MySQL 5.6 not starting (migrate MAMP 2 to MAMP 4) - mysql

Question

The old and the new MAMP: They don't boot MySQL server. Before the upgrade to MAMP 4, my MySQL server was working properly on OS X 10.11.6 El Capitan.
Now with MAMP is not possible to start the MySQL server (and migrate my old DB).
Note: "Tools > upgrade MySQL databases" is not accessible in the menu bar (remains gray) but no problem with Apache and PHP.
My chmod for all files from /Applications/MAMP/db/ is:
RW admin (group)
RW system
RW _mysql
RW _mysql (group)
RW everyone
and chmod for all files from /Applications/MAMP/tmp/mysql is:
RW admin (group)
RW system
RW everyone
MySQL last log error:
161007 12:20:26 mysqld_safe Starting mysqld daemon with databases from /Applications/MAMP/db/mysql56
2016-10-07 12:20:27 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2016-10-07 12:20:27 0 [Note] /Applications/MAMP/Library/bin/mysqld (mysqld 5.6.28) starting as process 16615 ...
2016-10-07 12:20:27 16615 [Warning] Setting lower_case_table_names=2 because file system for /Applications/MAMP/db/mysql56/ is case insensitive
2016-10-07 12:20:27 16615 [Note] Plugin 'FEDERATED' is disabled.
2016-10-07 12:20:27 16615 [Note] InnoDB: Using atomics to ref count buffer pool pages
2016-10-07 12:20:27 16615 [Note] InnoDB: The InnoDB memory heap is disabled
2016-10-07 12:20:27 16615 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2016-10-07 12:20:27 16615 [Note] InnoDB: Memory barrier is not used
2016-10-07 12:20:27 16615 [Note] InnoDB: Compressed tables use zlib 1.2.8
2016-10-07 12:20:27 16615 [Note] InnoDB: Using CPU crc32 instructions
2016-10-07 12:20:27 16615 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2016-10-07 12:20:27 16615 [Note] InnoDB: Completed initialization of buffer pool
2016-10-07 12:20:27 16615 [Note] InnoDB: Highest supported file format is Barracuda.
2016-10-07 12:20:27 16615 [Note] InnoDB: Log scan progressed past the checkpoint lsn 8276492
2016-10-07 12:20:27 16615 [Note] InnoDB: Database was not shutdown normally!
2016-10-07 12:20:27 16615 [Note] InnoDB: Starting crash recovery.
2016-10-07 12:20:27 16615 [Note] InnoDB: Reading tablespace information from the .ibd files...
2016-10-07 12:20:27 16615 [Note] InnoDB: Restoring possible half-written data pages
2016-10-07 12:20:27 16615 [Note] InnoDB: from the doublewrite buffer...
InnoDB: Doing recovery: scanned up to log sequence number 8280376
2016-10-07 12:20:27 16615 [Note] InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percent: 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
2016-10-07 12:20:27 16615 [Note] InnoDB: 128 rollback segment(s) are active.
2016-10-07 12:20:27 16615 [Note] InnoDB: Waiting for purge to start
2016-10-07 12:20:27 7000007ab000 InnoDB: Assertion failure in thread 123145310351360 in file dict0dict.cc line 3464
InnoDB: Failing assertion: for_table || ref_table
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/5.6/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
10:20:27 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 = 68101 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
0 mysqld 0x0000000106f73688 my_print_stacktrace + 72
1 mysqld 0x0000000106c3a9e8 handle_fatal_signal + 952
2 libsystem_platform.dylib 0x00007fff9fa7d52a _sigtramp + 26
3 ??? 0x020061d7b33d5471 0x0 + 144222767128859761
4 libsystem_c.dylib 0x00007fff9f4f66df abort + 129
5 mysqld 0x000000010700ba56 _Z25dict_foreign_add_to_cacheP14dict_foreign_tPPKcb17dict_err_ignore_t + 230
6 mysqld 0x0000000107026dba _ZL17dict_load_foreignPKcPS0_bb17dict_err_ignore_t + 1674
7 mysqld 0x000000010702601b _Z18dict_load_foreignsPKcPS0_bb17dict_err_ignore_t + 1115
8 mysqld 0x0000000107024996 _Z15dict_load_tablePKcm17dict_err_ignore_t + 2246
9 mysqld 0x0000000107026441 _Z21dict_load_table_on_idy17dict_err_ignore_t + 689
10 mysqld 0x0000000107004098 _ZL25dict_table_open_on_id_lowy17dict_err_ignore_t + 184
11 mysqld 0x0000000107003ee3 _Z21dict_table_open_on_idym15dict_table_op_t + 99
12 mysqld 0x000000010717dc75 _ZL24row_purge_parse_undo_recP12purge_node_tPhPbP9que_thr_t + 229
13 mysqld 0x000000010717d88f _ZL9row_purgeP12purge_node_tPhP9que_thr_t + 63
14 mysqld 0x000000010717d741 _Z14row_purge_stepP9que_thr_t + 305
15 mysqld 0x0000000107133d91 _ZL12que_thr_stepP9que_thr_t + 913
16 mysqld 0x00000001071334eb _ZL19que_run_threads_lowP9que_thr_t + 123
17 mysqld 0x00000001071332ee _Z15que_run_threadsP9que_thr_t + 110
18 mysqld 0x00000001071bc15a _Z9trx_purgemmb + 778
19 mysqld 0x00000001071aa673 _ZL12srv_do_purgemPm + 579
20 mysqld 0x00000001071a9be7 srv_purge_coordinator_thread + 679
21 libsystem_pthread.dylib 0x00007fff9328e99d _pthread_body + 131
22 libsystem_pthread.dylib 0x00007fff9328e91a _pthread_body + 0
23 libsystem_pthread.dylib 0x00007fff9328c351 thread_start + 13
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.
161007 12:20:27 mysqld_safe mysqld from pid file /Applications/MAMP/tmp/mysql/mysql.pid ended

Answer 1

I experienced the exact same problem and this is the only location (as of 10 Feb 2017) where I have found it reported as a problem.
If you don't need the content of the databases from MAMP 2, then this is easy:
Verify that MySQL is not running (via MAMP GUI and either Activity Monitor or Terminal process list)
Navigate to /Applications/MAMP/db/mysql56
Remove these three files: ib_logfile0, ib_logfile1, and ibdata1
Restart MySQL Server in MAMP
I found this solution here: http://www.randombugs.com/linux/crash-innodb-table.html. Note that the ibdata file is where InnoDB stores the data from your tables by default (https://serverfault.com/questions/487159/what-is-the-ibdata1-file-in-my-var-lib-mysql-directory) so it would be good to back-up these files before removing them; just in case something doesn't work out, you can restore back to your non-working configuration.
On the other hand, if you need the content of your MAMP 2 databases, then you will have needed to have completed a backup of them in the older/working version, preferably a MySQL dump so that restoration is as easy as copy/paste. Fortunately, I had a backup so in addition to deleting the "ib..." files listed above, I also deleted the directories of the databases that I intended to restore so that I could begin a restore with "CREATE DATABASE...".
I don't know whether this is a bug with MAMP, MySQL, OSX, but this is the solution that worked for me. I was able to restore the databases that I cared about and just didn't worry about losing the others for which I didn't have backed up.
Technical Data:
Old MAMP Version 2.1.2
Old MySQL Version 4.0.10.14
New MAMP Version 4.1.1
New MySQL Version 5.6.35
Mac OS 10.12.3