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I have a rather large stored procedure that processes over a hundred thousand records. This SP has been running beautifully until last week when the database server was hit with a ransomware attack. By a HUGE stroke of luck I took an offsite backup of the entire database the night before for testing. Historically the SP ran in under 3 minutes.

We have a new server, same OS, same MySQL version(5.7) same processors and memory(It's a VM) as the corrupted server. The only thing that was lost is the my.ini. IT didn't have the database server in their backup plan. IT found an older copy of the my.ini file which I ran with. The stored proc in now EXTREMELY slow, like a calculated 30 hours to run rather than 3 minutes. Barring something wrong with the VM setup I'm doubting the my.ini I was given.

Pertinent server specs(Where have I gone wrong?):

  • OS: Windows server 2012 R2 64 Bit

  • Available RAM: 9.41G

  • Available Virtual Memory: 6.67 GB

  • Processor:Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz, 2098 Mhz, 1 Core(s), 1 Logical Processor(s)

  • Page File Space: 1.81 GB

my.ini:

# Other default tuning values
# MySQL Server Instance Configuration File
# ----------------------------------------------------------------------
# Generated by the MySQL Server Instance Configuration Wizard
#
#
# Installation Instructions
# ----------------------------------------------------------------------
#
# On Linux you can copy this file to /etc/my.cnf to set global options,
# mysql-data-dir/my.cnf to set server-specific options
# (@localstatedir@ for this installation) or to
# ~/.my.cnf to set user-specific options.
#
# On Windows you should keep this file in the installation directory 
# of your server (e.g. C:\Program Files\MySQL\MySQL Server X.Y). To
# make sure the server reads the config file use the startup option 
# "--defaults-file". 
#
# To run run the server from the command line, execute this in a 
# command line shell, e.g.
# mysqld --defaults-file="C:\Program Files\MySQL\MySQL Server X.Y\my.ini"
#
# To install the server as a Windows service manually, execute this in a 
# command line shell, e.g.
# mysqld --install MySQLXY --defaults-file="C:\Program Files\MySQL\MySQL Server X.Y\my.ini"
#
# And then execute this in a command line shell to start the server, e.g.
# net start MySQLXY
#
#
# Guildlines for editing this file
# ----------------------------------------------------------------------
#
# In this file, you can use all long options that the program supports.
# If you want to know the options a program supports, start the program
# with the "--help" option.
#
# More detailed information about the individual options can also be
# found in the manual.
#
# For advice on how to change settings please see
# http://dev.mysql.com/doc/refman/5.7/en/server-configuration-defaults.html
#
#
# CLIENT SECTION
# ----------------------------------------------------------------------
#
# The following options will be read by MySQL client applications.
# Note that only client applications shipped by MySQL are guaranteed
# to read this section. If you want your own MySQL client program to
# honor these values, you need to specify it as an option during the
# MySQL client library initialization.
#
[client]

# pipe
# socket=0.0
port=3306

[mysql]
no-beep

default-character-set=utf8


# SERVER SECTION
# ----------------------------------------------------------------------
#
# The following options will be read by the MySQL Server. Make sure that
# you have installed the server correctly (see above) so it reads this 
# file.
#
# server_type=2
[mysqld]

# The next three options are mutually exclusive to SERVER_PORT below.
# skip-networking

# enable-named-pipe

# shared-memory

# shared-memory-base-name=MYSQL

# The Pipe the MySQL Server will use
# socket=MYSQL

# The TCP/IP Port the MySQL Server will listen on
port=3306

wait_timeout=2147483


# Path to installation directory. All paths are usually resolved relative to this.
# basedir="C:/Program Files/MySQL/MySQL Server 5.7/"

# Path to the database root
datadir=C:/ProgramData/MySQL/MySQL Server 5.7/Data

# The default character set that will be used when a new schema or table is
# created and no character set is defined
character-set-server=utf8

# The default storage engine that will be used when create new tables when
default-storage-engine=INNODB

# Set the SQL mode to strict
sql-mode="STRICT_TRANS_TABLES,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION"


#
# * Query Cache Configuration
#
query_cache_limit        = 2M
query_cache_min_res_unit = 512k
query_cache_size         = 200M



# General and Slow logging.
log-output=FILE
general-log=0
general_log_file="PUPIL-PBP.log"
slow-query-log=1
slow_query_log_file="PUPIL-PBP-slow.log"
long_query_time=10

# Binary Logging.
# log-bin

# Error Logging.
log-error="PUPIL-PBP.err"

# Server Id.
server-id=1

# Secure File Priv.
secure-file-priv="C:/ProgramData/MySQL/MySQL Server 5.7/Uploads"

# The maximum amount of concurrent sessions the MySQL server will
# allow. One of these connections will be reserved for a user with
# SUPER privileges to allow the administrator to login even if the
# connection limit has been reached.
max_connections=151

# The number of open tables for all threads. Increasing this value
# increases the number of file descriptors that mysqld requires.
# Therefore you have to make sure to set the amount of open files
# allowed to at least 4096 in the variable "open-files-limit" in
# section [mysqld_safe]
table_open_cache=2000

# Maximum size for internal (in-memory) temporary tables. If a table
# grows larger than this value, it is automatically converted to disk
# based table This limitation is for a single table. There can be many
# of them.
tmp_table_size=512M

# How many threads we should keep in a cache for reuse. When a client
# disconnects, the client's threads are put in the cache if there aren't
# more than thread_cache_size threads from before.  This greatly reduces
# the amount of thread creations needed if you have a lot of new
# connections. (Normally this doesn't give a notable performance
# improvement if you have a good thread implementation.)
thread_stack            = 192K
thread_cache_size       = 100

#*** MyISAM Specific options
# The maximum size of the temporary file MySQL is allowed to use while
# recreating the index (during REPAIR, ALTER TABLE or LOAD DATA INFILE.
# If the file-size would be bigger than this, the index will be created
# through the key cache (which is slower).
myisam_max_sort_file_size=100G

# If the temporary file used for fast index creation would be bigger
# than using the key cache by the amount specified here, then prefer the
# key cache method.  This is mainly used to force long character keys in
# large tables to use the slower key cache method to create the index.
myisam_sort_buffer_size=8M

# Size of the Key Buffer, used to cache index blocks for MyISAM tables.
# Do not set it larger than 30% of your available memory, as some memory
# is also required by the OS to cache rows. Even if you're not using
# MyISAM tables, you should still set it to 8-64M as it will also be
# used for internal temporary disk tables.
key_buffer_size=512M

# Size of the buffer used for doing full table scans of MyISAM tables.
# Allocated per thread, if a full scan is needed.
read_buffer_size=0

read_rnd_buffer_size=0

#*** INNODB Specific options ***
# innodb_data_home_dir=0.0

# Use this option if you have a MySQL server with InnoDB support enabled
# but you do not plan to use it. This will save memory and disk space
# and speed up some things.
# skip-innodb

# If set to 1, InnoDB will flush (fsync) the transaction logs to the
# disk at each commit, which offers full ACID behavior. If you are
# willing to compromise this safety, and you are running small
# transactions, you may set this to 0 or 2 to reduce disk I/O to the
# logs. Value 0 means that the log is only written to the log file and
# the log file flushed to disk approximately once per second. Value 2
# means the log is written to the log file at each commit, but the log
# file is only flushed to disk approximately once per second.
innodb_flush_log_at_trx_commit=0

# The size of the buffer InnoDB uses for buffering log data. As soon as
# it is full, InnoDB will have to flush it to disk. As it is flushed
# once per second anyway, it does not make sense to have it very large
# (even with long transactions).
innodb_log_buffer_size=256M

# InnoDB, unlike MyISAM, uses a buffer pool to cache both indexes and
# row data. The bigger you set this the less disk I/O is needed to
# access data in tables. On a dedicated database server you may set this
# parameter up to 80% of the machine physical memory size. Do not set it
# too large, though, because competition of the physical memory may
# cause paging in the operating system.  Note that on 32bit systems you
# might be limited to 2-3.5G of user level memory per process, so do not
# set it too high.
innodb_buffer_pool_size=4G

# Size of each log file in a log group. You should set the combined size
# of log files to about 25%-100% of your buffer pool size to avoid
# unneeded buffer pool flush activity on log file overwrite. However,
# note that a larger logfile size will increase the time needed for the
# recovery process.
innodb_log_file_size=1G

# Number of threads allowed inside the InnoDB kernel. The optimal value
# depends highly on the application, hardware as well as the OS
# scheduler properties. A too high value may lead to thread thrashing.
innodb_thread_concurrency=8

# The increment size (in MB) for extending the size of an auto-extend InnoDB system tablespace file when it becomes full.
innodb_autoextend_increment=64

# The number of regions that the InnoDB buffer pool is divided into.
# For systems with buffer pools in the multi-gigabyte range, dividing the buffer pool into separate instances can improve concurrency,
# by reducing contention as different threads read and write to cached pages.
innodb_buffer_pool_instances=8

# Determines the number of threads that can enter InnoDB concurrently.
innodb_concurrency_tickets=5000

# Specifies how long in milliseconds (ms) a block inserted into the old sublist must stay there after its first access before
# it can be moved to the new sublist.
innodb_old_blocks_time=1000

# It specifies the maximum number of .ibd files that MySQL can keep open at one time. The minimum value is 10.
innodb_open_files=300

# When this variable is enabled, InnoDB updates statistics during metadata statements.
innodb_stats_on_metadata=0

# When innodb_file_per_table is enabled (the default in 5.6.6 and higher), InnoDB stores the data and indexes for each newly created table
# in a separate .ibd file, rather than in the system tablespace.
innodb_file_per_table=1

# Use the following list of values: 0 for crc32, 1 for strict_crc32, 2 for innodb, 3 for strict_innodb, 4 for none, 5 for strict_none.
innodb_checksum_algorithm=0

# The number of outstanding connection requests MySQL can have.
# This option is useful when the main MySQL thread gets many connection requests in a very short time.
# It then takes some time (although very little) for the main thread to check the connection and start a new thread.
# The back_log value indicates how many requests can be stacked during this short time before MySQL momentarily
# stops answering new requests.
# You need to increase this only if you expect a large number of connections in a short period of time.
back_log=80

# If this is set to a nonzero value, all tables are closed every flush_time seconds to free up resources and
# synchronize unflushed data to disk.
# This option is best used only on systems with minimal resources.
flush_time=0

# The minimum size of the buffer that is used for plain index scans, range index scans, and joins that do not use
# indexes and thus perform full table scans.
join_buffer_size=256K

# The maximum size of one packet or any generated or intermediate string, or any parameter sent by the
# mysql_stmt_send_long_data() C API function.
max_allowed_packet=32M

# If more than this many successive connection requests from a host are interrupted without a successful connection,
# the server blocks that host from performing further connections.
max_connect_errors=100

# Changes the number of file descriptors available to mysqld.
# You should try increasing the value of this option if mysqld gives you the error "Too many open files".
open_files_limit=4161

# If you see many sort_merge_passes per second in SHOW GLOBAL STATUS output, you can consider increasing the
# sort_buffer_size value to speed up ORDER BY or GROUP BY operations that cannot be improved with query optimization
# or improved indexing.
sort_buffer_size=256K

# The number of table definitions (from .frm files) that can be stored in the definition cache.
# If you use a large number of tables, you can create a large table definition cache to speed up opening of tables.
# The table definition cache takes less space and does not use file descriptors, unlike the normal table cache.
# The minimum and default values are both 400.
table_definition_cache=1400

# Specify the maximum size of a row-based binary log event, in bytes.
# Rows are grouped into events smaller than this size if possible. The value should be a multiple of 256.
binlog_row_event_max_size=8K

# If the value of this variable is greater than 0, a replication slave synchronizes its master.info file to disk.
# (using fdatasync()) after every sync_master_info events.
sync_master_info=10000

# If the value of this variable is greater than 0, the MySQL server synchronizes its relay log to disk.
# (using fdatasync()) after every sync_relay_log writes to the relay log.
sync_relay_log=10000

# If the value of this variable is greater than 0, a replication slave synchronizes its relay-log.info file to disk.
# (using fdatasync()) after every sync_relay_log_info transactions.
sync_relay_log_info=10000

# Load mysql plugins at start."plugin_x ; plugin_y".
plugin_load="mysqlx"

# MySQL server's plugin configuration.
loose_mysqlx_port=33060

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  • 1
    Please consider reading this advice
    – mustaccio
    Feb 2, 2022 at 20:31
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    Additional information request, please. Any SSD or NVME devices on MySQL Host server? Post on pastebin.com and share the links. From your SSH login root, Text results of: A) SELECT COUNT(*) FROM information_schema.tables; B) SHOW GLOBAL STATUS; after minimum 24 hours UPTIME C) SHOW GLOBAL VARIABLES; D) SHOW FULL PROCESSLIST; for server workload tuning analysis to provide suggestions. Feb 2, 2022 at 20:47
  • Please post your COMPLETE my.ini - nothing removed so we can see what you are dealing with. ALERT, there is no [mysqld] section in what you have posted. Usually considered to be a SERIOUS omission in configuration. Feb 2, 2022 at 20:55
  • I must have been a little overzealous in removing the fluff. It has a mysqld section. Will re-post full fluffy my.ini
    – Mark Clark
    Feb 2, 2022 at 21:03
  • Thanks, that will help. Feb 2, 2022 at 21:04

1 Answer 1

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One thing to look at perhaps is the charset and collation on the new database. I had a similar situation, very slow stored procedures and there was a mismatch. Also see Stored Procedure Is Slower Than Query Due to Collation.

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