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Subject: Re: [OMPI users] MPI-Send for entire entire matrix when allocating memory dynamically
From: George Bosilca (bosilca_at_[hidden])
Date: 2009-10-31 13:32:22


Eugene is right, every time you create a new matrix you will have to
describe it with a new datatype (even when using MPI_BOTTOM).

george.

On Oct 30, 2009, at 18:11 , Natarajan CS wrote:

> Thanks for the replies guys! Definitely two suggestions worth
> trying. Definitely didn't consider a derived datatype. I wasn't
> really sure that the MPI_Send call overhead was significant enough
> that increasing the buffer size and decreasing the number of calls
> would cause any speed up. Will change the code over the weekend and
> see what happens! Also, maybe if one passes the absolute address
> maybe there is no need for creating multiple definitions of the
> datatype? Haven't gone through the man pages yet, so apologies for
> ignorance!
>
> On Fri, Oct 30, 2009 at 2:44 PM, Eugene Loh <Eugene.Loh_at_[hidden]>
> wrote:
> Wouldn't you need to create a different datatype for each matrix
> instance? E.g., let's say you create twelve 5x5 matrices. Wouldn't
> you need twelve different derived datatypes? I would think so
> because each time you create a matrix, the footprint of that matrix
> in memory will depend on the whims of malloc().
>
> George Bosilca wrote:
>
> Even with the original way to create the matrices, one can use
> MPI_Create_type_struct to create an MPI datatype (http://web.mit.edu/course/13/13.715/OldFiles/build/mpich2-1.0.6p1/www/www3/MPI_Type_create_struct.html
> ) using MPI_BOTTOM as the original displacement.
>
> On Oct 29, 2009, at 15:31 , Justin Luitjens wrote:
>
> Why not do something like this:
>
> double **A=new double*[N];
> double *A_data new double [N*N];
>
> for(int i=0;i<N;i++)
> A[i]=&A_data[i*N];
>
> This way you have contiguous data (in A_data) but can access it as
> a 2D array using A[i][j].
>
> (I haven't compiled this but I know we represent our matrices this
> way).
>
> On Thu, Oct 29, 2009 at 12:30 PM, Natarajan CS
> <csnataraj_at_[hidden]> wrote:
> Hi
> thanks for the quick response. Yes, that is what I meant. I thought
> there was no other way around what I am doing but It is always good
> to ask a expert rather than assume!
>
> Cheers,
>
> C.S.N
>
>
> On Thu, Oct 29, 2009 at 11:25 AM, Eugene Loh <Eugene.Loh_at_[hidden]>
> wrote:
> Natarajan CS wrote:
>
> Hello all,
> Firstly, My apologies for a duplicate post in LAM/MPI list I
> have the following simple MPI code. I was wondering if there was a
> workaround for sending a dynamically allocated 2-D matrix?
> Currently I can send the matrix row-by-row, however, since rows are
> not contiguous I cannot send the entire matrix at once. I realize
> one option is to change the malloc to act as one contiguous block
> but can I keep the matrix definition as below and still send the
> entire matrix in one go?
>
> You mean with one standard MPI call? I don't think so.
>
> In MPI, there is a notion of derived datatypes, but I'm not
> convinced this is what you want. A derived datatype is basically a
> static template of data and holes in memory. E.g., 3 bytes, then
> skip 7 bytes, then another 2 bytes, then skip 500 bytes, then 1
> last byte. Something like that. Your 2d matrices differ in two
> respects. One is that the pattern in memory is different for each
> matrix you allocate. The other is that your matrix definition
> includes pointer information that won't be the same in every
> process's address space. I guess you could overcome the first
> problem by changing alloc_matrix() to some fixed pattern in memory
> for some r and c, but you'd still have pointer information in there
> that you couldn't blindly copy from one process address space to
> another.
>
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