Leginon

Sorry about this. It was a bug in the patch I put in last Friday. It is fixed now. It should be o.k. now if you rerun.

Hi Anchi, thank you! Now, the installation gets stuck at "php /tmp/myami/install/newDBsetup.php -L leginondb -P projectdb -H localhost -U root -E xinhuolin@gmail.com"
It is taking forever and not moving forward.

Below are the screen msgs:

/sbin/chkconfig mysqld on

Please wait......(This may take a few minutes.)

/sbin/service mysqld stop

Please wait......(This may take a few minutes.)

180716 08:30:33 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
Stopping mysqld: [ OK ]

mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)'
Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!
180716 08:30:34 mysqld_safe Logging to '/var/log/mysqld.log'.
180716 08:30:34 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)'
Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!
mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)'
Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!
mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)'
Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!
mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)'
Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!
mysqld is alive
php /tmp/myami/install/newDBsetup.php -L leginondb -P projectdb -H localhost -U root -E xinhuolin@gmail.com

Please wait......(This may take a few minutes.)

Anchi Cheng wrote:

Sorry about this. It was a bug in the patch I put in last Friday. It is fixed now. It should be o.k. now if you rerun.

Another note is that the centOS7 autoinstallation script is also broken.

centOS7 autoinstallation script should not have the original error you reported regarding setupSinedonCfg()

The new error indicates that even though it was able to stop mysqld but it could not start it with

mysqld_safe --skip-grant-tables

As Anchi wrote, run mysqld_safe --skip-grant-tables and see why it's not starting. You can also cat /var/log/mysqld.log to see if there are any error messages there.

I am reading the log as shown below. So, I think it has something to do with the time zone table and the lock privilege tables. The last two lines are results of running the mysqld_safe

/var/log/mysqld.log
180716 13:26:02 InnoDB: Initializing buffer pool, size = 8.0M
180716 13:26:02 InnoDB: Completed initialization of buffer pool
180716 13:26:06 InnoDB: Started; log sequence number 0 44233
180716 13:26:06 [Warning] Can't open and lock time zone table: Table 'mysql.tim$
180716 13:26:06 [ERROR] Can't open and lock privilege tables: Table 'mysql.serv$
180716 13:26:06 [Note] /usr/libexec/mysqld: ready for connections.
Version: '5.1.73' socket: '/var/lib/mysql/mysql.sock' port: 3306 Source dist$
180716 13:29:08 mysqld_safe A mysqld process already exists
180716 13:30:53 mysqld_safe A mysqld process already exists

error msg from the installation
/sbin/chkconfig mysqld on

Please wait......(This may take a few minutes.)

/sbin/service mysqld stop

Please wait......(This may take a few minutes.)

180716 13:26:02 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
Stopping mysqld: [ OK ]

mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)'
Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!
180716 13:26:02 mysqld_safe Logging to '/var/log/mysqld.log'.
180716 13:26:02 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)'
Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!
mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)'
Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!
mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)'
Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!
mysqld is alive
php /tmp/myami/install/newDBsetup.php -L leginondb -P projectdb -H localhost -U root -E xinhuolin@gmail.com

Please wait......(This may take a few minutes.)

%%after key break

^CTraceback (most recent call last):
File "centosAutoInstallation_leginon.py", line 1343, in <module>
a.run()
File "centosAutoInstallation_leginon.py", line 1293, in run
result = self.setupDBServer()
File "centosAutoInstallation_leginon.py", line 314, in setupDBServer
self.runCommand(cmd)
File "centosAutoInstallation_leginon.py", line 176, in runCommand
stdoutResult = proc.stdout.read()
KeyboardInterrupt

It must be in some strange state. Reboot the server or kill all mysql processes (https://hoststud.com/resources/resolved-error-mysqld_safe-a-mysqld-process-already-exists.141/). Also, make sure all files in /var/lib/mysql/ are owned by mysql user.

I was able to solve the mysql problem, but now it says mysqladmin has problem connecting to 'localhost' and the entire error msg is below:

/sbin/chkconfig mysqld on

Please wait......(This may take a few minutes.)

/sbin/service mysqld stop

Please wait......(This may take a few minutes.)

180716 14:56:03 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
Stopping mysqld: [ OK ]

mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)'
Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!
180716 14:56:04 mysqld_safe Logging to '/var/log/mysqld.log'.
180716 14:56:04 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
mysqld is alive
php /tmp/myami/install/newDBsetup.php -L leginondb -P projectdb -H localhost -U root -E xinhuolin@gmail.com

Sargis Dallakyan wrote:

It must be in some strange state. Reboot the server or kill all mysql processes (https://hoststud.com/resources/resolved-error-mysqld_safe-a-mysqld-process-already-exists.141/). Also, make sure all files in /var/lib/mysql/ are owned by mysql user.

I found the problem. For some reason I don't have the mysql.sock file in /var/lib/mysql/

mysql.sock only exists when mysqld is alive. It seems that the log you show is normal.

I can reproduce

mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)'
Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!

mysqladmin -umysql ping

It takes some time for the database server to be ready to use.

Eventually, when the database is ready, the same ping gives no error and prints out

mysqld is alive

In other words, what you saw in log just means that the first ping found mysql-server not yet ready and our script was not able keep the error output from you as it try again. Eventually, it was able to move on.

It then ran the next part

php /tmp/myami/install/newDBsetup.php -L leginondb -P projectdb -H localhost -U root -E xinhuolin@gmail.com

So it seems that it has worked. What happened after that ? You can run the last command from shell and let us know what you get.

Hi Anchi,

Thank you for your reply. I am sorry for the delay in replying to your email. I am running mysql 5.1.73 and I modified the script so the installation is complete now. Now the problem I have is setting up the processing server. I am running everything on my workstation (users, storage, and processing). On the step 5 of the setup, it always shows "Local cluster does not exist. Please make sure the cluster exists." How do I just use the workstation itself to do the processing?

Just don't add any processing host. The default generates appion script commands that you copy and paste to your text terminal.