Re: [Pvfs2-users] kzalloc undefined

Wed, 21 Feb 2007 09:43:40 -0800 


On Feb 21, 2007, at 11:28 AM, Trach-Minh Tran wrote:


On 02/21/2007 06:10 PM, Sam Lang wrote:


On Feb 21, 2007, at 10:49 AM, Trach-Minh Tran wrote:


On 02/21/2007 05:18 PM, Sam Lang wrote:


Hi Minh,
I got the order of my AC_TRY_COMPILE arguments wrong. That was pretty 
sloppy on my part.  I've attached a patch that should fix the error
you're getting.  I'm not sure it will apply cleanly to the already
patched 2.6.2 source that you have. Better to start with a clean 2.6.2 
tarball.


Hi Sam,

Thanks for you prompt response. I can now load the module. I will do
some more tests with this 2.6.2 version. Until now, I've found
using my MPI-IO program, that this is not as stable as the 2.6.1 version: 
During about 1/2 hour running the test, already 2 data servers (out
of 8) have died!
That's surprising, the 2.6.2 release didn't include any changes to the servers from 2.6.1. Did you get any messages in the server logs on the 
nodes that died?



Do you think that I should stay with 2.6.1 + the misc-bug.patch from
Murali?


There aren't any other significant fixes in 2.6.2 besides support for
the latest Berkeley DB release, and the misc-bug patch that you mention, so using 2.6.1 shouldn't be a problem for you. That being said, if the 
servers crash for you on 2.6.2, its likely that they will do so with
2.6.1 and you just haven't hit it yet.  I'd also like to figure out
exactly what is causing the servers to crash. Can you send your MPI-IO 
program to us?



Hi Sam,
There is nothing in the server logs! May be tomorrow (it is now 6:30 pm 
here) I will have more infos from the mpi-io runs I've just submitted.
Rob thinks this might be related to the ROMIO ad_pvfs bug reported a couple days ago, but the even so, corruption on the client shouldn't cause the server's to segfault (esp. if the corruption is outside the PVFS system interfaces). If possible, it would be great to get a stack trace from one of the crashed servers. 

Thanks,

-sam



I have attached the mpi-io test program.

Best regards,   -Minh.
SUBROUTINE record(flag, n, r, z, phi, u, mu, w, vol, psi)
  IMPLICIT NONE
  INCLUDE 'mpif.h'
  CHARACTER*1, INTENT(in) :: flag
  INTEGER, INTENT(in) :: n
DOUBLE PRECISION, DIMENSION(n), INTENT(out):: r, z, phi, u, mu, w, vol, psi 
  INTEGER :: me, npes, ierr, comm=MPI_COMM_WORLD
  CHARACTER*128 :: fname="pvfs2:/scratch/ttran/io/io2.d"
!!$  CHARACTER*128 :: fname="io2.d"
  INTEGER, DIMENSION(:), ALLOCATABLE :: nplocs
  INTEGER :: i, nptot, fh, filetype
  INTEGER(kind=MPI_OFFSET_KIND) :: displ
! ______________________________________________________________________ __________ 
!   Prologue
!
  CALL mpi_comm_rank(comm, me, ierr)
  CALL mpi_comm_size(comm, npes, ierr)
! ______________________________________________________________________ __________ 
!   Define file layout
!
  ALLOCATE(nplocs(0:npes-1))
CALL mpi_allgather(n, 1, MPI_INTEGER, nplocs, 1, MPI_INTEGER, comm, ierr) 
  nptot = SUM(nplocs)
!!$  IF( me .EQ. 0 ) THEN
!!$     WRITE(*,'(a, 10(i10))') 'NPLOCS =', nplocs
!!$  END IF
CALL mpi_type_vector(8, n, nptot, MPI_DOUBLE_PRECISION, filetype, ierr) 
  CALL mpi_type_commit(filetype, ierr)
  displ = 0
  DO i=0,me-1
     displ = displ+8*nplocs(i)
  END DO
! ______________________________________________________________________ __________ 
!    Read restart file
!
  IF( flag .EQ. 'R' ) THEN
CALL mpi_file_open(comm, fname, MPI_MODE_RDONLY, MPI_INFO_NULL, fh, ierr) CALL mpi_file_set_view(fh, displ, MPI_DOUBLE_PRECISION, filetype, "native", & 
          &   MPI_INFO_NULL, ierr)
CALL mpi_file_read_all(fh, r, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_read_all(fh, z, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_read_all(fh, phi, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_read_all(fh, u, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_read_all(fh, mu, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_read_all(fh, w, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_read_all(fh, vol, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_read_all(fh, psi, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) 
  END IF
! ______________________________________________________________________ __________ 
!    Write restart file
!
  IF( flag .EQ. 'W' ) THEN
CALL mpi_file_open(comm, fname, MPI_MODE_WRONLY +MPI_MODE_CREATE, & 
          &   MPI_INFO_NULL, fh, ierr)
CALL mpi_file_set_view(fh, displ, MPI_DOUBLE_PRECISION, filetype, "native", & 
          &   MPI_INFO_NULL, ierr)
CALL mpi_file_write_all(fh, r, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_write_all(fh, z, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_write_all(fh, phi, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_write_all(fh, u, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_write_all(fh, mu, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_write_all(fh, w, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_write_all(fh, vol, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) CALL mpi_file_write_all(fh, psi, n, MPI_DOUBLE_PRECISION, MPI_STATUS_IGNORE, ierr) 
  END IF
! ______________________________________________________________________ __________ 
!   Epilogue
!
  DEALLOCATE(nplocs)
  CALL mpi_type_free(filetype, ierr)
  CALL mpi_file_close(fh, ierr)
!
END SUBROUTINE record
 PROGRAM main
!
! Parallel I/O benchmark
!
  IMPLICIT NONE
  INCLUDE 'mpif.h'
  INTEGER :: npes, me, ierr, comm=MPI_COMM_WORLD
  INTEGER :: npart, npart_mp=1, start, nploc
DOUBLE PRECISION, DIMENSION(:), ALLOCATABLE :: r, z, phi, u, mu, w, vol, psi 
  DOUBLE PRECISION :: t0, twrite, tread, mbytes
  INTEGER :: i, nit=1
  CHARACTER*1 :: flag
  INTEGER :: nerrors
! ______________________________________________________________________ __________ 
!   Init MPI
!
  CALL mpi_init(ierr)
  CALL mpi_comm_rank(comm, me, ierr)
  CALL mpi_comm_size(comm, npes, ierr)
! ______________________________________________________________________ __________ 
!   Input data of the run
!
  IF( me .EQ. 0 ) THEN
WRITE(*,*) 'Enter total number of particles (Mega Part.) and nits' 
     READ(*,*) npart_mp, nit
  END IF
  CALL mpi_bcast(npart_mp, 1, MPI_INTEGER, 0, comm, ierr)
  CALL mpi_bcast(nit, 1, MPI_INTEGER, 0, comm, ierr)
  npart = npart_mp*1024*1024
  CALL dist1d(0, npart, start, nploc)
! ______________________________________________________________________ __________ 
!   Init particle arrays
!
ALLOCATE(r(nploc), z(nploc), phi(nploc), u(nploc), mu(nploc), w (nploc), & 
       &   vol(nploc), psi(nploc))
  CALL initp(nploc, r, z, phi, u, mu, w, vol, psi)
  twrite=0.0
  tread=0.0
! ______________________________________________________________________ __________ 
!   Write arrays to file
!
  CALL mpi_barrier(comm, ierr)
  t0=mpi_wtime()
  DO i=1,nit
     CALL record('W', nploc, r, z, phi, u, mu, w, vol, psi)
  END DO
  CALL mpi_barrier(comm, ierr)
  twrite = mpi_wtime()-t0
! ______________________________________________________________________ __________ 
!   Read arrays to file
!
  CALL mpi_barrier(comm, ierr)
  t0=mpi_wtime()
  DO i=1,nit
r=0.0d0; z=0.0d0; phi=0.0d0; u=0.0d0; mu=0.0d0; w=0.0d0; vol=0.0d0; psi=0.0d0 
     CALL record('R', nploc, r, z, phi, u, mu, w, vol, psi)
  END DO
  CALL mpi_barrier(comm, ierr)
  tread = mpi_wtime()-t0
! ______________________________________________________________________ __________ 
!   Check read arrays
!
  CALL check(nploc, r, z, phi, u, mu, w, vol, psi, nerrors)
  i = nerrors
  CALL mpi_reduce(i, nerrors, 1, MPI_INTEGER, MPI_SUM, 0, comm, ierr)
  IF ( me .EQ. 0 ) THEN
WRITE(*, '(a,i12)' ) 'Number of errors return from CHECK:', nerrors 
  END IF
! ______________________________________________________________________ __________ 
!   Epilogue
!
  IF(me .EQ. 0 ) THEN
     twrite = twrite/REAL(nit)
     tread = tread/REAL(nit)
     mbytes = 8.0*8.0*REAL(npart)/1024.0/1024.0
     WRITE(*,'(a,f12.3,a)') 'Write/Read of', mbytes, 'MB'
WRITE(*,'(a,4(f8.3,a))') 'Write/Read performance:', twrite, ' s', & mbytes/twrite, ' MB/s', tread, ' s', mbytes/tread, ' MB/s' 
  END IF
  CALL mpi_finalize(ierr)
END PROGRAM main
!
SUBROUTINE initp(n, r, z, phi, u, mu, w, vol, psi)
  IMPLICIT NONE
  INCLUDE 'mpif.h'
  INTEGER, INTENT(in) :: n
DOUBLE PRECISION, DIMENSION(n), INTENT(out):: r, z, phi, u, mu, w, vol, psi 
  DOUBLE PRECISION :: x
  INTEGER :: me, ierr, comm=MPI_COMM_WORLD
  INTEGER :: i
! ______________________________________________________________________ __________ 
  CALL mpi_comm_rank(comm, me, ierr)
  x=0.0d0
  DO i=1,n
     x=x+1.0d0; r(i)   = x
     x=x+1.0d0; z(i)   = x
     x=x+1.0d0; phi(i) = x
     x=x+1.0d0; u(i)   = x
     x=x+1.0d0; mu(i)  = x
     x=x+1.0d0; w(i)   = x
     x=x+1.0d0; vol(i) = x
     x=x+1.0d0; psi(i) = x
  END DO
END SUBROUTINE initp
!
SUBROUTINE check(n, r, z, phi, u, mu, w, vol, psi, nerrs)
  IMPLICIT NONE
  INCLUDE 'mpif.h'
  INTEGER, INTENT(in) :: n
  INTEGER, INTENT(out) :: nerrs
DOUBLE PRECISION, DIMENSION(n), INTENT(in):: r, z, phi, u, mu, w, vol, psi 
  INTEGER :: i
  DOUBLE PRECISION :: x
! ______________________________________________________________________ __________ 
  nerrs = 0
  x=0.0d0
  DO i=1,n
     x=x+1.0d0; IF( r(i)   .NE. x ) nerrs=nerrs+1
     x=x+1.0d0; IF( z(i)   .NE. x ) nerrs=nerrs+1
     x=x+1.0d0; IF( phi(i) .NE. x ) nerrs=nerrs+1
     x=x+1.0d0; IF( u(i)   .NE. x ) nerrs=nerrs+1
     x=x+1.0d0; IF( mu(i)  .NE. x ) nerrs=nerrs+1
     x=x+1.0d0; IF( w(i)   .NE. x ) nerrs=nerrs+1
     x=x+1.0d0; IF( vol(i) .NE. x ) nerrs=nerrs+1
     x=x+1.0d0; IF( psi(i) .NE. x ) nerrs=nerrs+1
  END DO
END SUBROUTINE check
SUBROUTINE dist1d(s0, ntot, s, nloc)
  IMPLICIT NONE
  INCLUDE 'mpif.h'
  INTEGER, INTENT(in) :: s0, ntot
  INTEGER, INTENT(out) :: s, nloc
  INTEGER :: me, npes, ierr, naver, rem
!
  CALL MPI_COMM_SIZE(MPI_COMM_WORLD, npes, ierr)
  CALL MPI_COMM_RANK(MPI_COMM_WORLD, me, ierr)
  naver = ntot/npes
  rem = MODULO(ntot,npes)
  s = s0 + MIN(rem,me) + me*naver
  nloc = naver
  IF( me.LT.rem ) nloc = nloc+1
!
END SUBROUTINE dist1d


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