Identifying resource bottlenecks – CPU

One of the first steps when addressing a MySQL performance tuning problem is to perform a system audit of the physical hardware resources, then identify any obvious bottlenecks in these resources.

When dealing with CPU, a quick audit should include identifying the number of CPU cores your server has, and the types of these cores. The key file on Linux systems is /proc/cpuinfo.

Number of cores can be found via the command cat /proc/cpuinfo | grep “^processor” | wc -l

You need to look more closely at the file to determine the type of CPU (e.g. below the model name shows Intel(R) Xeon(R) CPU X3220 @ 2.40GHz. The combination of knowing the number of processors (cores) listed and physical id and siblings helps identify how many CPUs and how many cores per CPU exist.

$ cat /proc/cpuinfo
processor	: 0
vendor_id	: GenuineIntel
cpu family	: 6
model		: 15
model name	: Intel(R) Xeon(R) CPU           X3220  @ 2.40GHz
stepping	: 11
cpu MHz		: 2394.051
cache size	: 4096 KB
physical id	: 0
siblings	: 4
core id		: 0
cpu cores	: 4
fpu		: yes
fpu_exception	: yes
cpuid level	: 10
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall nx lm constant_tsc pni monitor ds_cpl vmx est tm2 cx16 xtpr lahf_lm
bogomips	: 4789.96
clflush size	: 64
cache_alignment	: 64
address sizes	: 36 bits physical, 48 bits virtual
power management:

...

Other commands that help with identifying CPU/cores include mpstat and top.

$ mpstat -P ALL 5

11:43:43 AM  CPU   %user   %nice    %sys %iowait    %irq   %soft  %steal   %idle    intr/s
11:43:48 AM  all    0.00    0.00    0.00    0.00    0.05    0.00    0.00   99.95   1033.00
11:43:48 AM    0    0.00    0.00    0.00    0.00    0.00    0.00    0.00  100.00   1000.40
11:43:48 AM    1    0.00    0.00    0.00    0.00    0.00    0.00    0.00  100.00      0.00
11:43:48 AM    2    0.00    0.00    0.00    0.00    0.00    0.00    0.00  100.00     31.40
11:43:48 AM    3    0.00    0.00    0.00    0.00    0.00    0.00    0.00  100.00      1.00
$ top
0

top - 11:42:09 up 36 days, 13:17,  2 users,  load average: 0.20, 0.24, 0.25
Tasks: 133 total,   1 running, 132 sleeping,   0 stopped,   0 zombie
Cpu0  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu1  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu2  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu3  :  0.0%us,  0.3%sy,  0.0%ni, 99.7%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Mem:   4050776k total,  3825584k used,   225192k free,   397580k buffers
Swap:  1052248k total,      128k used,  1052120k free,  2302408k cached

You can easily identify a CPU bottleneck using the vmstat command.

The following shows an idle system.

$ vmstat 1
procs -----------memory---------- ---swap-- -----io---- --system-- -----cpu------
 r  b   swpd   free   buff  cache   si   so    bi    bo   in   cs us sy id wa st
 0  0    128 234088 409632 2474372    0    0     0     0 1081  198  0  0 100  0  0
 0  0    128 234088 409632 2474396    0    0     0     0 1003   59  0  0 100  0  0
 0  0    128 234088 409636 2474392    0    0     0   100 1085  209  0  0 100  0  0
 0  0    128 233836 409636 2474396    0    0     0     0 1014  184  3  0 97  0  0
 0  0    128 233284 409636 2474396    0    0     0     0 1182  435  2  0 98  0  0
 0  0    128 233176 409636 2474396    0    0     0     0 1024  104  1  0 99  0  0
 0  0    128 233176 409636 2474396    0    0     0     0 1079  195  0  0 100  0  0
 1  0    128 233168 409644 2474396    0    0     0   232 1021  188  3  0 97  0  0
 0  0    128 233176 409644 2474396    0    0     0     0 1111  213  2  0 98  0  0
 0  0    128 233176 409644 2474396    0    0     0     0 1005   60  0  0 100  0  0

The key columns (from the man page are)

CPU – These are percentages of total CPU time.

  • us: Time spent running non-kernel code. (user time, including nice time)
  • sy: Time spent running kernel code. (system time)
  • id: Time spent idle. Prior to Linux 2.5.41, this includes IO-wait time.
  • wa: Time spent waiting for IO. Prior to Linux 2.5.41, included in idle.
  • st: Time stolen from a virtual machine. Prior to Linux 2.6.11, unknown.
  • Procs

  • r: The number of processes waiting for run time.

NOTE: The columns of vmstat may vary between different Linux Operating Systems.

If you system is CPU Bound then you will observe this. Look at id,us,sy,r

$ vmstat 1
procs -----------memory---------- ---swap-- -----io---- --system-- -----cpu------
 r  b   swpd   free   buff  cache   si   so    bi    bo   in   cs us sy id wa st
 3  0    128 275684 397176 2300672    0    0     0     0 1118  427 74  2 25  0  0
 3  0    128 217404 397176 2300672    0    0     0     0 1017  138 74  1 25  0  0
 6  0    128 239584 397176 2300672    0    0     0     0 1086  350 93  2  5  0  0
 4  0    128 269468 397176 2300672    0    0     0     0 1005  229 98  2  0  0  0
 4  0    128 217636 397180 2300668    0    0     0   168 1087  251 99  2  0  0  0
 4  0    128 240576 397180 2300668    0    0     0     0 1006  182 99  2  0  0  0
 4  0    128 270708 397180 2300668    0    0     0     0 1079  338 98  2  0  0  0
 4  0    128 218752 397180 2300684    0    0     0     0 1005  106 99  1  0  0  0
 4  0    128 226316 397180 2300684    0    0     0     0 1077  308 98  2  0  0  0
 4  0    128 198664 397184 2300680    0    0     0    76 1010  250 99  1  0  0  0
 4  0    128 179444 397184 2300680    0    0     0     0 1077  238 100  0  0  0  0
 4  0    128 185396 397184 2300688    0    0     0     0 1006  210 99  1  0  0  0
 4  0    128 199408 397184 2300688    0    0     0     0 1079  336 99  1  0  0  0

You should also be wary of a Single CPU Bound process. This is why knowing the number of cores is important. In this example, one CPU is bound.

$ vmstat 1
procs -----------memory---------- ---swap-- -----io---- --system-- -----cpu------
 r  b   swpd   free   buff  cache   si   so    bi    bo   in   cs us sy id wa st

 0  0    128  99592 412544 2477580    0    0     0     0 1017   89  0  0 100  0  0
 0  0    128  99592 412544 2477580    0    0     0     0 1090  222  0  0 100  0  0
 0  0    128  99592 412544 2477580    0    0     0     0 1019   98  0  0 100  0  0
 1  0    128  99592 412544 2477580    0    0     0     0 1096  347 14  0 86  0  0
 1  0    128  99592 412548 2477576    0    0     0    84 1030  194 25  0 75  0  0
 1  0    128  99592 412548 2477576    0    0     0     0 1094  300 25  0 75  0  0
 1  0    128  99592 412548 2477580    0    0     0     0 1012   76 25  0 75  0  0
 1  0    128  99592 412548 2477580    0    0     0     0 1096  318 25  0 75  0  0
 1  0    128  73192 412548 2477580    0    0     0     0 1039  273 29  0 70  0  0
 1  0    128  77284 412556 2477572    0    0     0   268 1122  373 25  1 75  0  0
 2  0    128  83592 412556 2477584    0    0     0     0 1036  374 27  1 72  0  0
 0  0    128  56220 412564 2477576    0    0     0   172 1017   84  7  0 94  0  0
 0  0    128  56220 412564 2477576    0    0     0     0 1078  192  0  0 100  0  0
$ mpstat -P ALL 1
12:15:55 PM  CPU   %user   %nice    %sys %iowait    %irq   %soft  %steal   %idle    intr/s
12:15:56 PM  all   25.00    0.00    0.00    0.00    0.00    0.00    0.00   75.00   1072.00
12:15:56 PM    0    0.00    0.00    0.00    0.00    0.00    0.00    0.00  100.00   1001.00
12:15:56 PM    1    0.00    0.00    0.00    0.00    0.00    0.00    0.00  100.00      0.00
12:15:56 PM    2    0.00    0.00    0.00    0.00    0.00    0.00    0.00  100.00     62.00
12:15:56 PM    3  100.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00      9.00

12:15:56 PM  CPU   %user   %nice    %sys %iowait    %irq   %soft  %steal   %idle    intr/s
12:15:57 PM  all   25.00    0.00    0.00    0.00    0.00    0.00    0.00   75.00   1021.00
12:15:57 PM    0    0.00    0.00    0.00    0.00    0.00    1.00    0.00   99.00   1001.00
12:15:57 PM    1    0.00    0.00    0.00    0.00    0.00    0.00    0.00  100.00      0.00
12:15:57 PM    2    0.00    0.00    0.00    0.00    0.00    0.00    0.00  100.00     18.00
12:15:57 PM    3  100.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00      2.00

I will be detailing identifying bottlenecks of Memory, Disk and Network in future posts. You can also find out more at the MySQL User Conference “Monitoring 101 – Simple stuff to save your bacon” session.

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