Rails bitnami, MYSQL is unable to start

Question

so im setting up bitnami ruby on AWS

Then i used this to setup mysql 5.6 https://www.digitalocean.com/community/tutorials/how-to-install-mysql-on-ubuntu-14-04

Mysql is not starting up when I tested using "service mysql status"

it kept giving me this "mysql stop/waiting"

so i tried this command "sudo service mysql start" where it kept on running and didnt complete

When i ran "mysqladmin -p -u root version " it did return me

/opt/bitnami/mysql/bin/mysqladmin.bin  Ver 8.42 Distrib 5.6.35, for linux-glibc2.5 on x86_64
Copyright (c) 2000, 2016, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Server version          5.6.35
Protocol version        10
Connection              Localhost via UNIX socket
UNIX socket             /opt/bitnami/mysql/tmp/mysql.sock
Uptime:                 14 min 59 sec

Threads: 1  Questions: 2  Slow queries: 0  Opens: 67  Flush tables: 1  Open tables: 60  Queries per second avg: 0.002

which seemed pretty normal to me, however checking service mysql status still showed me the mysql stop/waiting

i heard running mysqld would give me clues to solve my problem, but im quite lost here....

bitnami@ip-172-31-20-165:~/Projects/server-master$ mysqld
2017-03-08 16:08:24 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-03-08 16:08:24 0 [Note] --secure-file-priv is set to NULL. Operations related to importing and exporting data are disabled
2017-03-08 16:08:24 0 [Note] /opt/bitnami/mysql/bin/mysqld.bin (mysqld 5.6.35) starting as process 26956 ...
2017-03-08 16:08:24 26956 [Warning] Can't create test file /opt/bitnami/mysql/data/ip-172-31-20-165.lower-test
2017-03-08 16:08:24 26956 [Warning] Can't create test file /opt/bitnami/mysql/data/ip-172-31-20-165.lower-test
2017-03-08 16:08:24 26956 [Warning] Buffered warning: Changed limits: max_open_files: 1024 (requested 5000)

2017-03-08 16:08:24 26956 [Warning] Buffered warning: Changed limits: table_open_cache: 431 (requested 2000)

2017-03-08 16:08:24 26956 [Note] Plugin 'FEDERATED' is disabled.
/opt/bitnami/mysql/bin/mysqld.bin: Can't find file: './mysql/plugin.frm' (errno: 13 - Permission denied)
2017-03-08 16:08:24 26956 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2017-03-08 16:08:24 26956 [Note] InnoDB: Using atomics to ref count buffer pool pages
2017-03-08 16:08:24 26956 [Note] InnoDB: The InnoDB memory heap is disabled
2017-03-08 16:08:24 26956 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2017-03-08 16:08:24 26956 [Note] InnoDB: Memory barrier is not used
2017-03-08 16:08:24 26956 [Note] InnoDB: Compressed tables use zlib 1.2.3
2017-03-08 16:08:24 26956 [Note] InnoDB: Using Linux native AIO
2017-03-08 16:08:24 26956 [Note] InnoDB: Using CPU crc32 instructions
2017-03-08 16:08:24 26956 [Note] InnoDB: Initializing buffer pool, size = 16.0M
2017-03-08 16:08:24 26956 [Note] InnoDB: Completed initialization of buffer pool
2017-03-08 16:08:24 26956 [ERROR] InnoDB: ./ibdata1 can't be opened in read-write mode
2017-03-08 16:08:24 26956 [ERROR] InnoDB: The system tablespace must be writable!
2017-03-08 16:08:24 26956 [ERROR] Plugin 'InnoDB' init function returned error.
2017-03-08 16:08:24 26956 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2017-03-08 16:08:25 26956 [ERROR] Unknown/unsupported storage engine: InnoDB
2017-03-08 16:08:25 26956 [ERROR] Aborting

2017-03-08 16:08:25 26956 [Note] Binlog end
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'partition'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'ARCHIVE'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'BLACKHOLE'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_METRICS'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_CMPMEM'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_CMP'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_LOCKS'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'INNODB_TRX'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'CSV'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'MEMORY'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'MyISAM'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'MRG_MYISAM'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'sha256_password'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'mysql_old_password'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'mysql_native_password'
2017-03-08 16:08:25 26956 [Note] Shutting down plugin 'binlog'
2017-03-08 16:08:25 26956 [Note] /opt/bitnami/mysql/bin/mysqld.bin: Shutdown complete

And of course i tested running the rails on localhost:3000 which of course gave

Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)

Need help on this matter pleasee.

UPDATE 3/9/2017

I re-did everything without the mysql mumbo jumbo installation . and still got the "Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)"

Below i ran mysqld again

bitnami@ip-172-31-26-217:~/Projects/finowledge_server-master$ mysqld
2017-03-09 15:43:28 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-03-09 15:43:28 0 [Note] --secure-file-priv is set to NULL. Operations related to importing and exporting data are disabled
2017-03-09 15:43:28 0 [Note] /opt/bitnami/mysql/bin/mysqld.bin (mysqld 5.6.35) starting as process 10181 ...
2017-03-09 15:43:28 10181 [Warning] Can't create test file /opt/bitnami/mysql/data/ip-172-31-26-217.lower-test
2017-03-09 15:43:28 10181 [Warning] Can't create test file /opt/bitnami/mysql/data/ip-172-31-26-217.lower-test
2017-03-09 15:43:28 10181 [Warning] Buffered warning: Changed limits: max_open_files: 1024 (requested 5000)

2017-03-09 15:43:28 10181 [Warning] Buffered warning: Changed limits: table_open_cache: 431 (requested 2000)

2017-03-09 15:43:28 10181 [Note] Plugin 'FEDERATED' is disabled.
/opt/bitnami/mysql/bin/mysqld.bin: Can't find file: './mysql/plugin.frm' (errno: 13 - Permission denied)
2017-03-09 15:43:28 10181 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2017-03-09 15:43:28 10181 [Note] InnoDB: Using atomics to ref count buffer pool pages
2017-03-09 15:43:28 10181 [Note] InnoDB: The InnoDB memory heap is disabled
2017-03-09 15:43:28 10181 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2017-03-09 15:43:28 10181 [Note] InnoDB: Memory barrier is not used
2017-03-09 15:43:28 10181 [Note] InnoDB: Compressed tables use zlib 1.2.3
2017-03-09 15:43:28 10181 [Note] InnoDB: Using Linux native AIO
2017-03-09 15:43:28 10181 [Note] InnoDB: Using CPU crc32 instructions
2017-03-09 15:43:28 10181 [Note] InnoDB: Initializing buffer pool, size = 16.0M
2017-03-09 15:43:28 10181 [Note] InnoDB: Completed initialization of buffer pool
2017-03-09 15:43:28 10181 [ERROR] InnoDB: ./ibdata1 can't be opened in read-write mode
2017-03-09 15:43:28 10181 [ERROR] InnoDB: The system tablespace must be writable!
2017-03-09 15:43:28 10181 [ERROR] Plugin 'InnoDB' init function returned error.
2017-03-09 15:43:28 10181 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2017-03-09 15:43:28 10181 [ERROR] Unknown/unsupported storage engine: InnoDB
2017-03-09 15:43:28 10181 [ERROR] Aborting

2017-03-09 15:43:28 10181 [Note] Binlog end
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'partition'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'ARCHIVE'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'BLACKHOLE'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_METRICS'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_CMPMEM'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_CMP'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_LOCKS'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'INNODB_TRX'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'CSV'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'MEMORY'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'MyISAM'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'MRG_MYISAM'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'sha256_password'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'mysql_old_password'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'mysql_native_password'
2017-03-09 15:43:28 10181 [Note] Shutting down plugin 'binlog'
2017-03-09 15:43:28 10181 [Note] /opt/bitnami/mysql/bin/mysqld.bin: Shutdown complete

score 4 · Answer 1 · answered Mar 09 '17 at 10:25

4

Bitnami developer here.

You shouldn't follow those guides because it will point you in the bad direction. In the Bitnami Ruby stack mysql and postgresql are installed by default. To stop, start or see the status of the services you should use the ctlscript.sh, which is in /opt/bitnami/.

bitnami@ip-172-31-45-25:/opt/bitnami$ sudo ./ctlscript.sh help
usage: ./ctlscript.sh help
       ./ctlscript.sh (start|stop|restart|status)
       ./ctlscript.sh (start|stop|restart|status) mysql
       ./ctlscript.sh (start|stop|restart|status) postgresql
       ./ctlscript.sh (start|stop|restart|status) memcached
       ./ctlscript.sh (start|stop|restart|status) php-fpm
       ./ctlscript.sh (start|stop|restart|status) apache
       ./ctlscript.sh (start|stop|restart|status) nginx
       ./ctlscript.sh (start|stop|restart|status) redis

help       - this screen
start      - start the service(s)
stop       - stop  the service(s)
restart    - restart or start the service(s)
status     - show the status of the service(s)

And, if you execute this in the Bitnami Ruby stack:

bitnami@ip-172-31-45-25:/opt/bitnami$ sudo ./ctlscript.sh status
Nginx already running
php-fpm already running
apache already running
redis already running
mysql already running
postgresql already running
Memcached already running

You can see that mysql is running fine.

Here you have got the our mysql guides, I highly recommend you to read them: https://docs.bitnami.com/aws/components/mysql/

Also, here you have the FAQ's in aws: https://docs.bitnami.com/aws/faq/

Best regards.

answered Mar 09 '17 at 10:25

David Barranco

442
3
10

Hi, updated above. reinstalled without the mumbo jumbo mysql installation. and used your guide – Napmi Mar 09 '17 at 15:47
From this case: http://stackoverflow.com/questions/22132780/difference-between-mysql-mysqladmin-mysqld mysqld is the server executable. You should run `mysql -u root -p` and type the password in order to access to mysql. – David Barranco Mar 09 '17 at 15:59
hi thanks for taking your time for the explanation :) its just that i learn somewhere that mysqld would help solve or find these database errors.which i think i am facing now ? tho im still stuck with ""Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)" – Napmi Mar 09 '17 at 16:03
I'm not sure if executing `mysqld` would mess something. I recommend you to execute `sudo /opt/bitnami/ctlscript.sh restart` and see if in the restart of the mysql is there any problem. Then try to connect to mysql using the mysql client (`mysql -u root -p`) – David Barranco Mar 09 '17 at 16:13
i ran mysql -u root -p its all fine , still have same issue with socket – Napmi Mar 09 '17 at 16:19
Take into account that mysql operates in the `3306` port. Could it be different from the port that you have configured for your rail application? I'm telling you this because if you are able to connect the database using the `mysql` command the problem has to be with your app. – David Barranco Mar 09 '17 at 16:21

score 0 · Answer 2 · answered Mar 08 '17 at 20:57

0

It seems MySQL is having file permission problems in the mysql directory

2017-03-08 16:08:24 26956 [ERROR] InnoDB: ./ibdata1 can't be opened in read-write mode 2017-03-08 16:08:24 26956 [ERROR] InnoDB: The system tablespace must be writable

answered Mar 08 '17 at 20:57

R. Sierra

1,076
6
19

score 0 · Answer 3 · edited May 23 '17 at 12:25

0

So i fixed my issue. As it turns out bitnami uses 127.0.0.1 , so i shouldn't use "localhost" on my HOST but instead 127.0.0.1.

Original answer here Answer

edited May 23 '17 at 12:25

Community

1
1

answered Mar 09 '17 at 16:50

Napmi

521
2
13
32

Rails bitnami, MYSQL is unable to start

3 Answers3