Compute Engine MYSQL Server CPU Strange - php

Question

I couldn't think what else to title this strange problem.
We have a "Worker" Compute Engine which is a MySQL SLAVE. Its primary role is to process a large set of data and then place it back on the Master. All handled via a PHP Script.
Now the processing of data takes roughly 4 hours to complete. During this time we noticed the following CPU pattern.
What you can see above is the 50% solid CPU starts after a server reboot. Then after about 2 hours its starts to produce a ECG style pattern on the CPu. Around every 5/6 minutes CPU spikes to ~48% then drops over the 5 minutes.
My question is, why. Can anyoen please explain why. We ideally want this server to be Maxing out ots cpu at 100% (50% as there are 2 cores)
The spec of the server: 2 VCPU's with 7.5GB Memory.
As mentioned, if we can have this running full throttle it would be great. Below is the my.cnf
symbolic-links=0
max_connections=256
innodb_thread_concurrency = 0
innodb_additional_mem_pool_size = 1G
innodb_buffer_pool_size = 6G
innodb_flush_log_at_trx_commit = 1
innodb_io_capacity = 800
innodb_flush_method = O_DIRECT
innodb_log_file_size = 24M
query_cache_size = 1G
query_cache_limit = 512M
thread_cache_size = 32
key_buffer_size = 128M
max_allowed_packet = 64M
table_open_cache = 8000
table_definition_cache = 8000
sort_buffer_size = 128M
read_buffer_size = 8M
read_rnd_buffer_size = 4M
myisam_sort_buffer_size = 128M
tmp_table_size = 256M
query_cache_type = 1
join_buffer_size = 256M
wait_timeout = 300
server-id = 2
relay-log = /var/log/mysql/mysql-relay-bin.log
log_bin = /var/log/mysql/mysql-bin.log
log-error=/var/log/mysqld.log
read-only = 1
innodb_flush_log_at_trx_commit=2
I have cleaned up the above to remove any configs with private information which are not relevant to performance.
UPDATE
I have noticed when the VPU starts dropping during the heartbeat section of the graph the PHP script is no longer running. This is impossible, as the script I know takes 4 hours. No errors, and after another 4 hours the data is where I expected it.

Answer 1

Changing innodb_io_capacity = 800 to 1500 will likely reduce your 4 hour elapsed time to process by raising the limit to what you know you can achieve with your slave processing.

Answer 2

For your 7.5G indicated environment, configuration has
innodb_additional_mem_pool_size=1G
innodb_buffer_pool_size=6G
query_cache_size=1G
so before you start, you are overcommitted.
Another angle to consider, with
max_connections=256
max_allowed_packet=64M
could on a fully busy 256 connections need 16GB + just for this function to survive.
It is unlikely max_allowed_packet at 64M is reasonable.
Changing read_rnd_buffer_size = 4M to SET GLOBAL read_rnd_buffer_size=16384; could be significant on your slave then 24 hours later on master. They can be different but if it is significant in reducing your 4 hours on the slave, implement on both instances. Let us know what this single change does for you, please.
The 50% cpu utilization you are seeing is the script maxing out the --- single core that it is capable of utilizing --- . As indicated by PressingOnAlways recently. You can not tune around limit in your running script.
For a more thorough analysis, provide from SLAVE AND MASTER
RAM size (nnG)
SHOW GLOBAL STATUS
SHOW GLOBAL VARIABLES
SHOW INNODB STATUS

Answer 3

CPU % is measured by all the cores - so 100% cpu usage == both cores maxing out. PHP by default runs in a single thread and does not utilize multi-cores. The 50% cpu utilization you are seeing is the script maxing out the single core that it is capable of utilizing.
In order to utilize 100% cpu, consider spawning 2 PHP scripts that work on 2 separate datasets - e.g. script 1 processes records 1-1000000, while script 2 processes 1000001-2000000.
Other option is to rewrite the script to utilize threads. You may want to consider changing the language altogether for something that is more conducive to threads, like Golang? Though this might not be necessary if the main work is done within mysql.
The other issue you're seeing when the graph is below 50% may be due to IO wait. It's hard to tell from a graph though, you may be having a data flow transfer bottleneck where your CPU isn't working and waiting while large bits of data is transferred.
Optimizing CPU utilization is an exercise in finding the bottlenecks and removing them - good luck.

Answer 4

'Monitoring Service' could enabled to periodically capture a 'health check' of your system since it appears to be on a 6 minute cycle when you see spikes.
SHOW GLOBAL STATUS LIKE 'Com_show_%status' may confirm activity of this nature.
Divide your com_show_%status counters by (uptime/3600) to get rate-per-hour.
10 times an hour would be every 6 minutes.