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Subject: Re: [OMPI users] 1D and 2D arrays allocate memory by maloc() and MPI_Send and MPI_Recv problem.
From: George Bosilca (bosilca_at_[hidden])
Date: 2012-08-07 06:47:37


All MPI operations (including MPI_Send and MPI_Recv) consider any type of buffers (input and output) as a contiguous entity.

Therefore, you have two options:

1. Have a loop around MPI_Send & MPI_Recv similar to the allocation section.

2. Build an MPI Datatype representing the non-contiguous memory layout you really intend to send between peers.

  george.

On Aug 7, 2012, at 10:33 , Pawe³ Jaromin wrote:

> Hello all
>
> Sorry, may be this is a stupid question, bat a have a big problem with
> maloc() and matrix arrays.
> I want to make a program that do very simple thing like matriA *
> matrixB = matrixC.
> Because I need more matrix size than 100x100 (5000x5000), I have to
> use maloc() for memory allocation.
> First I tried this way:
>
> The typical form for dynamically allocating an NxM array of type T is:
> T **a = malloc(sizeof *a * N);
> if (a)
> {
> for (i = 0; i < N; i++)
> {
> a[i] = malloc(sizeof *a[i] * M);
> }
> }
> // the arrays are created before split to nodes
>
> No problem with create, fill array,but the problem started when I have
> send and receive it.
> Of course before send I calculated "cont" for MPI_Send.
> To be shore, that the count for MPI_Send i MPI_Recv is the same I also
> send "count".
>
> count = rows*matrix_size*sizeof (double); //part of matrix
> MPI_Send(&count, 1, MPI_INT, dest, mtype,MPI_COMM_WORLD);
> MPI_Send(&matrixA[offset][0], count, MPI_DOUBLE, dest, mtype, MPI_COMM_WORLD);
>
> from worker side the code looks like:
>
> MPI_Recv(&countA, 1, MPI_INT, source, mtype, MPI_COMM_WORLD, &status);
> MPI_Recv(&matrixA[0][0], countA, MPI_DOUBLE, source, mtype,
> MPI_COMM_WORLD, &status);
>
>
> An error looks like:
>
> [pawcioj-VirtualBox:01700] *** Process received signal ***
> [pawcioj-VirtualBox:01700] Signal: Segmentation fault (11)
> [pawcioj-VirtualBox:01700] Signal code: Address not mapped (1)
> [pawcioj-VirtualBox:01700] Failing at address: 0x88fa000
> [pawcioj-VirtualBox:01700] [ 0] [0xc2740c]
> [pawcioj-VirtualBox:01700] [ 1]
> /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x906c) [0x17606c]
> [pawcioj-VirtualBox:01700] [ 2]
> /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x6a1b) [0x173a1b]
> [pawcioj-VirtualBox:01700] [ 3]
> /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so(+0x3ae6) [0x7b7ae6]
> [pawcioj-VirtualBox:01700] [ 4]
> /usr/lib/libopen-pal.so.0(opal_progress+0x81) [0x406fa1]
> [pawcioj-VirtualBox:01700] [ 5]
> /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x48e5) [0x1718e5]
> [pawcioj-VirtualBox:01700] [ 6] /usr/lib/libmpi.so.0(MPI_Recv+0x165) [0x1ef9d5]
> [pawcioj-VirtualBox:01700] [ 7] macierz_V.02(main+0x927) [0x8049870]
> [pawcioj-VirtualBox:01700] [ 8] /lib/libc.so.6(__libc_start_main+0xe7)
> [0xddfce7]
> [pawcioj-VirtualBox:01700] [ 9] macierz_V.02() [0x8048b71]
> [pawcioj-VirtualBox:01700] *** End of error message ***
> --------------------------------------------------------------------------
> mpirun noticed that process rank 1 with PID 1700 on node
> pawcioj-VirtualBox exited on signal 11 (Segmentation fault).
>
>
> Because I have no result, I tied do that by 1D array but the problem
> seems similar.
>
> Probably I do something wrong, so I would like to ask you about advice
> how do that proper or maybe link to useful tutorial.
> I spend two weeks to find out how do that but unfortunately without result :(.
>
>
>
> --
> ------------------
> pozdrawiam
>
> Pawe³ Jaromin
>
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