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Subject: Re: [OMPI users] MPI-Send for entire entire matrix when allocating memory dynamically
From: Natarajan CS (csnataraj_at_[hidden])
Date: 2009-10-30 18:11:51


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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