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Subject: Re: [OMPI users] MPIRUN Error on Mac pro i7 laptop and linux desktop
From: christophe petit (christophe.petit09_at_[hidden])
Date: 2010-07-28 13:05:57


Thanks for your answers,

the execution of this parallel program works fine at my work, but we used
MPICH2. I thought this will run with OPEN-MPI too.

Here is the f90 source where MPI_CART_SHIFT is called :

      program heat
!**************************************************************************
!
! This program solves the heat equation on the unit square [0,1]x[0,1]
! | du/dt - Delta(u) = 0
! | u/gamma = cste
! by implementing a explicit scheme.
! The discretization is done using a 5 point finite difference scheme
! and the domain is decomposed into sub-domains.
! The PDE is discretized using a 5 point finite difference scheme
! over a (x_dim+2)*(x_dim+2) grid including the end points
! correspond to the boundary points that are stored.
!
! The data on the whole domain are stored in
! the following way :
!
! y
! ------------------------------------
! d | |
! i | |
! r | |
! e | |
! c | |
! t | |
! i | x20 |
! o /\ | |
! n | | x10 |
! | | |
! | | x00 x01 x02 ... |
! | ------------------------------------
! -------> x direction x(*,j)
!
! The boundary conditions are stored in the following submatrices
!
!
! x(1:x_dim, 0) ---> left temperature
! x(1:x_dim, x_dim+1) ---> right temperature
! x(0, 1:x_dim) ---> top temperature
! x(x_dim+1, 1:x_dim) ---> bottom temperature
!
!**************************************************************************
      implicit none
      include 'mpif.h'
! size of the discretization
      integer :: x_dim, nb_iter
      double precision, allocatable :: x(:,:),b(:,:),x0(:,:)
      double precision :: dt, h, epsilon
      double precision :: resLoc, result, t, tstart, tend
!
      integer :: i,j
      integer :: step, maxStep
      integer :: size_x, size_y, me, x_domains,y_domains
      integer :: iconf(5), size_x_glo
      double precision conf(2)
!
! MPI variables
      integer :: nproc, infompi, comm, comm2d, lda, ndims
      INTEGER, DIMENSION(2) :: dims
      LOGICAL, DIMENSION(2) :: periods
      LOGICAL, PARAMETER :: reorganisation = .false.
      integer :: row_type
      integer, parameter :: nbvi=4
      integer, parameter :: S=1, E=2, N=3, W=4
      integer, dimension(4) :: neighBor

!
      intrinsic abs
!
!
      call MPI_INIT(infompi)
      comm = MPI_COMM_WORLD
      call MPI_COMM_SIZE(comm,nproc,infompi)
      call MPI_COMM_RANK(comm,me,infompi)
!
!
      if (me.eq.0) then
          call readparam(iconf, conf)
      endif
      call MPI_BCAST(iconf,5,MPI_INTEGER,0,comm,infompi)
      call MPI_BCAST(conf,2,MPI_DOUBLE_PRECISION,0,comm,infompi)
!
      size_x = iconf(1)
      size_y = iconf(1)
      x_domains = iconf(3)
      y_domains = iconf(4)
      maxStep = iconf(5)
      dt = conf(1)
      epsilon = conf(2)
!
      size_x_glo = x_domains*size_x+2
      h = 1.0d0/dble(size_x_glo)
      dt = 0.25*h*h
!
!
      lda = size_y+2
      allocate(x(0:size_y+1,0:size_x+1))
      allocate(x0(0:size_y+1,0:size_x+1))
      allocate(b(0:size_y+1,0:size_x+1))
!
! Create 2D cartesian grid
      periods(:) = .false.

      ndims = 2
      dims(1)=x_domains
      dims(2)=y_domains
      CALL MPI_CART_CREATE(MPI_COMM_WORLD, ndims, dims, periods, &
        reorganisation,comm2d,infompi)
!
! Identify neighbors
!
      NeighBor(:) = MPI_PROC_NULL
! Left/West and right/Est neigbors
      CALL MPI_CART_SHIFT(comm2d,0,1,NeighBor(W),NeighBor(E),infompi)
! Bottom/South and Upper/North neigbors
      CALL MPI_CART_SHIFT(comm2d,1,1,NeighBor(S),NeighBor(N),infompi)
!
! Create row data type to coimmunicate with South and North neighbors
!
      CALL MPI_TYPE_VECTOR(size_x, 1, size_y+2, MPI_DOUBLE_PRECISION,
row_type,infompi)
      CALL MPI_TYPE_COMMIT(row_type, infompi)
!
! initialization
!
      call initvalues(x0, b, size_x+1, size_x )
!
! Update the boundaries
!
      call updateBound(x0,size_x,size_x, NeighBor, comm2d, row_type)

      step = 0
      t = 0.0
!
      tstart = MPI_Wtime()
! REPEAT
 10 continue
!
         step = step + 1
         t = t + dt
! perform one step of the explicit scheme
         call Explicit(x0,x,b, size_x+1, size_x, size_x, dt, h, resLoc)
! update the partial solution along the interface
         call updateBound(x0,size_x,size_x, NeighBor, comm2d, row_type)
! Check the distance between two iterates
         call MPI_ALLREDUCE(resLoc,result,1, MPI_DOUBLE_PRECISION,
MPI_SUM,comm,infompi)
         result= sqrt(result)
!
         if (me.eq.0) write(*,1002) t,result
!
       if ((result.gt.epsilon).and.(step.lt.maxStep)) goto 10
!
! UNTIL "Convergence"
!
       tend = MPI_Wtime()
       if (me.eq.0) then
         write(*,*)
         write(*,*) ' Convergence after ', step,' steps '
         write(*,*) ' Problem size ',
size_x*x_domains*size_y*y_domains
         write(*,*) ' Wall Clock ', tend-tstart

!
! Print the solution at each point of the grid
!
         write(*,*)
         write(*,*) ' Computed solution '
         write(*,*)
         do 30, j=size_x+1,0,-1
            write(*,1000)(x0(j,i),i=0,size_x+1)
 30 continue
       endif
!
      call MPI_FINALIZE(infompi)
!
      deallocate(x)
      deallocate(x0)
      deallocate(b)
!
! Formats available to display the computed values on the grid
!
1000 format(100(1x, f7.3))
1001 format(100(1x, e7.3))
1002 format(' At time ',E8.2,' Norm ', E8.2)

!
      stop
      end
!

------------------------------------------------------------------------------
2010/7/28 Jeff Squyres <jsquyres_at_[hidden]>

> According to the error message (especially since it's consistent across 2
> different platforms), it looks like you have an error in your application.
> Open MPI says that you're using an invalid communicator when calling
> MPI_Cart_shift. "Invalid" probably means that it's not a Cartesian
> communicator.
>
> You might want to double check the definition and requirements of the
> MPI_CART_SHIFT function (see the MPI_Cart_shift(3) man page).
>
>
>
> On Jul 28, 2010, at 12:28 PM, christophe petit wrote:
>
> > hello,
> >
> > i have a problem concerning the execution of a f90 program (explicitPar)
> compiled with openmpi-1.4.2. I get nearly the same error on my debian
> desktop ( AMD Phenom(tm) 9550 Quad-Core Processor) and my mac pro i7 laptop
> :
> >
> > on mac pro i7 :
> >
> > $ mpiexec -np 2 explicitPar
> > [macbook-pro-de-fab.livebox.home:48805] *** An error occurred in
> MPI_Cart_shift
> > [macbook-pro-de-fab.livebox.home:48805] *** on communicator
> MPI_COMM_WORLD
> > [macbook-pro-de-fab.livebox.home:48805] *** MPI_ERR_COMM: invalid
> communicator
> > [macbook-pro-de-fab.livebox.home:48805] *** MPI_ERRORS_ARE_FATAL (your
> MPI job will now abort)
> >
> --------------------------------------------------------------------------
> > mpiexec has exited due to process rank 1 with PID 48805 on
> > node macbook-pro-de-fab.livebox.home exiting without calling "finalize".
> This may
> > have caused other processes in the application to be
> > terminated by signals sent by mpiexec (as reported here).
> >
> >
> ---------------------------------------------------------------------------
> >
> > on my debian desktop :
> >
> > mpirun -np 2 explicitPar
> > [pablo:11665] *** An error occurred in MPI_Cart_shift
> > [pablo:11665] *** on communicator MPI_COMM_WORLD
> > [pablo:11665] *** MPI_ERR_COMM: invalid communicator
> > [pablo:11665] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> >
> --------------------------------------------------------------------------
> > mpirun has exited due to process rank 1 with PID 11665 on
> > node pablo exiting without calling "finalize". This may
> > have caused other processes in the application to be
> > terminated by signals sent by mpirun (as reported here).
> >
> --------------------------------------------------------------------------
> >
> >
> > I have installed openmpi-1.4.2 with the following options :
> >
> > ./configure --prefix=/usr/local/openmpi --enable-mpi-f77 --enable-mpi-f90
> >
> > with exported variables on bash shell : FC=gfortran F90=gfortran
> F77=gfortran CC=gcc CXX=g++
> >
> > The installation has been completed, the program compiles fine but i
> don't understand what's wrong. I note that with a single processor ("mpirun
> -np 1 explicitPar"), execution works fine.
> >
> > My debian desktop is a quad-core, so, theoretically, i can put up to 4
> for "np" parameter.
> > On my mac pro i7, i don't know how processors are there, but the "htop"
> command makes appear 4 cores too.
> >
> > Anyone has a solution ?
> >
> > Regards.
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > users mailing list
> > users_at_[hidden]
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> --
> Jeff Squyres
> jsquyres_at_[hidden]
> For corporate legal information go to:
> http://www.cisco.com/web/about/doing_business/legal/cri/
>
>
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