CPU Higher than expected in Node running in docker - node.js

Question

I have a vagrant machine running at 33% CPU on my Mac (10.9.5) when nothing is supposed to be happening. The VM machine is run by Kinematic. Looking inside one of the containers I see 2 node (v0.12.2) processes running at 3-4% CPU each.
root#49ab3ab54901:/usr/src# top -bc
top - 03:11:59 up 8:31, 0 users, load average: 0.13, 0.18, 0.22
Tasks: 7 total, 1 running, 6 sleeping, 0 stopped, 0 zombie
%Cpu(s): 0.2 us, 0.7 sy, 0.0 ni, 99.1 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
KiB Mem: 2051824 total, 1942836 used, 108988 free, 74572 buffers
KiB Swap: 1466848 total, 18924 used, 1447924 free. 326644 cached Mem
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
1 root 20 0 4332 672 656 S 0.0 0.0 0:00.10 /bin/sh -c node -e "require('./seed/seeder.js').seed().then(function (resp) { console.log('successfully seeded!'); pro+
15 root 20 0 737320 81008 13452 S 0.0 3.9 0:32.57 node /usr/local/bin/nodemon app/api.js
33 root 20 0 4332 740 652 S 0.0 0.0 0:00.00 sh -c node app/api.js
34 root 20 0 865080 68952 14244 S 0.0 3.4 0:01.70 node app/api.js
83 root 20 0 20272 3288 2776 S 0.0 0.2 0:00.11 bash
18563 root 20 0 20248 3152 2840 S 0.0 0.2 0:00.11 bash
18575 root 20 0 21808 2308 2040 R 0.0 0.1 0:00.00 top -bc
I went on and runned a node --prof and processed the log with node-tick-processor. It looks like that 99.3% of CPU is used in the syscall :
(for full output see http://pastebin.com/6qgFuFWK )
root#d6d78487e1ec:/usr/src# node-tick-processor isolate-0x26c0180-v8.log
...
Statistical profiling result from isolate-0x26c0180-v8.log, (130664 ticks, 0 unaccounted, 0 excluded).
...
[C++]:
ticks total nonlib name
129736 99.3% 99.3% syscall
160 0.1% 0.1% node::ContextifyScript::New(v8::FunctionCallbackInfo<v8::Value> const&)
124 0.1% 0.1% __write
73 0.1% 0.1% __xstat
18 0.0% 0.0% v8::internal::Heap::AllocateFixedArray(int, v8::internal::PretenureFlag)
18 0.0% 0.0% node::Stat(v8::FunctionCallbackInfo<v8::Value> const&)
17 0.0% 0.0% __lxstat
16 0.0% 0.0% node::Read(v8::FunctionCallbackInfo<v8::Value> const&)
...
1 0.0% 0.0% __fxstat
1 0.0% 0.0% _IO_default_xsputn
[GC]:
ticks total nonlib name
22 0.0%
[Bottom up (heavy) profile]:
Note: percentage shows a share of a particular caller in the total
amount of its parent calls.
Callers occupying less than 2.0% are not shown.
ticks parent name
129736 99.3% syscall
[Top down (heavy) profile]:
Note: callees occupying less than 0.1% are not shown.
inclusive self name
ticks total ticks total
129736 99.3% 129736 99.3% syscall
865 0.7% 0 0.0% Function: ~<anonymous> node.js:27:10
864 0.7% 0 0.0% LazyCompile: ~startup node.js:30:19
851 0.7% 0 0.0% LazyCompile: ~Module.runMain module.js:499:26
799 0.6% 0 0.0% LazyCompile: Module._load module.js:273:24
795 0.6% 0 0.0% LazyCompile: ~Module.load module.js:345:33
794 0.6% 0 0.0% LazyCompile: ~Module._extensions..js module.js:476:37
792 0.6% 0 0.0% LazyCompile: ~Module._compile module.js:378:37
791 0.6% 0 0.0% Function: ~<anonymous> /usr/src/app/api.js:1:11
791 0.6% 0 0.0% LazyCompile: ~require module.js:383:19
791 0.6% 0 0.0% LazyCompile: ~Module.require module.js:362:36
791 0.6% 0 0.0% LazyCompile: Module._load module.js:273:24
788 0.6% 0 0.0% LazyCompile: ~Module.load module.js:345:33
786 0.6% 0 0.0% LazyCompile: ~Module._extensions..js module.js:476:37
783 0.6% 0 0.0% LazyCompile: ~Module._compile module.js:378:37
644 0.5% 0 0.0% Function: ~<anonymous> /usr/src/app/api.authentication.js:1:11
627 0.5% 0 0.0%
...
A strace resulted in nothing abnormal:
% time seconds usecs/call calls errors syscall
------ ----------- ----------- --------- --------- ----------------
54.51 0.001681 76 22 clone
17.28 0.000533 4 132 epoll_ctl
16.80 0.000518 24 22 wait4
6.39 0.000197 2 110 66 stat
5.03 0.000155 1 176 close
0.00 0.000000 0 176 read
0.00 0.000000 0 88 write
0.00 0.000000 0 44 rt_sigaction
0.00 0.000000 0 88 rt_sigprocmask
0.00 0.000000 0 22 rt_sigreturn
0.00 0.000000 0 66 ioctl
0.00 0.000000 0 66 socketpair
0.00 0.000000 0 88 epoll_wait
0.00 0.000000 0 22 pipe2
------ ----------- ----------- --------- --------- ----------------
100.00 0.003084 1122 66 total
And the other node process:
% time seconds usecs/call calls errors syscall
------ ----------- ----------- --------- --------- ----------------
0.00 0.000000 0 14 epoll_wait
------ ----------- ----------- --------- --------- ----------------
100.00 0.000000 14 total
Am I missing something?
I wonder if it is VirtualBox's or Docker's layers consuming 4%.
When you have a few containers with 2 processes running at 4%, it adds up quickly.