MySQL is crashed -- please help fix it

[befree22]

MySQL is crashed and I'm getting "error connecting to database" on website. I'm unable to login to Kloxo-MR. Please help me fix this. I tried running command on http://forum.mratwork.com/kloxo-mr-technical-helps/i-cannot-acces-kloxo-mr-panel/msg28086/#msg28086 but mysql still crashed.

A. Kloxo-MR: 6.5.0.f-2014040701

B. OS: CentOS release 6.5 (Final) x86_64

C. Apps:
   1. MySQL: mysql-5.5.34-1.el6.x86_64
   2. PHP: php53u-5.3.28-2.ius.el6.x86_64
   3. Httpd: httpd-2.2.29-1.mr.el6.x86_64
   4. Lighttpd: --uninstalled--
   5. Nginx: --uninstalled--
   6. Qmail: qmail-toaster-1.03-1.3.38.mr.el6.x86_64
      - with: courier-imap-toaster-4.1.2-1.3.16.mr.el6.x86_64
   7. Dns: bind-9.9.5-1.el6.x86_64

D. Php-type (for Httpd/proxy):

E. Memory:
                total       used       free     shared    buffers     cached
   Mem:          4096       1111       2984          0          0        605
   -/+ buffers/cache:        505       3590
   Swap:         1024          1       1022

[MRatWork]

Inform here 'cat /var/log/mysqld.log' (enough latest 20 lines)

[befree22]

141008 20:54:48 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
141008 20:54:48 [Note] Plugin 'FEDERATED' is disabled.
141008 20:54:48 InnoDB: The InnoDB memory heap is disabled
141008 20:54:48 InnoDB: Mutexes and rw_locks use GCC atomic builtins
141008 20:54:48 InnoDB: Compressed tables use zlib 1.2.3
141008 20:54:48 InnoDB: Initializing buffer pool, size = 128.0M
141008 20:54:48 InnoDB: Completed initialization of buffer pool
141008 20:54:48 InnoDB: highest supported file format is Barracuda.
InnoDB: Log scan progressed past the checkpoint lsn 57364192755
141008 20:54:48  InnoDB: Database was not shut down normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
InnoDB: Error: tried to read 1048576 bytes at offset 0 1048576.
InnoDB: Was only able to read 507904.
InnoDB: Fatal error: cannot read from file. OS error number 17.
141008 20:54:53  InnoDB: Assertion failure in thread 139743683688416 in file os0file.c line 2538
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/5.5/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
00:54:53 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.
We will try our best to scrape up some info that will hopefully help
diagnose the problem, but since we have already crashed,
something is definitely wrong and this may 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 = 338508 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
/usr/libexec/mysqld(my_print_stacktrace+0x2e)[0x78b18e]
/usr/libexec/mysqld(handle_fatal_signal+0x493)[0x6741b3]
/lib64/libpthread.so.0(+0xf710)[0x7f189c5eb710]
/lib64/libc.so.6(gsignal+0x35)[0x7f189aa34925]
/lib64/libc.so.6(abort+0x175)[0x7f189aa36105]
/usr/libexec/mysqld[0x8bda60]
/usr/libexec/mysqld[0x886461]
/usr/libexec/mysqld[0x82bdb3]
/usr/libexec/mysqld[0x8b53f2]
/usr/libexec/mysqld[0x8b60a2]
/usr/libexec/mysqld[0x818deb]
/usr/libexec/mysqld[0x7e4860]
/usr/libexec/mysqld(_Z24ha_initialize_handlertonP13st_plugin_int+0x41)[0x676eb1]
/usr/libexec/mysqld[0x58d4d8]
/usr/libexec/mysqld(_Z11plugin_initPiPPci+0x8c8)[0x590db8]
/usr/libexec/mysqld[0x518078]
/usr/libexec/mysqld(_Z11mysqld_mainiPPc+0x3fd)[0x51b1dd]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x7f189aa20d1d]
/usr/libexec/mysqld[0x510ee5]
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.
141008 20:54:53 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended

[MRatWork]

Run 'sh /script/set-mysql-default' (and then try 'service mysqld restart' for testing) and then 'sh /script/mysql-convert engine=myisam'.

[befree22]

sh /script/set-mysql-default
sh: /script/set-mysql-default: No such file or directory

The malicious hacker deleted some of the files.

[MRatWork]

Above script exist in Kloxo-MR 7. If using 6.5, add:

Code: [Select]

innodb_use_native_aio=0
skip-innodb
default-storage-engine=myisamunder '[mysqld]' if not exists in /etc/my.cnf.

[befree22]

I ran the command but I'm still unable to login to Kloxo admin.

[MRatWork]

Sorry, I mean above code must entry to /etc/my.cnf

[befree22]

I was able to login to Kloxo-MR using the command above. However, I'm unable to restore from an admin {Backup Home} file I created in summer. I keep getting the message that all accounts (admin, reseller, website directories) and roundcube already exist. How do I help me restore this backup so my website can get back online? Since that bast*&^ crashed MySQL all data from PHPMyAdmin is returning innodb error.

[befree22]

In phpmyadmin, when I click on a database table, I get the following error message:

"1286 Unknown storage engine InnoDB".

1. I changed the mysql engine from innodb to myisam by running the given code above but there's a conflict. I want to change it back to innodb -- what code do I run and which file needs changing?

2. I also tried upgrading to the latest version but I'm getting error.

this log is appearing when I try to upgrade mysql

Transaction Check Error:
  file /etc/my.cnf from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/lib64/mysql/libmysqlclient.so.18.0.0 from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/Index.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/armscii8.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/ascii.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/cp1250.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/cp1256.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/cp1257.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/cp850.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/cp852.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/cp866.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/dec8.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/geostd8.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/greek.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/hebrew.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/hp8.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/keybcs2.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/koi8r.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/koi8u.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/latin1.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/latin2.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/latin5.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/latin7.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/macce.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/macroman.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64
  file /usr/share/mysql/charsets/swe7.xml from install of mysql55-libs-5.5.40-1.ius.el6.x86_64 conflicts with file from package mysql-libs-5.5.34-1.el6.x86_64

Please help me fix these problems.
 

[MRatWork]

Kloxo-MR using mysql55 branch install mysql branch to make sure using mysql 5.5 version. Original mysql from OS is version 5.0 or 5.1 and have trouble with panel itself. It's why Kloxo-MR using mysql55.

Inform here 'yum list installed mysql*'.

[befree22]

yum list installed mysql*
Loaded plugins: fastestmirror, priorities, protectbase, replace
Loading mirror speeds from cached hostfile
 * base: mirror.rackspace.com
 * extras: ftpmirror.your.org
 * mratwork-epel: mirror.steadfast.net
 * mratwork-ius-stable: dl.iuscommunity.org
 * updates: mirror.fdcservers.net
0 packages excluded due to repository protections
Installed Packages
mysql.x86_64                                                   5.5.34-1.el6                                                @mratwork-centalt
mysql-libs.x86_64                                              5.5.34-1.el6                                                @mratwork-centalt
mysql-server.x86_64                                            5.5.34-1.el6                                                @mratwork-centalt
mysqlclient16.x86_64                                           5.1.61-4.ius.el6                                            @mratwork-ius

[MRatWork]

Try 'yum replace mysql --replace-with=mysql55'

[befree22]

Log below. What is my next step? Restart server? And how do I switch back to innodb?

yum replace mysql --replace-with=mysql55
Loaded plugins: fastestmirror, priorities, protectbase, replace
Loading mirror speeds from cached hostfile
 * base: mirror.rackspace.com
 * extras: mirror.cs.uwp.edu
 * mratwork-epel: mirror.steadfast.net
 * mratwork-ius-stable: dl.iuscommunity.org
 * updates: centos.chi.host-engine.com
0 packages excluded due to repository protections
Replacing packages takes time, please be patient...

WARNING: Unable to resolve all providers: ['libmysqlclient.so.18(libmysqlclient_18)(64bit)', 'mysql-libs(x86-64)', 'mysql-client', 'mysql(x86-64)', 'libpinba_engine.so.0()(64bit)', 'mysql-server(x86-64)']

This may be normal depending on the package.  Continue? [y/N] y
Resolving Dependencies
--> Running transaction check
---> Package mysql.x86_64 0:5.5.34-1.el6 will be erased
---> Package mysql-libs.x86_64 0:5.5.34-1.el6 will be erased
--> Processing Dependency: libmysqlclient.so.18(libmysqlclient_18)(64bit) for package: php52s-5.2.17-11.mr.el6.x86_64
---> Package mysql-server.x86_64 0:5.5.34-1.el6 will be erased
---> Package mysql55.x86_64 0:5.5.40-1.ius.el6 will be installed
---> Package mysql55-libs.x86_64 0:5.5.40-1.ius.el6 will be installed
---> Package mysql55-server.x86_64 0:5.5.40-1.ius.el6 will be installed
--> Running transaction check
---> Package php52s.x86_64 0:5.2.17-11.mr.el6 will be erased
--> Finished Dependency Resolution
--> Running transaction check
---> Package php52s.x86_64 0:5.2.17-11.mr.el6 will be erased
--> Processing Dependency: libmysqlclient.so.18(libmysqlclient_18)(64bit) for package: php52s-5.2.17-11.mr.el6.x86_64
--> Running transaction check
---> Package php52s.x86_64 0:5.2.17-11.mr.el6 will be erased
--> Finished Dependency Resolution

Dependencies Resolved

============================================================================================================================================
 Package                       Arch                  Version                            Repository                                     Size
============================================================================================================================================
Installing:
 mysql55                       x86_64                5.5.40-1.ius.el6                   mratwork-ius-stable                           9.1 M
 mysql55-libs                  x86_64                5.5.40-1.ius.el6                   mratwork-ius-stable                           786 k
 mysql55-server                x86_64                5.5.40-1.ius.el6                   mratwork-ius-stable                           9.6 M
Removing:
 mysql                         x86_64                5.5.34-1.el6                       @mratwork-centalt                              29 M
 mysql-libs                    x86_64                5.5.34-1.el6                       @mratwork-centalt                             4.1 M
 mysql-server                  x86_64                5.5.34-1.el6                       @mratwork-centalt                              45 M
Removing for dependencies:
 php52s                        x86_64                5.2.17-11.mr.el6                   @mratwork-release-version-arch                 20 M

Transaction Summary
============================================================================================================================================
Install       3 Package(s)
Remove        4 Package(s)

Total size: 19 M
Total download size: 19 M
Is this ok [y/N]: y
Downloading Packages:
(1/2): mysql55-5.5.40-1.ius.el6.x86_64.rpm                                                                           | 9.1 MB     00:00     
(2/2): mysql55-server-5.5.40-1.ius.el6.x86_64.rpm                                                                    | 9.6 MB     00:00     
--------------------------------------------------------------------------------------------------------------------------------------------
Total                                                                                                        10 MB/s |  19 MB     00:01     
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing : mysql55-libs-5.5.40-1.ius.el6.x86_64                                                                                     1/7
warning: /etc/my.cnf created as /etc/my.cnf.rpmnew
  Installing : mysql55-5.5.40-1.ius.el6.x86_64                                                                                          2/7
  Installing : mysql55-server-5.5.40-1.ius.el6.x86_64                                                                                   3/7
  Erasing    : mysql-server-5.5.34-1.el6.x86_64                                                                                         4/7
  Erasing    : mysql-5.5.34-1.el6.x86_64                                                                                                5/7
  Erasing    : php52s-5.2.17-11.mr.el6.x86_64                                                                                           6/7
  Erasing    : mysql-libs-5.5.34-1.el6.x86_64                                                                                           7/7
  Verifying  : mysql55-server-5.5.40-1.ius.el6.x86_64                                                                                   1/7
  Verifying  : mysql55-5.5.40-1.ius.el6.x86_64                                                                                          2/7
  Verifying  : mysql55-libs-5.5.40-1.ius.el6.x86_64                                                                                     3/7
  Verifying  : php52s-5.2.17-11.mr.el6.x86_64                                                                                           4/7
  Verifying  : mysql-5.5.34-1.el6.x86_64                                                                                                5/7
  Verifying  : mysql-server-5.5.34-1.el6.x86_64                                                                                         6/7
  Verifying  : mysql-libs-5.5.34-1.el6.x86_64                                                                                           7/7

Removed:
  mysql.x86_64 0:5.5.34-1.el6               mysql-libs.x86_64 0:5.5.34-1.el6               mysql-server.x86_64 0:5.5.34-1.el6             

Dependency Removed:
  php52s.x86_64 0:5.2.17-11.mr.el6                                                                                                         

Installed:
  mysql55.x86_64 0:5.5.40-1.ius.el6         mysql55-libs.x86_64 0:5.5.40-1.ius.el6         mysql55-server.x86_64 0:5.5.40-1.ius.el6       

Complete!

[MRatWork]

Try 'service mysqld restart'.