I've successfully configured my Ubuntu server so MySQL can use hugepages. Problem is when I want to enable memlock option in my.cnf and /proc/sys/vm/hugetlb_shm_group is set to another group (MySQL is a member of this group).
# uname -a
Linux hostname 3.13.0-32-generic #57~precise1-Ubuntu SMP Tue Jul 15 03:51:20 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
# mysqld --version
mysqld Ver 5.5.53-0ubuntu0.12.04.1 for debian-linux-gnu on x86_64 ((Ubuntu))
# egrep ^Huge /proc/meminfo
HugePages_Total: 15000
HugePages_Free: 15000
HugePages_Rsvd: 0
HugePages_Surp: 0
# id mysql
uid=107(mysql) gid=113(mysql) groups=113(mysql),117(hugetlb)
If /proc/sys/vm/hugetlb_shm_group is set to 113 everything goes well no matter of memlock option.
But if I set /proc/sys/vm/hugetlb_shm_group to 117 it works only without the memlock option. If I enable it I get this error when MySQL starts:
InnoDB: HugeTLB: Warning: Failed to allocate 21978152960 bytes. errno 1
InnoDB HugeTLB: Warning: Using conventional memory pool
Any idea what can be wrong?
Turned out to be a problem with ulimit. Settings in /etc/security/limits.conf are ignored so I got it working with simple edit in /etc/init/mysql.conf:
exec /usr/bin/mysqld
changed to
script
ulimit -l unlimited
/usr/bin/mysqld
end script
Related
I am running a MariaDB server on my Ubuntu machine mysql Ver 15.1 Distrib 10.1.44-MariaDB, for debian-linux-gnu (x86_64) using readline 5.2. When trying to create a new table in a custom datadir with DATA DIRECTORY='/home/myuser/ext', the MySQL error log tells me
7f70acb77700 InnoDB: Operating system error number 13 in a file operation.
InnoDB: The error means mysqld does not have the access rights to
InnoDB: the directory.
mysqld is running as mysql user:
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
30450 mysql 20 0 695572 206208 16432 S 0,0 1,3 0:43.48 mysqld
data directory is owned by mysql user:
$ ls -l
drwxr-xr-x 4 mysql mysql 4096 Feb 13 11:16 ext
ownership and permissons on original datadir:
$ ll /var/lib/mysql/
total 1355856
drwxr-xr-x 7 mysql mysql 4096 Feb 13 12:00 ./
apparmor apparently is not intefering. content of /etc/apparmor.d/usr.sbin.mysqld
# This file is intensionally empty to disable apparmor by default for newer
# versions of MariaDB, while providing seamless upgrade from older versions
# and from mysql, where apparmor is used.
#
# By default, we do not want to have any apparmor profile for the MariaDB
# server. It does not provide much useful functionality/security, and causes
# several problems for users who often are not even aware that apparmor
# exists and runs on their system.
#
# Users can modify and maintain their own profile, and in this case it will
# be used.
#
# When upgrading from previous version, users who modified the profile
# will be promptet to keep or discard it, while for default installs
# we will automatically disable the profile.
/etc/apparmor.d/local/usr.sbin.mysqld is nonexistent.
I am out of ideas here... What else could it be?
I am on Mac 10.11.3 (15D21)
About Docker I have:
$ docker version
Client:
Version: 1.10.3
API version: 1.22
Go version: go1.5.3
Git commit: 20f81dd
Built: Thu Mar 10 21:49:11 2016
OS/Arch: darwin/amd64
Server:
Version: 1.10.3
API version: 1.22
Go version: go1.5.3
Git commit: 20f81dd
Built: Thu Mar 10 21:49:11 2016
OS/Arch: linux/amd64
For Mysql
$ docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
mysql latest 7a5866c2edbf 12 days ago 361.3 MB
...
I did the following:
mkdir -p /Users/me/docker/mysql/data
chmod -R 777 /Users/me/docker/mysql/data
(Even with sudo for each command)
It from Pro Docker and from: Permission denied when mounting Docker volume in OSX
Even doing:
docker -v /Users/me/docker/mysql/data:/var/lib/mysql mysql chown -R mysql /var/lib/mysql
It from: Database Fails to Start - Host Directory as a Data Volume
When I execute: (showing in multiple lines for better visualisation)
docker run -v /Users/me/docker/mysql/data:/var/lib/mysql --name manolitomysql
-e MYSQL_DATABASE='mysqldb' -e MYSQL_USER='mysql' -e MYSQL_PASSWORD='mysql'
-e MYSQL_ALLOW_EMPTY_PASSWORD='yes' -e MYSQL_ROOT_PASSWORD='' -d mysql
I always get:
$ docker logs manolitomysql
Initializing database
2016-03-27T16:04:33.520170Z 0 [Warning] Setting lower_case_table_names=2 because file system for /var/lib/mysql/ is case insensitive
2016-03-27T16:04:35.089907Z 0 [ERROR] InnoDB: Operating system error number 13 in a file operation.
2016-03-27T16:04:35.090006Z 0 [ERROR] InnoDB: The error means mysqld does not have the access rights to the directory.
2016-03-27 16:04:35 0x7f061a050740 InnoDB: Assertion failure in thread 139664183068480 in file fil0fil.cc line 868
InnoDB: Failing assertion: success
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
16:04:35 UTC - mysqld got signal 6 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
Attempting to collect some information that could help diagnose the problem.
As this is a crash and something is definitely wrong, the information
collection process might fail.
key_buffer_size=8388608
read_buffer_size=131072
max_used_connections=0
max_threads=151
thread_count=0
connection_count=0
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 68188 K bytes of memory
Hope that's ok; if not, decrease some variables in the equation.
Thread pointer: 0x0
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 0 thread_stack 0x40000
mysqld(my_print_stacktrace+0x2c)[0xe57c7c]
mysqld(handle_fatal_signal+0x459)[0x7896b9]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xf8d0)[0x7f0619c2d8d0]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37)[0x7f061841b067]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x148)[0x7f061841c448]
mysqld[0x75fc29]
mysqld[0x1180f68]
mysqld(_Z40fil_open_log_and_system_tablespace_filesv+0xe4)[0x1185a74]
mysqld[0x107afe0]
mysqld(_Z34innobase_start_or_create_for_mysqlv+0x3692)[0x107eb12]
mysqld[0xf4a05d]
mysqld(_Z24ha_initialize_handlertonP13st_plugin_int+0x51)[0x7d3981]
mysqld[0xc53716]
mysqld(_Z11plugin_initPiPPci+0x5c8)[0xc5a5c8]
mysqld[0x782164]
mysqld(_Z11mysqld_mainiPPc+0x7b2)[0x7835d2]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f0618407b45]
mysqld[0x77a274]
The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains
information that should help you find out what is causing the crash.
What extra configuration is need it?
For the audience, the following works:
1 Create a Dockerfile with
FROM mysql:latest
RUN deluser mysql
RUN useradd mysql
RUN mkdir -p /Users/me/docker/mysql/data
RUN chmod -R 777 /Users/me/docker/mysql/data
2 Create a new image using the previous Dockerfile
3 Run your new container using the previous new image
You may have better control using a Dockerfile with the following instructions:
RUN useradd mysql
RUN mkdir /var/lib/mysql && chown -R mysql:mysql /var/lib/mysql
I tried that restarting EC2 instance and sudo service httpd restart.
But I still get this message:
[ec2-user#ip-* ~]$ sudo service mysqld start
MySQL Daemon failed to start.
Starting mysqld: [FAILED]
Also I get this message:
[ec2-user#ip-* ~]$ mysqld
160127 7:01:48 [Note] mysqld (mysqld 5.5.46) starting as process 2745 ...
160127 7:01:48 [Warning] Can't create test file /var/lib/mysql/ip-*.lower-test
160127 7:01:48 [Warning] Can't create test file /var/lib/mysql/ip-*.lower-test
160127 7:01:48 [Note] Plugin 'FEDERATED' is disabled.
mysqld: Can't find file: './mysql/plugin.frm' (errno: 13)
160127 7:01:48 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
160127 7:01:48 InnoDB: The InnoDB memory heap is disabled
160127 7:01:48 InnoDB: Mutexes and rw_locks use GCC atomic builtins
160127 7:01:48 InnoDB: Compressed tables use zlib 1.2.8
160127 7:01:48 InnoDB: Using Linux native AIO
160127 7:01:48 InnoDB: Initializing buffer pool, size = 128.0M
160127 7:01:48 InnoDB: Completed initialization of buffer pool
160127 7:01:48 InnoDB: Operating system error number 13 in a file operation.
InnoDB: The error means mysqld does not have the access rights to
InnoDB: the directory.
InnoDB: File name ./ibdata1
InnoDB: File operation call: 'open'.
InnoDB: Cannot continue operation.
I don't know what should I do..
Cheers!
EDIT
(+ I'm also using amazon RDS.)
Now, I tried sudo chown -R mysql:mysql /var/lib/mysql too.
But
[ec2-user#ip-* ~]$ mysql_upgrade
Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
FATAL ERROR: Upgrade failed
[ec2-user#ip-* ~]$ ls -lh /var/lib/mysql/
합계 29M
-rw-rw---- 1 mysql mysql 5.0M 1월 27 06:52 ib_logfile0
-rw-rw---- 1 mysql mysql 5.0M 1월 27 06:12 ib_logfile1
-rw-rw---- 1 mysql mysql 18M 1월 27 06:52 ibdata1
drwx------ 2 mysql mysql 4.0K 1월 20 07:03 mysql
drwx------ 2 mysql mysql 4.0K 1월 20 07:03 performance_schema
drwx------ 2 mysql mysql 4.0K 1월 20 07:03 test
As per today the nano instances with 0.5GiB memory do not allow running mysqld - they do not have enough memory. Running a micro instance with 1GiB memory fixes the problem completely. I think guys at AWS should have made a note about this in the LAMP installation instructions, as this research costed me several hours or even a day before I figured it out.
I answer myself to my question to help other people in the same problem.
I resolved this problem from these steps:
Restart your EC2 instance.
Type sudo service httpd restart. (I don't know why I should do these two steps.)
Type sudo chown -R mysql:mysql /var/lib/mysql. - Before typing this command, check your user= option in your /etc/my.cnf. If there is no user= option, your user is "mysql". (Visit https://stackoverflow.com/a/21435052/1570534)
Change the innodb_buffer_pool_size option inside /etc/my.cnf from 128 (can be different) to 500M. If you don't have innodb_buffer_pool_size option in your /etc/my.cnf, add innodb_buffer_pool_size=500M in [mysqld] section.
I hope it helps you!
I also faced the same issue when setting up an instance on Lightsail with the lowest cost instance (512MB, 1 vCPU, 20 GB SSD).
I was able to solve the issue by adding a swap file in the instance.
Here is the step to create a swap:
Use the dd command to create a swap file on the root file system, where "bs" is the block size and "count" is the number of blocks. In this example the swap file is 1 GB:
$ sudo dd if=/dev/zero of=/swapfile bs=1M count=1000
Update the read and write permissions for the swap file:
$ chmod 600 /swapfile
Set up a Linux swap area:
$ mkswap /swapfile
Make the swap file available for immediate use by adding the swap file to swap space:
$ swapon /swapfile
Verify that the procedure was successful:
$ swapon -s
Enable the swap file at boot time by editing the /etc/fstab file:
$ vi /etc/fstab
$ /swapfile swap swap defaults 0 0
If the issue is in Amazon Linux OS, please check whether you have free swap.
I faced the same issue, when I add more swap, mysql service start working.
You can see more from here http://www.linuxblackmagic.com/2018/04/mysql-daemon-failed-to-start-in-amazon.html
This will surely work for you.
Shivin Vijai
I had this problem, similar to #Michael Zelensky, when I tried to make use of an Amazon t3.nano machine. (FWIW t3.micro needed no extra adjustments on my end, but I was trying to see "how low could I go" )
I was able to find a workaround that seems to be working for now. Simply add:
table_definition_cache=400
.. to the [mysqld] section in /etc/my.cnf . This apparently lowered some of the memory usage enough to allow me to then perform a service mysqld start and the service came up (along with my Wordpress websites :) )
Thanks to some AWS support specialists and also this website for helping me figure this out: http://www.tocker.ca/2014/03/10/configuring-mysql-to-use-minimal-memory.html
I'm having an issue where MySQL 5.1.54 is restarting every 30 minutes on Ubuntu 11.04. When this occurs, the following appears in the MySQL log:
111030 12:01:52 [Note] /usr/sbin/mysqld: Normal shutdown
111030 12:01:52 [Note] Event Scheduler: Purging the queue. 0 events
111030 12:01:52 InnoDB: Starting shutdown...
111030 12:01:54 InnoDB: Shutdown completed; log sequence number 0 875122
111030 12:01:54 [Note] /usr/sbin/mysqld: Shutdown complete
111030 12:01:55 [Note] Plugin 'FEDERATED' is disabled.
111030 12:01:55 InnoDB: Initializing buffer pool, size = 256.0M
111030 12:01:55 InnoDB: Completed initialization of buffer pool
111030 12:01:55 InnoDB: Started; log sequence number 0 875122
111030 12:01:55 [Note] Event Scheduler: Loaded 0 events
111030 12:01:55 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.1.54-1ubuntu4-log' socket: '/var/run/mysqld/mysqld.sock' port: 3306 (Ubuntu)
This occurs like clockwork every 30 minutes, so it's obviously some service restarting it.
I have checked the crontab of every user on the system (including system users), and none of them have a crontab setup, as you can see in the output below:
# awk -F: '{print $1}' /etc/passwd | xargs -n 1 -i crontab -u {} -l
no crontab for root
no crontab for daemon
no crontab for bin
no crontab for sys
no crontab for sync
no crontab for games
no crontab for man
no crontab for lp
no crontab for mail
no crontab for news
no crontab for uucp
no crontab for proxy
no crontab for www-data
no crontab for backup
no crontab for list
no crontab for irc
no crontab for gnats
no crontab for nobody
no crontab for libuuid
no crontab for syslog
no crontab for sshd
no crontab for landscape
no crontab for ubuntu
no crontab for statd
no crontab for myproxy
no crontab for condor
no crontab for messagebus
no crontab for avahi
no crontab for joe
no crontab for smmta
no crontab for smmsp
no crontab for postfix
no crontab for deploy
no crontab for mysql
no crontab for redis
My dmesg contains the following each time it is restarted. I'm not an apparmor expert, but I believe this is a normal message obtained each time the MySQL service starts:
[1165328.780405] type=1400 audit(1319976114.984:74): apparmor="STATUS" operation="profile_replace" name="/usr/sbin/mysqld" pid=31985 comm="apparmor_parser"
Also, here are the contents of the MySQL upstart configuration in /etc/init/mysql.conf:
# MySQL Service
description "MySQL Server"
author "Mario Limonciello <superm1#ubuntu.com>"
start on (net-device-up
and local-filesystems
and runlevel [2345])
stop on runlevel [016]
respawn
env HOME=/etc/mysql
umask 007
# The default of 5 seconds is too low for mysql which needs to flush buffers
kill timeout 300
pre-start script
#Sanity checks
[ -r $HOME/my.cnf ]
[ -d /var/run/mysqld ] || install -m 755 -o mysql -g root -d /var/run/mysqld
/lib/init/apparmor-profile-load usr.sbin.mysqld
LC_ALL=C BLOCKSIZE= df --portability /var/lib/mysql/. | tail -n 1 | awk '{ exit ($4<4096) }'
end script
exec /usr/sbin/mysqld
post-start script
for i in `seq 1 30` ; do
/usr/bin/mysqladmin --defaults-file="${HOME}"/debian.cnf ping && {
exec "${HOME}"/debian-start
# should not reach this line
exit 2
}
sleep 1
done
exit 1
end script
Any idea what might be causing this? It doesn't cause any problems, other than Monit alerts stating that "PID changed Service mysqld" (I have Monit monitoring mysqld -- but it reports no errors with the mysqld process, other than the fact that every 30 minutes, it has its PID changed since MySQL is restarted).
Thanks in advance.
are you using chef or puppet, which might be doing something that triggers the reboot?
can you check (and probably post) the definition of your mysql job in upstart? (/etc/init/mysql.conf). OK = try removing the "respawn". It does not work as documented in the upstart documentation. Generally it's used to respawn the process if it's killed by other process, but it seems it does not function as expected. You can see why the apparmour is always loading - because of the pre-start stanza in the script.
As upstart is very new, and is still evolving, better is to use the SysV way.
You should try to run it without AppArmor: just run /usr/bin/mysqld_safe or /usr/bin/mysqld without using upstart and wait 30 minutes. If mysql does not auto-restart, then disable AppArmor in the /etc/init/mysql.conf file, or configure it differently.
If the problem is still there, read mysql's log. If the log is not enabled by default, you can use the option --log-error=/tmp/mysql.log --log-warnings when launching mysqld.
Seems converting the /etc/init.d/mysql start up script to sysV style rather than as an upstart script seemed to correct the problem for me.
I had this same problem upgrading to Ubuntu 14.04. I found this question because it mentions the AppArmor log message, so thanks! I may not have realised MySQL was restarting otherwise.
Upon investigating /var/log/daemon.log, I found the output of /etc/mysql/debian-start appearing repeatedly. The relevant part was this:
May 18 06:48:18 tom /etc/mysql/debian-start[15525]: Upgrading MySQL tables if necessary.
May 18 06:48:18 tom /etc/mysql/debian-start[15528]: /usr/bin/mysql_upgrade: the '--basedir' option is always ignored
May 18 06:48:18 tom /etc/mysql/debian-start[15528]: Looking for 'mysql' as: /usr/bin/mysql
May 18 06:48:18 tom /etc/mysql/debian-start[15528]: Looking for 'mysqlcheck' as: /usr/bin/mysqlcheck
May 18 06:48:18 tom /etc/mysql/debian-start[15528]: Error: Server version (5.5.35-1ubuntu1) does not match with the version of
May 18 06:48:18 tom /etc/mysql/debian-start[15528]: the server (5.5.37) with which this program was built/distributed. You can
May 18 06:48:18 tom /etc/mysql/debian-start[15528]: use --skip-version-check to skip this check.
May 18 06:48:18 tom /etc/mysql/debian-start[15528]: FATAL ERROR: Upgrade failed
I read through the /etc/mysql/debian-start script and tried running the upgrade command as in the script, hoping to debug it (MySQL server needs to be running at the time):
/usr/bin/mysql_upgrade --defaults-extra-file=/etc/mysql/debian.cnf
I then found that this worked without complaint and everything simply worked from that point onward. I don't know why it was failing in the first place, but that seemed to fix it. MySQL hasn't restarted itself since.
I've installed MySQL on my personal/development machine using the .dmg package, according to the instructions here: http://dev.mysql.com/doc/refman/5.5/en/macosx-installation-pkg.html including installing the startup item and the preferences pane. And yet, I can't seem to use MySQL at all.
running:
/Library/StartupItems/MySQLCOM/MySQLCOM start
or
/Library/StartupItems/MySQLCOM/MySQLCOM restart
"appears" to work -- in that, it gives me a message like "Starting MySQL database server" -- but afterward, I still can't go into mysql at the command-line, or connect to it in a Rails 2.3.8 application running in script/server. I get the error denoted in the question title.
Also, the MySQL preferences pane doesn't seem to work either. If I click the "Start MySQL Server" button, I'm asked for my password, but then nothing happens -- the pane continues to say that the server is stopped.
(I believe I had a MacPorts version of MySQL installed previously, and it's also possible that there was one built from source at some time in the past -- but I'm reasonably sure I've uninstalled these and deleted all the files having to do with it that I could find.)
I'm also trying mysqld start in terminal. here's the output:
110127 15:40:28 [Warning] Can't create test file /usr/local/mysql-5.5.8-osx10.6-x86_64/data/Lucky-Charm.lower-test
110127 15:40:28 [Warning] Can't create test file /usr/local/mysql-5.5.8-osx10.6-x86_64/data/Lucky-Charm.lower-test
110127 15:40:28 [Note] Plugin 'FEDERATED' is disabled.
mysqld: Can't find file: './mysql/plugin.frm' (errno: 13)
110127 15:40:28 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
InnoDB: The InnoDB memory heap is disabled
InnoDB: Mutexes and rw_locks use GCC atomic builtins
InnoDB: Compressed tables use zlib 1.2.3
110127 15:40:28 InnoDB: Initializing buffer pool, size = 128.0M
110127 15:40:28 InnoDB: Completed initialization of buffer pool
110127 15:40:28 InnoDB: Operating system error number 13 in a file operation.
InnoDB: The error means mysqld does not have the access rights to
InnoDB: the directory.
InnoDB: File name ./ibdata1
InnoDB: File operation call: 'open'.
InnoDB: Cannot continue operation.
Tried following the message about running mysql_upgrade but that just gives me my original error again.
UPDATE:
OK I've been pursuing the theory that it's a permissions problem. Seeing that the datadir was owned by root, I chown -R it to _mysql. In response to Mike, here's where that now stands:
$ ls -al /usr/local/mysql-5.5.8-osx10.6-x86_64
total 296
drwxr-xr-x 16 root wheel 544 Dec 3 12:53 .
drwxrwxr-x 12 root staff 408 Jan 27 14:38 ..
-rw-r--r-- 1 root wheel 17987 Dec 3 11:58 COPYING
-rw-r--r-- 1 root wheel 12388 Dec 3 11:58 INSTALL-BINARY
-rw-r--r-- 1 root wheel 113534 Dec 3 11:58 README
drwxr-xr-x 44 root wheel 1496 Dec 3 12:53 bin
drwxr-xr-x 9 _mysql wheel 306 Jan 27 16:46 data
drwxr-xr-x 4 root wheel 136 Dec 3 12:53 docs
drwxr-xr-x 47 root wheel 1598 Dec 3 12:53 include
drwxr-xr-x 12 root wheel 408 Jan 27 14:38 lib
drwxr-xr-x 4 root wheel 136 Dec 3 12:53 man
drwxr-xr-x 19 root wheel 646 Jan 27 14:38 mysql-test
drwxr-xr-x 3 root wheel 102 Dec 3 12:53 scripts
drwxr-xr-x 32 root wheel 1088 Dec 3 12:53 share
drwxr-xr-x 28 root wheel 952 Dec 3 12:53 sql-bench
drwxr-xr-x 16 root wheel 544 Dec 3 12:53 support-files
I was trying to do mysqld start in the Terminal because it was the only thing giving me anything that seemed like meaningful error message output (see https://gist.github.com/799436) but I'm told by folks in #mysql that that's not intended to be run directly (and if I try sudo mysqld start i get a message bitching me out for trying to run mysql as root).
I seem to have something working now: mysqld_safe & successfully gets a MySQL server running. What still doesn't work is the "normal" method of starting up the server (the Startup Item or Preferences Pane)
... leading someone in #mysql to tell me that apparently MySQL is fine, it's the startup item that's borked.
Ok there were several things, mostly having to do with permissions/ownership, that were tried to make the binary-installed MySQL work nicely.
You may need to make sure that the startup item is owned by root:
sudo chown -R root:wheel /Library/StartupItems/MySQLCOM
Maybe you need a /etc/my.cnf file with this in it:
[mysqld]
socket=/tmp/mysql.sock
datadir=/usr/local/mysql/data
You might need to fill in these variables in /usr/local/mysql/support-files/mysql.server (the line will be there with blank values):
basedir=/usr/local/mysql
datadir=/usr/local/mysql/data
(see can't start MySql in Mac OS 10.6 Snow Leopard regarding the above)
That may be enough to do it, but if not, try making sure the mysql user (_mysql) can write to the data directory (owns it and has write permissions to everything in it).
Anyway, now the Preferences Panel and Startup Item actually seem to work for me.
After going over this a second time on another machine, I've made some edits and removed some unnecessary bit from what I answered yesterday.
Overall here's what I suggest you do to get the binary-installed MySQL working nice in OSX 10.6. Warning, you might end up deleting any databases you already had in the first couple steps, but as this is intended to be for your development machine, that shouldn't be any big deal. Back stuff up with mysqldump first if you must.
Make sure you don't have a mysql server running right now: ps aux | grep mysql will show you their processes. Stop it with mysqladmin shutdown or if that won't work because something is borked, sudo kill the process numbers.
Remove any prior installed versions of mysql -- check port list installed, check for a homebrew-installed one, sudo find / -name mysql looking for compiled-from-source ones and delete them, whatever it takes. You could even remove the startup item by deleting the /Library/StartupItems/MySQLCOM directory if you want.
Run the mysql-whatever-version.pkg install package
Test it by typing sudo mysqld_safe & at the terminal. If you get "command not found," add /usr/local/mysql/bin to your path and try again. If you get any scary error messages, check for a /etc/my.cnf file as described above and try again. If it still doesn't work, then maybe try recursively chowning and chmoding the /usr/local/mysql/data directory to make sure _mysql can write to it. Once you get it to appear to start up OK, enter mysql at terminal. If you get a MySQL command prompt, all is well (enter exit to get out of it) -- in fact, if you get anything other than the ol' "Can't connect to local MySQL server through socket" then you can conclude that the MySQL server works -- shut down or kill the server and move on.
Next we'll install the startup item. Run MySQLStartupItem.pkg
Test the startup item at the terminal by entering sudo /Library/StartupItems/MySQLCOM/MySQLCOM start. It will give you a message claiming that it is starting up the server, but if it's unsuccessful it won't give you any indication, so try going into mysql again to test that the server is running. If so, enter sudo /Library/StartupItems/MySQLCOM/MySQLCOM stop to stop the server (and to test that the startup item can stop the server as well as start it :D) If it didn't work, try making the settings described above in /usr/local/mysql/support-files/mysql.server. If that still doesn't do it, try the bit up at the top about sudo chown -R root:wheel /Library/StartupItems/MySQLCOM.
Once that works, run/install the MySQL.prefPane. This should give you a MySQL item in your System Preferences near the bottom, and if you go in there, you should see a button that you can click which will stop/start the MySQL server. Try it, and if it doesn't work by now, I'm not sure what else I can tell you.
I had experienced the same error after removing my old mac ports and installing mysql in a new mac ports directory ( a new /opt/local ).
I fixed it by setting the correct permissions for the mysql directories in the ports tree:
chown -R _mysql:_mysql /opt/local/var/db/mysql5
chown -R _mysql:_mysql /opt/local/var/run/mysql5/
chmod -R 755 /opt/local/var/run/mysql5
I'm not sure if the chmod was needed. Of course ports had already done the job of creating the _mysql user and group.