Interval timer problem

To resume, you want to produce strobe with various durations.

This strobe signal is on an OUTPUT FPGA pin (destination : other device)

right ?

If you want hard real time (I mean that durations are strictly constrained and if one time is missed then fatal error), I don't recommand using software interrupts, because of what you have seen.

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It’s hard to realize this staff on FPGA logic because it works closely to other subprograms.

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To produce strobe at various duration is not hard. You can load the value to a external (but inside FPGA) counter which produce strobe.

To load the value, just employ a PIO ins Qsys.

could you describe more of your project ? could you give a basic algorithm and structure of this part of your project (moslty relation between strobe and (sub)program)?

Not enough info to help you and still confusing.