[mpich-discuss] MPI-IO issue

[Wei-keng Liao]

Hi,

I am guessing the problem is the datatype you created.
Please check the type extent to see if it equals to the
size of entire array, using MPI_Type_extent(). If not,
the file pointer after the first read will not move to
the beginning of the second array you expected, which
leads to reading data from a wrong file location.

Also, if each process reads a block subarray, I suggest
to use MPI_Type_create_subarray to create the new datatype.


Wei-keng


On Feb 8, 2012, at 3:46 PM, Grismer, Matthew J Civ USAF AFMC AFRL/RBAT wrote:

> I am attempting to use MPI-IO to read block, structured data from a
> file.  Three three-dimensional coordinate arrays are stored in the file,
> one after another with Fortran ordering and in binary (not Fortran
> unformatted):
> 
> header info
> (((x(i,j,k),i=1,ie),j=1,je),k=1,ke)
> (((y(i,j,k),i=1,ie),j=1,je),k=1,ke)
> (((z(i,j,k),i=1,ie),j=1,je),k=1,ke)
> 
> Each processor reads a block subset of the arrays, and I've defined a
> derived type using MPI_TYPE_INDEXED for the blocks that go to each
> processor.  MPI_TYPE_INDEXED takes as arguments the number of blocks,
> block size, and block displacement;  I created (and committed) the
> datatype with the number of blocks/displacements 3 times (i.e.
> subsetie*subsetje*subsetke*3) what I need for one variable above on a
> given processor.  Then I used the following to read the file across the
> processors:
> 
> count = subsetie*subsetje*subsetke
> call MPI_FILE_SET_VIEW ( fh, skipheader, mpi_real8, newdatatype,
> "native", mpi_info_null, ierror )
> call MPI_FILE_READ_ALL ( fh, x, count, mpi_real8, ierror )
> call MPI_FILE_READ_ALL ( fh, y, count, mpi_real8, ierror ) 
> call MPI_FILE_READ_ALL ( fh, z, count, mpi_real8, ierror ) 
> 
> The result from this is x is read correctly, y and z are not.  However,
> if I define one variable xyz(subsetie,subsetje,subsetke,3) and read all
> the data in one call:
> 
> count = subsetie*subsetje*subsetke*3
> call MPI_FILE_SET_VIEW ( fh, skipheader, mpi_real8, newdatatype,
> "native", mpi_info_null, ierror )
> call MPI_FILE_READ_ALL ( fh, xyz, count, mpi_real8, ierror )
> 
> everything is read correctly, which also verifies my derived type is
> correct.  Alternatively I can reset the view (with correct
> displacements) after each READ_ALL and read into the individual
> variables.
> 
> Is this the expected behavior?  If so I do not understand how to make
> successive collective reads from a file without resetting the view
> before every read, which will take a toll on performance when I continue
> to read many additional variables from the file.
> 
> Matt
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