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Subject: [OMPI users] 1D and 2D arrays allocate memory by maloc() and MPI_Send and MPI_Recv problem.
From: Pawe³ Jaromin (jaromin.pawel_at_[hidden])
Date: 2012-08-07 04:33:14


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