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Timing problems

Hello!

We are programming a small program for the practical weeks at the University, which controls a small experiment. Unfortunately we are total Labview beginners and have large problems with the timing of our program. It would be nice, if the program could switch an external device with an accuracy of 1-5 ms. But unfortunately it already needs an extra 100ms with simple waiting for loops to finish.

For example: It takes about 300ms to get data from a photodiode, when it should only measure and average for 10ms (last frame of the sequence). And then it only took one value.
We attached our program. It would be really nice, if you could give us a few tips on how to improve timing.
As interface we use a National Instruments card: Ni-PCI-6024E
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