I certainly wouldn't isolate 3 of 4 cores on a j1900. I might try 1 or 2 of them just for comparison. And it often pays to try isolating different cores or combinations of them. (The i5 i'm playing with right now gives best results with isolcpues=3.) But depending on the setup you have it may not even be worth the effort.
I let the last one run for a lot longer and also ran a latency-test -1ms. Results below:
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During both of these I was ssh'd into the box and using apt-get, 7 glxgears, and ncftp to transfer files for my machine to linuxcnc/configs/
so the numbers are not as good.
Still nearly 1000000 ns latency
I still suspect you have a power management option (say C states >C1 enabled) enabled in the BIOS or bad hardware (bad drives can do this)
