Problems with mysql

[lfontanez]

Hello,
Tried docker-compose up -d on my Mac after installing Docker and cloning the repo.

The mysql container aborts after some errors.

Initial entries in log:

Initializing database
mysqld: Can't create/write to file '/var/lib/mysql/is_writable' (Errcode: 13 - Permission denied)

I see a 'mysql' folder being created in the repo, so I gave group and everyone Read&Write Access

docker-compose down then docker-compose up -d again.

It aborts for other reasons.

Complete log:

Initializing database
2017-03-27T21:04:28.677202Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-03-27T21:04:28.684345Z 0 [Warning] Setting lower_case_table_names=2 because file system for /var/lib/mysql/ is case insensitive
2017-03-27T21:04:29.299513Z 0 [ERROR] InnoDB: Operating system error number 13 in a file operation.
2017-03-27T21:04:29.299676Z 0 [ERROR] InnoDB: The error means mysqld does not have the access rights to the directory.
2017-03-27 21:04:29 0x7fd11e0a8740 InnoDB: Assertion failure in thread 140536128898880 in file fil0fil.cc line 896
InnoDB: Failing assertion: success
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/5.7/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
21:04:29 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.
Attempting to collect some information that could help diagnose the problem.
As this is a crash and something is definitely wrong, the information
collection process might fail.
2017-03-27T21:04:29.301563531Z
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 = 68190 K bytes of memory
Hope that's ok; if not, decrease some variables in the equation.
2017-03-27T21:04:29.301585958Z
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
mysqld(my_print_stacktrace+0x2c)[0xe7fdcc]
mysqld(handle_fatal_signal+0x459)[0x7a9d39]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xf890)[0x7fd11dc85890]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37)[0x7fd11c68e067]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x148)[0x7fd11c68f448]
mysqld[0x7804a7]
mysqld[0x11baeb6]
mysqld(_Z40fil_open_log_and_system_tablespace_filesv+0xe4)[0x11bf954]
mysqld[0x10b2190]
mysqld(_Z34innobase_start_or_create_for_mysqlv+0x3692)[0x10b5cc2]
mysqld[0xf7e1e8]
mysqld(_Z24ha_initialize_handlertonP13st_plugin_int+0x51)[0x7f4af1]
mysqld[0xc76196]
mysqld(_Z11plugin_initPiPPci+0x5b8)[0xc7d1c8]
mysqld[0x7a255e]
mysqld(_Z11mysqld_mainiPPc+0x7e8)[0x7a3b78]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7fd11c67ab45]
mysqld[0x79a664]
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.
Initializing database
2017-03-27T21:04:29.715620Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-03-27T21:04:29.718876Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.
2017-03-27T21:04:29.719044Z 0 [ERROR] Aborting
2017-03-27T21:04:29.720495956Z
Initializing database
2017-03-27T21:04:30.169146Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-03-27T21:04:30.171343Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.
2017-03-27T21:04:30.171430Z 0 [ERROR] Aborting
2017-03-27T21:04:30.172388435Z
Initializing database
2017-03-27T21:04:30.827091Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-03-27T21:04:30.829169Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.
2017-03-27T21:04:30.829256Z 0 [ERROR] Aborting
2017-03-27T21:04:30.830013677Z
Initializing database
2017-03-27T21:04:31.880473Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-03-27T21:04:31.882845Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.
2017-03-27T21:04:31.884271Z 0 [ERROR] Aborting
2017-03-27T21:04:31.885417164Z
Initializing database
2017-03-27T21:04:33.739927Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-03-27T21:04:33.742316Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.
2017-03-27T21:04:33.742411Z 0 [ERROR] Aborting
2017-03-27T21:04:33.743256752Z
Initializing database
2017-03-27T21:04:37.187048Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-03-27T21:04:37.189442Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.
2017-03-27T21:04:37.189537Z 0 [ERROR] Aborting
2017-03-27T21:04:37.190081904Z
Initializing database
2017-03-27T21:04:43.834879Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-03-27T21:04:43.838534Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.
2017-03-27T21:04:43.838654Z 0 [ERROR] Aborting
2017-03-27T21:04:43.839550165Z
Initializing database
2017-03-27T21:04:56.898769Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-03-27T21:04:56.900907Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.
2017-03-27T21:04:56.900995Z 0 [ERROR] Aborting
2017-03-27T21:04:56.901318881Z

[lfontanez]

Hello,

I was using Docker Toolbox. Switched to Docker for Mac and everything worked correctly.
Port 80 not available in my machine, but I explored the files and managed to configure to a different port.

All is working after making all the minor adjustments needed.