Timed sequence doesn't work right with external timing source

I'll describe first what I want to accomplish and
then maybe someone can read further and suggest why the attached VI
doesn't work. I have a SMU (PXI 4130) that takes differing amounts of
time to set a current depending on if the setting spans a range
boundary. I want to be able to make that SMU setting and then wait a
specific amount of time (sometimes 1 msec). If the SMU takes a little
longer to return then I want that extra time to come out of the wait
time. To do this I figured I would need an external time source to
control a timed sequence to give better than the normal 1 msec
resolution. So now onto the problems I'm having.
I've
got two problems here that I would really appreciate some insight on.
The attached VI is the subject of both problems (as is the VI is
worthless, but it illustrates the problem). Note that you need some
type of DAQ board with a counter on it to run it.
I can't
figure out why this timed sequence doesn't work with an external timing
source. It works mostly as expected (see next problem) with the
internal source, but fails miserably with the external source. Run the
VI as is to get a baseline. Then connect the DAQmx Create Timing Source
VI to the Source Name input of the timed structure. It seems like it
should run exactly the same both ways.
Problem 2 (run with the
internal timing source). The VI should take the same amount of time to
execute regardless of the input to the Wait VI (within reason of
course). That's actually the main impetus for this whole exercise. But
according to the Actual End indicator it runs faster with a longer wait
time.
George
Attachments:
test timed sequence.vi ‏144 KB

Hi George, I have been playing with the code that you have posted and I think I am seeing what your concern is with regards to the first problem that you stated.  Without running the code I would expect both internal and external timing to cause the VI to run in the exact same manner, however obviously that is not the case.  I am currently looking into this behavior and I will post you a response as soon as I have an answer for you. 
As for the second problem, If you look at the manner in which you have coded this VI, a 1ms wait in the first frame will lead to a calculation of 1999ms wait in the second frame, and thus 5 iterations of 1999ms or about 99,995ms total running time.  If you increase the wait in the first frame to say 50ms, then an overall all wait of 1950ms is calculated in the second frame so not the overall iteration time is now 1950 which, over 5 iteration leads to 99,750ms thus as you increase the wait in the first loop the overall loop duration will be less.  This is expected behavior.
Again I will post back once I have a clarification on the internal vs external timing.
Chris_K 
National Instruments
Applications Engineer

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