Featured CentOS 7.x How to help test .08 CentOS 7 Betas with Github code ?

Added the new official MariaDB 10 YUM repo config for CentOS 7. Previously, .08 beta used the CentOS 6 version even for CentOS 7.

with new official MariaDB 10 YUM repo for CentOS 7 the startup/restart scripts change from init.d to systemd method

---

commit at Commits · centminmod/centminmod · GitHub

 

added an upgrade section to 1st post CentOS 7.x - How to help test .08 CentOS 7 Betas with Github code ? | Centmin Mod Community

 

For nginx versions are the same unless specifically a .08 beta commit changes something with nginx compile options would you need to recompile/update Nginx.

YUM update is outside of Centmin Mod script, so you can update whenever. But if you mean getting that new MariaDB 10 CentOS 7 repo instead of MariaDB 10 CentOS 6 repo, you won't be able to with any yum updates or using latest .08 beta download as there is no code specifically made for switching that MariaDB 10 YUM repo from CentOS 6 to CentOS 7 one right now. Pretty much the same for MariaDB 10, just CentOS 6 repo uses init.d and CentOS 7 repo uses systemd

 

totally depends on what was updated as not all changes can be grabbed or utilised by just downloading the latest .08 beta code and running menu based updates.

which updated library you talking about Commits · centminmod/centminmod · GitHub ? you mean update EPEL 7 release rpm download url update EPEL 7 release download version · 4ea5c3d · centminmod/centminmod · GitHub ? Yes that change and any changes for inc/downloadlinks.inc can usually be obtained by grabbing latest .08 beta zip download but there's no need to run any YUM commands as that download is only installed once at initial install time to install EPEL YUM repo. So it's only a problem you'd encounter on fresh .08 beta installs.

 

Updated .08 beta and switched the random number generator to /dev/urandom which doubles the number of generated random digits Commits · centminmod/centminmod · GitHub

 

seem to resulted in a bug by switching to urandom reported on Github Unattended installer fails to create Memcached status page · Issue #31 · centminmod/centminmod · GitHub

fixed with this commit fix randomised generator to remove space · 1f641ac · centminmod/centminmod · GitHub

 

FYI, was just doing some yum updates for a CentOS 7.0 512MB VPS and ran out of memory with 0 swap assigned. So added a 2GB Swap file to the VPS and tried yum updates again and saw swap used was up to 480MB. So it does seem true that for CentOS 7.0 you need a minimum of 1GB of memory to get by given that the yum update easily consumed 512MB + 480MB = 992MB of memory.

So be aware if you want to use CentOS 7.0 either a minimum of 1GB of memory is required or at least 512MB of memory + ample swap disk allocation is required !

these were the YUM updated packages involved.

Code:

 tail -80 /var/log/yum.log | grep 'Oct 02'
Oct 02 04:34:52 Updated: nss-util-3.16.2-2.el7_0.x86_64
Oct 02 04:34:52 Updated: systemd-libs-208-11.el7_0.2.x86_64
Oct 02 04:34:52 Updated: mesa-libglapi-9.2.5-6.20131218.el7_0.x86_64
Oct 02 04:34:52 Updated: centos-release-7-0.1406.el7.centos.2.5.x86_64
Oct 02 04:34:54 Updated: systemd-208-11.el7_0.2.x86_64
Oct 02 04:34:54 Updated: libgudev1-208-11.el7_0.2.x86_64
Oct 02 04:34:55 Updated: initscripts-9.49.17-1.el7_0.1.x86_64
Oct 02 04:34:55 Updated: 12:dhcp-libs-4.2.5-27.el7.centos.1.x86_64
Oct 02 04:34:55 Updated: policycoreutils-2.2.5-11.el7_0.1.x86_64
Oct 02 04:34:55 Updated: nss-softokn-freebl-3.16.2-2.el7_0.x86_64
Oct 02 04:34:56 Updated: nss-softokn-3.16.2-2.el7_0.x86_64
Oct 02 04:34:56 Updated: nss-3.16.2-7.el7_0.x86_64
Oct 02 04:34:56 Updated: nss-sysinit-3.16.2-7.el7_0.x86_64
Oct 02 04:34:56 Updated: 1:NetworkManager-glib-0.9.9.1-26.git20140326.4dba720.el7_0.x86_64
Oct 02 04:47:42 Updated: MariaDB-common-10.0.14-1.el6.x86_64
Oct 02 04:47:42 Updated: MariaDB-compat-10.0.14-1.el6.x86_64
Oct 02 04:47:45 Updated: MariaDB-client-10.0.14-1.el6.x86_64
Oct 02 04:47:45 Updated: 12:dhcp-common-4.2.5-27.el7.centos.1.x86_64
Oct 02 04:47:45 Updated: 12:dhclient-4.2.5-27.el7.centos.1.x86_64
Oct 02 04:47:45 Updated: kernel-tools-libs-3.10.0-123.8.1.el7.x86_64
Oct 02 04:47:45 Updated: systemd-sysv-208-11.el7_0.2.x86_64
Oct 02 04:47:45 Updated: 1:NetworkManager-0.9.9.1-26.git20140326.4dba720.el7_0.x86_64
Oct 02 04:47:46 Updated: mesa-libgbm-9.2.5-6.20131218.el7_0.x86_64
Oct 02 04:47:49 Updated: linux-firmware-20140804-0.1.git6bce2b0.el7_0.noarch
Oct 02 04:47:56 Installed: kernel-3.10.0-123.8.1.el7.x86_64
Oct 02 04:47:56 Updated: mesa-libEGL-9.2.5-6.20131218.el7_0.x86_64
Oct 02 04:47:56 Updated: 1:NetworkManager-tui-0.9.9.1-26.git20140326.4dba720.el7_0.x86_64
Oct 02 04:47:56 Updated: kernel-tools-3.10.0-123.8.1.el7.x86_64
Oct 02 04:48:07 Updated: MariaDB-server-10.0.14-1.el6.x86_64
Oct 02 04:48:09 Updated: MariaDB-devel-10.0.14-1.el6.x86_64
Oct 02 04:48:09 Updated: MariaDB-shared-10.0.14-1.el6.x86_64
Oct 02 04:48:10 Updated: kernel-headers-3.10.0-123.8.1.el7.x86_64
Oct 02 04:48:10 Updated: iwl6000g2b-firmware-17.168.5.2-35.el7_0.noarch
Oct 02 04:48:10 Updated: 1:iwl1000-firmware-39.31.5.1-35.el7_0.noarch
Oct 02 04:48:10 Updated: iwl100-firmware-39.31.5.1-35.el7_0.noarch
Oct 02 04:48:10 Updated: iwl5150-firmware-8.24.2.2-35.el7_0.noarch
Oct 02 04:48:10 Updated: iwl2000-firmware-18.168.6.1-35.el7_0.noarch
Oct 02 04:48:10 Updated: iwl3945-firmware-15.32.2.9-35.el7_0.noarch
Oct 02 04:48:10 Updated: epel-release-7-2.noarch
Oct 02 04:48:10 Updated: iwl135-firmware-18.168.6.1-35.el7_0.noarch
Oct 02 04:48:10 Updated: libertas-sd8686-firmware-20140804-0.1.git6bce2b0.el7_0.noarch
Oct 02 04:48:10 Updated: iwl7260-firmware-22.0.7.0-35.el7_0.noarch
Oct 02 04:48:10 Updated: iwl4965-firmware-228.61.2.24-35.el7_0.noarch
Oct 02 04:48:28 Installed: kernel-devel-3.10.0-123.8.1.el7.x86_64
Oct 02 04:48:28 Updated: mesa-libGL-9.2.5-6.20131218.el7_0.x86_64
Oct 02 04:48:29 Updated: iwl6050-firmware-41.28.5.1-35.el7_0.noarch
Oct 02 04:48:29 Updated: iwl2030-firmware-18.168.6.1-35.el7_0.noarch
Oct 02 04:48:29 Updated: nss-tools-3.16.2-7.el7_0.x86_64
Oct 02 04:48:29 Updated: iwl6000g2a-firmware-17.168.5.3-35.el7_0.noarch
Oct 02 04:48:29 Updated: libertas-sd8787-firmware-20140804-0.1.git6bce2b0.el7_0.noarch
Oct 02 04:48:29 Updated: 2:libertas-usb8388-firmware-20140804-0.1.git6bce2b0.el7_0.noarch
Oct 02 04:48:30 Updated: tzdata-2014g-1.el7.noarch
Oct 02 04:49:37 Updated: selinux-policy-targeted-3.12.1-153.el7_0.11.noarch
Oct 02 04:49:38 Updated: iwl105-firmware-18.168.6.1-35.el7_0.noarch
Oct 02 04:49:39 Updated: ca-certificates-2014.1.98-70.0.el7_0.noarch
Oct 02 04:49:39 Updated: iwl5000-firmware-8.83.5.1_1-35.el7_0.noarch
Oct 02 04:49:39 Updated: iwl6000-firmware-9.221.4.1-35.el7_0.noarch
Oct 02 04:49:40 Updated: iwl3160-firmware-22.0.7.0-35.el7_0.noarch
Oct 02 04:49:40 Updated: kexec-tools-2.0.4-32.el7.centos.4.x86_64

 

Updated inc/phpsededit.inc moving the initial PHP php.ini tweaks from /usr/local/lib/php.ini to /etc/centminmod/php.d/custom_php.ini so they are preserved on PHP upgrades. Commit Commits · centminmod/centminmod · GitHub

 

about time @Matt

Discovered a bug in initial MariaDB install routine which affects both .07 stable and .08 betas when InnoDB is enabled the InnoDB engine may fail to load as there is a mismatched innodb_log_file_size from what was initially created size of 5MB at install and the custom /etc/my.cnf size of 48MB or 64MB - you can see this in MariaDB error log when you enable InnoDB for the first time. I had a workaround for this, but mistakenly placed the work around too early in the install routine before the custom /etc/my.cnf was set. The workaround should be placed after the custom /etc/my.cnf is set.

So committed fixes for both branches

• .07 stable update inc/mariadb_install.inc move ib_logfile workaround · 81aaeae · centminmod/centminmod · GitHub
• .08centos7beta01 and .08geoip update inc/mariadb_install.inc move ib_logfile workaround · c0bd030 · centminmod/centminmod · GitHub

If it's your first time enabling innodb in /etc/my.cnf and you're on Centmin Mod prior to the committed fixes, you'd want to first check your MariaDB error log /var/log/mysqld.log to make sure you are experiencing the same exact error messages outlined here (for failed innodb engine and innodb_log_file_size) and follow the commands to rectify them outlined here or below.

check your error logs for mysql

Code:

tail -50 /var/log/mysqld.log

Code:

141007 19:37:42 [Note] /usr/sbin/mysqld: Normal shutdown

141007 19:37:42 [Note] Event Scheduler: Purging the queue. 0 events
141007 19:37:42 [Note] /usr/sbin/mysqld: Shutdown complete

141007 19:37:42 mysqld_safe mysqld from pid file /var/lib/mysql/vla01.centminmod.com.pid ended
141007 19:37:46 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
141007 19:37:46 InnoDB: The InnoDB memory heap is disabled
141007 19:37:46 InnoDB: Mutexes and rw_locks use GCC atomic builtins
141007 19:37:46 InnoDB: Compressed tables use zlib 1.2.3
141007 19:37:46 InnoDB: Using Linux native AIO
141007 19:37:46 InnoDB: Initializing buffer pool, size = 16.0M
141007 19:37:46 InnoDB: Completed initialization of buffer pool
InnoDB: Error: log file ./ib_logfile0 is of different size 0 5242880 bytes
InnoDB: than specified in the .cnf file 0 67108864 bytes!
InnoDB: Possible causes for this error:
(a) Incorrect log file is used or log file size is changed
(b) In case default size is used this log file is from 10.0
(c) Log file is corrupted or there was not enough disk space
In case (b) you need to set innodb_log_file_size = 48M
141007 19:37:46 [ERROR] Plugin 'InnoDB' init function returned error.
141007 19:37:46 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
141007 19:37:46 [Note] Plugin 'FEDERATED' is disabled.
141007 19:37:46 [Note] Plugin 'ARCHIVE' is disabled.
141007 19:37:46 [Note] Plugin 'FEEDBACK' is disabled.
141007 19:37:46 [Note] Server socket created on IP: '0.0.0.0'.
141007 19:37:46 [Note] Event Scheduler: Loaded 0 events
141007 19:37:46 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.39-MariaDB'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MariaDB Server

InnoDB engine failed to load as it seems somewhere in MariaDB install routine it creates a 5MB sized innodb log file prior to the custom tweaked my.cnf I created is read which has a 48MB sized innodb log file so it causes problems until you stop mysql server and remove the 5MB innodblog files ib_logfile* from /var/lib/mysql

Manual fix after enabling innodb in /etc/my.cnf for the very first time.

Code:

mysqladmin flush-tables
sleep 30
service mysql stop
sleep 30
rm -rf /var/lib/mysql/ib_logfile*
service mysql start

 

just check if mysql variable have_innodb is YES

via command

Code:

 mysqladmin var | grep have_innodb

will show YES if innodb engine is enabled

Code:

mysqladmin var | grep have_innodb
| have_innodb                                       | YES 

killall not found is okay as mysql stop command already stopped mysqld

 

MariaDB 10 doesn't have that variable. So need to verify to see if any innodb variables are listed, if not then innodb engine wasn't loaded, if it returns variables then innodb engine is enabled and loaded

Code:

mysqladmin var | grep innodb | tr -s ' '

i.e.

Spoiler: sample output for innodb variables

Code:

mysqladmin var | grep innodb | tr -s ' '
| ignore_builtin_innodb | OFF |
| innodb_adaptive_flushing | ON |
| innodb_adaptive_flushing_lwm | 10 |
| innodb_adaptive_hash_index | ON |
| innodb_adaptive_hash_index_partitions | 1 |
| innodb_adaptive_max_sleep_delay | 150000 |
| innodb_additional_mem_pool_size | 8388608 |
| innodb_api_bk_commit_interval | 5 |
| innodb_api_disable_rowlock | OFF |
| innodb_api_enable_binlog | OFF |
| innodb_api_enable_mdl | OFF |
| innodb_api_trx_level | 0 |
| innodb_autoextend_increment | 64 |
| innodb_autoinc_lock_mode | 1 |
| innodb_buffer_pool_dump_at_shutdown | OFF |
| innodb_buffer_pool_dump_now | OFF |
| innodb_buffer_pool_filename | ib_buffer_pool |
| innodb_buffer_pool_instances | 8 |
| innodb_buffer_pool_load_abort | OFF |
| innodb_buffer_pool_load_at_startup | OFF |
| innodb_buffer_pool_load_now | OFF |
| innodb_buffer_pool_populate | OFF |
| innodb_buffer_pool_size | 50331648 |
| innodb_change_buffer_max_size | 25 |
| innodb_change_buffering | all |
| innodb_checksum_algorithm | innodb |
| innodb_checksums | ON |
| innodb_cleaner_lsn_age_factor | high_checkpoint |
| innodb_cmp_per_index_enabled | OFF |
| innodb_commit_concurrency | 0 |
| innodb_compression_failure_threshold_pct | 5 |
| innodb_compression_level | 6 |
| innodb_compression_pad_pct_max | 50 |
| innodb_concurrency_tickets | 5000 |
| innodb_corrupt_table_action | assert |
| innodb_data_file_path | ibdata1:10M:autoextend |
| innodb_data_home_dir | |
| innodb_disable_sort_file_cache | OFF |
| innodb_doublewrite | ON |
| innodb_empty_free_list_algorithm | backoff |
| innodb_fake_changes | OFF |
| innodb_fast_shutdown | 1 |
| innodb_file_format | Antelope |
| innodb_file_format_check | ON |
| innodb_file_format_max | Antelope |
| innodb_file_per_table | ON |
| innodb_flush_log_at_timeout | 1 |
| innodb_flush_log_at_trx_commit | 2 |
| innodb_flush_method | O_DIRECT |
| innodb_flush_neighbors | 1 |
| innodb_flushing_avg_loops | 30 |
| innodb_force_load_corrupted | OFF |
| innodb_force_recovery | 0 |
| innodb_foreground_preflush | exponential_backoff |
| innodb_ft_aux_table | |
| innodb_ft_cache_size | 8000000 |
| innodb_ft_enable_diag_print | OFF |
| innodb_ft_enable_stopword | ON |
| innodb_ft_max_token_size | 84 |
| innodb_ft_min_token_size | 3 |
| innodb_ft_num_word_optimize | 2000 |
| innodb_ft_result_cache_limit | 2000000000 |
| innodb_ft_server_stopword_table | |
| innodb_ft_sort_pll_degree | 2 |
| innodb_ft_total_cache_size | 640000000 |
| innodb_ft_user_stopword_table | |
| innodb_io_capacity | 100 |
| innodb_io_capacity_max | 2000 |
| innodb_kill_idle_transaction | 0 |
| innodb_large_prefix | OFF |
| innodb_lock_wait_timeout | 50 |
| innodb_locking_fake_changes | ON |
| innodb_locks_unsafe_for_binlog | OFF |
| innodb_log_arch_dir | ./ |
| innodb_log_arch_expire_sec | 0 |
| innodb_log_archive | OFF |
| innodb_log_block_size | 512 |
| innodb_log_buffer_size | 8388608 |
| innodb_log_checksum_algorithm | innodb |
| innodb_log_compressed_pages | ON |
| innodb_log_file_size | 67108864 |
| innodb_log_files_in_group | 2 |
| innodb_log_group_home_dir | ./ |
| innodb_lru_scan_depth | 1024 |
| innodb_max_bitmap_file_size | 104857600 |
| innodb_max_changed_pages | 1000000 |
| innodb_max_dirty_pages_pct | 75 |
| innodb_max_dirty_pages_pct_lwm | 0 |
| innodb_max_purge_lag | 0 |
| innodb_max_purge_lag_delay | 0 |
| innodb_mirrored_log_groups | 1 |
| innodb_monitor_disable | |
| innodb_monitor_enable | |
| innodb_monitor_reset | |
| innodb_monitor_reset_all | |
| innodb_old_blocks_pct | 37 |
| innodb_old_blocks_time | 1000 |
| innodb_online_alter_log_max_size | 134217728 |
| innodb_open_files | 1000 |
| innodb_optimize_fulltext_only | OFF |
| innodb_page_size | 16384 |
| innodb_print_all_deadlocks | OFF |
| innodb_purge_batch_size | 300 |
| innodb_purge_threads | 1 |
| innodb_random_read_ahead | OFF |
| innodb_read_ahead_threshold | 56 |
| innodb_read_io_threads | 2 |
| innodb_read_only | OFF |
| innodb_replication_delay | 0 |
| innodb_rollback_on_timeout | OFF |
| innodb_rollback_segments | 128 |
| innodb_sched_priority_cleaner | 19 |
| innodb_show_locks_held | 10 |
| innodb_show_verbose_locks | 0 |
| innodb_simulate_comp_failures | 0 |
| innodb_sort_buffer_size | 2097152 |
| innodb_spin_wait_delay | 6 |
| innodb_stats_auto_recalc | ON |
| innodb_stats_method | nulls_equal |
| innodb_stats_on_metadata | OFF |
| innodb_stats_persistent | ON |
| innodb_stats_persistent_sample_pages | 20 |
| innodb_stats_sample_pages | 8 |
| innodb_stats_transient_sample_pages | 8 |
| innodb_status_output | OFF |
| innodb_status_output_locks | OFF |
| innodb_strict_mode | OFF |
| innodb_support_xa | ON |
| innodb_sync_array_size | 1 |
| innodb_sync_spin_loops | 30 |
| innodb_table_locks | ON |
| innodb_thread_concurrency | 0 |
| innodb_thread_sleep_delay | 10000 |
| innodb_track_changed_pages | OFF |
| innodb_undo_directory | . |
| innodb_undo_logs | 128 |
| innodb_undo_tablespaces | 0 |
| innodb_use_atomic_writes | OFF |
| innodb_use_fallocate | OFF |
| innodb_use_global_flush_log_at_trx_commit | ON |
| innodb_use_native_aio | ON |
| innodb_use_stacktrace | OFF |
| innodb_use_sys_malloc | ON |
| innodb_version | 5.6.20-68.0 |
| innodb_write_io_threads | 2 |

also double check your mysql error log as per MariaDB - mysql problems the mysqltuner & tuning-primer | Centmin Mod Community and see if you experienced the same problem

 

@Andy you fixed the innodb_log_file_size errors as seen in mysqld error log and shows you have InnoDB engine loaded and enabled

Code:

141008  1:52:09 [Note] InnoDB: Setting log file ./ib_logfile101 size to 64 MB
141008  1:52:09 [Note] InnoDB: Setting log file ./ib_logfile1 size to 64 MB
141008  1:52:09 [Note] InnoDB: Renaming log file ./ib_logfile101 to ./ib_logfile0
141008  1:52:09 [Warning] InnoDB: New log files created, LSN=2006070

However, you have another set of errors for mysql.gtid_slave.pos and mysql.innodb_table_stats system tables being corrupted or mismatched data from the *ibd files and innodb table space.

Code:

141008  1:52:09 [Warning] InnoDB: Cannot open table mysql/gtid_slave_pos from the internal data dictionary of InnoDB though the .frm file for the table exists. See http://dev.mysql.com/doc/refman/5.6/en/innodb-troubleshooting.html for how you can resolve the problem.
141008  1:52:09 [Warning] Failed to load slave replication state from table mysql.gtid_slave_pos: 1932: Table 'mysql.gtid_slave_pos' doesn't exist in engine
141008  1:52:09 [Note] /usr/sbin/mysqld: ready for connections.
Version: '10.0.14-MariaDB'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MariaDB Server
2014-10-08 02:30:15 7f61ed584700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.

The fix can be complicated and isn't 100% guaranteed. However, I written a quick shell script to do all the leg work, mariadb10fix.sh.

This problem and fix is only if you're running MariaDB 10. The script will:

1. make a full backup of all your databases on your server at /home/mysql10fix/all_databases_backup.sql
2. download the most common 3 missing innodb tables schema (with no-data) create tables structure sql file named mariadb10_3tables.sql - which was created from a working MariaDB 10.0.x database system
3. stop mysql server and nginx and remove physically the *.ibd data files for the 3 common innodb tables within mysql database for gtid_slave_pos, innodb_table_stats and innodb_index_stats and then start up mysql server and nginx again. I stopped nginx so you don't get email bombarded with mysql error messages
4. then discard those tables from innodb tablespace
5. then import the mysql databases 3 innodb tables structures from mariadb10_3tables.sql file
6. then restart mysql server, and move old mysql error log file from /var/log/mysqld.log to /var/log/mysqld.log-oldlog and create a new empty fresh old file
7. then run mysql_upgrade forced option to check and repair all mysql database tables.
8. then tail the last 25 lines of mysql error log /var/log/mysqld.log to check if mysql restarted clean and without errors (as shown in below example)

how to download and run mariadb10fix.sh

Code:

wget -cnv https://gist.github.com/centminmod/ee2befd9f8807561cd0a/raw/mariadb10fix.sh
chmod +x mariadb10fix.sh
./mariadb10fix.sh

example output below

Code:

---------------------------------------------------------
creating work directory at /home/mysql10fix
---------------------------------------------------------
changing to /home/mysql10fix
---------------------------------------------------------
backuping up all databases first including system tables
backup time depends on size of all your databases
---------------------------------------------------------
downloading missing tables sql file
2014-10-08 04:52:20 URL:https://gist.githubusercontent.com/centminmod/9bb511a8e59a9df7190f/raw/417ac17a855fc2c00a297ce100808fdb444c95f3/mariadb10_3tables.sql [3530] -> "mariadb10_3tables.sql" [1]
---------------------------------------------------------
stopping mysql server
Shutting down MySQL.. SUCCESS!
---------------------------------------------------------
check missing table files
-rw------- 1 mysql mysql 1.0K Sep 20 01:19 gtid_slave_pos.frm
-rw------- 1 mysql mysql  96K Sep 20 01:19 gtid_slave_pos.ibd
-rw------- 1 mysql mysql 4.9K Sep 20 01:19 innodb_index_stats.frm
-rw------- 1 mysql mysql  96K Sep 20 01:19 innodb_index_stats.ibd
-rw------- 1 mysql mysql 1.5K Sep 20 01:19 innodb_table_stats.frm
-rw------- 1 mysql mysql  96K Sep 20 01:19 innodb_table_stats.ibd
---------------------------------------------------------
removing missing tables' files
---------------------------------------------------------
starting mysql server
Starting MySQL. SUCCESS!
---------------------------------------------------------
discarding missing table spaces
---------------------------------------------------------
importing missing tables create sql file
---------------------------------------------------------
restart mysql server
Shutting down MySQL.. SUCCESS!
Starting MySQL. SUCCESS!

---------------------------------------------------------
mysql_upgrade --force mysql
Phase 1/3: Running 'mysql_fix_privilege_tables'...
Processing databases
mysql
mysql.column_stats                                 OK
mysql.columns_priv                                 OK
mysql.db                                           OK
mysql.event                                        OK
mysql.func                                         OK
mysql.gtid_slave_pos                               OK
mysql.help_category                                OK
mysql.help_keyword                                 OK
mysql.help_relation                                OK
mysql.help_topic                                   OK
mysql.host                                         OK
mysql.index_stats                                  OK
mysql.innodb_index_stats                           OK
mysql.innodb_table_stats                           OK
mysql.plugin                                       OK
mysql.proc                                         OK
mysql.procs_priv                                   OK
mysql.proxies_priv                                 OK
mysql.roles_mapping                                OK
mysql.servers                                      OK
mysql.table_stats                                  OK
mysql.tables_priv                                  OK
mysql.time_zone                                    OK
mysql.time_zone_leap_second                        OK
mysql.time_zone_name                               OK
mysql.time_zone_transition                         OK
mysql.time_zone_transition_type                    OK
mysql.user                                         OK
Phase 2/3: Fixing table and database names
Phase 3/3: Checking and upgrading tables
Processing databases
information_schema
performance_schema
OK

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check mysql error log
141008  4:52:23 [Note] InnoDB: Starting shutdown...
141008  4:52:25 [Note] InnoDB: Shutdown completed; log sequence number 1617174
141008  4:52:25 [Note] /usr/sbin/mysqld: Shutdown complete

141008 04:52:25 mysqld_safe mysqld from pid file /var/lib/mysql/centos65np.localdomain.pid ended
141008 04:52:26 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
141008  4:52:26 [Note] InnoDB: Using mutexes to ref count buffer pool pages
141008  4:52:26 [Note] InnoDB: The InnoDB memory heap is disabled
141008  4:52:26 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
141008  4:52:26 [Note] InnoDB: Compressed tables use zlib 1.2.3
141008  4:52:26 [Note] InnoDB: Using Linux native AIO
141008  4:52:26 [Note] InnoDB: Not using CPU crc32 instructions
141008  4:52:26 [Note] InnoDB: Initializing buffer pool, size = 48.0M
141008  4:52:26 [Note] InnoDB: Completed initialization of buffer pool
141008  4:52:26 [Note] InnoDB: Highest supported file format is Barracuda.
141008  4:52:26 [Note] InnoDB: 128 rollback segment(s) are active.
141008  4:52:26 [Note] InnoDB: Waiting for purge to start
141008  4:52:26 [Note] InnoDB:  Percona XtraDB (http://www.percona.com) 5.6.19-67.0 started; log sequence number 1617174
141008  4:52:26 [Note] Plugin 'FEDERATED' is disabled.
141008  4:52:26 [Note] Plugin 'ARCHIVE' is disabled.
141008  4:52:26 [Note] Plugin 'FEEDBACK' is disabled.
141008  4:52:26 [Note] Server socket created on IP: '::'.
141008  4:52:26 [Note] Event Scheduler: Loaded 0 events
141008  4:52:26 [Note] /usr/sbin/mysqld: ready for connections.
Version: '10.0.13-MariaDB'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MariaDB Server
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