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Subject: Re: [OMPI users] problems on parallel writing
From: jody (jody.xha_at_[hidden])
Date: 2010-02-24 02:29:45


Hi
I know nearly nothing about fortran
but it looks to me as the pointer 'temp' in

> call MPI_FILE_WRITE(FH, temp, COUNT, MPI_REAL8, STATUS, IERR)

is not defined (or perhaps NULL?) for all processors except processor 0 :

> if ( myid == 0 ) then
> count = 1
> else
> count = 0
> end if
>
> if (count .gt. 0) then
> allocate(temp(count))
> temp(1) = 2122010.0d0
> end if

In C/C++ something like this would almost certainly lead to a crash,
but i don't know if this would be the case in Fortran...
jody

On Wed, Feb 24, 2010 at 4:38 AM, w k <thuwk99_at_[hidden]> wrote:
> Hello everyone,
>
>
> I'm trying to implement some functions in my code using parallel writing.
> Each processor has an array, say q, whose length is single_no(could be zero
> on some processors). I want to write q down to a common file, but the
> elements of q would be scattered to their locations in this file. The
> locations of the elements are described by a map. I wrote my testing code
> according to an example in a MPI-2 tutorial which can be found here:
> www.npaci.edu/ahm2002/ahm_ppt/Parallel_IO_MPI_2.ppt. This way of writing is
> called "Accessing Irregularly Distributed Arrays" in this tutorial and the
> example is given in page 42.
>
> I tested my code with mvapich and got the result as expected. But when I
> tested it with openmpi, it didn't work. I tried the version 1.2.8 and 1.4
> and both didn't work. I tried two clusters. Both of them are intel chips
> (woodcrest and nehalem), DDR infiniband with Linux system. I got some error
> message like
>
> +++++++++++++++++++++++++++++++++++++++++++++++++++
> [n0883:08251] *** Process received signal ***
> [n0883:08249] *** Process received signal ***
> [n0883:08249] Signal: Segmentation fault (11)
> [n0883:08249] Signal code: Address not mapped (1)
> [n0883:08249] Failing at address: (nil)
> [n0883:08251] Signal: Segmentation fault (11)
> [n0883:08251] Signal code: Address not mapped (1)
> [n0883:08251] Failing at address: (nil)
> [n0883:08248] *** Process received signal ***
> [n0883:08250] *** Process received signal ***
> [n0883:08248] Signal: Segmentation fault (11)
> [n0883:08248] Signal code: Address not mapped (1)
> [n0883:08248] Failing at address: (nil)
> [n0883:08250] Signal: Segmentation fault (11)
> [n0883:08250] Signal code: Address not mapped (1)
> [n0883:08250] Failing at address: (nil)
> [n0883:08251] [ 0] /lib64/libpthread.so.0 [0x2b4f0a2f0d60]
> +++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
> My testing code is here:
>
> ===========================================================================================================
> program test_MPI_write_adv2
>
>
>   !-- Template for any mpi program
>
>   implicit none
>
>   !--Include the mpi header file
>   include 'mpif.h'              ! --> Required statement
>
>   !--Declare all variables and arrays.
>   integer :: fh, ierr, myid, numprocs, itag, etype, filetype, info
>   integer :: status(MPI_STATUS_SIZE)
>   integer :: irc, ip
>   integer(kind=mpi_offset_kind) :: offset, disp
>   integer :: i, j, k
>
>   integer :: num
>
>   character(len=64) :: filename
>
>   real(8), pointer :: q(:), temp(:)
>   integer, pointer :: map(:)
>   integer :: single_no, count
>
>
>   !--Initialize MPI
>   call MPI_INIT( ierr )         ! --> Required statement
>
>   !--Who am I? --- get my rank=myid
>   call MPI_COMM_RANK( MPI_COMM_WORLD, myid, ierr )
>
>   !--How many processes in the global group?
>   call MPI_COMM_SIZE( MPI_COMM_WORLD, numprocs, ierr )
>
>   if ( myid == 0 ) then
>      single_no = 4
>   elseif ( myid == 1 ) then
>      single_no = 2
>   elseif ( myid == 2 ) then
>      single_no = 2
>   elseif ( myid == 3 ) then
>      single_no = 3
>   else
>      single_no = 0
>   end if
>
>   if (single_no .gt. 0) allocate(map(single_no))
>
>   if ( myid == 0 ) then
>      map = (/ 0, 2, 5, 6 /)
>   elseif ( myid == 1 ) then
>      map = (/ 1, 4 /)
>   elseif ( myid == 2 ) then
>      map = (/ 3, 9 /)
>   elseif ( myid == 3 ) then
>      map = (/ 7, 8, 10 /)
>   end if
>
>   if (single_no .gt. 0) allocate(q(single_no))
>
>   if (single_no .gt. 0) then
>      do i = 1,single_no
>         q(i) = dble(myid+1)*100.0d0 + dble(map(i)+1)
>      end do
>   end if
>
>   if (single_no .gt. 0) map = map + 1
>
>   if ( myid == 0 ) then
>      count = 1
>   else
>      count = 0
>   end if
>
>   if (count .gt. 0) then
>      allocate(temp(count))
>      temp(1) = 2122010.0d0
>   end if
>
>   write(filename,'(a)') 'test_write.bin'
>
>   call MPI_FILE_OPEN(MPI_COMM_WORLD, filename,
> MPI_MODE_RDWR+MPI_MODE_CREATE, MPI_INFO_NULL, fh, ierr)
>
>   call MPI_FILE_WRITE(FH, temp, COUNT, MPI_REAL8, STATUS, IERR)
>
>   call MPI_TYPE_CREATE_INDEXED_BLOCK(single_no, 1, map,
> MPI_DOUBLE_PRECISION, filetype, ierr)
>   call MPI_TYPE_COMMIT(filetype, ierr)
>   disp = 0
>   call MPI_FILE_SET_VIEW(fh, disp, MPI_DOUBLE_PRECISION, filetype, 'native',
> MPI_INFO_NULL, ierr)
>   call MPI_FILE_WRITE_ALL(fh, q, single_no, MPI_DOUBLE_PRECISION, status,
> ierr)
>   call MPI_FILE_CLOSE(fh, ierr)
>
>
>   if (single_no .gt. 0) deallocate(map)
>
>   if (single_no .gt. 0) deallocate(q)
>
>   if (count .gt. 0) deallocate(temp)
>
>   !--Finilize MPI
>   call MPI_FINALIZE(irc)        ! ---> Required statement
>
>   stop
>
>
> end program test_MPI_write_adv2
> ===========================================================================================================
>
>
> The expected result is (should be in binary but the values are as follows) :
>
>    2122010.00000000
>    101.000000000000
>    202.000000000000
>    103.000000000000
>    304.000000000000
>    205.000000000000
>    106.000000000000
>    107.000000000000
>    408.000000000000
>    409.000000000000
>    310.000000000000
>    411.000000000000
>
>
> Can anyone help me on this problem?
>
>
> Thanks a lot,
> Kan
>
>
>
>
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