Recover MySQL /var/lib/mysql after update - mysql

I did an update from Mysql 5.5 to 8.0 in a Centos 6 server without dumping the databases to a .sql file, I just copied the /var/lib/mysql directory to another location.
Now if I try to load mysqld service it crashes.
Being naive I deleted all the content of /var/lib/mysql and installed the service again, now it runs but now I do not know how to manually import the DB files to the directory (copy & paste of the folder does not work) in order to do a check of the DB and/or repair it.

rysnc should likely already be installed, but if it isn't you would:
sudo yum install rsync
Then
#make sure mysql isn't running
sudo service mysqld stop
#double check that there is no MySQL PID running
sudo ps aux | grep mysql
#move the new MySQL 8.0 data files out of the way
sudo mv /var/lib/mysql /var/lib/mysql.bak
#copy the original data files back to /var/lib/mysql
#note that the trailing / is required for both paths
sudo rsync -av /path/to/original/mysql/db/files/ /var/lib/mysql/
#change user and group ownership to mysql
sudo chown -R mysql:mysql /var/lib/mysql
#start MySQL
sudo service mysqld start
#run mysql_upgrade, replace {usernamehere} with the actual username
sudo mysql_upgrade -u {usernamehere} -p
Update:
You will need to downgrade the binaries to 5.5. Take a backup of each database once MySQL is running again and then upgrade in the following order:
5.6
5.7
8.0
You will need to run mysql_upgrade after each upgrade.

Related

Installation of MySQL 5.7 issue on Centos 7-directory initialization issue

While installing MySQL 5.7 on centos7, I am struggling with the data directory initialization step:
bin/mysqld --initialize --user=mysql
I am getting an error as
bin/mysqld:Error on realpath on 'var\lib\mysql-files'
Failed to access directory for --secure-file-priv. Please make sure that directory exists and is accessible by MYSQL server.Supplied value : /var/lib/mysql-files
.
Please suggest.
As described in the MySQL documentation,
/var/lib/mysql-files is the (default) directory where mysql allows import/export operations to work only with files, and the directory MUST exist.
You could try either:
Make sure the directory exists and give access to mysql
sudo mkdir -p /var/lib/mysql-files
sudo chown -R mysql:mysql /var/lib/mysql-files
sudo chmod -R 770 /var/lib/mysql-files
Or:
Disable this option from my.cnf

MySQL community server suddenly stopped working [duplicate]

My problem started off with me not being able to log in as root any more on my mysql install. I was attempting to run mysql without passwords turned on... but whenever I ran the command
# mysqld_safe --skip-grant-tables &
I would never get the prompt back. I was trying to follow these instructions to recover the password.
The screen just looks like this:
root#jj-SFF-PC:/usr/bin# mysqld_safe --skip-grant-tables
120816 11:40:53 mysqld_safe Logging to syslog.
120816 11:40:53 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
and I don't get a prompt to start typing the SQL commands to reset the password.
When I kill it by pressing CTRL + C, I get the following message:
error: 'Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)'
Check that mysqld is running and that the socket: '/var/run/mysqld/mysqld.sock' exists!
If I retry the command and leave it long enough, I do get the following series of messages:
root#jj-SFF-PC:/run/mysqld# 120816 13:15:02 mysqld_safe Logging to syslog.
120816 13:15:02 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
120816 13:16:42 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
[1]+ Done mysqld_safe --skip-grant-tables
root#jj-SFF-PC:/run/mysqld#
But then if I try to log in as root by doing:
# mysql -u root
I get the following error message:
ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)
I checked and /var/run/mysqld/mysqld.sock file doesn't not exist. The folder does, but not the file.
Also, I don't know if this helps or not, but I ran find / -name mysqld and it came up with:
/var/run/mysqld - folder
/usr/sbin/mysqld - file
/run/mysqld - folder
I don't know if this is normal or not. But I'm including this info just in case it helps.
I finally decided to uninstall and reinstall mysql.
apt-get remove mysql-server
apt-get remove mysql-client
apt-get remove mysql-common
apt-get remove phpmyadmin
After reinstalling all packages again in the same order as above, during the phpmyadmin install, I got the same error:
ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)
So I tried again to uninstall/reinstall. This time, after I uninstalled the packages, I also manually renamed all mysql files and directories to mysql.bad in their respective locations.
/var/lib/mysql
/var/lib/mysql/mysql
/var/log/mysql
/usr/lib/perl5/DBD/mysql
/usr/lib/perl5/auto/DBD/mysql
/usr/lib/mysql
/usr/bin/mysql
/usr/share/mysql
/usr/share/dbconfig-common/internal/mysql
/etc/init.d/mysql
/etc/apparmor.d/abstractions/mysql
/etc/mysql
Then I tried to reinstall mysql-server and mysql-client again. But I've noticed that it doesn't prompt me for a password. Isn't it supposed to ask for an admin password?
Try this command,
sudo service mysql start
To find all socket files on your system run:
sudo find / -type s
My Mysql server system had the socket open at /var/lib/mysql/mysql.sock
Once you find where the socket is being opened, add or edit the line to your /etc/my.cnf file with the path to the socket file:
socket=/var/lib/mysql/mysql.sock
Sometimes the system startup script that launched the command line executable specifies a flag --socket=path. This flag could override the my.cnf location, and that would result in a socket not being found where the my.cnf file indicates it should be. Then when you try to run the mysql command line client, it will read my.cnf to find the socket, but it will not find it since it deviates from where the server created one. So, Unless you care where the socket resides, just changing the my.cnf to match should work.
Then, stop the mysqld process. How you do this will vary by system.
If you're super user in the linux system, try one of the following if you don't know the specific method your Mysql setup uses:
service mysqld stop
/etc/init.d/mysqld stop
mysqladmin -u root -p shutdown
Some systems aren't setup to have an elegant way to stop mysql (or for some reason mysql doesn't respond) and you can force terminate mysql with either:
One step: pkill -9 mysqld
Two step (least preferred):
Find the process id of mysql with either pgrep mysql or ps aux | grep mysql | grep -v grep
Assuming the process id is 4969 terminate with kill -9 4969
After you do this you might want to look for a pid file in /var/run/mysqld/ and delete it
Make sure the permissions on your socket is such that whatever user mysqld is running as can read/write to it. An easy test is to open it up to full read/write and see if it still works:
chmod 777 /var/run/mysqld/mysqld.sock
If that fixes the issue, you can tailor the permissions and ownership of the socket as needed based on your security settings.
Also, the directory the socket resides in has to be reachable by the user running the mysqld process.
This error occurs due to multiple installations of mysql.
Run the command:
ps -A|grep mysql
Kill the process by using:
sudo pkill mysql
and then run command:
ps -A|grep mysqld
Also Kill this process by running:
sudo pkill mysqld
Now you are fully set just run the following commands:
service mysql restart
mysql -u root -p
Have very well working mysql again
The solution is way easier.
First, you have to locate(in Terminal with "sudo find / -type s") where your mysql.sock file is located. In my case it was in /opt/lampp/var/mysql/mysql.sock
Fire up Terminal and issue
sudo Nautilus
This starts your Files manager with super user privileges
From Nautilus navigate to where your mysql.sock file is located
Right click on the file and select Make Link
Rename the Link File to mysqld.sock then Right click on the file and Cut it
Go to /var/run and create a folder called mysqld and enter it
Now right click and Paste the Link File
Voila! You will now have a mysqld.sock file at /var/run/mysqld/mysqld.sock :)
Just Need to Start MySQL Service after installation:
For Ubuntu:
sudo service mysql start;
For CentOS or RHEL:
sudo service mysqld start;
There is a bug on Ubuntu with MySQL 5.6 and 5.7 where var/run/mysqld/ would disappear whenever MySQL service stopped or is rebooted. This prevents MySQL from running at all. Found this workaround, which isn't perfect, but at least it gets it running after stopping/reboot:
mkdir /var/run/mysqld/
chown mysqld /var/run/mysqld/
Make sure your inaccessible socket file path is same as '/var/run/mysqld/mysqld.sock', otherwise change the path as yours.
Stop the mysqld
$ sudo /etc/init.d/mysqld stop
If the process still runing;
$ sudo pkill -9 mysqld
Remove the mysql directory where socket going to create. For me it did not allowed to remove, so I had to forcefully remove.
$ sudo mkdir -p /var/run/mysqld
Set the ownership to the dirctory
$ sudo chown mysql:mysql /var/run/mysqld
Start mysql
$ sudo /etc/init.d/mysql start
Trying to connect mysql
$ sudo mysql -u dbuser -p
Okay just copy and paste these codes: This should be done in the terminal, inside a server, when your mysql database is not properly installed, and when you are getting this error: 'Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)'.
Stop MySql
sudo /etc/init.d/mysqld stop
Restart it or start it
sudo /etc/init.d/mysqld restart or sudo /etc/init.d/mysqld start
Make a link like this and give it to the system
ln -s /tmp/mysql.sock /var/lib/mysql/mysql.sock
Run a secure installation which guides all the process you need to do to configure mysql
/usr/bin/mysql_secure_installation
I faced same error and found that it was due to upgradation of packages, So after restarting my system I resolved error.
I think due to sql libraries/ packages update that error occured, So try this if you are doing some upgrading :)
There is a lots of reason for this issue, but sometimes just restart the mysql server, it will fix the issue.
sudo service mysql restart
The answer of the user load step worked for me.
Sometimes is need edit the file in /etc/mysql/my.cnf add line to client
[client]
password = your_mysql_root_password
port = 3306
host = 127.0.0.1
socket = /var/lib/mysql/mysql.sock
Using XAMPP on ubuntu:
Create a folder called mysqld inside /var/run directory. You can accomplish that using the command sudo mkdir /var/run/mysqld.
Create a symbolic link to mysql.sock file that is created by the XAMPP server when it is started. You can use the command sudo ln -s /opt/lampp/var/mysql/mysql.sock /var/run/mysqld/mysqld.sock.
Note: The mysql.sock file is created when the server is started and removed when the server is stopped, so sometimes the link you created might appear to be broken but it should work as long as you have started the server using either sudo /opt/lampp/lampp start or any other means.
Start the server if it's not already running and try executing your program again.
Good luck! I hope you'll get away with it this time.
I think your MySQL server has not started. So start the server using one of the following commands.
#services mysql start
or
#/etc/init.d/mysql start
Why getting this error
I received new updates of mysql libraries so i updated my Kubuntu OS after that getting these errors.
Commands i tried and how i fixed it.
MySql-server is running correctly but when i tried to connect its giving
Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock'.
I checked /var/run/mysqld/mysqld.sock'. this directory.
My files did not existed.
I also tried these commands to connect but did not worked for me.
mysql -h 127.0.0.1 -P 3306 -u root -p
sudo service mysql start
After wasting round about 2 hours i found the solution
sudo apt-get clean
sudo apt-get update
sudo apt-get upgrade -f
After that everything fixed for me.
*Error: 'Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)'
solutions
finally uninstall and reinstall mysql. **
sudo apt-get remove mysql-server
sudo apt-get remove mysql-client
sudo apt-get remove mysql-common
sudo apt-get remove phpmyadmin
then install again by
sudo apt-get install mysql-server-5.6
After this operation, 164 MB of additional disk space will be used.
Do you want to continue? [Y/n] Y press YES for complete installations
......
.......
At last you will get these lines....
Setting up libhtml-template-perl (2.95-1) ...
Setting up mysql-common-5.6 (5.6.16-1~exp1) ...
Processing triggers for libc-bin (2.19-0ubuntu6)
Processing triggers for ureadahead (0.100.0-16) ...
And then
root#ubuntu1404:~# mysql -u root -p (for every password first u
should use )
Enter password:
Note :Entered password should be same as the installation time
password of mysql(like .root,system,admin,rahul etc...)
Then type
USE rahul_db(database name);
Thanks.**
Temporary Solution
Maybe someone facing this problem. I am using Mysql Workbench on Ubuntu 14 and got this error.
mysqldump: Got error: 2002: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2) when trying to connect
Find your socket file by running sudo find / -type s, in my case it was /run/mysqld/mysqld.sock
So, I just created a link to this file in tmp directory.
sudo ln -s /var/run/mysqld/mysqld.sock /tmp/mysql.sock
Please note that this is a temporary solution since the file created will be under /tmp. See other answers for a permanent solution.
ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)
in /etc/my.cnf add this lines:
[client]
socket=/var/lib/mysql/mysql.sock <= this path should be also same as is[mysqld]
And restart the service with:
service mysql restart
this worked for me
This was mentioned a couple of times already, but this worked immediately for me:
service mysql restart
you can find mysqld.sock in /var/run/mysqld if you have already installed mysql-server
by sudo apt-get install mysql-server
I just had this problem on Ubuntu 14.10
Turns that mysql-server was no longer installed (somehow it had been removed) but I couldn't just install it because there were some broken packages and dependency issues/conflicts.
In the end I had to reinstall mysql
sudo apt-get remove mysql-client
sudo apt-get install mysql-server
I had the exactly same issue. After struggling for an hour, I found a way of correcting it without reinstalling mysql-common, mysql-client, mysql-server.
First of all, go to "/var/run/mysqld". You will find that the mysql.sock does not exist. Simply remove the entire mysqld directory and recreate it and provide it necessary privileges.
# rm -rf /var/run/mysqld && mkdir /var/run/mysqld && chown mysql /var/run/mysqld/
Now, Kill the mysql process in it's entirety. It might be possible that it will show you "waiting for page cleaner" on running "/etc/init.d/mysql status" command even after shutting down the service.
To completely close the service, use
# pkill -9 mysqld
Once the process is killed, try starting it again using
# /etc/init.d/mysql start
And you will see that it works good! And also there will be no issue in stopping it too.
In My case two mysqld processes were running..
killed the optional processs by using
pkill -9 mysqld
If you have a lot of databases and tables on your system, and if you have innodb_file_per_table set in my.cnf, then your mysql server might have run out of opened objects / files (or rather the descriptors for these objects)
Set a new max number with
open-files-limit = 2048
and restart mysql.
This approach might help when the socket is not created at all, but really this might not not be the real problem, there is an underlying problem.
My solution;
Ubuntu 18.04 (WSL)
/etc/mysql/my.cnf
!includedir /etc/mysql/conf.d/
!includedir /etc/mysql/mysql.conf.d/
/etc/mysql/mysql.conf.d/mysqld.cnf
[mysqld]
user = mysql
pid-file = /var/run/mysqld/mysqld.pid
socket = /var/run/mysqld/mysqld.sock
port = 3306
I changed the port. It's worked for me. You can write another port. Example 3355
I am using XAMPP on Ubuntu. I found this error when connecting database through terminal. I solve it without any configuration because default socket file path in XAMPP is written in "/opt/lampp/etc/my.cnf" as following:
[client]
#password = your_password
port = 3306
socket = /opt/lampp/var/mysql/mysql.sock
now you can connect just by giving this socket path parameter with mysql command on terminal like:
mysql -u root --socket /opt/lampp/var/mysql/mysql.sock
and it's done without any configuration.
If you don't want to type socket path everytime, then go for changing default path in my.cnf by "/var/run/mysqld/mysqld.sock". Provide permissions and restart mysql server.
Edit:
Recently I've installed Ubuntu 20.04 and trying to install MySQL server but my system were crashing and not working at all. So I've just completely removed MySQL and installed MariaDB. Its working like a charm without any problems.
Changing the host to 127.0.0.1 worked for me.
Edit the file in /etc/mysql/my.cnf and add the below mentioned line to the section: client
[client]
port = 3306
host = 127.0.0.1
socket = /var/lib/mysql/mysql.sock
After you are done with it. Execute the following command.
sudo service mysql start
I had similar problem on a CentOS VPS. If MySQL won't start or keeps crashing right after it starts, try these steps:
1) Find my.cnf file (mine was located in /etc/my.cnf) and add the line:
innodb_force_recovery = X
replacing X with a number from 1 to 6, starting from 1 and then incrementing if MySQL won't start. Setting to 4, 5 or 6 can delete your data so be carefull and read http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html before.
2) Restart MySQL service. Only SELECT will run and that's normal at this point.
3) Dump all your databases/schemas with mysqldump one by one, do not compress the dumps because you'd have to uncompress them later anyway.
4) Move (or delete!) only the bd's directories inside /var/lib/mysql, preserving the individual files in the root.
5) Stop MySQL and then uncomment the line added in 1). Start MySQL.
6) Recover all bd's dumped in 3).
Good luck!
I uninstalled mysql in Ubuntu 16.04 https://askubuntu.com/questions/172514/how-do-i-uninstall-mysql
I reinstalled mysql
https://www.digitalocean.com/community/tutorials/how-to-install-mysql-on-ubuntu-16-04
This seemed to work.
First create dir /var/run/mysqld
with command:
mkdir -p /var/run/mysqld
then add rigths to the dir
chown mysql:mysql /var/run/mysqld
after this try
mysql -u root
You must install mysql-server
apt install mysql-server

How to create mysql volume which exists even if i remove the docker container

I created docker container with mysql using -v option:
-v /storage/mysql1/mysql-datadir:/var/lib/mysql
When i removed container i lost database saved in /var/lib/mysql .
How can i create mysql container with -v option (to see everything from the host) and not lost the data?
Have you tried restarting the mysql service in your host?
This is something like restoring MYSQL db from physical file.
When you perform db operations inside container, it saves real-data and indexes in /var/lib/mysql path or the path that you specify while installing.
But, for Host machine, MYSQL service still does not know about the change.
Restart the MYSQL service by service mysql restart.
Additionally check the owner and permission in the MYSQL data folder like below:
sudo chown -R mysql:mysql /var/lib/mysql
sudo chmod -R 660 /var/lib/mysql/
sudo chown -R mysql.mysql /var/log/mysql
While running container, mount /var/log/mysql as well along with data folder.

MySQL Job failed to start

I'm on Kubuntu 12.04, and after installing mysql via an apt-get (mysql ver: 5.5.35), i'm trying to start mysql service, but I got this error:
sudo service mysql start
start: Job failed to start
So I googled this problem, it says i have to go to the /var/log/mysql/error.log
But my error.log file is empty :(
Then I checked the permissions
:
drwxr-s--- 2 mysql adm 4096 Apr 7 11:21 mysql
-rw-r----- 1 mysql adm 0 Apr 7 11:21 error.log
So I don't know what to do... Why this error ? Why is the error file empty ?
First make a backup of your /var/lib/mysql/ directory just to be safe.
sudo mkdir /home/<your username>/mysql/
cd /var/lib/mysql/
sudo cp * /home/<your username>/mysql/ -R
Next purge MySQL (this will remove php5-mysql and phpmyadmin as well as a number of other libraries so be prepared to re-install some items after this.
sudo apt-get purge mysql-server-5.1 mysql-common
Remove the folder /etc/mysql/ and it's contents
sudo rm /etc/mysql/ -R
Next check that your old database files are still in /var/lib/mysql/ if they are not then copy them back in to the folder then chown root:root
(only run these if the files are no longer there)
sudo mkdir /var/lib/mysql/
sudo chown root:root /var/lib/mysql/ -R
cd ~/mysql/
sudo cp * /var/lib/mysql/ -R
Next install mysql server
sudo apt-get install mysql-server
Finally re-install any missing packages like phpmyadmin and php5-mysql.
My problem was running out of memory. Digital ocean has great instruction for adding swap memory for Ubuntu: https://www.digitalocean.com/community/tutorials/how-to-add-swap-on-ubuntu-14-04
This solved the issue and enabled me to restart the Mysql that otherwise would not start.
Reinstallation will works because it will reset all the value to default. It is better to find what the real culprits (my.cnf editing mistake does happens, e.g. bad/outdated parameter suggestion during mysql tuning.)
Here is the mysql diagnosis if you suspect some value is wrong inside my.cnf : Run the mysqld to show you the results.
sudo -u mysql mysqld
Afterwards, fix all the my.cnf key error that pop out from the screen until mysqld startup successfully.
Then restart it using
sudo service mysql restart
In my case, it simply because the disk is full.
Just clear some disk space and restart and everything is fine.
In most cases, just purging the mysql-server package and re-installing it will do the job.
Run,
sudo apt-get purge mysql-server-5.1 mysql-common
followed by
sudo apt-get install mysql-server
This line did solve the issue in my case,
sudo apt clean
In my case, i do:
sudo nano /etc/mysql/my.cnf
search for bind names and IPs
remove the specific, and let only localhost 127.0.0.1 and the hostname
Check the file permissions, if edited
Fail:
$ sudo chmod 776 /etc/mysql/my.cnf
$ sudo service mysql restart
mysql stop/waiting
start: Job failed to start
Ok:
$ sudo chmod 774 /etc/mysql/my.cnf
$ sudo service mysql restart
stop: Unknown instance:
mysql start/running, process 9564
To help others who do not have a full disk to troubleshoot this problem, first inspect your error log (for me the path is given in my /etc/mysql/my.cnf file):
tail /var/log/mysql/error.log
My problem turned out to be a new IP address allocated after some network router reconfiguration, so I needed to change the bind-address variable.
In my case the problem was the /var/log disk full (check with df -h)
Just deleted some log files and mysql started, no big deal!
The given solution requires enough free HDD, the actual problem was the HDD memory shortage. So If you don't have an alternative server or free disk space, you need some other alternative.
I faced this error with my production server (Linode VPS) when I was running a bulk download into MySQL. Its not a proper solution but VERY QUICK FIX, which we often need in production to bring things UP FAST.
Resize our VPS Server to higher Hard Disk size
Start MySQL, it works.
Login to your MySQL instance and make appropriate adjustments that caused this error (e.g. remove some records, table, or take DB backup to your local machine that are not required at production, etc. After all you know, what caused this issue.)
Downgrade your VPS Server to previous package you was already using
In my case:
restart server
restart mysql
create .socket in directory
I had the same problem. But i discover that my hd is full.
$ sudo cat /var/log/upstart/mysql.log
/proc/self/fd/9: ERROR: The partition with /var/lib/mysql is too full!
So, I run
$ df -h
And I got the message
/dev/xvda1 7.8G 7.4G 0 100% /
Then I found out which folder was full by running the following command on the terminal
$ cd /var/www
$ for i in *; do echo $i; find $i |wc -l; done
This give me the number of files on each folder on /var/www. I logged into the folder with most files, and deleted some backup files, and i continued deleting useless files and cache files.
then I run $ sudo /etc/init.d/mysql start and it work again

MySQL Start Error

I am trying to install MySQL 5.6.17 on Ubuntu Linux and I am having difficulties doing so. I opened the MySQL Reference and opened "Installing MySQL on Unix/Linux Using Generic Binaries". I followed the following step:
shell> groupadd mysql
shell> useradd -r -g mysql mysql
shell> cd /usr/local
shell> tar zxvf /path/to/mysql-VERSION-OS.tar.gz
shell> ln -s full-path-to-mysql-VERSION-OS mysql
shell> cd mysql
shell> chown -R mysql .
shell> chgrp -R mysql .
shell> scripts/mysql_install_db --user=mysql
shell> chown -R root .
shell> chown -R mysql data
shell> bin/mysqld_safe --user=mysql &
//Next command is optional
shell> cp support-files/mysql.server /etc/init.d/mysql.server
After that when I try to start MySQL using /etc/init.d/mysql.server start I get the following error:
Couldn't find MySQL server (/usr/bin/mysqld_safe)
I looked in /usr/bin and I found mysqld_safe. Any suggestions on how to fix that problem. Please reply with a detailed solution.
Thank You
It seems you have installed Mysql in "/usr/local" and init script is looking for binaries in "/usr"
Change the "basedir" in /etc/init.d/mysql.server to :
basedir=/usr/local
The fact that you found /usr/bin/mysqld_safe suggests that MySQL in some shape or form was preinstalled on your OS. This can cause some confusion, in particular due to location of config files.
So for instance, on some versions of Ubuntu, the packages mysql-common is pre-installed, which means you might have an /etc/mysql/my.conf file with some defaults in it. When you install from the tar file to /usr/local, follow the INSTALL-BINARIES (or equivalent) instructions, and try to start /etc/init.d/mysql.server start you might get errors as the one you report ("Couldn't find MySQL server (/usr/bin/mysqld_safe)"), because the default configuration in /etc/init.d/mysql.server and any /etc/my.cnf that you created (optional step during install) is getting over-ridden by a setting in the OS installed /etc/mysql/my.conf. Note that this might happen even if you change the values in /etc/init.d/mysql.server and/or /etc/my.cnf.
One way out is to merge /etc/my.cnf and /etc/mysql/my.cnf into a single file at one of these locations, with the correct defaults that you wish to use.