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Subject: Re: [OMPI users] problems on parallel writing
From: jody (jody.xha_at_[hidden])
Date: 2010-02-24 15:46:53


Hi
I can't answer your question about the array q offhand,
but i will try to translate your program to C and see if
it fails the same way.

Jody

On Wed, Feb 24, 2010 at 7:40 PM, w k <thuwk99_at_[hidden]> wrote:
> Hi Jordy,
>
> I don't think this part caused the problem. For fortran, it doesn't matter
> if the pointer is NULL as long as the count requested from the processor is
> 0. Actually I tested the code and it passed this part without problem. I
> believe it aborted at MPI_FILE_SET_VIEW part.
>
> Just curious, how does C handle the case that we need to collect data in
> array q but only part of the processors has q with a length greater than 0?
>
> Thanks for your reply,
> Kan
>
>
>
>
> On Wed, Feb 24, 2010 at 2:29 AM, jody <jody.xha_at_[hidden]> wrote:
>>
>> 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
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > users mailing list
>> > users_at_[hidden]
>> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>> >
>>
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