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Parfor loop just hangs, CPU usage goes to zero

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JohnDapper
JohnDapper on 14 Mar 2016
Commented: David Saidman on 14 Jan 2020
Hi all. Here is a sample code of what I am attempting to run.
parfor i = 1:num
answer(:,i) = someFunction(someData(:,i));
end
Key information: "someFunction" is a C++ mex file. "someData" is a memmapfile (memmapfilename.data) because it is too large to be loaded onto each worker
Oddly, the parfor loop just hangs, the CPU usage goes to zero, and when I CTRL+C, here is what I get:
Operation terminated by user during distcomp.remoteparfor/getCompleteIntervals (line
127)
In parallel_function>distributed_execution (line 820)
[tags, out] = P.getCompleteIntervals(chunkSize);
In parallel_function (line 587)
R = distributed_execution(...
This isn't an issue if I replace the "parfor" with a simple "for" - everything works fine. What seems to happen is that some of the workers become unresponsive. After the above issue is encountered, even running a simple command such as
pctRunOnAll 1+1
will return "2" on only some, but not all, workers.
Any help would be great. A fresh re-installation did not help. Validation for "parpool" passed.

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Cole
Cole on 4 Jan 2018
I tried MATLAB 2014a, but the same error occurred.
John Tencer
John Tencer on 3 Apr 2018
I'm observing this behavior with 2017b.
David Saidman
David Saidman on 14 Jan 2020
Did anybody get any success with this? I'm having exact same 2017b, definitely no keyboard statement.
If I wait a bit, it ends up running but on a single CPU (event tho I have 18 in my pool on a cpu with 20 physical and 40 logical cores, about 10gb spare memory in performance monitor).

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Answers (4)

Dave Behera
Dave Behera on 24 Mar 2016
It seems that there is a deadlock when the workers are trying to the access the file using the same object (that you got from memmapfile). Due to that, the progress is getting stalled with zero CPU usage and no abort message.
Can you try creating a separate memmapfile object within each parfor iteration and passing it to the someFunction function? This may make the file access thread-safe.
Also, could you try the same workflow with spmd?

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Sanjay Manohar
Sanjay Manohar on 19 Dec 2017
Happened suddenly after I set a breakpoint within a subfunction.
Cole
Cole on 4 Jan 2018
I have just tried SPMD, but it doesn't work. The similar problem still exists.

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arvid Martens
arvid Martens on 9 Jan 2018
I noticed that the problem started to occur after I updated the drivers of the GPUs that are being used during the calculations. Rolling back the drivers resolved the problem. However, new GPU hardware is on its way, as the current ones are pretty old. So I hope the problem is resolved by then.
Is there a way to throw an error when this stalling occurs? I could write an error handling to reduce the time lost by this stalling.

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Andrea Stevanato
Andrea Stevanato on 13 Jul 2018
I have the same error with matlab 2018a.

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Sanjay Manohar
Sanjay Manohar on 3 Jun 2019
Edited: Sanjay Manohar on 3 Jun 2019
I was having the same parfor problem, until I noticed I had a "keyboard" instruction in my code.

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