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....@sun.com>
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
<csnata...@gmail.com> 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....@sun.com>
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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