[petsc-users] Error with file linking

[Satish Balay]

This is too confusing..


On Wed, 12 May 2010, Wee-Beng TAY wrote:

> Hi,
> 
> my code works fine with petsc-3.0. However I have problem linking when using
> petsc3.1. I used the same linking command as that given by make ex1f, which is
> :

This is not the compile for ex1f - I see ' a.out global.o ...'
> 
> /app1/mvapich/current/bin/mpif90 -r8 -w95 -fPIC -g -O3 -o a.out global.o
> grid.o flux_area.o bc.o bc_impl.o bc_semi.o set_matrix.o inter_step.o
> mom_disz.o poisson.o petsc_sub.o cell_data.o fractional.o ns2d_c.o
> -Wl,-rpath,/home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib
> -L/home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib -lpetsc
> -Wl,-rpath,/home/svu/g0306332/lib/hypre-2.6.0b_atlas5/lib
> -L/home/svu/g0306332/lib/hypre-2.6.0b_atlas5/lib -lHYPRE -lmpichcxx -lstdc++
> -Wl,-rpath,/app1/intel/mkl/10.0.5.025/lib/em64t
> -L/app1/intel/mkl/10.0.5.025/lib/em64t -lmkl_lapack -lmkl -lguide -lpthread
> -L/app1/mvapich2/1.4/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -ldl -lmpich
> -lpthread -lrdmacm -libverbs -libumad -lrt -lgcc_s -lmpichf90
> -L/app1/intel/Compiler/11.0/074/lib/intel64 -lifport -lifcore -limf -lsvml -lm
> -lipgo -lirc -lirc_s -lm -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich
> -lpthread -lrdmacm -libverbs -libumad -lrt -lgcc_s -ldl
> 
> The compiling command is:
> 
> /app1/mvapich/current/bin/mpif90 -r8 -132 -fPIC -g -w90 -w -w95 -c -O3
> -I/home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/include
> -I/home/svu/g0306332/codes/petsc-3.1-p0/include
> -I/home/svu/g0306332/lib/hypre-2.6.0b_atlas5/include
> -I/app1/mvapich2/1.4/include -I/app1/mvapich2/current/include
> -I/home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/include
> -I/home/svu/g0306332/lib/hypre-2.6.0b_atlas5/include
> -I/app1/mvapich2/1.4/include -I/app1/mvapich2/current/include

The above compile command is incomplete. Why truncate it?

What about the link command?

> 
> The error msgs are:
> 
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(mpinit.o):
> In function `PetscOpenMPSpawn':
> /home/svu/g0306332/codes/petsc-3.1-p0/src/sys/objects/mpinit.c:72: undefined
> reference to `MPI_Comm_get_parent'

Clearly you are not linking with the library that provides MPI_Comm_get_parent.

Why not use petsc makefiles - and avoid these hasseles?

Satish


> /home/svu/g0306332/codes/petsc-3.1-p0/src/sys/objects/mpinit.c:79: undefined
> reference to `MPI_Comm_spawn'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(gr2.o):
> In function `DAArrayMPIIO':
> /home/svu/g0306332/codes/petsc-3.1-p0/src/dm/da/src/gr2.c:482: undefined
> reference to `MPI_Type_get_extent'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(binv.o):
> In function `PetscViewerBinaryMPIIO':
> /home/svu/g0306332/codes/petsc-3.1-p0/src/sys/viewer/impls/binary/binv.c:563:
> undefined reference to `MPI_Type_get_extent'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(vpscat.o):
> In function `VecScatterDestroy_PtoP':
> /home/svu/g0306332/codes/petsc-3.1-p0/src/vec/vec/utils/vpscat.c:169:
> undefined reference to `MPI_Win_free'
> /home/svu/g0306332/codes/petsc-3.1-p0/src/vec/vec/utils/vpscat.c:170:
> undefined reference to `MPI_Win_free'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(vpscat.o):
> In function `VecScatterBegin_1':
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:64:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:67:
> undefined reference to `MPI_Put'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:69:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:52:
> undefined reference to `MPI_Alltoallw'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(vpscat.o):
> In function `VecScatterCreateCommon_PtoS':
> /home/svu/g0306332/codes/petsc-3.1-p0/src/vec/vec/utils/vpscat.c:1896:
> undefined reference to `MPI_Win_create'
> /home/svu/g0306332/codes/petsc-3.1-p0/src/vec/vec/utils/vpscat.c:1909:
> undefined reference to `MPI_Win_create'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(vpscat.o):
> In function `VecScatterBegin_12':
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:64:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:67:
> undefined reference to `MPI_Put'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:69:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:52:
> undefined reference to `MPI_Alltoallw'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(vpscat.o):
> In function `VecScatterBegin_8':
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:64:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:67:
> undefined reference to `MPI_Put'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:69:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:52:
> undefined reference to `MPI_Alltoallw'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(vpscat.o):
> In function `VecScatterBegin_7':
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:64:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:67:
> undefined reference to `MPI_Put'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:69:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:52:
> undefined reference to `MPI_Alltoallw'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(vpscat.o):
> In function `VecScatterBegin_6':
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:64:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:67:
> undefined reference to `MPI_Put'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:69:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:52:
> undefined reference to `MPI_Alltoallw'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(vpscat.o):
> In function `VecScatterBegin_5':
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:64:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:67:
> undefined reference to `MPI_Put'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:69:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:52:
> undefined reference to `MPI_Alltoallw'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(vpscat.o):
> In function `VecScatterBegin_4':
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:64:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:67:
> undefined reference to `MPI_Put'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:69:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:52:
> undefined reference to `MPI_Alltoallw'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(vpscat.o):
> In function `VecScatterBegin_3':
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:64:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:67:
> undefined reference to `MPI_Put'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:69:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:52:
> undefined reference to `MPI_Alltoallw'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(vpscat.o):
> In function `VecScatterBegin_2':
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:64:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:67:
> undefined reference to `MPI_Put'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:69:
> undefined reference to `MPI_Win_fence'
> /home/svu/g0306332/codes/petsc-3.1-p0/include/../src/vec/vec/utils/vpscat.h:52:
> undefined reference to `MPI_Alltoallw'
> /home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib/libpetsc.a(vecio.o):
> In function `VecLoad_Binary':
> /home/svu/g0306332/codes/petsc-3.1-p0/src/vec/vec/utils/vecio.c:276: undefined
> reference to `MPI_Type_get_extent'
> 
> May I know what's wrong?
> 
>