On 05/07/2014 11:36 AM, Rob Latham wrote:
On 05/05/2014 09:20 PM, Richard Shaw wrote:
Hello,
I think I've come across a bug when using ROMIO to read in a 2D
distributed array. I've attached a test case to this email.
Thanks for the bug report and the test case.
I've opened MPICH bug (because this is ROMIO's fault, not OpenMPI's
fault... until I can prove otherwise ! :>)
This bug appears to be OpenMPIs fault now.
I'm looking at OpenMPI's "pulled it from git an hour ago" version, and
ROMIO's flattening code overruns arrays: the OpenMPI datatype processing
routines return too few blocks for ranks 1 and 3.
Michael Raymond told me off-list "I tracked this down to MPT not marking
HVECTORs / STRUCTs with 0-sized counts as contiguous. Once I changed
this, the memory corruption and the data mismatches both went away. ".
Could something similar be happening in OpenMPI ?
==rob
http://trac.mpich.org/projects/mpich/ticket/2089
==rob
In the testcase I first initialise an array of 25 doubles (which will be
a 5x5 grid), then I create a datatype representing a 5x5 matrix
distributed in 3x3 blocks over a 2x2 process grid. As a reference I use
MPI_Pack to pull out the block cyclic array elements local to each
process (which I think is correct). Then I write the original array of
25 doubles to disk, and use MPI-IO to read it back in (performing the
Open, Set_view, and Real_all), and compare to the reference.
Running this with OMPI, the two match on all ranks.
> mpirun -mca io ompio -np 4 ./darr_read.x
=== Rank 0 === (9 elements)
Packed: 0.0 1.0 2.0 5.0 6.0 7.0 10.0 11.0 12.0
Read: 0.0 1.0 2.0 5.0 6.0 7.0 10.0 11.0 12.0
=== Rank 1 === (6 elements)
Packed: 15.0 16.0 17.0 20.0 21.0 22.0
Read: 15.0 16.0 17.0 20.0 21.0 22.0
=== Rank 2 === (6 elements)
Packed: 3.0 4.0 8.0 9.0 13.0 14.0
Read: 3.0 4.0 8.0 9.0 13.0 14.0
=== Rank 3 === (4 elements)
Packed: 18.0 19.0 23.0 24.0
Read: 18.0 19.0 23.0 24.0
However, using ROMIO the two differ on two of the ranks:
> mpirun -mca io romio -np 4 ./darr_read.x
=== Rank 0 === (9 elements)
Packed: 0.0 1.0 2.0 5.0 6.0 7.0 10.0 11.0 12.0
Read: 0.0 1.0 2.0 5.0 6.0 7.0 10.0 11.0 12.0
=== Rank 1 === (6 elements)
Packed: 15.0 16.0 17.0 20.0 21.0 22.0
Read: 0.0 1.0 2.0 0.0 1.0 2.0
=== Rank 2 === (6 elements)
Packed: 3.0 4.0 8.0 9.0 13.0 14.0
Read: 3.0 4.0 8.0 9.0 13.0 14.0
=== Rank 3 === (4 elements)
Packed: 18.0 19.0 23.0 24.0
Read: 0.0 1.0 0.0 1.0
My interpretation is that the behaviour with OMPIO is correct.
Interestingly everything matches up using both ROMIO and OMPIO if I set
the block shape to 2x2.
This was run on OS X using 1.8.2a1r31632. I have also run this on Linux
with OpenMPI 1.7.4, and OMPIO is still correct, but using ROMIO I just
get segfaults.
Thanks,
Richard
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Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA
