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110926 12:09:41  InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percents: 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
InnoDB: Apply batch completed
InnoDB: Last MySQL binlog file position 0 3329, file name /var/lib/mysql/mysql-bin.004279
110926 12:09:42  InnoDB: Started; log sequence number 46 4210009908
110926 12:09:42 [Note] Recovering after a crash using /var/lib/mysql/mysql-bin
110926 12:09:42 [Note] Starting crash recovery...
110926 12:09:42 [Note] Crash recovery finished.
110926 12:09:42 [Note] /usr/libexec/mysqld: ready for connections.
Version: '5.0.45-log'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  Source distribution

from web admin:

#2002 - The server is not responding (or the local MySQL server's socket is not correctly configured)

Every time I access the DB, it crashes as far as I can tell

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more log output: looks like I/O error: –  v2k Sep 26 '11 at 19:16
    
Version: '5.0.45-log' socket: '/var/lib/mysql/mysql.sock' port: 3306 Source distribution InnoDB: Error: tried to read 16384 bytes at offset 2 64110592. InnoDB: Was only able to read -1. 110926 12:14:39 InnoDB: Operating system error number 5 in a file operation. InnoDB: Error number 5 means 'Input/output error'. InnoDB: Some operating system error numbers are described at InnoDB: dev.mysql.com/doc/refman/5.0/en/… InnoDB: File operation call: 'read'. InnoDB: Cannot continue operation. –  v2k Sep 26 '11 at 19:16
    
Problem was HDD: test ` === START OF READ SMART DATA SECTION === SMART overall-health self-assessment test result: PASSED Please note the following marginal Attributes: ID# ATTRIBUTE_NAME FLAG VALUE WORST THRESH TYPE UPDATED WHEN_FAILED RAW_VALUE 190 Temperature_Celsius 0x0022 045 032 045 Old_age Always FAILING_NOW 55` –  v2k Oct 4 '11 at 20:28

3 Answers 3

MySQL was failing to read parts of the database due to a failing HDD.

mysqldump would fail because of this as well.

I ended up writing a python script to pull out all the readable parts of the Innodb database.

In summary:

  1. img'd hard drive with dd (http://www.thegeekstuff.com/2010/10/dd-command-examples/)
  2. backed up database via mysqldump (with python script to skip unreadables)
  3. imported into new system
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p.s. I tested the HDD via cyberciti.biz/tips/linux-find-out-if-harddisk-failing.html –  v2k Oct 4 '11 at 20:35

Based on what you say, have you tried to do a FORCED FULL fsck of the disk where the database information resides?

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Restart webmin after you restart MySQL. Depending on your distribution it could be

service webin restart

or

/ect/init.d/webin restart
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1  
What does this have to do with the question? –  John Gardeniers Sep 27 '11 at 0:06
    
My thoughts exactly, @JohnGardeniers. Hence the downvote... –  EEAA Sep 27 '11 at 3:28
    
Good question. I must have had some other question in my mind. My bad. –  jdw Sep 27 '11 at 12:24
    
Actually, I take it back. He's getting errors from webmin as well as MySQL. My thought is that once he restarts MySQL he should also restart Webmin. So, while it may not work, it is a valid answer that addresses the problem. –  jdw Sep 27 '11 at 12:25

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