 |
| Sort_range | 0 |
| Sort_rows | 0 |
| Sort_scan | 0 |
| Table_locks_immediate | 4065218 |
| Table_locks_waited | 196 |
| Tc_log_max_pages_used | 0 |
| Tc_log_page_size | 0 |
| Tc_log_page_waits | 0 |
| Threads_cached | 51 |
| Threads_connected | 1 |
| Threads_created | 52 |
| Threads_running | 1 |
| Uptime | 334856 |
+-----------------------------------+------------+
225 rows in set (0.00 sec)

SHOW STATUS; command gives plenty of useful info, however it is not showing the exact list of queries currently processed by the SQL server. Therefore sometimes it is exactly a stucked (slow queries) execution, you need to debug in order to fix a lagging SQL. One way to track this slow queries is via enabling mysql slow-query.log. Anyways enabling the slow-query requires a MySQL server restart and some critical productive database servers are not so easy to restart and the SQL slow queries have to be tracked "on the fly" so to say.
Therefore, to check the exact (slow) queries processed by the SQL server (without restarting it), do
 

mysql> SHOW processlist;
+——+——+—————+——+———+——+————–+——————————————————————————————————+
| Id | User | Host | db | Command | Time | State | Info |
+——+——+—————+——+———+——+————–+——————————————————————————————————+
| 609 | root | localhost | blog | Sleep | 5 | | NULL |
| 1258 | root | localhost | NULL | Sleep | 85 | | NULL |
| 1308 | root | localhost | NULL | Query | 0 | NULL | show processlist |
| 1310 | blog | pcfreak:64033 | blog | Query | 0 | Sending data | SELECT comment_author, comment_author_url, comment_content, comment_post_ID, comment_ID, comment_aut |
+——+——+—————+——+———+——+————–+——————————————————————————————————+
4 rows in set (0.00 sec)
mysql>

SHOW processlist gives a good view on what is happening inside the SQL.

To get more complete information on SQL query threads use the full extra option:

mysql> SHOW full processlist;

This gives pretty full info on running threads, but unfortunately it is annoying to re-run the command again and again – constantly to press UP Arrow + Enter keys.

Hence it is useful to get the same command output, refresh periodically every few seconds. This is possible by running it through the watch command:

debian:~# watch "'show processlist' | mysql -u root -p'secret_password'"

watch will run SHOW processlist every 2 secs (this is default watch refresh time, for other timing use watch -n 1, watch -n 10 etc. etc.

The produced output will be similar to:

Every 2.0s: echo 'show processlist' | mysql -u root -p'secret_password' Thu May 10 17:24:19 2012

Id User Host db Command Time State Info
609 root localhost blog Sleep 3 NULL1258 root localhost NULL Sleep 649 NULL1542 blog pcfreak:64981 blog Query 0 Copying to tmp table \
SELECT p.ID, p.post_title, p.post_content,p.post_excerpt, p.pos
t_date, p.comment_count, count(t_r.o
1543 root localhost NULL Query 0 NULL show processlist

Though this "hack" is one of the possible ways to get some interactivity on what is happening inside SQL server databases and tables table. for administering hundred or thousand SQL servers running dozens of queries per second – monitor their behaviour few times aday using mytop or mtop is times easier.

Though, the names of the two tools are quite similar and I used to think both tools are one and the same, actually they're not but both are suitable for monitoring sql database execution in real time.

As a sys admin, I've used mytop and mtop, on almost each Linux server with MySQL server installed.
Both tools has helped me many times in debugging oddities with sql servers. Therefore my personal view is mytop and mtop should be along with the Linux sysadmin most useful command tools outfit, still I'm sure many administrators still haven't heard about this nice goodies.

1. Installing mytop on Debian, Ubuntu and other deb based GNU / Linux-es

mytop is available for easy install on Debian and across all debian / ubuntu and deb derivative distributions via apt.

Here is info obtained with apt-cache show

debian:~# apt-cache show mytop|grep -i description -A 3
Description: top like query monitor for MySQL
Mytop is a console-based tool for monitoring queries and the performance
of MySQL. It supports version 3.22.x, 3.23.x, 4.x and 5.x servers.
It's written in Perl and support connections using TCP/IP and UNIX sockets.

Installing the tool is done with the trivial:

debian:~# apt-get --yes install mytop
....

mtop used to be available for apt-get-ting in Debian Lenny and prior Debian releases but in Squeeze onwards, only mytop is included (probably due to some licensing incompitabilities with mtop??).

For those curious on how mtop / mytop works – both are perl scripts written to periodically connects to the SQL server and run commands similar to SHOW FULL PROCESSLIST;. Then, the output is parsed and displayed to the user.

Here how mytop running, looks like:

MyTOP showing queries running on Ubuntu 8.04 Linux - Debugging interactively top like MySQL

2. Installing mytop on RHEL and CentOS

By default in RHEL and CentOS and probably other RedHat based Linux-es, there is neither mtop nor mytop available in package repositories. Hence installing the tools on those is only available from 3rd parties. As of time of writting an rpm builds for RHEL and CentOS, as well as (universal rpm distros) src.rpm package is available on http://pkgs.repoforge.org/mytop/. For the sake of preservation – if in future those RPMs disappear, I made a mirror of mytop rpm's here

Mytop rpm builds depend on a package perl(Term::ReadKey), my attempt to install it on CentOS 5.6, returned following err:

[root@cenots ~]# rpm -ivh mytop-1.4-2.el5.rf.noarch.rpm
warning: mytop-1.4-2.el5.rf.noarch.rpm: Header V3 DSA signature: NOKEY, key ID 6b8d79e6
error: Failed dependencies:
perl(Term::ReadKey) is needed by mytop-1.4-2.el5.rf.noarch

The perl(Term::ReadKey package is not available in CentOS 5.6 and (probably other centos releases default repositories so I had to google perl(Term::ReadKey) I found it on http://rpm.pbone.net/ package repository, the exact url to the rpm dependency as of time of writting this post is:

ftp://ftp.pbone.net/mirror/yum.trixbox.org/centos/5/old/perl-Term-ReadKey-2.30-2.rf.i386.rpm

Quickest, way to install it is:

[root@centos ~]# rpm -ivh ftp://ftp.pbone.net/mirror/yum.trixbox.org/centos/5/old/perl-Term-ReadKey-2.30-2.rf.i386.rpmRetrieving ftp://ftp.pbone.net/mirror/yum.trixbox.org/centos/5/old/perl-Term-ReadKey-2.30-2.rf.i386.rpmPreparing... ########################################### [100%]
1:perl-Term-ReadKey ########################################### [100%]

This time mytop, install went fine:

[root@centos ~]# rpm -ivh mytop-1.4-2.el5.rf.noarch.rpm
warning: mytop-1.4-2.el5.rf.noarch.rpm: Header V3 DSA signature: NOKEY, key ID 6b8d79e6
Preparing... ########################################### [100%]
1:mytop ########################################### [100%]

To use it further, it is the usual syntax:

mytop -u username -p 'secret_password' -d database

CentOS Linux MyTOP MySQL query benchmark screenshot - vpopmail query

3. Installing mytop and mtop on FreeBSD and other BSDs

To debug the running SQL queries in a MySQL server running on FreeBSD, one could use both mytop and mtop – both are installable via ports:

a) To install mtop exec:

freebsd# cd /usr/ports/sysutils/mtop
freebsd# make install clean
....

b) To install mytop exec:

freebsd# cd /usr/ports/databases/mytop
freebsd# make install clean
....

I personally prefer to use mtop on FreeBSD, because once run it runs prompts the user to interactively type in the user/pass

freebsd# mtop

Then mtop prompts the user with "interactive" dialog screen to type in user and pass:

Mtop interactive type in username and password screenshot on FreeBSD 7.2

It is pretty annoying, same mtop like syntax don't show user/pass prompt:

freebsd# mytop
Cannot connect to MySQL server. Please check the:

* database you specified "test" (default is "test")
* username you specified "root" (default is "root")
* password you specified "" (default is "")
* hostname you specified "localhost" (default is "localhost")
* port you specified "3306" (default is 3306)
* socket you specified "" (default is "")
The options my be specified on the command-line or in a ~/.mytop
config file. See the manual (perldoc mytop) for details.
Here's the exact error from DBI. It might help you debug:
Unknown database 'test'

The correct syntax to run mytop instead is:

freebsd# mytop -u root -p 'secret_password' -d 'blog'

Or the longer more descriptive:

freebsd# mytop --user root --pass 'secret_password' --database 'blog'

By the way if you take a look at mytop's manual you will notice a tiny error in documentation, where the three options –user, –pass and –database are wrongly said to be used as -user, -pass, -database:

freebsd# mytop -user root -pass 'secret_password' -database 'blog'
Cannot connect to MySQL server. Please check the:

* database you specified "atabase" (default is "test")
* username you specified "ser" (default is "root")
* password you specified "ass" (default is "")
* hostname you specified "localhost" (default is "localhost")
* port you specified "3306" (default is 3306)
* socket you specified "" (default is "")a
...
Access denied for user 'ser'@'localhost' (using password: YES)

Actually it is interesting mytop, precededed historically mtop.
mtop was later written (probably based on mytop), to run on FreeBSD OS by a famous MySQL (IT) spec — Jeremy Zawodny .
Anyone who has to do frequent MySQL administration tasks, should already heard Zawodny's name.
For those who haven't, Jeremy used to be a head database administrators and developer in Yahoo! Inc. some few years ago.
His website contains plenty of interesting thoughts and writtings on MySQL server and database management
 

How to add a new MySQL user to have INSERT,UPDATE,DELETE permissions to a Database

Tuesday, October 25th, 2011

I needed to add a newly created MySQL user with no access to any database with no special permissions (user is created from phpmyadmin) with some permissions to a specific database which is used for the operation of a website, here are the MySQL CLI client commands I issued to make it work:

# mysql -u root -p
mysql> GRANT ALL ON Sql_User_DB.* TO Sql_User@localhost;
mysql> FLUSH PRIVILEGES;

Where in the Example Sql_User_DB is my example database to which the user is granted access and my sample user is Sql_User .
Note that without FLUSH PRIVILEGES; new privileges might not be active. 

To test further if all is fine login with Sql_User and try to list database tables.

$ mysql -u Sql_User -p
password:
mysql> USE Sql_User_DB;
mysql> SHOW TABLES;
...

How to get rid of “PHP Warning: PHP Startup: Unable to load dynamic library ‘/usr/lib/php5/20090626/suhosin.so'” on Debian GNU / Linux

Tuesday, October 25th, 2011

PHP-warning-how-to-fix-warnings-and-errors-php-logo

After a recent new Debian Squeeze Apache+PHP server install and moving a website from another server host running on CentOS 5.7 Linux server, some of the PHP scripts running via crontab started displaying the following annoying PHP Warnings :

debian:~# php /home/website/www/cron/update.php

PHP Warning: PHP Startup: Unable to load dynamic library '/usr/lib/php5/20090626/suhosin.so' – /usr/lib/php5/20090626/suhosin.so: cannot open shared object file: No such file or directory in Unknown on line 0

Obviously the error revealed that PHP cli is not happy that, I've previously removes the suhosin php5-suhosin module from the system.
I wouldn't have removed php5-suhosin if sometimes it doesn't produced some odd experiences with the Apache webserver.
To fix the PHP Warning, I used first grep to see, where exactly the suhosin module gets included in debian's php.ini config files. debian:~# cd /etc/php5
debian:/etc/php5# grep -rli suhosin *
apache2/conf.d/suhosin.ini
cgi/conf.d/suhosin.ini
cli/conf.d/suhosin.ini
conf.d/suhosin.ini

Yeah that's right Debian has three php.ini php config files. One for the php cli/usr/bin/php, another for the Apache webserver loaded php library/usr/lib/apache2/modules/libphp5.so and one for Apache's cgi module/usr/lib/apache2/modules/mod_fcgid.so .

I was too lazy to edit all the above found declarations trying to include the suhosin module in PHP, hence I remembered that probably all this obsolete suhosin module declaration are still present because probably the php5-suhosin package is still not purged from the system.

A quick check with dpkg , further strenthened my assumption as the php5-suhosin module was still hanging around as an (rc – remove candidate);

debian:~# dpkg -l |grep -i suhosin
rc php5-suhosin 0.9.32.1-1 advanced protection module for php5

Hence to remove the obsolete package config and directories completely out of the system and hence solve the PHP Warning I used dpkg –purge, like so:

debian:~# dpkg --purge php5-suhosin
(Reading database ... 76048 files and directories currently installed.)
Removing php5-suhosin ...
Purging configuration files for php5-suhosin ...
Processing triggers for libapache2-mod-php5 ...
Reloading web server config: apache2.

Further on to make sure the PHP Warning is solved I did the cron php script another go and it produced no longer errors:

debian:~# php /home/website/www/cron/update.php
debian:~#

How to change MySQL server root password

Friday, July 29th, 2011

MySQL pass dialog Debian

I had to change my mysql root password for one of the servers since during the install I mispasted the password in the MySQL password prompt I needed the pwd to be changed.

Here is how I changed it to my desired one:

linux:~# /usr/bin/mysqladmin -u root -p'OLD_PASSWORD_STRING' password NEW_PASSWORD_STRING
linux:~#

The password gets changed immediately 😉

If a new password has to be set to a passwordless mysql server, the command to be issued is:

linux:~# /usr/bin/mysqladmin -u root password PASSWORD_STRING

Changing the MySQL password is also possible with mysql cli, after connecting to the sql server, though this method is a bit more time consuming. Here is how to do it from mysql console:

linux:~# mysql -u root -p
Server version: 5.1.49-3 (Debian)

Copyright (c) 2000, 2010, Oracle and/or its affiliates. All rights reserved.
This software comes with ABSOLUTELY NO WARRANTY. This is free software,
and you are welcome to modify and redistribute it under the GPL v2 license

Type ‘help;’ or ‘h’ for help. Type ‘c’ to clear the current input statement.
mysql> use mysql;
mysql> update user set password=PASSWORD(“NEW_PASSWORD”) where User=’root’;mysql> flush privileges;

Of course it’s possible to do change the root pass via phpmyadmin
Cheers 😉