christophe petit wrote:
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.
In your input deck, how big are x_domains and y_domains -- that is,
iconf(3) and iconf(4)? Do they have to be changed if you change the
number of processes you run on? Off hand, it looks like
x_domains*y_domains = iconf(3)*iconf(4) should equal nproc. If you can
run with nproc=1 and don't change the input deck, you won't be able to
run on nproc/=1.
Given that the problem is in MPI_Cart_shift, could you produce a much
smaller program that illustrates the error you're trying to understand?
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 <jsquy...@cisco.com>
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.
>
>
>
>
>
>
>
--
Jeff Squyres
jsquy...@cisco.com
For corporate legal information go to:
http://www.cisco.com/web/about/doing_business/legal/cri/
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