Swap used when there is enough free RAM. Performance impacted - c++

Question

I wrote a simple program to study the performance when using a lot of RAM on Linux (64bit Red Hat Enterprise Linux Server release 6.4). (Please ignore the memory leak.)
#include <sys/time.h>
#include <time.h>
#include <stdio.h>
#include <string.h>
#include <iostream>
#include <vector>
using namespace std;
double getWallTime()
{
struct timeval time;
if (gettimeofday(&time, NULL))
{
return 0;
}
return (double)time.tv_sec + (double)time.tv_usec * .000001;
}
int main()
{
int *a;
int n = 1000000000;
do
{
time_t mytime = time(NULL);
char * time_str = ctime(&mytime);
time_str[strlen(time_str)-1] = '\0';
printf("Current Time : %s\n", time_str);
double start = getWallTime();
a = new int[n];
for (int i = 0; i < n; i++)
{
a[i] = 1;
}
double elapsed = getWallTime()-start;
cout << elapsed << endl;
cout << "Allocated." << endl;
}
while (1);
return 0;
}
The output is
Current Time : Tue May 8 11:46:55 2018
3.73667
Allocated.
Current Time : Tue May 8 11:46:59 2018
64.5222
Allocated.
Current Time : Tue May 8 11:48:03 2018
110.419
The top output is as below. We can see swap increased though there was enough free RAM. The consequence was the runtime soared from 3 seconds to 64 seconds.
top - 11:46:55 up 21 days, 1:14, 18 users, load average: 1.24, 1.25, 0.95
Tasks: 819 total, 3 running, 816 sleeping, 0 stopped, 0 zombie
Cpu(s): 1.6%us, 1.4%sy, 0.0%ni, 97.1%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
Mem: 132110088k total, 127500344k used, 4609744k free, 262288k buffers
Swap: 10485752k total, 4112k used, 10481640k free, 45988192k cached
top - 11:47:01 up 21 days, 1:14, 18 users, load average: 1.38, 1.27, 0.96
Tasks: 819 total, 2 running, 817 sleeping, 0 stopped, 0 zombie
Cpu(s): 0.5%us, 2.1%sy, 0.0%ni, 97.4%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
Mem: 132110088k total, 131620156k used, 489932k free, 262288k buffers
Swap: 10485752k total, 4112k used, 10481640k free, 45844228k cached
top - 11:47:53 up 21 days, 1:15, 18 users, load average: 1.25, 1.26, 0.97
Tasks: 819 total, 2 running, 817 sleeping, 0 stopped, 0 zombie
Cpu(s): 0.1%us, 2.5%sy, 0.0%ni, 97.4%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
Mem: 132110088k total, 131626300k used, 483788k free, 262276k buffers
Swap: 10485752k total, 5464k used, 10480288k free, 43056696k cached
top - 11:47:56 up 21 days, 1:15, 18 users, load average: 1.23, 1.26, 0.97
Tasks: 819 total, 2 running, 817 sleeping, 0 stopped, 0 zombie
Cpu(s): 0.1%us, 2.5%sy, 0.0%ni, 97.4%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
Mem: 132110088k total, 131627568k used, 482520k free, 262276k buffers
Swap: 10485752k total, 5792k used, 10479960k free, 42949788k cached
top - 11:47:59 up 21 days, 1:15, 18 users, load average: 1.21, 1.25, 0.97
Tasks: 819 total, 2 running, 817 sleeping, 0 stopped, 0 zombie
Cpu(s): 0.1%us, 2.5%sy, 0.0%ni, 97.4%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
Mem: 132110088k total, 131623080k used, 487008k free, 262276k buffers
Swap: 10485752k total, 6312k used, 10479440k free, 42840068k cached
top - 11:48:02 up 21 days, 1:15, 18 users, load average: 1.21, 1.25, 0.97
Tasks: 819 total, 2 running, 817 sleeping, 0 stopped, 0 zombie
Cpu(s): 0.1%us, 2.5%sy, 0.0%ni, 97.4%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
Mem: 132110088k total, 131620016k used, 490072k free, 262276k buffers
Swap: 10485752k total, 6772k used, 10478980k free, 42729276k cached
I read this and this. My questions are
Why would Linux sacrifice the performance rather than totally using cached RAM? Memory fragmentation? But putting data on swap will certainly create fragmentation too.
Is there a workaround to get consistent 3 seconds until reaching the physical RAM size?
Thanks.
Update 1:
Add more output from top.
Update 2:
Per David's suggestions, looking at /proc//io shows my program doesn't I/O. So David's first answer should explain this observation. Now comes to my second question. How to improve the performance as a non-root user (can't modify swappiness, etc.).
Update 3: I switched to another machine since I needed to sudo some commands. This is a real machine (no virtual machine) with Intel(R) Xeon(R) CPU E5-2680 0 # 2.70GHz. The machine has 16 physical cores.
uname -a
2.6.32-642.4.2.el6.x86_64 #1 SMP Tue Aug 23 19:58:13 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Running osgx's modified code with more iterations gives
Iteration 451
Time to malloc: 1.81198e-05
Time to fill with data: 0.109081
Fill rate with data: **916**.75 Mints/sec, 3667Mbytes/sec
Time to second write access of data: 0.049731
Access rate of data: 2010.82 Mints/sec, 8043.27Mbytes/sec
Time to third write access of data: 0.0478709
Access rate of data: 2088.95 Mints/sec, 8355.81Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 180800Mbytes
Iteration 452
Time to malloc: 1.09673e-05
Time to fill with data: 5.16316
Fill rate with data: **19**.368 Mints/sec, 77.4719Mbytes/sec
Time to second write access of data: 0.0495219
Access rate of data: 2019.31 Mints/sec, 8077.23Mbytes/sec
Time to third write access of data: 0.0439548
Access rate of data: 2275.06 Mints/sec, 9100.25Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 181200Mbytes
I did see kernel switched from 2MB page to 4KB page when slowdown occurred.
vmstat 1 60
procs -----------memory---------- ---swap-- -----io---- --system-- -----cpu-----
r b swpd free buff cache si so bi bo in cs us sy id wa st
2 0 1217396 11506356 5911040 47499184 0 2 35 47 0 0 14 2 84 0 0
2 0 1217396 11305860 5911040 47499184 4 0 4 36 5163 3460 7 6 87 0 0
2 0 1217396 11112744 5911040 47499188 0 0 0 0 4326 3451 7 6 87 0 0
2 0 1217396 10980556 5911040 47499188 0 0 0 0 4801 3385 7 6 87 0 0
2 0 1217396 10845940 5911040 47499192 0 0 0 20 4650 3596 7 6 87 0 0
2 0 1217396 10712508 5911040 47499200 0 0 0 0 5743 3562 7 6 87 0 0
2 0 1217396 10583380 5911040 47499200 0 0 0 40 4531 3622 7 6 87 0 0
2 0 1217396 10449096 5911040 47499200 0 0 0 0 4516 3629 7 6 87 0 0
2 0 1217396 10187856 5911040 47499200 0 0 0 0 4499 3456 7 6 87 0 0
2 0 1217396 10053256 5911040 47499204 0 0 0 8 5334 3507 7 6 87 0 0
2 0 1217396 9921624 5911040 47499204 0 0 0 0 6310 3593 6 6 87 0 0
2 0 1217396 9788532 5911040 47499208 0 0 0 44 5794 3516 7 6 87 0 0
2 0 1217396 9660516 5911040 47499208 0 0 0 0 4894 3535 7 6 87 0 0
2 0 1217396 9527552 5911040 47499212 0 0 0 0 4686 3570 7 6 87 0 0
2 0 1217396 9396536 5911040 47499212 0 0 0 0 4805 3538 7 6 87 0 0
2 0 1217396 9238664 5911040 47499212 0 0 0 0 5940 3459 7 6 87 0 0
2 0 1217396 9000136 5911040 47499216 0 0 0 32 5239 3333 7 6 87 0 0
2 0 1217396 8861132 5911040 47499220 0 0 0 0 5579 3351 7 6 87 0 0
2 0 1217396 8733688 5911040 47499220 0 0 0 0 4910 3199 7 6 87 0 0
2 0 1217396 8596600 5911040 47499224 0 0 0 44 5075 3453 7 6 87 0 0
2 0 1217396 8338468 5911040 47499232 0 0 0 0 5328 3444 7 6 87 0 0
2 0 1217396 8207732 5911040 47499232 0 0 0 52 5474 3370 7 6 87 0 0
2 0 1217396 8071212 5911040 47499236 0 0 0 0 5442 3419 7 6 87 0 0
2 0 1217396 7807736 5911040 47499236 0 0 0 0 6139 3456 7 6 87 0 0
2 0 1217396 7676080 5911044 47499232 0 0 0 16 4533 3430 6 6 87 0 0
2 0 1217396 7545728 5911044 47499236 0 0 0 0 6712 3957 7 6 87 0 0
4 0 1217396 7412444 5911044 47499240 0 0 0 68 6110 3547 7 6 87 0 0
procs -----------memory---------- ---swap-- -----io---- --system-- -----cpu-----
r b swpd free buff cache si so bi bo in cs us sy id wa st
2 0 1217396 7280148 5911048 47499244 0 0 0 68 6140 3516 7 7 86 0 0
2 0 1217396 7147836 5911048 47499244 0 0 0 0 4434 3400 7 6 87 0 0
2 0 1217396 6886980 5911048 47499248 0 0 0 16 7354 3393 7 6 87 0 0
2 0 1217396 6752868 5911048 47499248 0 0 0 0 5286 3573 7 6 87 0 0
2 0 1217396 6621772 5911048 47499248 0 0 0 0 5353 3410 7 6 87 0 0
2 0 1217396 6489760 5911048 47499252 0 0 0 48 5172 3454 7 6 87 0 0
2 0 1217396 6248732 5911048 47499256 0 0 0 0 5266 3411 7 6 87 0 0
2 0 1217396 6092804 5911048 47499260 0 0 0 4 6345 3473 7 6 87 0 0
2 0 1217396 5962544 5911048 47499260 0 0 0 0 7399 3712 7 6 87 0 0
2 0 1217396 5828492 5911048 47499264 0 0 0 0 5804 3516 7 6 87 0 0
2 0 1217396 5566720 5911048 47499264 0 0 0 44 5800 3370 7 6 87 0 0
2 0 1217396 5434204 5911048 47499264 0 0 0 0 6716 3446 7 6 87 0 0
2 0 1217396 5240724 5911048 47499268 0 0 0 68 3948 3346 7 6 87 0 0
2 0 1217396 5051688 5911008 47484936 0 0 0 0 4743 3734 7 6 87 0 0
2 0 1217396 4925680 5910500 47478444 0 0 136 0 5978 3779 7 6 87 0 0
2 0 1217396 4801744 5908552 47471820 0 0 0 32 4573 3237 7 6 87 0 0
2 0 1217396 4675772 5908552 47463984 0 0 0 0 6594 3276 7 6 87 0 0
2 0 1217396 4486472 5908444 47455736 0 0 0 4 6096 3256 7 6 87 0 0
2 0 1217396 4299908 5908392 47446964 0 0 0 0 5569 3525 7 6 87 0 0
2 0 1217396 4175444 5906884 47440024 0 0 0 0 4975 3141 7 6 87 0 0
2 0 1217396 4063472 5905976 47423860 0 0 0 56 6255 3147 6 6 87 0 0
2 0 1217396 3939816 5905796 47415596 0 0 0 0 5396 3143 7 6 87 0 0
2 0 1217396 3686540 5905796 47407152 0 0 0 44 6471 3201 7 6 87 0 0
2 0 1217396 3557596 5905796 47398892 0 0 0 0 7581 3727 7 6 87 0 0
2 0 1217396 3445536 5905796 47381812 0 0 0 0 5560 3222 7 6 87 0 0
2 0 1217396 3250272 5905796 47373364 0 0 0 60 5594 3343 7 6 87 0 0
2 0 1217396 3065232 5903744 47367156 0 0 0 0 5595 3182 7 6 87 0 0
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 1217396 2951704 5903028 47350792 0 0 0 12 5210 3262 7 6 87 0 0
2 0 1217396 2829228 5902928 47342444 0 0 0 0 5724 3758 7 6 87 0 0
2 0 1217396 2575248 5902580 47334472 0 0 0 0 4377 3369 7 6 87 0 0
2 0 1217396 2527996 5897796 47322436 0 0 0 60 5550 3570 7 6 87 0 0
2 0 1217396 2398672 5893572 47322324 0 0 0 0 5603 3225 7 6 87 0 0
2 0 1217396 2272536 5889364 47322228 0 0 0 16 6924 3310 7 6 87 0 0
iostat -xyz 1 60
Linux 2.6.32-642.4.2.el6.x86_64 05/09/2018 _x86_64_ (16 CPU)
avg-cpu: %user %nice %system %iowait %steal %idle
6.64 0.00 6.26 0.00 0.00 87.10
Device: rrqm/s wrqm/s r/s w/s rsec/s wsec/s avgrq-sz avgqu-sz await r_await w_await svctm %util
avg-cpu: %user %nice %system %iowait %steal %idle
7.00 0.06 5.69 0.00 0.00 87.24
I managed to do "sudo perf top", and saw this in the top line when slowdown occurred.
16.84% [kernel] [k] compaction_alloc
From top. There were several other processes running (not shown).
Tasks: 799 total, 5 running, 787 sleeping, 4 stopped, 3 zombie
Cpu(s): 23.1%us, 16.7%sy, 0.0%ni, 60.0%id, 0.0%wa, 0.0%hi, 0.1%si, 0.0%st
Mem: 264503640k total, 256749480k used, 7754160k free, 5830508k buffers
Swap: 409259004k total, 1217112k used, 408041892k free, 50458600k cached
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
23559 toddwz 20 0 165g 164g 1204 R 93.0 65.4 2:05.51 a.out
Update 4
After turning off THP, I see the following. Fill rate is consistent around 550 Mints/sec (900 with THP on) until my program uses 240GB RAM (cached RAM < 1GB). And then swap kicks in, so fill rate drops.
Iteration 610
Time to malloc: 1.3113e-05
Time to fill with data: 0.181151
Fill rate with data: 552.025 Mints/sec, 2208.1Mbytes/sec
Time to second write access of data: 0.04074
Access rate of data: 2454.59 Mints/sec, 9818.36Mbytes/sec
Time to third write access of data: 0.0420492
Access rate of data: 2378.17 Mints/sec, 9512.67Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 244400Mbytes
Iteration 611
Time to malloc: 1.88351e-05
Time to fill with data: 0.306215
Fill rate with data: 326.568 Mints/sec, 1306.27Mbytes/sec
Time to second write access of data: 0.045784
Access rate of data: 2184.17 Mints/sec, 8736.68Mbytes/sec
Time to third write access of data: 0.0441492
Access rate of data: 2265.05 Mints/sec, 9060.19Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 244800Mbytes
Iteration 612
Time to malloc: 2.21729e-05
Time to fill with data: 1.33305
Fill rate with data: 75.016 Mints/sec, 300.064Mbytes/sec
Time to second write access of data: 0.048573
Access rate of data: 2058.76 Mints/sec, 8235.02Mbytes/sec
Time to third write access of data: 0.0495481
Access rate of data: 2018.24 Mints/sec, 8072.96Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 245200Mbytes
Conclusion
The behavior of my program is more transparent to me with transparent huge page (THP) turned off so I'll continue with THP off. For my particular program, the cause is THP not swap. Thanks to all who helped.

Answer 1

First iterations of the test probably uses huge pages (2 MB pages) due to THP: Transparent Hugepage - https://www.kernel.org/doc/Documentation/vm/transhuge.txt -
check your /sys/kernel/mm/transparent_hugepage/enabled and grep AnonHugePages /proc/meminfo during the execution of test.
The reason applications are running faster is because of two
factors. The first factor is almost completely irrelevant and it's not
of significant interest because it'll also have the downside of
requiring larger clear-page copy-page in page faults which is a
potentially negative effect. The first factor consists in taking a
single page fault for each 2M virtual region touched by userland (so
reducing the enter/exit kernel frequency by a 512 times factor). This
only matters the first time the memory is accessed for the lifetime of
a memory mapping.
Allocation of huge amounts of memory with new or malloc is served by single syscall mmap, which usually don't "populate" the virtual memory with physical pages, check man mmap around MADV_POPULATE:
MAP_POPULATE (since Linux 2.5.46)
Populate (prefault) page tables for a mapping. ... This will help
to reduce blocking on page faults later.
This memory is just registered by mmap (without MAP_POPULATE) as virtual and write access is prohibited in page table. When your test tries to do first write to any memory page, page fault exception is generated and handled by OS kernel. Linux kernel will allocate some physical memory and map virtual page to physical (populate the page). With THP enabled (it is often enabled) kernel may allocate single huge page of 2MB, if it has some free huge physical pages. If there is no free huge pages, kernel will allocate 4KB page. So, without hugepages you will have 512 times more page faults (it can be checked by running vmstat 1 180 in another console while test is running, or by perf stat -I 1000).
Next accesses to populated pages will not have page faults, so you can extend your test with second (third) for i in (0..N-1): a[i] = 1; loop and measure time of both loops.
Your results still sounds strange. Is your system real or virtualized? Hypervisors may support 2 MB pages, and virtual systems may have much more cost for memory allocation and exception handling.
On my PC with less memory I have something like 10% slowdown when page faults switches from huge page allocation down to 4KB page allocation (check page-faults strings from perf stat - there were only around 2 thousands page faults per seconds with 2MB pages and >200 thousands page faults with 4KB pages):
$ cat /sys/kernel/mm/transparent_hugepage/enabled
[always] madvise never
$ perf stat -I1000 ./a.out
Iteration 0
Time to malloc: 8.10623e-06
Time to fill with data: 0.364378
Fill rate with data: 274.44 Mints/sec, 1097.76Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 400Mbytes
Iteration 1
Time to malloc: 1.90735e-05
Time to fill with data: 0.357983
Fill rate with data: 279.343 Mints/sec, 1117.37Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 800Mbytes
Iteration 2
Time to malloc: 1.69277e-05
# time counts unit events
1.000414902 999.893040 task-clock (msec)
1.000414902 1 context-switches # 0.001 K/sec
1.000414902 0 cpu-migrations # 0.000 K/sec
1.000414902 2,024 page-faults # 0.002 M/sec
1.000414902 2,664,963,857 cycles # 2.665 GHz
1.000414902 3,072,781,834 instructions # 1.15 insn per cycle
1.000414902 559,551,437 branches # 559.611 M/sec
1.000414902 25,176 branch-misses # 0.00% of all branches
Time to fill with data: 0.357014
Fill rate with data: 280.101 Mints/sec, 1120.4Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 1200Mbytes
Iteration 3
Time to malloc: 1.71661e-05
Time to fill with data: 0.358964
Fill rate with data: 278.579 Mints/sec, 1114.32Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 1600Mbytes
Iteration 4
Time to malloc: 1.69277e-05
Time to fill with data: 0.356918
Fill rate with data: 280.177 Mints/sec, 1120.71Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 2000Mbytes
Iteration 5
Time to malloc: 1.50204e-05
2.000779126 1000.703872 task-clock (msec)
2.000779126 1 context-switches # 0.001 K/sec
2.000779126 0 cpu-migrations # 0.000 K/sec
2.000779126 2,280 page-faults # 0.002 M/sec
2.000779126 2,686,072,244 cycles # 2.685 GHz
2.000779126 3,094,777,285 instructions # 1.16 insn per cycle
2.000779126 563,593,105 branches # 563.425 M/sec
2.000779126 9,661 branch-misses # 0.00% of all branches
Time to fill with data: 0.371785
Fill rate with data: 268.973 Mints/sec, 1075.89Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 2400Mbytes
Iteration 6
Time to malloc: 1.90735e-05
Time to fill with data: 0.418562
Fill rate with data: 238.913 Mints/sec, 955.653Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 2800Mbytes
Iteration 7
Time to malloc: 2.09808e-05
3.001146481 1000.436128 task-clock (msec)
3.001146481 1 context-switches # 0.001 K/sec
3.001146481 0 cpu-migrations # 0.000 K/sec
3.001146481 217,415 page-faults # 0.217 M/sec
3.001146481 2,687,783,783 cycles # 2.687 GHz
3.001146481 3,100,713,038 instructions # 1.16 insn per cycle
3.001146481 560,207,049 branches # 560.014 M/sec
3.001146481 83,230 branch-misses # 0.01% of all branches
Time to fill with data: 0.416297
Fill rate with data: 240.213 Mints/sec, 960.853Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 3200Mbytes
Iteration 8
Time to malloc: 1.38283e-05
Time to fill with data: 0.41672
Fill rate with data: 239.969 Mints/sec, 959.877Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 3600Mbytes
Iteration 9
Time to malloc: 1.40667e-05
Time to fill with data: 0.424997
Fill rate with data: 235.296 Mints/sec, 941.183Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 4000Mbytes
Iteration 10
Time to malloc: 1.28746e-05
4.001467773 1000.378604 task-clock (msec)
4.001467773 2 context-switches # 0.002 K/sec
4.001467773 0 cpu-migrations # 0.000 K/sec
4.001467773 232,690 page-faults # 0.233 M/sec
4.001467773 2,655,313,682 cycles # 2.654 GHz
4.001467773 3,087,157,016 instructions # 1.15 insn per cycle
4.001467773 557,266,313 branches # 557.070 M/sec
4.001467773 95,433 branch-misses # 0.02% of all branches
Time to fill with data: 0.413271
Fill rate with data: 241.972 Mints/sec, 967.888Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 4400Mbytes
Iteration 11
Time to malloc: 1.21593e-05
Time to fill with data: 0.414624
Fill rate with data: 241.182 Mints/sec, 964.73Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 4800Mbytes
Iteration 12
Time to malloc: 1.5974e-05
5.001792272 1000.372602 task-clock (msec)
5.001792272 2 context-switches # 0.002 K/sec
5.001792272 0 cpu-migrations # 0.000 K/sec
5.001792272 236,260 page-faults # 0.236 M/sec
5.001792272 2,687,340,230 cycles # 2.686 GHz
5.001792272 3,134,864,968 instructions # 1.17 insn per cycle
5.001792272 565,846,287 branches # 565.644 M/sec
5.001792272 104,634 branch-misses # 0.02% of all branches
Time to fill with data: 0.412331
Fill rate with data: 242.524 Mints/sec, 970.094Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 5200Mbytes
Iteration 13
Time to malloc: 1.3113e-05
Time to fill with data: 0.414433
Fill rate with data: 241.294 Mints/sec, 965.174Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 5600Mbytes
Iteration 14
Time to malloc: 1.88351e-05
Time to fill with data: 0.417277
Fill rate with data: 239.649 Mints/sec, 958.596Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 6000Mbytes
6.002129544 1000.404270 task-clock (msec)
6.002129544 1 context-switches # 0.001 K/sec
6.002129544 0 cpu-migrations # 0.000 K/sec
6.002129544 215,269 page-faults # 0.215 M/sec
6.002129544 2,676,269,667 cycles # 2.675 GHz
6.002129544 3,286,469,282 instructions # 1.23 insn per cycle
6.002129544 578,367,266 branches # 578.156 M/sec
6.002129544 345,470 branch-misses # 0.06% of all branches
....
After disabling THP with root command from https://access.redhat.com/solutions/46111 I always have ~200 thousands page faults per second and around 950 MB/s:
$ cat /sys/kernel/mm/transparent_hugepage/enabled
always [madvise] never
$ perf stat -I1000 ./a.out
Iteration 0
Time to malloc: 1.50204e-05
Time to fill with data: 0.422322
Fill rate with data: 236.786 Mints/sec, 947.145Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 400Mbytes
Iteration 1
Time to malloc: 1.50204e-05
Time to fill with data: 0.415068
Fill rate with data: 240.924 Mints/sec, 963.698Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 800Mbytes
Iteration 2
Time to malloc: 2.19345e-05
# time counts unit events
1.000162191 999.429856 task-clock (msec)
1.000162191 14 context-switches # 0.014 K/sec
1.000162191 0 cpu-migrations # 0.000 K/sec
1.000162191 232,727 page-faults # 0.233 M/sec
1.000162191 2,664,896,604 cycles # 2.666 GHz
1.000162191 3,080,713,267 instructions # 1.16 insn per cycle
1.000162191 555,116,838 branches # 555.434 M/sec
1.000162191 102,262 branch-misses # 0.02% of all branches
Time to fill with data: 0.440695
Fill rate with data: 226.914 Mints/sec, 907.658Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 1200Mbytes
Iteration 3
Time to malloc: 2.09808e-05
Time to fill with data: 0.414463
Fill rate with data: 241.276 Mints/sec, 965.104Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 1600Mbytes
Iteration 4
Time to malloc: 1.81198e-05
2.000544564 1000.142465 task-clock (msec)
2.000544564 16 context-switches # 0.016 K/sec
2.000544564 0 cpu-migrations # 0.000 K/sec
2.000544564 229,697 page-faults # 0.230 M/sec
2.000544564 2,621,180,984 cycles # 2.622 GHz
2.000544564 3,041,358,811 instructions # 1.15 insn per cycle
2.000544564 547,910,242 branches # 548.027 M/sec
2.000544564 93,682 branch-misses # 0.02% of all branches
Time to fill with data: 0.428383
Fill rate with data: 233.436 Mints/sec, 933.744Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 2000Mbytes
Iteration 5
Time to malloc: 1.5974e-05
Time to fill with data: 0.421986
Fill rate with data: 236.975 Mints/sec, 947.899Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 2400Mbytes
Iteration 6
Time to malloc: 1.5974e-05
Time to fill with data: 0.413477
Fill rate with data: 241.851 Mints/sec, 967.406Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 2800Mbytes
Iteration 7
Time to malloc: 1.88351e-05
3.000866438 999.980461 task-clock (msec)
3.000866438 20 context-switches # 0.020 K/sec
3.000866438 0 cpu-migrations # 0.000 K/sec
3.000866438 231,194 page-faults # 0.231 M/sec
3.000866438 2,622,484,960 cycles # 2.623 GHz
3.000866438 3,061,610,229 instructions # 1.16 insn per cycle
3.000866438 551,533,361 branches # 551.616 M/sec
3.000866438 104,561 branch-misses # 0.02% of all branches
Time to fill with data: 0.448333
Fill rate with data: 223.048 Mints/sec, 892.194Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 3200Mbytes
Iteration 8
Time to malloc: 1.50204e-05
Time to fill with data: 0.410566
Fill rate with data: 243.566 Mints/sec, 974.265Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 3600Mbytes
Iteration 9
Time to malloc: 1.3113e-05
4.001231042 1000.098860 task-clock (msec)
4.001231042 17 context-switches # 0.017 K/sec
4.001231042 0 cpu-migrations # 0.000 K/sec
4.001231042 228,532 page-faults # 0.229 M/sec
4.001231042 2,586,146,024 cycles # 2.586 GHz
4.001231042 3,026,679,955 instructions # 1.15 insn per cycle
4.001231042 545,236,541 branches # 545.284 M/sec
4.001231042 115,251 branch-misses # 0.02% of all branches
Time to fill with data: 0.441442
Fill rate with data: 226.53 Mints/sec, 906.121Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 4000Mbytes
Iteration 10
Time to malloc: 1.5974e-05
Time to fill with data: 0.42898
Fill rate with data: 233.111 Mints/sec, 932.445Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 4400Mbytes
Iteration 11
Time to malloc: 2.00272e-05
5.001547227 999.982415 task-clock (msec)
5.001547227 19 context-switches # 0.019 K/sec
5.001547227 0 cpu-migrations # 0.000 K/sec
5.001547227 225,796 page-faults # 0.226 M/sec
5.001547227 2,560,990,918 cycles # 2.561 GHz
5.001547227 3,005,384,743 instructions # 1.15 insn per cycle
5.001547227 542,275,580 branches # 542.315 M/sec
5.001547227 116,537 branch-misses # 0.02% of all branches
Time to fill with data: 0.414212
Fill rate with data: 241.422 Mints/sec, 965.689Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 4800Mbytes
Iteration 12
Time to malloc: 1.69277e-05
Time to fill with data: 0.411084
Fill rate with data: 243.259 Mints/sec, 973.037Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 5200Mbytes
Iteration 13
Time to malloc: 1.40667e-05
Time to fill with data: 0.413644
Fill rate with data: 241.754 Mints/sec, 967.015Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 5600Mbytes
Iteration 14
Time to malloc: 1.28746e-05
6.001849796 999.913923 task-clock (msec)
6.001849796 18 context-switches # 0.018 K/sec
6.001849796 0 cpu-migrations # 0.000 K/sec
6.001849796 236,912 page-faults # 0.237 M/sec
6.001849796 2,685,445,660 cycles # 2.686 GHz
6.001849796 3,153,464,551 instructions # 1.20 insn per cycle
6.001849796 568,989,467 branches # 569.032 M/sec
6.001849796 125,943 branch-misses # 0.02% of all branches
Time to fill with data: 0.444891
Fill rate with data: 224.774 Mints/sec, 899.097Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 6000Mbytes
Test modified for perf stat with rate printing and limited iteration count:
$ cat test.c; g++ test.c
#include <sys/time.h>
#include <time.h>
#include <stdio.h>
#include <string.h>
#include <iostream>
#include <vector>
using namespace std;
double getWallTime()
{
struct timeval time;
if (gettimeofday(&time, NULL))
{
return 0;
}
return (double)time.tv_sec + (double)time.tv_usec * .000001;
}
#define M 1000000
int main()
{
int *a;
int n = 100000000;
int j;
double total = 0;
for(j=0; j<15; j++)
{
cout << "Iteration " << j << endl;
double start = getWallTime();
a = new int[n];
cout << "Time to malloc: " << getWallTime() - start << endl;
for (int i = 0; i < n; i++)
{
a[i] = 1;
}
double elapsed = getWallTime()-start;
cout << "Time to fill with data: " << elapsed << endl;
cout << "Fill rate with data: " << n/elapsed/M << " Mints/sec, " << n*sizeof(int)/elapsed/M << "Mbytes/sec" << endl;
total += n*sizeof(int)*1./M;
cout << "Allocated " << n*sizeof(int)*1./M << " Mbytes, with total memory allocated " << total << "Mbytes" << endl;
}
return 0;
}
Test modified for second and third write access
$ g++ second.c -o second
$ cat second.c
#include <sys/time.h>
#include <time.h>
#include <stdio.h>
#include <string.h>
#include <iostream>
#include <vector>
using namespace std;
double getWallTime()
{
struct timeval time;
if (gettimeofday(&time, NULL))
{
return 0;
}
return (double)time.tv_sec + (double)time.tv_usec * .000001;
}
#define M 1000000
int main()
{
int *a;
int n = 100000000;
int j;
double total = 0;
for(j=0; j<15; j++)
{
cout << "Iteration " << j << endl;
double start = getWallTime();
a = new int[n];
cout << "Time to malloc: " << getWallTime() - start << endl;
for (int i = 0; i < n; i++)
{
a[i] = 1;
}
double elapsed = getWallTime()-start;
cout << "Time to fill with data: " << elapsed << endl;
cout << "Fill rate with data: " << n/elapsed/M << " Mints/sec, " << n*sizeof(int)/elapsed/M << "Mbytes/sec" << endl;
start = getWallTime();
for (int i = 0; i < n; i++)
{
a[i] = 2;
}
elapsed = getWallTime()-start;
cout << "Time to second write access of data: " << elapsed << endl;
cout << "Access rate of data: " << n/elapsed/M << " Mints/sec, " << n*sizeof(int)/elapsed/M << "Mbytes/sec" << endl;
start = getWallTime();
for (int i = 0; i < n; i++)
{
a[i] = 3;
}
elapsed = getWallTime()-start;
cout << "Time to third write access of data: " << elapsed << endl;
cout << "Access rate of data: " << n/elapsed/M << " Mints/sec, " << n*sizeof(int)/elapsed/M << "Mbytes/sec" << endl;
total += n*sizeof(int)*1./M;
cout << "Allocated " << n*sizeof(int)*1./M << " Mbytes, with total memory allocated " << total << "Mbytes" << endl;
}
return 0;
}
Without THP - around 1.25 GB/s for second and third access:
$ cat /sys/kernel/mm/transparent_hugepage/enabled
always [madvise] never
$ ./second
Iteration 0
Time to malloc: 9.05991e-06
Time to fill with data: 0.426387
Fill rate with data: 234.529 Mints/sec, 938.115Mbytes/sec
Time to second write access of data: 0.318292
Access rate of data: 314.177 Mints/sec, 1256.71Mbytes/sec
Time to third write access of data: 0.321722
Access rate of data: 310.827 Mints/sec, 1243.31Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 400Mbytes
Iteration 1
Time to malloc: 3.50475e-05
Time to fill with data: 0.411859
Fill rate with data: 242.802 Mints/sec, 971.206Mbytes/sec
Time to second write access of data: 0.317989
Access rate of data: 314.476 Mints/sec, 1257.91Mbytes/sec
Time to third write access of data: 0.321637
Access rate of data: 310.91 Mints/sec, 1243.64Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 800Mbytes
Iteration 2
Time to malloc: 2.81334e-05
Time to fill with data: 0.411918
Fill rate with data: 242.767 Mints/sec, 971.067Mbytes/sec
Time to second write access of data: 0.318647
Access rate of data: 313.827 Mints/sec, 1255.31Mbytes/sec
Time to third write access of data: 0.321041
Access rate of data: 311.487 Mints/sec, 1245.95Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 1200Mbytes
Iteration 3
Time to malloc: 2.5034e-05
Time to fill with data: 0.411138
Fill rate with data: 243.227 Mints/sec, 972.909Mbytes/sec
Time to second write access of data: 0.318429
Access rate of data: 314.042 Mints/sec, 1256.17Mbytes/sec
Time to third write access of data: 0.321332
Access rate of data: 311.205 Mints/sec, 1244.82Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 1600Mbytes
Iteration 4
Time to malloc: 3.71933e-05
Time to fill with data: 0.410922
Fill rate with data: 243.355 Mints/sec, 973.421Mbytes/sec
Time to second write access of data: 0.320262
Access rate of data: 312.244 Mints/sec, 1248.98Mbytes/sec
Time to third write access of data: 0.319223
Access rate of data: 313.261 Mints/sec, 1253.04Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 2000Mbytes
Iteration 5
Time to malloc: 2.19345e-05
Time to fill with data: 0.418508
Fill rate with data: 238.944 Mints/sec, 955.777Mbytes/sec
Time to second write access of data: 0.320419
Access rate of data: 312.092 Mints/sec, 1248.37Mbytes/sec
Time to third write access of data: 0.319752
Access rate of data: 312.742 Mints/sec, 1250.97Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 2400Mbytes
Iteration 6
Time to malloc: 3.19481e-05
Time to fill with data: 0.410054
Fill rate with data: 243.87 Mints/sec, 975.481Mbytes/sec
Time to second write access of data: 0.320244
Access rate of data: 312.262 Mints/sec, 1249.05Mbytes/sec
Time to third write access of data: 0.319546
Access rate of data: 312.944 Mints/sec, 1251.78Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 2800Mbytes
Iteration 7
Time to malloc: 3.19481e-05
Time to fill with data: 0.409491
Fill rate with data: 244.206 Mints/sec, 976.822Mbytes/sec
Time to second write access of data: 0.318501
Access rate of data: 313.971 Mints/sec, 1255.88Mbytes/sec
Time to third write access of data: 0.320052
Access rate of data: 312.449 Mints/sec, 1249.8Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 3200Mbytes
Iteration 8
Time to malloc: 2.5034e-05
Time to fill with data: 0.409922
Fill rate with data: 243.949 Mints/sec, 975.795Mbytes/sec
Time to second write access of data: 0.320583
Access rate of data: 311.932 Mints/sec, 1247.73Mbytes/sec
Time to third write access of data: 0.319478
Access rate of data: 313.011 Mints/sec, 1252.04Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 3600Mbytes
Iteration 9
Time to malloc: 2.69413e-05
Time to fill with data: 0.41104
Fill rate with data: 243.285 Mints/sec, 973.141Mbytes/sec
Time to second write access of data: 0.320389
Access rate of data: 312.121 Mints/sec, 1248.48Mbytes/sec
Time to third write access of data: 0.319762
Access rate of data: 312.733 Mints/sec, 1250.93Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 4000Mbytes
Iteration 10
Time to malloc: 2.59876e-05
Time to fill with data: 0.412612
Fill rate with data: 242.358 Mints/sec, 969.434Mbytes/sec
Time to second write access of data: 0.318304
Access rate of data: 314.165 Mints/sec, 1256.66Mbytes/sec
Time to third write access of data: 0.319453
Access rate of data: 313.035 Mints/sec, 1252.14Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 4400Mbytes
Iteration 11
Time to malloc: 2.98023e-05
Time to fill with data: 0.412428
Fill rate with data: 242.467 Mints/sec, 969.866Mbytes/sec
Time to second write access of data: 0.318467
Access rate of data: 314.004 Mints/sec, 1256.02Mbytes/sec
Time to third write access of data: 0.319716
Access rate of data: 312.778 Mints/sec, 1251.11Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 4800Mbytes
Iteration 12
Time to malloc: 2.69413e-05
Time to fill with data: 0.410515
Fill rate with data: 243.597 Mints/sec, 974.386Mbytes/sec
Time to second write access of data: 0.31832
Access rate of data: 314.149 Mints/sec, 1256.6Mbytes/sec
Time to third write access of data: 0.319569
Access rate of data: 312.921 Mints/sec, 1251.69Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 5200Mbytes
Iteration 13
Time to malloc: 2.28882e-05
Time to fill with data: 0.412385
Fill rate with data: 242.492 Mints/sec, 969.967Mbytes/sec
Time to second write access of data: 0.318929
Access rate of data: 313.549 Mints/sec, 1254.2Mbytes/sec
Time to third write access of data: 0.31949
Access rate of data: 312.999 Mints/sec, 1252Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 5600Mbytes
Iteration 14
Time to malloc: 2.90871e-05
Time to fill with data: 0.41235
Fill rate with data: 242.512 Mints/sec, 970.05Mbytes/sec
Time to second write access of data: 0.340456
Access rate of data: 293.724 Mints/sec, 1174.89Mbytes/sec
Time to third write access of data: 0.319716
Access rate of data: 312.778 Mints/sec, 1251.11Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 6000Mbytes
With THP - bit faster allocation but same speed of second and third access:
$ cat /sys/kernel/mm/transparent_hugepage/enabled
[always] madvise never
$ ./second
Iteration 0
Time to malloc: 1.50204e-05
Time to fill with data: 0.365043
Fill rate with data: 273.94 Mints/sec, 1095.76Mbytes/sec
Time to second write access of data: 0.320503
Access rate of data: 312.01 Mints/sec, 1248.04Mbytes/sec
Time to third write access of data: 0.319442
Access rate of data: 313.046 Mints/sec, 1252.18Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 400Mbytes
...
Iteration 14
Time to malloc: 2.7895e-05
Time to fill with data: 0.409294
Fill rate with data: 244.323 Mints/sec, 977.293Mbytes/sec
Time to second write access of data: 0.318422
Access rate of data: 314.049 Mints/sec, 1256.19Mbytes/sec
Time to third write access of data: 0.322098
Access rate of data: 310.465 Mints/sec, 1241.86Mbytes/sec
Allocated 400 Mbytes, with total memory allocated 6000Mbytes

Answer 2

From updates and the chat:
I did see kernel switched from 2MB page to 4KB page when slowdown occurred.
I managed to do "sudo perf top", and saw this in the top line when slowdown occurred.
16.84% [kernel] [k] compaction_alloc
perf top -g
- 31.27% 31.03% [kernel] [k] compaction_alloc \u2592
- compaction_alloc \u2592
- migrate_pages \u2592
compact_zone \u2592
compact_zone_order \u2592
try_to_compact_pages \u2592
__alloc_pages_direct_compact \u2592
__alloc_pages_nodemask \u2592
alloc_pages_vma \u2592
do_huge_pmd_anonymous_page \u2592
handle_mm_fault \u2592
__do_page_fault \u2592
do_page_fault \u2592
page_fault
Slowdown is connected with enabled THP and slow page faults of 4KB. After 4 KB switch page faults are very slow from some linux kernel internal compaction mechanisms (is kernel still trying to get some more huge pages?) - http://lwn.net/Articles/368869 and http://lwn.net/Articles/591998. More problems from THP on NUMA, both from THP and NUMA code.
The original problem is
we launch several solvers simultaneously based on memory set by user. In this case, use may want to use all 230G free RAM.
we do dynamic memory allocation/deallocation. when we reach the memory limit, in this case, could be say 150 GB (not 230 GB), we see dramatic slowdown.
I observe high system cpu usage, and swap usage. So I make up this little program, which seems to show my original problem
I can suggest globally disable THP (https://unix.stackexchange.com/questions/99154/disable-transparent-hugepage or http://www.olivierdoucet.info/blog/2012/05/19/debugging-a-mysql-stall/), or free most of "cached" (by echo 3 > /proc/sys/vm/drop_caches from root) - this is temporary (and not fast) workaround. With freed cached memory there will be less need for compaction (but it will make programs of other users slower - they will need to re-read their data from disks/nfs).
Huge swap on slow (rotating) disk can kill all performance from the moment it will be used (and swap on ssd is fast enough, and swap on NVMe is very fast).
You may also want to change huge allocations in your software from default new/delete to manual calling of anonymous mmap for allocation and munmap for deallocation to control flags (there are mmap and madvise flags for huge page and there is populate - http://man7.org/linux/man-pages/man2/mmap.2.html http://man7.org/linux/man-pages/man2/madvise.2.html).
With MAP_POPULATE you will have (very?) slow allocation, but all memory allocated will be really used from the moment of allocation (all accesses will be fast).