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Here is a screenshot from the Latency Test of the old configuration. Only for the Kernel-Infos.
The latency was horrible at this time (without irq-optimisation at this time)
   

I don't know much about cos sin. The whole processor is available for you to do all sorts of processing.
The ethercat part is the easy one I would say.
Every cycle you calculate a new encoder value, set a pdo variable and the soes library does the rest.

Edit. But I checked quickly. So you need to take in two analogue signals and calculate the phase angle.
Absolutely doable, could be a nice application.
Start a project thread and I'll give you a hand with the ethercat stuff.

Edit 2. The ADCs on STM32F4 are only 12-bit, you may need 16-bit ADC for this. Another processor? 
External 16-bit ADC unit?

Edit 3. IC-NV instead of ADCs of course.

Hi,

I also did a fresh installation on a DELL Optiplex 3060 Micro PC (RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller)
Everything incl. IRQ-Optimizing (Latency) works fine, but i also run into this error "Error finishing read" with my MESA 7i96s.


In my old installation (at this PC) i run the 3.6.0 rt11 Kernel and did not have this problems, so i think, last time i updated it for the same reason. Sadly i don`t know how to do this update again.
Is there an easy way only updating the kernel?
(Sorry but I`m not in the Linux-Space, so its a little hard for me)

Thanks a lot
Jens