Personal blog of Yzmir Ramirez

In this blog post, we’ll look at does the Meltdown fix affect performance for MySQL on bare metal servers.

Since the news about the Meltdown bug, there were a lot of reports on the performance hit from proposed fixes. We have looked at how the fix affects MySQL (Percona Server for MySQL) under a sysbench workload.

In this case, we used bare metal boxes with the following specifications:

• Two-socket Intel(R) Xeon(R) CPU E5-2683 v3 @ 2.00GHz (in total 56 entries in /proc/cpuinfo)
• Ubuntu 16.04
• Memory: 256GB
• Storage: Samsung SM863 1.9TB SATA SSD
• Percona Server for MySQL 5.7.20
• Kernel (vulnerable) 4.13.0-21
• Kernel (with Meltdown fix) 4.13.0-25

Please note, the current kernel for Ubuntu 16.04 contains only a Meltdown fix, and not one for Spectre.

We performed the validation with the https://github.com/speed47/spectre-meltdown-checker tool. The database size is 100GB in a sysbench workload with 100 tables, 4mln rows each with Pareto distribution.

We have used a socket connection and TCP host connection to measure a possible overhead from the TCP network connection. We also perform read-write and read-only benchmarks.

The results are below for a various number of threads:

Where

• Nokpti: kernel without KPTI patch (4.13.0-21)
• Pti: kernel with KPTI patch (4.13.0-25), with PTI enabled
• Nopti: kernel with KPTI patch (4.13.0-25), with PTI disabled

 

	testname	bp	socket	threads	pti	nopti	nokpti	nopti_pct	pti_pct
1	OLTP_RO	in-memory	tcp_socket	1	709.93	718.47	699.50	-2.64	-1.47
4	OLTP_RO	in-memory	tcp_socket	8	5473.05	5500.08	5483.40	-0.30	0.19
3	OLTP_RO	in-memory	tcp_socket	64	21716.18	22036.98	21548.46	-2.22	-0.77
2	OLTP_RO	in-memory	tcp_socket	128	21606.02	22010.36	21548.62	-2.10	-0.27
5	OLTP_RO	in-memory	unix_socket	1	750.41	759.33	776.88	2.31	3.53
8	OLTP_RO	in-memory	unix_socket	8	5851.80	5896.86	5986.89	1.53	2.31
7	OLTP_RO	in-memory	unix_socket	64	23052.10	23552.26	23191.48	-1.53	0.60
6	OLTP_RO	in-memory	unix_socket	128	23215.38	23602.64	23146.42	-1.93	-0.30
9	OLTP_RO	io-bound	tcp_socket	1	364.03	369.68	370.51	0.22	1.78
12	OLTP_RO	io-bound	tcp_socket	8	3205.05	3225.21	3210.63	-0.45	0.17
11	OLTP_RO	io-bound	tcp_socket	64	15324.66	15456.44	15364.25	-0.60	0.26
10	OLTP_RO	io-bound	tcp_socket	128	17705.29	18007.45	17748.70	-1.44	0.25
13	OLTP_RO	io-bound	unix_socket	1	421.74	430.10	432.88	0.65	2.64
16	OLTP_RO	io-bound	unix_socket	8	3322.19	3367.46	3367.34	-0.00	1.36
15	OLTP_RO	io-bound	unix_socket	64	15977.28	16186.59	16248.42	0.38	1.70
14	OLTP_RO	io-bound	unix_socket	128	18729.10	19111.55	18962.02	-0.78	1.24
17	OLTP_RW	in-memory	tcp_socket	1	490.76	495.21	489.49	-1.16	-0.26
20	OLTP_RW	in-memory	tcp_socket	8	3445.66	3459.16	3414.36	-1.30	-0.91
19	OLTP_RW	in-memory	tcp_socket	64	11165.77	11167.44	10861.44	-2.74	-2.73
18	OLTP_RW	in-memory	tcp_socket	128	12176.96	12226.17	12204.85	-0.17	0.23
21	OLTP_RW	in-memory	unix_socket	1	530.08	534.98	540.27	0.99	1.92
24	OLTP_RW	in-memory	unix_socket	8	3734.93	3757.98	3772.17	0.38	1.00
23	OLTP_RW	in-memory	unix_socket	64	12042.27	12160.86	12138.01	-0.19	0.80
22	OLTP_RW	in-memory	unix_socket	128	12930.34	12939.02	12844.78	-0.73	-0.66
25	OLTP_RW	io-bound	tcp_socket	1	268.08	270.51	270.71	0.07	0.98
28	OLTP_RW	io-bound	tcp_socket	8	1585.39	1589.30	1557.58	-2.00	-1.75
27	OLTP_RW	io-bound	tcp_socket	64	4828.30	4782.42	4620.57	-3.38	-4.30
26	OLTP_RW	io-bound	tcp_socket	128	5158.66	5172.82	5321.03	2.87	3.15
29	OLTP_RW	io-bound	unix_socket	1	280.54	282.06	282.35	0.10	0.65
32	OLTP_RW	io-bound	unix_socket	8	1582.69	1584.52	1601.26	1.06	1.17
31	OLTP_RW	io-bound	unix_socket	64	4519.45	4485.72	4515.28	0.66	-0.09
30	OLTP_RW	io-bound	unix_socket	128	5524.28	5460.03	5275.53	-3.38	-4.50

 

As you can see, there is very little difference between runs (in 3-4% range), which fits into variance during the test.

Similar experiments were done on different servers and workloads:

• https://github.com/Percona-Lab-results/201701-meltdown-OLTP-ro/blob/master/smperf-ubuntu-results.md
• https://github.com/Percona-Lab-results/201701-meltdown-OLTP-ro/blob/master/centos-res.md

There also we see a negligible difference that fits into measurement variance.

Overhead analysis

To understand why we do not see much effect in MySQL (InnoDB workloads), let’s take a look where we expect to see the overhead from the proposed fix.

The main overhead is expected from a system call, so let’s test syscall execution on the kernel before the fix and after the fix (thanks for Alexey Kopytov for an idea how to test it with sysbench).

We will use the following script syscall.lua:

ffi.cdef[[long syscall(long, long, long, long);]]
function event()
 for i = 1, 10000 do
 ffi.C.syscall(0, 0, 0, 0)
 end
end

Basically, we measure the time for executing 10000 system calls (this will be one event).

To run benchmark:

sysbench syscall.lua --time=60 --report-interval=1 run

 

And the results are following:

• On the kernel without the fix (4.13.0-21): 455 events/sec
• On the kernel with the fix (4.13.0-26): 250 events/sec

This means that time to execute 10000 system calls increased from 2.197ms to 4ms.

While this increase looks significant, it does not have much effect on MySQL (InnoDB engine). In MySQL, you can expect most system calls done for IO or network communication.

We can assume that the time to execute 10000 IO events on the fast storage takes 1000ms, so adding an extra 2ms for the system calls corresponds to adding 0.2% in overhead (which is practically invisible in MySQL workloads).

I expect the effect will be much more visible if we work with MyISAM tables cached in OS memory. In this case, the syscall overhead would be much more visible when accessing data in memory.

Conclusion:

From our results, we do not see a measurable effect from KPTI patches (to mitigate the Meltdown vulnerability) running on bare metal servers with Ubuntu 16.04 and 4.13 kernel series.

Reference commands and configs:

sysbench oltp_read_only.lua   {--mysql-socket=/tmp/mysql.sock|--mysql-host=127.0.0.1} --mysql-user=root
--mysql-db=sbtest100t4M --rand-type=pareto  --tables=100  --table-size=4000000 --num-threads=$threads --report-interval=1
--max-time=180 --max-requests=0  run

RW:

sysbench oltp_read_write.lua   {--mysql-socket=/tmp/mysql.sock|--mysql-host=127.0.0.1} --mysql-user=root
--mysql-db=sbtest100t4M --rand-type=pareto  --tables=100  --table-size=4000000 --num-threads=$threads --report-interval=1
--max-time=180 --max-requests=0  run

mysqld:
Percona Server 5.7.20-19

numactl --physcpubind=all --interleave=all   /usr/bin/env LD_PRELOAD=/data/opt/alexey.s/bin64_5720.ps/lib/mysql/libjemalloc.so.1 ./bin/mysqld
--defaults-file=/data/opt/alexey.s/my-perf57.cnf --basedir=. --datadir=/data/sam/sbtest100t4M   --user=root  --innodb_flush_log_at_trx_commit=1
--innodb-buffer-pool-size=150GB --innodb-log-file-size=10G --innodb-buffer-pool-instances=8  --innodb-io-capacity-max=20000
--innodb-io-capacity=10000 --loose-innodb-page-cleaners=8 --ssl=0

My.cnf file:

[mysqld]
user=root
port=3306
innodb_status_file=0
innodb_data_file_path=ibdata1:100M:autoextend
innodb_flush_log_at_trx_commit = 1
innodb_file_per_table = true
innodb_log_buffer_size = 128M
innodb_log_file_size = 10G
innodb_log_files_in_group = 2
innodb_write_io_threads=8
innodb_read_io_threads=8
innodb_io_capacity=15000
innodb_io_capacity_max=25000
innodb_lru_scan_depth=8192
#innodb_buffer_pool_size=${BP}G
innodb_doublewrite=1
innodb_thread_concurrency=0
innodb-checksum-algorithm=strict_crc32
innodb_flush_method=O_DIRECT_NO_FSYNC
innodb_purge_threads=8
loose-innodb-page-cleaners=8
innodb_buffer_pool_instances=8
innodb_change_buffering=none
innodb_adaptive_hash_index=OFF
sync_binlog=0
max_connections=5000
table_open_cache=5000
query_cache_type=OFF
thread_cache_size=16
back_log=2000
connect_timeout=15
skip-grant-tables
sort_buffer_size=262144
key_buffer_size=8388608
join_buffer_size=262144
server-id=1
max_connections=50000
skip_name_resolve=ON
max_prepared_stmt_count=1048560
performance_schema=OFF
performance-schema-instrument='wait/synch/%=ON'
innodb_monitor_enable=all
innodb_flush_neighbors=0
metadata_locks_hash_instances=256
table_open_cache_instances=64