Cyclic task issue with 4.9.47-rt37

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Hi,
I'm writing since i am experiencing some difficulties through the
development of an application which execute a cyclic task every 1 ms.
The computer where this application should run is an embedded pc with
an intel celeron j1900 quad core, 2G of ram and 32G of ssd. I have
installed debian 9.2.1 on it, from a netinst iso image, with no
graphical environment. I've downloaded the latest stable kernel source
(4.9.47) with the respective rt patch (4.9.47-rt37) and followed the
instructions as described in the web page "how to set up preempt_rt
properly".
I patched the kernel and then i ticked the box with the "Fully
Preemptible Kernel" option, and compiled it (make, make
modules_install, make install). Rebooted the pc, i checked that the
new kernel was running (uname -a) and i wrote a small cpp application
following the example of "how to build a simple rt application" web
page and "how to build a basic cyclic application" web page. Then to
be sure that the cycle keeps at a constant rate of 1 ms, i took the
time in nano seconds (clock_gettime) each time the thread finished
sleeping and woke up, and compared it with the previous woke up time
by subtraction. In theory i should get this time to be around 1000000
ns, but what i get is that it varies continuosly from 800000 to
1100000. Sometimes when i launch the program it stays around the
desired cycle time, but if i stop and restart the program then it
starts to behave as before. I am really confused, what am i doing
wrong or am i missing to do? Any suggestion is appreciated. Thanks in
advance.
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