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Subject: Re: [OMPI users] MPI-IO Inconsistency over Lustre using OMPI 1.3
From: Nathan Baca (nathan.baca_at_[hidden])
Date: 2009-03-03 22:49:49


Thanks for the quick reply and suggestions.

I have tried both isolating the output to a single OST and striping across
multiple OSTs. Both will produce the same result. I have tried compiling
with multiple versions of both pathscale and intel compilers all with the
same result.

The odd thing is that this seems to work using hpmpi 2.03 compiled with
pathscale 3.2 and intel 10.1.018. The operating system is XC 3.2.1 which is
essentially rhel4.5. The kernel is 2.6.9-67.9hp.7sp.XCsmp. Lustre version is
lustre-1.4.11-2.3_0.6_xc3.2.1_k2.6.9_67.9hp.7sp.XCsmp.

Thanks for the info, Nate

On Tue, Mar 3, 2009 at 11:10 AM, Brian Dobbins <bdobbins_at_[hidden]> wrote:

>
> 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]
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>
>
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-- 
Nathan Baca
nathan.baca_at_[hidden]