Gilles,
Thanks for the confirmation and patch. Do you expect the fix to be implemented
in OpenMPI 1.10.2?
Thanks,
Dan
________________________________________
From: users [users-boun...@open-mpi.org] on behalf of GARMANN, DANIEL J DR-02
USAF AFMC AFRL/RQVA [daniel.garm...@us.af.mil]
Sent: Tuesday, December 08, 2015 12:56 PM
To: us...@open-mpi.org
Subject: [OMPI users] Odd behavior with subarray datatypes in OpenMPI 1.10.1
Hello all,
I've noticed a change in behavior with subarray datatypes in OpenMPI 1.10.1
where the lower bounds and extents are different than previous versions. This
leads to incorrect displacements when using the subarrays with MPI-IO. I've
attached a sample code for 2 processors the shows the issue. When run on 2
processors, the program will decompose a 10x10 array of real(8) elements into
two subarrays, dimensioned 5x10 each. It then serially writes a file with two
full arrays, x and y, with values between 1.0 and 10.0, that will then be read
in via MPI-IO with the unique subarrays created on each processor, where rank 0
gets all x <= 5.0, and rank 1 gets all x > 5.0.
--- OpenMPI version 1.10.0 gives the correct behavior with the following output:
FULL ARRAY SIZE: 10 10
RANK = 0
SUBARRAY DIMENSIONS : 5, 10
SUBARRAY INDICES : 0, 0
LOWER BOUND : 0
EXTENT : 800
X-VALUES : 1.0 2.0 3.0 4.0 5.0
Y-VALUES : 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0
RANK = 1
SUBARRAY DIMENSIONS : 5, 10
SUBARRAY INDICES : 5, 0
LOWER BOUND : 0
EXTENT : 800
X-VALUES : 6.0 7.0 8.0 9.0 10.0
Y-VALUES : 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0
--- OpenMPI version 1.10.1 results in the following, where you will notice
different lower bounds and extents resulting in the wrong y-values on rank 0:
RANK = 0
SUBARRAY DIMENSIONS : 5, 10
SUBARRAY INDICES : 0, 0
LOWER BOUND : 0
EXTENT : 760
X-VALUES : 1.0 2.0 3.0 4.0 5.0
Y-VALUES : 6.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0
RANK = 1
SUBARRAY DIMENSIONS : 5, 10
SUBARRAY INDICES : 5, 0
LOWER BOUND : 40
EXTENT : 760
X-VALUES : 6.0 7.0 8.0 9.0 10.0
Y-VALUES : 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0
Is this a bug with OpenMPI 1.10.1 or am I assuming something incorrectly in my
program? I realize it would be best to read all the data through one call to
MPI_FILE_READ_ALL; however, this sample program is a very simple example of a
much more complex program that cannot buffer the I/O so easily, so I am
compelled to stick with successive reads of the subarray datatypes.
Any help is greatly appreciated!
Best regards,
Dan Garmann
PROGRAM test_extent
IMPLICIT NONE
INCLUDE 'mpif.h'
INTEGER, PARAMETER :: num_dims = 2
INTEGER :: ierr, num_procs, i, j, n, myrank, subarray_type, subsize,
arrsize, fid
INTEGER, DIMENSION(num_dims) :: arrdim, subdim, subind
INTEGER(KIND=MPI_ADDRESS_KIND) :: lower_bound, extent
REAL(KIND=8), DIMENSION(10,10) :: x, y
REAL(KIND=8), DIMENSION( 5,10) :: xsub, ysub
CALL MPI_INIT( ierr )
CALL MPI_COMM_RANK( mpi_comm_world, myrank, ierr )
CALL MPI_COMM_SIZE( mpi_comm_world, num_procs, ierr )
arrdim = (/ 10, 10 /) ! Full array dimensions
subdim = (/ 5, 10 /) ! Sub-array dimensions
subind = (/ myrank*5, 0 /) ! Sub-array stating index in full array (base 0)
arrsize = PRODUCT(arrdim) ! number of elements in full array
subsize = PRODUCT(subdim) ! number of elements in sub-array
CALL MPI_TYPE_CREATE_SUBARRAY( num_dims, arrdim, subdim, subind, &
& MPI_ORDER_FORTRAN, MPI_REAL8, subarray_type,
ierr )
CALL MPI_TYPE_COMMIT ( subarray_type, ierr )
CALL MPI_TYPE_GET_EXTENT( subarray_type, lower_bound, extent, ierr )
! Write temporary file for testing MPI-IO
IF (myrank == 0) THEN
DO j = 1, 10
DO i = 1, 10
x(i,j) = REAL(i,KIND=8)
y(i,j) = REAL(j,KIND=8)
END DO
END DO
OPEN(UNIT=1,FILE='io_test.dat',FORM='UNFORMATTED',ACCESS='STREAM',ACTION='WRITE',STATUS='REPLACE')
WRITE(1) x, y
CLOSE(1)
END IF
! Open test file and read using MPI-IO with the sub-array datatype
CALL MPI_FILE_OPEN( mpi_comm_world, 'io_test.dat', MPI_MODE_RDONLY,
MPI_INFO_NULL, fid, ierr )
CALL MPI_FILE_SET_VIEW( fid, 0_MPI_OFFSET_KIND, MPI_REAL8, subarray_type,
'NATIVE', MPI_INFO_NULL, ierr )
CALL MPI_FILE_READ_ALL( fid, xsub, subsize, MPI_REAL8, MPI_STATUS_IGNORE,
ierr )
CALL MPI_FILE_READ_ALL( fid, ysub, subsize, MPI_REAL8, MPI_STATUS_IGNORE,
ierr )
CALL MPI_FILE_CLOSE( fid, ierr )
! Write output to screen
IF (myrank == 0) WRITE(*,'(A,I0,1X,I0)') 'FULL ARRAY SIZE: ', arrdim
DO n = 0, num_procs-1
IF (myrank == n) THEN
WRITE(*,'(/A,I0)') 'RANK = ', myrank
WRITE(*,'(3X,A,I2,", ",I2)') 'SUBARRAY DIMENSIONS : ', subdim
WRITE(*,'(3X,A,I2,", ",I2)') 'SUBARRAY INDICES : ', subind
WRITE(*,'(2(3X,A,I0))') 'LOWER BOUND : ', lower_bound
WRITE(*,'(3X,A,I0)') 'EXTENT : ', extent
WRITE(*,'(3X,A, 5F5.1)') 'X-VALUES : ', xsub(:,1)
WRITE(*,'(3X,A,10F5.1)') 'Y-VALUES : ', ysub(1,:)
END IF
CALL MPI_BARRIER( mpi_comm_world, ierr )
END DO
CALL MPI_FINALIZE( ierr )
STOP
END PROGRAM test_extent
