E_WARNING: Error while sending STMT_PREPARE packet. PID=*

Re Slowlog: Show us your my.cnf. Were the changes in the [mysqld] section? Test it via SELECT SLEEP(12);, then look both in the file and the table.

Alternate way to find the query: Since the query is taking several minutes, do SHOW FULL PROCESSLIST; when you think it might be running.

How much RAM do you have? Do not have max_allowed_packet=300M unless you have at least 30GB of RAM. Else you are risking swapping (or even crashing). Keep that setting under 1% of RAM.

For further analysis of tunables, please provide (1) RAM size, (2) SHOW VARIABLES; and (3) SHOW GLOBAL STATUS;.

Re deleted_at: That link you gave starts with "The column deleted_at is not a good index candidate". You misinterpreted it. It is talking about a single-column INDEX(deleted_at). I am suggesting a composite index such as INDEX(contact_id, job_class_name, execute_at, deleted_at).

158 seconds for a simple query on a small table? It could be that there is a lot of other stuff going on. Get the PROCESSLIST.

Re Separate indexes versus composite: Think of two indexes: INDEX(last_name) and INDEX(first_name). You flip through the last_name index to find "James", then what can you do? Flipping through the other index for "Rick" won't help you find me.

Analysis of VARIABLES and GLOBAL STATUS

Observations:

• Version: 5.7.22-log
• 1.00 GB of RAM
• Uptime = 16d 10:30:19
• Are you sure this was a SHOW GLOBAL STATUS ?
• You are not running on Windows.
• Running 64-bit version
• You appear to be running entirely (or mostly) InnoDB.

The More Important Issues:

innodb_buffer_pool_size -- I thought you had it at 213M, not 10M. 10M is much too small. On the other hand, you seem to have less than that much data.

Since the RAM is so small, I recommend dropping tmp_table_size and max_heap_table_size and max_allowed_packet to 8M.And lower table_open_cache, table_definition_cache, and innodb_open_files to 500.

What causes so many simultaneous connections?

Details and other observations:

( innodb_buffer_pool_size / _ram ) = 10M / 1024M = 0.98% -- % of RAM used for InnoDB buffer_pool

( innodb_buffer_pool_size ) = 10M -- InnoDB Data + Index cache

( innodb_lru_scan_depth ) = 1,024-- "InnoDB: page_cleaner: 1000ms intended loop took ..." may be fixed by lowering lru_scan_depth

( Innodb_buffer_pool_pages_free / Innodb_buffer_pool_pages_total ) = 375 / 638 = 58.8% -- Pct of buffer_pool currently not in use-- innodb_buffer_pool_size is bigger than necessary?

( Innodb_buffer_pool_bytes_data / innodb_buffer_pool_size ) = 4M / 10M = 40.0% -- Percent of buffer pool taken up by data-- A small percent may indicate that the buffer_pool is unnecessarily big.

( innodb_log_buffer_size / _ram ) = 16M / 1024M = 1.6% -- Percent of RAM used for buffering InnoDB log writes.-- Too large takes away from other uses for RAM.

( innodb_log_file_size * innodb_log_files_in_group / innodb_buffer_pool_size ) = 48M * 2 / 10M = 960.0% -- Ratio of log size to buffer_pool size. 50% is recommended, but see other calculations for whether it matters.-- The log does not need to be bigger than the buffer pool.

( innodb_flush_method ) = innodb_flush_method = -- How InnoDB should ask the OS to write blocks. Suggest O_DIRECT or O_ALL_DIRECT (Percona) to avoid double buffering. (At least for Unix.) See chrischandler for caveat about O_ALL_DIRECT

( innodb_flush_neighbors ) = 1 -- A minor optimization when writing blocks to disk.-- Use 0 for SSD drives; 1 for HDD.

( innodb_io_capacity ) = 200 -- I/O ops per second capable on disk . 100 for slow drives; 200 for spinning drives; 1000-2000 for SSDs; multiply by RAID factor.

( innodb_print_all_deadlocks ) = innodb_print_all_deadlocks = OFF -- Whether to log all Deadlocks.-- If you are plagued with Deadlocks, turn this on. Caution: If you have lots of deadlocks, this may write a lot to disk.

( min( tmp_table_size, max_heap_table_size ) / _ram ) = min( 16M, 16M ) / 1024M = 1.6% -- Percent of RAM to allocate when needing MEMORY table (per table), or temp table inside a SELECT (per temp table per some SELECTs). Too high may lead to swapping.-- Decrease tmp_table_size and max_heap_table_size to, say, 1% of ram.

( net_buffer_length / max_allowed_packet ) = 16,384 / 16M = 0.10%

( local_infile ) = local_infile = ON-- local_infile = ON is a potential security issue

( Select_scan / Com_select ) = 111,324 / 264144 = 42.1% -- % of selects doing full table scan. (May be fooled by Stored Routines.)-- Add indexes / optimize queries

( long_query_time ) = 10 -- Cutoff (Seconds) for defining a "slow" query.-- Suggest 2

( Max_used_connections / max_connections ) = 152 / 151 = 100.7% -- Peak % of connections-- increase max_connections and/or decrease wait_timeout

You have the Query Cache half-off. You should set both query_cache_type = OFF and query_cache_size = 0 . There is (according to a rumor) a 'bug' in the QC code that leaves some code on unless you turn off both of those settings.

Abnormally small:

( Innodb_pages_read + Innodb_pages_written ) / Uptime = 0.186Created_tmp_files = 0.015 /HRHandler_write = 0.21 /secInnodb_buffer_pool_bytes_data = 3 /secInnodb_buffer_pool_pages_data = 256Innodb_buffer_pool_pages_total = 638Key_reads+Key_writes + Innodb_pages_read+Innodb_pages_written+Innodb_dblwr_writes+Innodb_buffer_pool_pages_flushed = 0.25 /secTable_locks_immediate = 2.8 /HRTable_open_cache_hits = 0.44 /secinnodb_buffer_pool_chunk_size = 5MB

Abnormally large:

Com_create_db = 0.41 /HRCom_drop_db = 0.41 /HRConnection_errors_peer_address = 2Performance_schema_file_instances_lost = 9Ssl_default_timeout = 500

Abnormal strings:

ft_boolean_syntax = + -><()~*:&have_ssl = YEShave_symlink = DISABLEDinnodb_fast_shutdown = 1optimizer_trace = enabled=off,one_line=offoptimizer_trace_features = greedy_search=on, range_optimizer=on, dynamic_range=on, repeated_subselect=onsession_track_system_variables = time_zone, autocommit, character_set_client, character_set_results, character_set_connectionslave_rows_search_algorithms = TABLE_SCAN,INDEX_SCAN

I encountered the same situation on a long-running PHP CLI script (it listens on a Redis list ; each action is quick but the script basically runs for ever).

I create the PDO object and a prepared statement at the beginning, then reuse them afterwards.

The day after I started the script, I got the exact same errors:

PHP Warning:  Error while sending STMT_EXECUTE packet. PID=9438 in /...redacted.../myscript.php on line 39SQLSTATE[HY000]: General error: 2006 MySQL server has gone away

In my case, it's a development server, there is no load, MySQL is on the same box... so it's unlikely to come from external factors.It's most likely related to the fact I used the same MySQL connection for too long, and it timed out. And PDO doesn't bother, so any subsequent query will just return "MySQL server has gone away".

Checking the value of "wait_timeout" in MySQL:

mysql> show variables like 'wait_timeout';+---------------+-------+| Variable_name | Value |+---------------+-------+| wait_timeout  | 28800 |+---------------+-------+1 row in set (0.06 sec)mysql> show local variables like 'wait_timeout';+---------------+-------+| Variable_name | Value |+---------------+-------+| wait_timeout  | 28800 |+---------------+-------+1 row in set (0.00 sec)

I see 28800 seconds = 8 hours, which seems coherent with the timing of my errors.

In my case, restarting the MySQL server, or setting wait_timeout very low, while keeping the same PHP worker running, makes it very easy to reproduce the issue.

Overall:

• PDO doesn't care if the connection times out, and will not automatically reconnect. If you put a try/catch around your PDO queries, the script will never crash and keep using the obsolete PDO instance.
• the STMT_EXECUTE warning is probably incidental ; just because the script whose connection timed out was using prepared statements, and the first query post-timeout happened to be using a prepared statement

To get back to your case

• in theory Laravel 5 is immune to this issue: https://blog.armen.im/en/laravel-4-and-stmt_prepare-error/ ; do you use something other than Illuminate, or even bare PDO directly? Also, I'm not sure what Laravel does when it detects a lost connection (does it reconnect and rebuild prepared statements?), it might be worth digging further.
• check your MySQL wait_timeout value, and increase it if it's too low
• if it's not happening all the time, see if the errors correlate with server / DB load. High load can make things (especially big SQL queries) several times slower, to the point some other MySQL timeout like max_execution_time gets reached.
• see if you wrapped PDO queries in a try / catch block and use it to retry the query ; it might be preventing the connection error from bubbling up.

If you see this message randomly, possible reasons:

1. Your MySQL is behind a proxy, and they are using different timeout config.

2. You are using PHP's persist connection.

You may try to dig into the problem by these steps:

1. Make sure your connections to MySQL have long enough timeout (eg: proxy setting, MySQL's wait_timeout / interactive_timeout)

2. Disable the persist connection at PHP side.

3. Do some tcpdump if you can to see what happend when you got the error message.