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Our site is having issues with writing to the server and to the db
Add comments here to get more clarity or context around a question. To answer a question, use the “Answer” field below.
Please you need to share more information with us in order to help you.
What db are you using? Is the disk full? Do you use instance or block storage?
Once you share more info we can help.
It’s a drupal site with a CiviCRM integration. MySQL db. The disk is not full. Here are the error logs:
2019-05-01 09:31:16 0x7fd98023e700 InnoDB: Assertion failure in thread 140572134467328 in file row0mysql.cc line 4536
InnoDB: Failing assertion: table->n_rec_locks == 0
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: about forcing recovery.
09:31:16 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.
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 101423 K bytes of memory
Hope that's ok; if not, decrease some variables in the equation.
Thread pointer: 0x7fd8e008d8a0
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
stack_bottom = 7fd98023de70 thread_stack 0x30000
Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (7fd8e009a6a0): is an invalid pointer
Connection ID (thread ID): 17043
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.
2019-05-01T09:31:17.441758Z 0 [Warning] Changed limits: max_open_files: 1024 (requested 5000)
2019-05-01T09:31:17.441819Z 0 [Warning] Changed limits: max_connections: 214 (requested 600)
2019-05-01T09:31:17.441824Z 0 [Warning] Changed limits: table_open_cache: 400 (requested 2000)
2019-05-01T09:31:17.618392Z 0 [Warning] option 'max_allowed_packet': unsigned value 104857600000 adjusted to 1073741824
2019-05-01T09:31:17.618450Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2019-05-01T09:31:17.620726Z 0 [Note] /usr/sbin/mysqld (mysqld 5.7.26-0ubuntu0.16.04.1) starting as process 26973 ...
2019-05-01T09:31:17.626689Z 0 [Note] InnoDB: PUNCH HOLE support available
2019-05-01T09:31:17.626712Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2019-05-01T09:31:17.626723Z 0 [Note] InnoDB: Uses event mutexes
2019-05-01T09:31:17.626730Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2019-05-01T09:31:17.626736Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.8
2019-05-01T09:31:17.626752Z 0 [Note] InnoDB: Using Linux native AIO
2019-05-01T09:31:17.627136Z 0 [Note] InnoDB: Number of pools: 1
2019-05-01T09:31:17.627286Z 0 [Note] InnoDB: Using CPU crc32 instructions
2019-05-01T09:31:17.629588Z 0 [Note] InnoDB: Initializing buffer pool, total size = 32G, instances = 8, chunk size = 128M
2019-05-01T09:31:20.452548Z 0 [Note] InnoDB: Completed initialization of buffer pool
2019-05-01T09:31:21.019893Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2019-05-01T09:31:21.032387Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2019-05-01T09:31:21.470986Z 0 [Note] InnoDB: Log scan progressed past the checkpoint lsn 2525015194905
2019-05-01T09:31:21.491046Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 2525016775564
2019-05-01T09:31:21.491603Z 0 [Note] InnoDB: Database was not shutdown normally!
2019-05-01T09:31:21.491628Z 0 [Note] InnoDB: Starting crash recovery.
2019-05-01T09:31:21.604529Z 0 [Note] InnoDB: 1 transaction(s) which must be rolled back or cleaned up in total 3 row operations to undo
2019-05-01T09:31:21.604565Z 0 [Note] InnoDB: Trx id counter is 1485434368
2019-05-01T09:31:21.627951Z 0 [Note] InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percent: 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 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
2019-05-01T09:31:24.254228Z 0 [Note] InnoDB: Apply batch completed
2019-05-01T09:31:25.119176Z 0 [Note] InnoDB: Starting in background the rollback of uncommitted transactions
2019-05-01T09:31:25.119255Z 0 [Note] InnoDB: Rolling back trx with id 1485433997, 3 rows to undo
2019-05-01T09:31:25.122520Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2019-05-01T09:31:25.122538Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2019-05-01T09:31:25.122602Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2019-05-01T09:31:25.122953Z 0 [Note] InnoDB: Rollback of trx with id 1485433997 completed
2019-05-01T09:31:25.122975Z 0 [Note] InnoDB: Rollback of non-prepared transactions completed
2019-05-01T09:31:25.144212Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2019-05-01T09:31:25.145457Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2019-05-01T09:31:25.145473Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2019-05-01T09:31:25.146205Z 0 [Note] InnoDB: 5.7.26 started; log sequence number 2525016775564
2019-05-01T09:31:25.146211Z 0 [Note] InnoDB: page_cleaner: 1000ms intended loop took 4127ms. The settings might not be optimal. (flushed=0 and evicted=0, during the time.)
2019-05-01T09:31:25.146668Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
2019-05-01T09:31:25.146800Z 0 [Note] Plugin 'FEDERATED' is disabled.
2019-05-01T09:31:25.154755Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key
2019-05-01T09:31:25.154793Z 0 [Note] Server hostname (bind-address): '127.0.0.1'; port: 3306
2019-05-01T09:31:25.154816Z 0 [Note] - '127.0.0.1' resolves to '127.0.0.1';
2019-05-01T09:31:25.154871Z 0 [Note] Server socket created on IP: '127.0.0.1'.
2019-05-01T09:31:25.167106Z 0 [Note] Event Scheduler: Loaded 0 events
2019-05-01T09:31:25.167356Z 0 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.7.26-0ubuntu0.16.04.1' socket: '/var/run/mysqld/mysqld.sock' port: 3306 (Ubuntu)
# The MySQL database server configuration file.
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
# For explanations see
# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
# Here is entries for some specific programs
# The following values assume you have at least 32M ram
socket = /var/run/mysqld/mysqld.sock
nice = 0
# * Basic Settings
user = mysql
pid-file = /var/run/mysqld/mysqld.pid
socket = /var/run/mysqld/mysqld.sock
port = 3306
basedir = /usr
datadir = /var/lib/mysql
tmpdir = /tmp
lc-messages-dir = /usr/share/mysql
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address = 127.0.0.1
# * Fine Tuning
key_buffer_size = 16M
max_allowed_packet = 100000M
thread_stack = 192K
thread_cache_size = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover-options = BACKUP
max_connections = 200
sql_mode = STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION
#table_cache = 64
#thread_concurrency = 10
# * Query Cache Configuration
query_cache_limit = 1M
query_cache_size = 16M
# * Logging and Replication
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file = /var/log/mysql/mysql.log
#general_log = 1
# Error log - should be very few entries.
log_error = /var/log/mysql/error.log
# Here you can see queries with especially long duration
#log_slow_queries = /var/log/mysql/mysql-slow.log
#long_query_time = 10
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
# other settings you may need to change.
#server-id = 1
#log_bin = /var/log/mysql/mysql-bin.log
expire_logs_days = 10
max_binlog_size = 100M
#binlog_do_db = include_database_name
#binlog_ignore_db = include_database_name
# * InnoDB
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
# * Security Features
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
innodb_buffer_pool_size = 32G
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