I think here you may use cellfun to get rif of for ... endfor and see what happens into the master.
The master will be responsible for this huge amount of data.
After that you send the smaller matrixes to the slaves, do the calculations and send the results back to the master.
The idea is to check if the master may work with GNU Octave with all this local data ...before the MPI_Send ...
The slaves do not need to see the whole dataset but just a small part ...
I realized I sent a wrong version of the example code. Please see the
correct version attached.
On Tue, May 14, 2013 at 1:01 PM, Sukanta Basu <
address@hidden> wrote:
> Dear Riccardo and Jordi,
>
> I created this simple for-loop problem for testing the
memory issue in
> openmpi. If I run this code in serial mode with the same loop
> operation, the memory leak does not happen!
>
> Two related notes:
> (i) I used to use MatlabMPI with Matlab for the same code. I never
> witnessed this memory increase issue.
> (ii) The same code without openmpi (i.e., serial version) does not
> cause memory issue.
>
> In my research code, I have more than several dozens of functions
> within this iterative loop (a time-dependent operation in a CFD code).
> This loop cannot be vectorized.
>
> Also, deleting the variables from the workspace (after MPI_Send
> operation) is not an option. Because, some of the variables are needed
> in different functions. Since these variables are not growing in size
> with time/iteration, they should not increase memory consumption in
> any serious manner.
>
> Thanks for
the links. I have been using Matlab/Octave for more than a
> decade and I am quite familiar with vectorization issues. Based on my
> experience (as an user and not a developer of Octave), vectorization
> helps tremendously in speeding up the operations. Having JIT compiler
> makes things really faster. However, I do not see why it should cause
> memory increase issues. May be I am missing something.
>
> Best regards,
> Sukanta
>
> On Tue, May 14, 2013 at 12:31 PM, Jordi Gutiérrez Hermoso
> <
address@hidden> wrote:
>> On 14 May 2013 12:23, Riccardo Corradini <
address@hidden> wrote:
>>> After sending to the master , clear all variables within each slave
>>>
http://www.mathworks.it/it/help/matlab/ref/cellfun.html>>>
http://yagtom.googlecode.com/svn/trunk/html/speedup.html>>> Also search vectorizaction tips on octave mailing list archive.
>>
>> Is this documentation any good?
>>
>>
http://www.gnu.org/software/octave/doc/interpreter/Vectorization-and-Faster-Code-Execution.html>>
>> - Jordi G. H.
>
>
>
> --
> Sukanta Basu
> Associate Professor
> North Carolina State University
>
http://www4.ncsu.edu/~sbasu5/--
Sukanta Basu
Associate Professor
North Carolina State University
http://www4.ncsu.edu/~sbasu5/