Help with "Check that you can ping the server mysql"

Support
#1

Situation
I am running OpenEMR in AWS. Last thursday (Sept. 12th) I got an error saying the Site ID was missing - so I logged into AWS and restarted the ec2 instance, and it cleared up. However the following morning, the problem was there again - so I once again restarted the ec2 instance and started getting a different error “Check that you can ping the server mysql.”

I saw that others were having problems relatively recently in AWS, and was hoping it would just clear up. Since then I’ve restarted the instance multiple times each day, I still cannot access openemr at all - currently, with the same mysql error.

I do have experience developing in PHP, however, I have zero experience working with AWS, it sadly is overwhelming. (I don’t even know how to access the php files or ftp in to the site.)

I really need to fix this soon - any help and suggestions would be greatly appreciated. And I apologize in advance, but I’ll probably need dummy instructions on how to do anything beyond restarting the instance in AWS.

OpenEMR Version
I’m using OpenEMR version… not sure, 5.01+

Browser:
I’m using: opera, chrome, firefox

Operating System
I’m using: win 7, win 10

Blank screen on first start of OpenEMR 5.0.2
#2

hi @susmitahunter, which package are you using?

#3

I installed the express version a year ago… i think at that time it was 5.0.1 at the time

#4

would have created a key pair to use to ssh into that instance

#5

It did create the .pem file, and I followed those instructions… got the error message saying the permissions are too open.

#6
#7

I think I got in. I followed the instructions on how to use putty to get in, with the modification of using ubuntu as the username. What should I do next?

#8

check on the dockers with

sudo bash
docker ps

further help is at openemr-devops/packages/express at master · openemr/openemr-devops · GitHub

#9

i was able to run those commands and it gave me :
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
88f8a6baf98c openemr/openemr:5.0.1 “./run_openemr.sh” 16 months ago Up 24 hours 0.0.0.0:80->80/tcp, 0.0.0.0:443->443/tcp lightsail_openemr_1

I then went to that first link and tried the general commands, the apache one worked, and got me to a new prompt, at which point I wasn’t sure what I was doing. I also tried the mysql docker command, but that gave me an error saying the docker exec command requires at least 2 arguments.

I’m sorry again for needing my hand held, but I’m still at a loss as to what is actually wrong and what I’m supposed to do… with tools I’ve really never played with before. So thank you again for your continued help.

#10

ok, so the mysql container isn’t running, you should be seeing something like the below in addition to the openemr container

5bceca97b5b2        openemr/mysql-xtrabackup:latest   "docker-entrypoint..."   9 months ago        Up 11 days          3306/tcp

from the root bash prompt something like
root@ip-10-0-1-118:~#
what does
docker ps -a
show you?

#11 
CONTAINER ID        IMAGE                             COMMAND                  C                                                                                        REATED             STATUS                    PORTS                                                                                                                              NAMES
88f8a6baf98c        openemr/openemr:5.0.1             "./run_openemr.sh"       1                                                                                        6 months ago       Up 28 hours               0.0.0.0:80->80/tcp, 0.0.0.0:443->44                                                                                        3/tcp   lightsail_openemr_1
d05167f16b1f        openemr/mysql-xtrabackup:latest   "docker-entrypoint..."   1                                                                                        6 months ago       Exited (1) 28 hours ago                                                                                                                                      lightsail_mysql_1
#12

how about
docker logs d05167f16b1f

#13 
Initializing database
2018-04-28T18:20:14.578848Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is                                                                                                                                                              deprecated. Please use --explicit_defaults_for_timestamp server option (see doc                                                                                                                                                             umentation for more details).
2018-04-28T18:20:15.698529Z 0 [Warning] InnoDB: New log files created, LSN=45790
2018-04-28T18:20:15.952408Z 0 [Warning] InnoDB: Creating foreign key constraint                                                                                                                                                              system tables.
2018-04-28T18:20:16.020103Z 0 [Warning] No existing UUID has been found, so we a                                                                                                                                                             ssume that this is the first time that this server has been started. Generating                                                                                                                                                              a new UUID: ccac40c5-4b10-11e8-8f58-0242ac120002.
2018-04-28T18:20:16.022331Z 0 [Warning] Gtid table is not ready to be used. Tabl                                                                                                                                                             e 'mysql.gtid_executed' cannot be opened.
2018-04-28T18:20:16.023204Z 1 [Warning] root@localhost is created with an empty                                                                                                                                                              password ! Please consider switching off the --initialize-insecure option.
2018-04-28T18:20:16.878650Z 1 [Warning] 'user' entry 'root@localhost' ignored in                                                                                                                                                              --skip-name-resolve mode.
2018-04-28T18:20:16.878748Z 1 [Warning] 'user' entry 'mysql.session@localhost' i                                                                                                                                                             gnored in --skip-name-resolve mode.
2018-04-28T18:20:16.878779Z 1 [Warning] 'user' entry 'mysql.sys@localhost' ignor                                                                                                                                                             ed in --skip-name-resolve mode.
2018-04-28T18:20:16.878812Z 1 [Warning] 'db' entry 'performance_schema mysql.ses                                                                                                                                                             sion@localhost' ignored in --skip-name-resolve mode.
2018-04-28T18:20:16.878847Z 1 [Warning] 'db' entry 'sys mysql.sys@localhost' ign                                                                                                                                                             ored in --skip-name-resolve mode.
2018-04-28T18:20:16.878901Z 1 [Warning] 'proxies_priv' entry '@ root@localhost'                                                                                                                                                              ignored in --skip-name-resolve mode.
2018-04-28T18:20:16.878961Z 1 [Warning] 'tables_priv' entry 'user mysql.session@                                                                                                                                                             localhost' ignored in --skip-name-resolve mode.
2018-04-28T18:20:16.878987Z 1 [Warning] 'tables_priv' entry 'sys_config mysql.sy                                                                                                                                                             s@localhost' ignored in --skip-name-resolve mode.
Database initialized
Initializing certificates
Generating a 2048 bit RSA private key
....+++
................................................................................                                                                                                                                                             ....................+++
unable to write 'random state'
writing new private key to 'ca-key.pem'
-----
Generating a 2048 bit RSA private key
..+++
...................+++
unable to write 'random state'
writing new private key to 'server-key.pem'
-----
Generating a 2048 bit RSA private key
......................+++
..............+++
unable to write 'random state'
writing new private key to 'client-key.pem'
-----
Certificates initialized
MySQL init process in progress...
2018-04-28T18:20:19.899688Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is                                                                                                                                                              deprecated. Please use --explicit_defaults_for_timestamp server option (see doc                                                                                                                                                             umentation for more details).
2018-04-28T18:20:19.907481Z 0 [Note] mysqld (mysqld 5.7.22) starting as process                                                                                                                                                              88 ...
2018-04-28T18:20:19.913267Z 0 [Note] InnoDB: PUNCH HOLE support available
2018-04-28T18:20:19.913331Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic                                                                                                                                                              builtins
2018-04-28T18:20:19.913354Z 0 [Note] InnoDB: Uses event mutexes
2018-04-28T18:20:19.913374Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence()                                                                                                                                                              is used for memory barrier
2018-04-28T18:20:19.913393Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2018-04-28T18:20:19.913411Z 0 [Note] InnoDB: Using Linux native AIO
2018-04-28T18:20:19.913806Z 0 [Note] InnoDB: Number of pools: 1
2018-04-28T18:20:19.913959Z 0 [Note] InnoDB: Using CPU crc32 instructions
2018-04-28T18:20:19.921574Z 0 [Note] InnoDB: Initializing buffer pool, total siz                                                                                                                                                             e = 128M, instances = 1, chunk size = 128M
2018-04-28T18:20:19.942729Z 0 [Note] InnoDB: Completed initialization of buffer                                                                                                                                                              pool
2018-04-28T18:20:19.945182Z 0 [Note] InnoDB: If the mysqld execution user is aut                                                                                                                                                             horized, page cleaner thread priority can be changed. See the man page of setpri                                                                                                                                                             ority().
2018-04-28T18:20:19.957760Z 0 [Note] InnoDB: Highest supported file format is Ba                                                                                                                                                             rracuda.
2018-04-28T18:20:19.991212Z 0 [Note] InnoDB: Creating shared tablespace for temp                                                                                                                                                             orary tables
2018-04-28T18:20:19.991437Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12                                                                                                                                                              MB. Physically writing the file full; Please wait ...
2018-04-28T18:20:20.035590Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2018-04-28T18:20:20.037144Z 0 [Note] InnoDB: 96 redo rollback segment(s) found.                                                                                                                                                              96 redo rollback segment(s) are active.
2018-04-28T18:20:20.037203Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are                                                                                                                                                              active.
2018-04-28T18:20:20.041215Z 0 [Note] InnoDB: 5.7.22 started; log sequence number                                                                                                                                                              2589156
2018-04-28T18:20:20.041773Z 0 [Note] Plugin 'FEDERATED' is disabled.
2018-04-28T18:20:20.043929Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/li                                                                                                                                                             b/mysql/ib_buffer_pool
2018-04-28T18:20:20.054279Z 0 [Note] Found ca.pem, server-cert.pem and server-ke                                                                                                                                                             y.pem in data directory. Trying to enable SSL support using them.
2018-04-28T18:20:20.055362Z 0 [Warning] CA certificate ca.pem is self signed.
2018-04-28T18:20:20.055939Z 0 [Note] InnoDB: Buffer pool(s) load completed at 18                                                                                                                                                             0428 18:20:20
2018-04-28T18:20:20.066637Z 0 [Warning] Insecure configuration for --pid-file: L                                                                                                                                                             ocation '/var/run/mysqld' in the path is accessible to all OS users. Consider ch                                                                                                                                                             oosing a different directory.
2018-04-28T18:20:20.069159Z 0 [Warning] 'user' entry 'root@localhost' ignored in                                                                                                                                                              --skip-name-resolve mode.
2018-04-28T18:20:20.069361Z 0 [Warning] 'user' entry 'mysql.session@localhost' i                                                                                                                                                             gnored in --skip-name-resolve mode.
2018-04-28T18:20:20.069449Z 0 [Warning] 'user' entry 'mysql.sys@localhost' ignor                                                                                                                                                             ed in --skip-name-resolve mode.
2018-04-28T18:20:20.069489Z 0 [Warning] 'db' entry 'performance_schema mysql.ses                                                                                                                                                             sion@localhost' ignored in --skip-name-resolve mode.
2018-04-28T18:20:20.069511Z 0 [Warning] 'db' entry 'sys mysql.sys@localhost' ign                                                                                                                                                             ored in --skip-name-resolve mode.
2018-04-28T18:20:20.069683Z 0 [Warning] 'proxies_priv' entry '@ root@localhost'                                                                                                                                                              ignored in --skip-name-resolve mode.
2018-04-28T18:20:20.072632Z 0 [Warning] 'tables_priv' entry 'user mysql.session@                                                                                                                                                             localhost' ignored in --skip-name-resolve mode.
2018-04-28T18:20:20.072692Z 0 [Warning] 'tables_priv' entry 'sys_config mysql.sy                                                                                                                                                             s@localhost' ignored in --skip-name-resolve mode.
2018-04-28T18:20:20.084728Z 0 [Note] Event Scheduler: Loaded 0 events
2018-04-28T18:20:20.085204Z 0 [Note] mysqld: ready for connections.
Version: '5.7.22'  socket: '/var/run/mysqld/mysqld.sock'  port: 0  MySQL Communi                                                                                                                                                             ty Server (GPL)
Warning: Unable to load '/usr/share/zoneinfo/iso3166.tab' as time zone. Skipping                                                                                                                                                              it.
Warning: Unable to load '/usr/share/zoneinfo/leap-seconds.list' as time zone. Sk                                                                                                                                                             ipping it.
Warning: Unable to load '/usr/share/zoneinfo/zone.tab' as time zone. Skipping it                                                                                                                                                             .
2018-04-28T18:20:25.864150Z 4 [Warning] 'user' entry 'root@localhost' ignored in                                                                                                                                                              --skip-name-resolve mode.
2018-04-28T18:20:25.864263Z 4 [Warning] 'user' entry 'mysql.sys@localhost' ignor                                                                                                                                                             ed in --skip-name-resolve mode.
2018-04-28T18:20:25.864312Z 4 [Warning] 'db' entry 'performance_schema mysql.ses                                                                                                                                                             sion@localhost' ignored in --skip-name-resolve mode.
2018-04-28T18:20:25.864385Z 4 [Warning] 'db' entry 'sys mysql.sys@localhost' ign                                                                                                                                                             ored in --skip-name-resolve mode.
2018-04-28T18:20:25.864431Z 4 [Warning] 'proxies_priv' entry '@ root@localhost'                                                                                                                                                              ignored in --skip-name-resolve mode.
2018-04-28T18:20:25.864495Z 4 [Warning] 'tables_priv' entry 'user mysql.session@                                                                                                                                                             localhost' ignored in --skip-name-resolve mode.
2018-04-28T18:20:25.864523Z 4 [Warning] 'tables_priv' entry 'sys_config mysql.sy                                                                                                                                                             s@localhost' ignored in --skip-name-resolve mode.

2018-04-28T18:20:25.878199Z 0 [Note] Giving 0 client threads a chance to die gra                                                                                                                                                             cefully
2018-04-28T18:20:25.878262Z 0 [Note] Shutting down slave threads
2018-04-28T18:20:25.878285Z 0 [Note] Forcefully disconnecting 0 remaining client                                                                                                                                                             s
2018-04-28T18:20:25.878306Z 0 [Note] Event Scheduler: Purging the queue. 0 event                                                                                                                                                             s
2018-04-28T18:20:25.878801Z 0 [Note] Binlog end
2018-04-28T18:20:25.879586Z 0 [Note] Shutting down plugin 'ngram'
2018-04-28T18:20:25.879737Z 0 [Note] Shutting down plugin 'BLACKHOLE'
2018-04-28T18:20:25.879764Z 0 [Note] Shutting down plugin 'partition'
2018-04-28T18:20:25.879808Z 0 [Note] Shutting down plugin 'ARCHIVE'
2018-04-28T18:20:25.879827Z 0 [Note] Shutting down plugin 'MEMORY'
2018-04-28T18:20:25.879847Z 0 [Note] Shutting down plugin 'INNODB_SYS_VIRTUAL'
2018-04-28T18:20:25.879864Z 0 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2018-04-28T18:20:25.879881Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACE                                                                                                                                                             S'
2018-04-28T18:20:25.879897Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_CO                                                                                                                                                             LS'
2018-04-28T18:20:25.879912Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2018-04-28T18:20:25.880054Z 0 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2018-04-28T18:20:25.880078Z 0 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2018-04-28T18:20:25.880094Z 0 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2018-04-28T18:20:25.880156Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS                                                                                                                                                             '
2018-04-28T18:20:25.880177Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2018-04-28T18:20:25.880192Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE                                                                                                                                                             '
2018-04-28T18:20:25.880208Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE                                                                                                                                                             '
2018-04-28T18:20:25.880224Z 0 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2018-04-28T18:20:25.880590Z 0 [Note] Shutting down plugin 'INNODB_FT_BEING_DELET                                                                                                                                                             ED'
2018-04-28T18:20:25.880615Z 0 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2018-04-28T18:20:25.880632Z 0 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STO                                                                                                                                                             PWORD'
2018-04-28T18:20:25.880673Z 0 [Note] Shutting down plugin 'INNODB_METRICS'
2018-04-28T18:20:25.880691Z 0 [Note] Shutting down plugin 'INNODB_TEMP_TABLE_INF                                                                                                                                                             O'
2018-04-28T18:20:25.880707Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_ST                                                                                                                                                             ATS'
2018-04-28T18:20:25.880724Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LR                                                                                                                                                             U'
2018-04-28T18:20:25.880780Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2018-04-28T18:20:25.880801Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_                                                                                                                                                             RESET'
2018-04-28T18:20:25.880856Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2018-04-28T18:20:25.880877Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2018-04-28T18:20:25.880893Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM'
2018-04-28T18:20:25.880909Z 0 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2018-04-28T18:20:25.880925Z 0 [Note] Shutting down plugin 'INNODB_CMP'
2018-04-28T18:20:25.880940Z 0 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2018-04-28T18:20:25.880956Z 0 [Note] Shutting down plugin 'INNODB_LOCKS'
2018-04-28T18:20:25.880971Z 0 [Note] Shutting down plugin 'INNODB_TRX'
2018-04-28T18:20:25.881128Z 0 [Note] Shutting down plugin 'InnoDB'
2018-04-28T18:20:25.881224Z 0 [Note] InnoDB: FTS optimize thread exiting.
2018-04-28T18:20:25.881467Z 0 [Note] InnoDB: Starting shutdown...
2018-04-28T18:20:25.981957Z 0 [Note] InnoDB: Dumping buffer pool(s) to /var/lib/                                                                                                                                                             mysql/ib_buffer_pool
2018-04-28T18:20:25.982633Z 0 [Note] InnoDB: Buffer pool(s) dump completed at 18                                                                                                                                                             0428 18:20:25
2018-04-28T18:20:27.292584Z 0 [Note] InnoDB: Shutdown completed; log sequence nu                                                                                                                                                             mber 12193308
2018-04-28T18:20:27.293330Z 0 [Note] InnoDB: Removed temporary tablespace data f                                                                                                                                                             ile: "ibtmp1"
2018-04-28T18:20:27.293482Z 0 [Note] Shutting down plugin 'MyISAM'
2018-04-28T18:20:27.293548Z 0 [Note] Shutting down plugin 'MRG_MYISAM'
2018-04-28T18:20:27.293588Z 0 [Note] Shutting down plugin 'CSV'
2018-04-28T18:20:27.293606Z 0 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2018-04-28T18:20:27.293649Z 0 [Note] Shutting down plugin 'sha256_password'
2018-04-28T18:20:27.293675Z 0 [Note] Shutting down plugin 'mysql_native_password                                                                                                                                                             '
2018-04-28T18:20:27.293975Z 0 [Note] Shutting down plugin 'binlog'
2018-04-28T18:20:27.295173Z 0 [Note] mysqld: Shutdown complete


MySQL init process done. Ready for start up.

2018-04-28T18:20:27.561704Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is                                                                                                                                                              deprecated. Please use --explicit_defaults_for_timestamp server option (see doc                                                                                                                                                             umentation for more details).
2018-04-28T18:20:27.565916Z 0 [Note] mysqld (mysqld 5.7.22) starting as process                                                                                                                                                              1 ...
2018-04-28T18:20:27.581875Z 0 [Note] InnoDB: PUNCH HOLE support available
2018-04-28T18:20:27.582061Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic                                                                                                                                                              builtins
2018-04-28T18:20:27.582100Z 0 [Note] InnoDB: Uses event mutexes
2018-04-28T18:20:27.582140Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence()                                                                                                                                                              is used for memory barrier
2018-04-28T18:20:27.582159Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2018-04-28T18:20:27.582178Z 0 [Note] InnoDB: Using Linux native AIO
2018-04-28T18:20:27.582894Z 0 [Note] InnoDB: Number of pools: 1
2018-04-28T18:20:27.583181Z 0 [Note] InnoDB: Using CPU crc32 instructions
2018-04-28T18:20:27.587805Z 0 [Note] InnoDB: Initializing buffer pool, total siz                                                                                                                                                             e = 128M, instances = 1, chunk size = 128M
2018-04-28T18:20:27.604328Z 0 [Note] InnoDB: Completed initialization of buffer                                                                                                                                                              pool
2018-04-28T18:20:27.607841Z 0 [Note] InnoDB: If the mysqld execution user is aut                                                                                                                                                             horized, page cleaner thread priority can be changed. See the man page of setpri                                                                                                                                                             ority().
2018-04-28T18:20:27.621769Z 0 [Note] InnoDB: Highest supported file format is Ba                                                                                                                                                             rracuda.
2018-04-28T18:20:27.646979Z 0 [Note] InnoDB: Creating shared tablespace for temp                                                                                                                                                             orary tables
2018-04-28T18:20:27.647101Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12                                                                                                                                                              MB. Physically writing the file full; Please wait ...
2018-04-28T18:20:27.694897Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2018-04-28T18:20:27.696539Z 0 [Note] InnoDB: 96 redo rollback segment(s) found.                                                                                                                                                              96 redo rollback segment(s) are active.
2018-04-28T18:20:27.696594Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are                                                                                                                                                              active.
2018-04-28T18:20:27.697368Z 0 [Note] InnoDB: Waiting for purge to start
2018-04-28T18:20:27.747651Z 0 [Note] InnoDB: 5.7.22 started; log sequence number                                                                                                                                                              12193308
2018-04-28T18:20:27.748244Z 0 [Note] Plugin 'FEDERATED' is disabled.
2018-04-28T18:20:27.748569Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/li                                                                                                                                                             b/mysql/ib_buffer_pool
2018-04-28T18:20:27.760257Z 0 [Note] Found ca.pem, server-cert.pem and server-ke                                                                                                                                                             y.pem in data directory. Trying to enable SSL support using them.
2018-04-28T18:20:27.760722Z 0 [Warning] CA certificate ca.pem is self signed.
2018-04-28T18:20:27.764237Z 0 [Note] Server hostname (bind-address): '*'; port:                                                                                                                                                              3306
2018-04-28T18:20:27.764524Z 0 [Note] IPv6 is available.
2018-04-28T18:20:27.764676Z 0 [Note]   - '::' resolves to '::';
2018-04-28T18:20:27.764727Z 0 [Note] Server socket created on IP: '::'.
2018-04-28T18:20:27.768375Z 0 [Note] InnoDB: Buffer pool(s) load completed at 18                                                                                                                                                             0428 18:20:27
2018-04-28T18:20:27.768848Z 0 [Warning] Insecure configuration for --pid-file: L                                                                                                                                                             ocation '/var/run/mysqld' in the path is accessible to all OS users. Consider ch                                                                                                                                                             oosing a different directory.
2018-04-28T18:20:27.772682Z 0 [Warning] 'user' entry 'root@localhost' ignored in                                                                                                                                                              --skip-name-resolve mode.
2018-04-28T18:20:27.772780Z 0 [Warning] 'user' entry 'mysql.sys@localhost' ignor                                                                                                                                                             ed in --skip-name-resolve mode.
2018-04-28T18:20:27.772821Z 0 [Warning] 'db' entry 'performance_schema mysql.ses                                                                                                                                                             sion@localhost' ignored in --skip-name-resolve mode.
2018-04-28T18:20:27.772886Z 0 [Warning] 'db' entry 'sys mysql.sys@localhost' ign                                                                                                                                                             ored in --skip-name-resolve mode.
2018-04-28T18:20:27.772914Z 0 [Warning] 'proxies_priv' entry '@ root@localhost'                                                                                                                                                              ignored in --skip-name-resolve mode.
2018-04-28T18:20:27.779197Z 0 [Warning] 'tables_priv' entry 'user mysql.session@                                                                                                                                                             localhost' ignored in --skip-name-resolve mode.
2018-04-28T18:20:27.779269Z 0 [Warning] 'tables_priv' entry 'sys_config mysql.sy                                                                                                                                                             s@localhost' ignored in --skip-name-resolve mode.
2018-04-28T18:20:27.829512Z 0 [Note] Event Scheduler: Loaded 0 events
2018-04-28T18:20:27.829855Z 0 [Note] mysqld: ready for connections.
Version: '5.7.22'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  MySQL Comm                                                                                                                                                             unity Server (GPL)
2018-04-28T18:21:36.864024Z 0 [Note] Giving 0 client threads a chance to die gra                                                                                                                                                             cefully
2018-04-28T18:21:36.864054Z 0 [Note] Shutting down slave threads
2018-04-28T18:21:36.864059Z 0 [Note] Forcefully disconnecting 0 remaining client                                                                                                                                                             s
2018-04-28T18:21:36.864068Z 0 [Note] Event Scheduler: Purging the queue. 0 event                                                                                                                                                             s
2018-04-28T18:21:36.864103Z 0 [Note] Binlog end
2018-04-28T18:21:36.865478Z 0 [Note] Shutting down plugin 'ngram'
2018-04-28T18:21:36.865527Z 0 [Note] Shutting down plugin 'BLACKHOLE'
2018-04-28T18:21:36.865548Z 0 [Note] Shutting down plugin 'partition'
2018-04-28T18:21:36.865566Z 0 [Note] Shutting down plugin 'ARCHIVE'
2018-04-28T18:21:36.865581Z 0 [Note] Shutting down plugin 'MEMORY'
2018-04-28T18:21:36.865599Z 0 [Note] Shutting down plugin 'INNODB_SYS_VIRTUAL'
2018-04-28T18:21:36.865615Z 0 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2018-04-28T18:21:36.865632Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACE                                                                                                                                                             S'
2018-04-28T18:21:36.865648Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_CO                                                                                                                                                             LS'
2018-04-28T18:21:36.865685Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2018-04-28T18:21:36.865771Z 0 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2018-04-28T18:21:36.865791Z 0 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2018-04-28T18:21:36.865807Z 0 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2018-04-28T18:21:36.865824Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS                                                                                                                                                             '
2018-04-28T18:21:36.865864Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2018-04-28T18:21:36.865880Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE                                                                                                                                                             '
2018-04-28T18:21:36.865896Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE                                                                                                                                                             '
2018-04-28T18:21:36.865911Z 0 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2018-04-28T18:21:36.865927Z 0 [Note] Shutting down plugin 'INNODB_FT_BEING_DELET                                                                                                                                                             ED'
2018-04-28T18:21:36.865943Z 0 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2018-04-28T18:21:36.865958Z 0 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STO                                                                                                                                                             PWORD'
2018-04-28T18:21:36.865974Z 0 [Note] Shutting down plugin 'INNODB_METRICS'
2018-04-28T18:21:36.865996Z 0 [Note] Shutting down plugin 'INNODB_TEMP_TABLE_INF                                                                                                                                                             O'
2018-04-28T18:21:36.866026Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_ST                                                                                                                                                             ATS'
2018-04-28T18:21:36.866042Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LR                                                                                                                                                             U'
2018-04-28T18:21:36.866058Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2018-04-28T18:21:36.866081Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_                                                                                                                                                             RESET'
2018-04-28T18:21:36.866097Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2018-04-28T18:21:36.866113Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2018-04-28T18:21:36.866129Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM'
2018-04-28T18:21:36.866145Z 0 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2018-04-28T18:21:36.866179Z 0 [Note] Shutting down plugin 'INNODB_CMP'
2018-04-28T18:21:36.866196Z 0 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2018-04-28T18:21:36.866212Z 0 [Note] Shutting down plugin 'INNODB_LOCKS'
2018-04-28T18:21:36.866228Z 0 [Note] Shutting down plugin 'INNODB_TRX'
2018-04-28T18:21:36.866243Z 0 [Note] Shutting down plugin 'InnoDB'
2018-04-28T18:21:36.867007Z 0 [Note] InnoDB: FTS optimize thread exiting.
2018-04-28T18:21:36.867146Z 0 [Note] InnoDB: Starting shutdown...
2018-04-28T18:21:36.967473Z 0 [Note] InnoDB: Dumping buffer pool(s) to /var/lib/                                                                                                                                                             mysql/ib_buffer_pool
2018-04-28T18:21:36.967748Z 0 [Note] InnoDB: Buffer pool(s) dump completed at 18                                                                                                                                                             0428 18:21:36
2018-04-28T18:21:38.282482Z 0 [Note] InnoDB: Shutdown completed; log sequence nu                                                                                                                                                             mber 40839846
2018-04-28T18:21:38.282945Z 0 [Note] InnoDB: Removed temporary tablespace data f                                                                                                                                                             ile: "ibtmp1"
2018-04-28T18:21:38.282997Z 0 [Note] Shutting down plugin 'MyISAM'
2018-04-28T18:21:38.283025Z 0 [Note] Shutting down plugin 'MRG_MYISAM'
2018-04-28T18:21:38.283067Z 0 [Note] Shutting down plugin 'CSV'
2018-04-28T18:21:38.283083Z 0 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2018-04-28T18:21:38.283123Z 0 [Note] Shutting down plugin 'sha256_password'
2018-04-28T18:21:38.283161Z 0 [Note] Shutting down plugin 'mysql_native_password                                                                                                                                                             '
2018-04-28T18:21:38.283295Z 0 [Note] Shutting down plugin 'binlog'
2018-04-28T18:21:38.284312Z 0 [Note] mysqld: Shutdown complete

2018-06-12T19:12:16.861328Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is                                                                                                                                                              deprecated. Please use --explicit_defaults_for_timestamp server option (see doc                                                                                                                                                             umentation for more details).
2018-06-12T19:12:16.862868Z 0 [Note] mysqld (mysqld 5.7.22) starting as process                                                                                                                                                              1 ...
2018-06-12T19:12:16.867103Z 0 [Note] InnoDB: PUNCH HOLE support available
2018-06-12T19:12:16.867162Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic                                                                                                                                                              builtins
2018-06-12T19:12:16.867185Z 0 [Note] InnoDB: Uses event mutexes
2018-06-12T19:12:16.867205Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence()                                                                                                                                                              is used for memory barrier
2018-06-12T19:12:16.867223Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2018-06-12T19:12:16.867241Z 0 [Note] InnoDB: Using Linux native AIO
2018-06-12T19:12:16.868450Z 0 [Note] InnoDB: Number of pools: 1
2018-06-12T19:12:16.870631Z 0 [Note] InnoDB: Using CPU crc32 instructions
2018-06-12T19:12:16.872342Z 0 [Note] InnoDB: Initializing buffer pool, total siz                                                                                                                                                             e = 128M, instances = 1, chunk size = 128M
2018-06-12T19:12:16.881099Z 0 [Note] InnoDB: Completed initialization of buffer                                                                                                                                                              pool
2018-06-12T19:12:16.883847Z 0 [Note] InnoDB: If the mysqld execution user is aut                                                                                                                                                             horized, page cleaner thread priority can be changed. See the man page of setpri                                                                                                                                                             ority().
2018-06-12T19:12:16.903051Z 0 [Note] InnoDB: Highest supported file format is Ba                                                                                                                                                             rracuda.
2018-06-12T19:12:17.016466Z 0 [Note] InnoDB: Creating shared tablespace for temp                                                                                                                                                             orary tables
2018-06-12T19:12:17.016616Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12                                                                                                                                                              MB. Physically writing the file full; Please wait ...
2018-06-12T19:12:17.079635Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2018-06-12T19:12:17.080620Z 0 [Note] InnoDB: 96 redo rollback segment(s) found.                                                                                                                                                              96 redo rollback segment(s) are active.
2018-06-12T19:12:17.080675Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are                                                                                                                                                              active.
2018-06-12T19:12:17.081505Z 0 [Note] InnoDB: Waiting for purge to start
2018-06-12T19:12:17.131756Z 0 [Note] InnoDB: 5.7.22 started; log sequence number                                                                                                                                                              40839846
2018-06-12T19:12:17.132230Z 0 [Note] Plugin 'FEDERATED' is disabled.
2018-06-12T19:12:17.132539Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/li                                                                                                                                                             b/mysql/ib_buffer_pool
2018-06-12T19:12:17.148606Z 0 [Note] Found ca.pem, server-cert.pem and server-ke                                                                                                                                                             y.pem in data directory. Trying to enable SSL support using them.
2018-06-12T19:12:17.149500Z 0 [Warning] CA certificate ca.pem is self signed.
2018-06-12T19:12:17.153243Z 0 [Note] Server hostname (bind-address): '*'; port:                                                                                                                                                              3306
2018-06-12T19:12:17.153326Z 0 [Note] IPv6 is available.
2018-06-12T19:12:17.153353Z 0 [Note]   - '::' resolves to '::';
2018-06-12T19:12:17.153396Z 0 [Note] Server socket created on IP: '::'.
2018-06-12T19:12:17.156349Z 0 [Warning] Insecure configuration for --pid-file: L                                                                                                                                                             ocation '/var/run/mysqld' in the path is accessible to all OS users. Consider ch                                                                                                                                                             oosing a different directory.
2018-06-12T19:12:17.303192Z 0 [Warning] 'user' entry 'root@localhost' ignored in                                                                                                                                                              --skip-name-resolve mode.
2018-06-12T19:12:17.303311Z 0 [Warning] 'user' entry 'mysql.sys@localhost' ignor                                                                                                                                                             ed in --skip-name-resolve mode.
2018-06-12T19:12:17.303586Z 0 [Warning] 'db' entry 'performance_schema mysql.ses                                                                                                                                                             sion@localhost' ignored in --skip-name-resolve mode.
2018-06-12T19:12:17.303634Z 0 [Warning] 'db' entry 'sys mysql.sys@localhost' ign                                                                                                                                                             ored in --skip-name-resolve mode.
error from daemon in stream: Error grabbing logs: invalid character 'l' after ob                                                                                                                                                             ject key:value pair
#14

the last error is 2018-06-12, probably should be something more recent if it was working as recently as a few days ago

#15

yes, was definitely working as of last week. what should i be trying to do at this point?

#16

how about

 docker logs --tail d05167f16b1f
#17

maybe i’m typing that in wrong, i get the error that “docker logs” requires exactly 1 argument(s).

#18

right, try 20 so

 docker logs --tail 20 d05167f16b1f
#19 
root@ip-172-31-31-206:~# docker logs --tail 20 d05167f16b1f
2019-09-18T13:38:35.439327Z 0 [Note] InnoDB: Using CPU crc32 instructions
2019-09-18T13:38:35.441269Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2019-09-18T13:38:35.453940Z 0 [Note] InnoDB: Completed initialization of buffer pool
2019-09-18T13:38:35.458411Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2019-09-18T13:38:35.490242Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2019-09-18T13:38:35.681606Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2019-09-18T13:38:35.681677Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2019-09-18T13:38:35.681837Z 0 [Warning] InnoDB: Retry attempts for writing partial data failed.
2019-09-18T13:38:35.681849Z 0 [ERROR] InnoDB: Write to file ./ibtmp1failed at offset 0, 1048576 bytes should have been written, only 0 were written. Operating system error number 28. Check that your OS and file system support files of this size. Check also that the disk is not full or a disk quota exceeded.
2019-09-18T13:38:35.681859Z 0 [ERROR] InnoDB: Error number 28 means 'No space left on device'
2019-09-18T13:38:35.681863Z 0 [Note] InnoDB: Some operating system error numbers are described at http://dev.mysql.com/doc/refman/5.7/en/operating-system-error-codes.html
2019-09-18T13:38:35.681867Z 0 [ERROR] InnoDB: Could not set the file size of './ibtmp1'. Probably out of disk space
2019-09-18T13:38:35.681871Z 0 [ERROR] InnoDB: Unable to create the shared innodb_temporary
2019-09-18T13:38:35.681874Z 0 [ERROR] InnoDB: Plugin initialization aborted with error Generic error
2019-09-18T13:38:36.182872Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2019-09-18T13:38:36.182900Z 0 [ERROR] Plugin 'InnoDB' init function returned error.
2019-09-18T13:38:36.182905Z 0 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2019-09-18T13:38:36.182910Z 0 [ERROR] Failed to initialize builtin plugins.
2019-09-18T13:38:36.182912Z 0 [ERROR] Aborting
#20

ok, there it is, no more room on the storage, maybe @jesdynf has some easy to follow advice on how to create more room on the mysql volume?