parallelization and mex-compiled code

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martin 2014-2-6

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评论： martin 2014-2-9

I want to optimize a mex-compiled function (fortran-90 source) defined over an 1D interval by computing its values on a sufficiently fine sampling. It works fine with a for-loop but when I try parfor (for speed) I get crashes in the mex-compiled code (getting a error from one of the workers). Is this a documented problem, and does anyone have suggestions how to localize what goes wrong?

I run MatlabR2013a and Ubuntu 13.10 on a 16 core (32 virtual) machine and I get 12 workers when I do matlabpool.

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Matt J 2014-2-6

No, there is no general prohibition against using mex files with parfor. Show us the plain for-loop and the parfor version.

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Answer 1

Matt J 2014-2-6

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编辑：Matt J 2014-2-6

在 MATLAB Online 中打开

You should try running a plain for-loop first, but with the iterations in random order, i.e., instead of

 for i=1:n
   ...
 end

run as

 for i=randperm(n)
   ...
 end

This is a good way to test whether your code is independent of the order of the iterations (a basic requirement of parfor) before the Parallel Computing Toolbox even gets involved.

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martin 2014-2-6

编辑：Matt J 2014-2-6

在 MATLAB Online 中打开

My script:

    cat timeme_straightsearch.m
  stupidvector=zeros(1,360);
  disp('search with conventional for-loop:')
  tic
  for countindex = 1:360
  stupidvector(countindex)=localsearchstrul_valuespectral(countindex);
  end
  [foundpsi,whichelement]=min(stupidvector)
  toc
  disp('search with  parfor-loop:')
  tic
  parfor countindex = 1:360
  stupidvector(countindex)=localsearchstrul_valuespectral(countindex);
  end
  [foundpsi,whichelement]=min(stupidvector)
  toc

and in matlab:

>> matlabpool 
Starting matlabpool using the 'local' profile ... connected to 12 workers.
>> timeme_straightsearch
search with conventional for-loop:
foundpsi =
     -5.3948
whichelement =
     121
Elapsed time is 186.328337 seconds.
search with  parfor-loop:
Error using distcomp.remoteparfor/getCompleteIntervals (line 22)
The session that parfor is using has shut down.
Error in timeme_straightsearch (line 13)
parfor countindex = 1:360
Caused by:
    Error using distcomp.remoteparfor/getCompleteIntervals (line
    22)
    The session that parfor is using has shut down.
The client lost connection to lab 1. This might be due to network
problems, or the interactive matlabpool job might have errored.

Matt J 2014-2-6

Can you try it on a different machine to see if it's hardware problem? I don't see anything wrong with the code.

martin 2014-2-9

Thanks for your input, I will try another machine asap. Just an additional observation: The program crashes on the fortran90 statement "call mxCopyPtrToReal8(inptr_xdim,realxdim,1)" i.e a standardconstruction right out of the manualmapges for mex

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