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Subject: Re: [OMPI users] OMPI link error with petsc 2.3.3
From: Yann JOBIC (jobic_at_[hidden])
Date: 2008-10-08 09:58:11


Hello,

I just tried to link with mpif90. And that's working! I don't have the
warning.
(the small change from your command : PIC, not fPIC)

I'm trying to compile PETSC with the new linker.

How come we don't have the warning ?

Thanks,

Yann

Terry Dontje wrote:
> Yann,
>
> Your whole compile process in your email below shows you using mpicc
> to link your executable. Can you please try and do the following for
> linkage instead?
>
> mpif90 -fPIC -m64 -o solv_ksp solv_ksp.o
> -R/opt/lib/petsc/lib/amd-64-openmpi_no_debug
> -L/opt/lib/petsc/lib/amd-64-openmpi_no_debug -lpetscsnes -lpetscksp
> -lpetscdm -lpetscmat -lpetscvec -lpetsc -lX11 -lsunperf -lsunmath
> -lm -ldl -R/opt/mx/lib/amd64 -R/opt/SUNWhpc/HPC8.0/lib/amd64
> -R/opt/SUNWhpc/HPC8.0/lib/amd64 -L/opt/SUNWhpc/HPC8.0/lib/amd64 -lmpi
> -lopen-rte -lopen-pal -lnsl -lrt -lm -lsocket
> -R/opt/SUNWspro/lib/amd64 -R/opt/SUNWspro/lib/amd64
> -L/opt/SUNWspro/lib/amd64 -R/opt/SUNWspro/prod/lib/amd64
> -L/opt/SUNWspro/prod/lib/amd64 -R/usr/ccs/lib/amd64
> -L/usr/ccs/lib/amd64 -R/lib/64 -L/lib/64 -R/usr/lib/64 -L/usr/lib/64
> -lm -lfui -lfai -lfsu -lsunmath -lmtsk -lm -ldl -R/usr/ucblib
>
> --td
>> Date: Wed, 08 Oct 2008 14:14:50 +0200 From: "Yann JOBIC"
>> <jobic_at_[hidden]> Subject: Re: [OMPI users] OMPI link
>> error with petsc 2.3.3 To: Open MPI Users <users_at_[hidden]>
>> Message-ID: <48ECA43A.1060202_at_[hidden]> Content-Type:
>> text/plain; charset=ISO-8859-1; format=flowed Hello, I used cc to
>> compile. I tried to use mpicc/mpif90 to compile PETSC, but it changed
>> nothing. I still have the same error. I'm giving you the whole
>> compile proccess : 4440p-jobic% gmake solv_ksp mpicc -o solv_ksp.o -c
>> -fPIC -m64 -I/opt/lib/petsc
>> -I/opt/lib/petsc/bmake/amd-64-openmpi_no_debug
>> -I/opt/lib/petsc/include -I/opt/SUNWhpc/HPC8.0/include
>> -I/opt/SUNWhpc/HPC8.0/include/amd64 -I. -D__SDIR__="" solv_ksp.c
>> mpicc -fPIC -m64 -o solv_ksp solv_ksp.o
>> -R/opt/lib/petsc/lib/amd-64-openmpi_no_debug
>> -L/opt/lib/petsc/lib/amd-64-openmpi_no_debug -lpetscsnes -lpetscksp
>> -lpetscdm -lpetscmat -lpetscvec -lpetsc -lX11 -lsunperf -lsunmath -lm
>> -ldl -R/opt/mx/lib/amd64 -R/opt/SUNWhpc/HPC8.0/lib/amd64
>> -R/opt/SUNWhpc/HPC8.0/lib/amd64 -L/opt/SUNWhpc/HPC8.0/lib/amd64 -lmpi
>> -lopen-rte -lopen-pal -lnsl -lrt -lm -lsocket -lmpi_f77 -lmpi_f90
>> -R/opt/SUNWspro/lib/amd64 -R/opt/SUNWspro/lib/amd64
>> -L/opt/SUNWspro/lib/amd64 -R/opt/SUNWspro/prod/lib/amd64
>> -L/opt/SUNWspro/prod/lib/amd64 -R/usr/ccs/lib/amd64
>> -L/usr/ccs/lib/amd64 -R/lib/64 -L/lib/64 -R/usr/lib/64 -L/usr/lib/64
>> -lm -lfui -lfai -lfsu -lsunmath -lmtsk -lm -ldl -R/usr/ucblib ld:
>> warning: symbol `mpi_fortran_status_ignore_' has differing sizes:
>> (file /opt/SUNWhpc/HPC8.0/lib/amd64/libmpi.so value=0x8; file
>> /opt/SUNWhpc/HPC8.0/lib/amd64/libmpi_f90.so value=0x14);
>> /opt/SUNWhpc/HPC8.0/lib/amd64/libmpi.so definition taken /usr/bin/rm
>> -f solv_ksp.o Thanks for your help, Yann Terry Dontje wrote:
>>> > Yann,
>>> >
>>> > How were you trying to link your code with PETSc? Did you use
>>> mpif90 > or mpif77 wrappers or were you using cc or mpicc wrappers?
>>> I ran some > basic tests that test the usage of MPI_STATUS_IGNORE
>>> using mpif90 (and > mpif77) and it works fine. However I was able
>>> to generate a similar > error as you did when tried to link things
>>> with the cc program. > If you are using cc to link could you
>>> possibly try to use mpif90 to > link your code?
>>> >
>>> > --td
>>> >
>>> > Date: Tue, 07 Oct 2008 16:55:14 +0200
>>> > From: "Yann JOBIC" <jobic_at_[hidden]>
>>> > Subject: [OMPI users] OMPI link error with petsc 2.3.3
>>> > To: Open MPI Users <users_at_[hidden]>
>>> > Message-ID: <48EB7852.6070404_at_[hidden]>
>>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>> >
>>> > Hello,
>>> >
>>> > I'm using openmpi 1.3r19400 (ClusterTools 8.0), with sun studio
>>> 12, > and solaris 10u5
>>> >
>>> > I've got this error when linking a PETSc code :
>>> > ld: warning: symbol `mpi_fortran_status_ignore_' has differing sizes:
>>> > (file /opt/SUNWhpc/HPC8.0/lib/amd64/libmpi.so value=0x8;
>>> file > /opt/SUNWhpc/HPC8.0/lib/amd64/libmpi_f90.so value=0x14);
>>> > /opt/SUNWhpc/HPC8.0/lib/amd64/libmpi.so definition taken
>>> >
>>> >
>>> > Isn't it very strange ?
>>> >
>>> > Have you got any idea on the way to solve it ?
>>> >
>>> > Many thanks,
>>> >
>>> > Yann
>>> >
>>>
>>>> >>
>>> >
>>> > _______________________________________________
>>> > users mailing list
>>> > users_at_[hidden]
>>> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>>
>>
>> -- ___________________________ Yann JOBIC HPC engineer Polytech
>> Marseille DME IUSTI-CNRS UMR 6595 Technop?le de Ch?teau Gombert 5 rue
>> Enrico Fermi 13453 Marseille cedex 13 Tel : (33) 4 91 10 69 39 ou
>> (33) 4 91 10 69 43 Fax : (33) 4 91 10 69 69
>
> _______________________________________________
> users mailing list
> users_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/users

-- 
___________________________
Yann JOBIC
HPC engineer
Polytech Marseille DME
IUSTI-CNRS UMR 6595
Technopôle de Château Gombert
5 rue Enrico Fermi
13453 Marseille cedex 13
Tel : (33) 4 91 10 69 39
  ou  (33) 4 91 10 69 43
Fax : (33) 4 91 10 69 69