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Subject: Re: [OMPI users] MPI-IO Inconsistency over Lustre using OMPI 1.3
From: Brian Dobbins (bdobbins_at_[hidden])
Date: 2009-03-03 13:10:49


Hi Nathan,

  I just ran your code here and it worked fine - CentOS 5 on dual Xeons w/
IB network, and the kernel is 2.6.18-53.1.14.el5_lustre.1.6.5smp. I used an
OpenMPI 1.3.0 install compiled with Intel 11.0.081 and, independently, one
with GCC 4.1.2. I tried a few different times with varying numbers of
processors.

  (Both executables were compiled with -O2)

  I'm sure the main OpenMPI guys will have better ideas, but in the meantime
what kernel, OS and compilers are you using? And does it happen when you
write to a single OST? Make a directory and try setting the stripe-size to
1 (eg, lfs setstripe <directory name> 1048576 0 1' will give you, I think, a
1MB stripe size starting at OST 0 and of size 1.) I'm just wondering
whether it's something with your hardware, maybe a particular OST, since it
seems to work for me.

  ... Sorry I can't be of more help, but I imagine the regular experts will
chime in shortly.

  Cheers,
  - Brian

On Tue, Mar 3, 2009 at 12:51 PM, Nathan Baca <nathan.baca_at_[hidden]> wrote:

> Hello,
>
> I am seeing inconsistent mpi-io behavior when writing to a Lustre file
> system using open mpi 1.3 with romio. What follows is a simple reproducer
> and output. Essentially one or more of the running processes does not read
> or write the correct amount of data to its part of a file residing on a
> Lustre (parallel) file system.
>
> Any help figuring out what is happening is greatly appreciated. Thanks,
> Nate
>
> program gcrm_test_io
> implicit none
> include "mpif.h"
>
> integer X_SIZE
>
> integer w_me, w_nprocs
> integer my_info
>
> integer i
> integer (kind=4) :: ierr
> integer (kind=4) :: fileID
>
> integer (kind=MPI_OFFSET_KIND) :: mylen
> integer (kind=MPI_OFFSET_KIND) :: offset
> integer status(MPI_STATUS_SIZE)
> integer count
> integer ncells
> real (kind=4), allocatable, dimension (:) :: array2
> logical sync
>
> call mpi_init(ierr)
> call MPI_COMM_SIZE(MPI_COMM_WORLD,w_nprocs,ierr)
> call MPI_COMM_RANK(MPI_COMM_WORLD,w_me,ierr)
>
> call mpi_info_create(my_info, ierr)
> ! optional ways to set things in mpi-io
> ! call mpi_info_set (my_info, "romio_ds_read" , "enable" , ierr)
> ! call mpi_info_set (my_info, "romio_ds_write", "enable" , ierr)
> ! call mpi_info_set (my_info, "romio_cb_write", "enable" , ierr)
>
> x_size = 410011 ! A 'big' number, with bigger numbers it is more
> likely to fail
> sync = .true. ! Extra file synchronization
>
> ncells = (X_SIZE * w_nprocs)
>
> ! Use node zero to fill it with nines
> if (w_me .eq. 0) then
> call MPI_FILE_OPEN (MPI_COMM_SELF, "output.dat",
> MPI_MODE_CREATE+MPI_MODE_WRONLY, my_info, fileID, ierr)
> allocate (array2(ncells))
> array2(:) = 9.0
> mylen = ncells
> offset = 0 * 4
> call MPI_FILE_SET_VIEW(fileID,offset, MPI_REAL,MPI_REAL,
> "native",MPI_INFO_NULL,ierr)
> call MPI_File_write(fileID, array2, mylen , MPI_REAL,
> status,ierr)
> call MPI_Get_count(status,MPI_INTEGER, count, ierr)
> if (count .ne. mylen) print*, "Wrong initial write count:",
> count,mylen
> deallocate(array2)
> if (sync) call MPI_FILE_SYNC (fileID,ierr)
> call MPI_FILE_CLOSE (fileID,ierr)
> endif
>
> ! All nodes now fill their area with ones
> call MPI_BARRIER(MPI_COMM_WORLD,ierr)
> allocate (array2( X_SIZE))
> array2(:) = 1.0
> offset = (w_me * X_SIZE) * 4 ! multiply by four, since it is real*4
> mylen = X_SIZE
> call MPI_FILE_OPEN (MPI_COMM_WORLD,"output.dat",MPI_MODE_WRONLY,
> my_info, fileID, ierr)
> print*,"node",w_me,"starting",(offset/4) +
> 1,"ending",(offset/4)+mylen
> call MPI_FILE_SET_VIEW(fileID,offset, MPI_REAL,MPI_REAL,
> "native",MPI_INFO_NULL,ierr)
> call MPI_File_write(fileID, array2, mylen , MPI_REAL, status,ierr)
> call MPI_Get_count(status,MPI_INTEGER, count, ierr)
> if (count .ne. mylen) print*, "Wrong write count:", count,mylen,w_me
> deallocate(array2)
> if (sync) call MPI_FILE_SYNC (fileID,ierr)
> call MPI_FILE_CLOSE (fileID,ierr)
>
> ! Read it back on node zero to see if it is ok data
> if (w_me .eq. 0) then
> call MPI_FILE_OPEN (MPI_COMM_SELF, "output.dat",
> MPI_MODE_RDONLY, my_info, fileID, ierr)
> mylen = ncells
> allocate (array2(ncells))
> call MPI_File_read(fileID, array2, mylen , MPI_REAL, status,ierr)
>
> call MPI_Get_count(status,MPI_INTEGER, count, ierr)
> if (count .ne. mylen) print*, "Wrong read count:", count,mylen
> do i=1,ncells
> if (array2(i) .ne. 1) then
> print*, "ERROR", i,array2(i), ((i-1)*4),
> ((i-1)*4)/(1024d0*1024d0) ! Index, value, # of good bytes,MB
> goto 999
> end if
> end do
> print*, "All done with nothing wrong"
> 999 deallocate(array2)
> call MPI_FILE_CLOSE (fileID,ierr)
> call MPI_file_delete ("output.dat",MPI_INFO_NULL,ierr)
> endif
>
> call mpi_finalize(ierr)
>
> end program gcrm_test_io
>
> 1.3 Open MPI
> node 0 starting 1 ending
> 410011
> node 1 starting 410012 ending
> 820022
> node 2 starting 820023 ending
> 1230033
> node 3 starting 1230034 ending
> 1640044
> node 4 starting 1640045 ending
> 2050055
> node 5 starting 2050056 ending
> 2460066
> All done with nothing wrong
>
>
> node 0 starting 1 ending
> 410011
> node 1 starting 410012 ending
> 820022
> node 2 starting 820023 ending
> 1230033
> node 5 starting 2050056 ending
> 2460066
> node 4 starting 1640045 ending
> 2050055
> node 3 starting 1230034 ending
> 1640044
> Wrong write count: 228554 410011 2
> Wrong read count: 1048576 2460066
> ERROR 1048577 0.0000000E+00 4194304 4.00000000000000
>
>
> node 1 starting 410012 ending
> 820022
> node 0 starting 1 ending
> 410011
> node 2 starting 820023 ending
> 1230033
> node 3 starting 1230034 ending
> 1640044
> node 4 starting 1640045 ending
> 2050055
> node 5 starting 2050056 ending
> 2460066
> Wrong read count: 1229824 2460066
> ERROR 1229825 0.0000000E+00 4919296 4.69140625000000
>
> --
> Nathan Baca
> nathan.baca_at_[hidden]
>
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