[petsc-users] test failed on 2 processes and segmentation fault while initializing in deal.II

[Jed Brown]

On Thu, Aug 4, 2011 at 09:16, huyaoyu <huyaoyu1986 at gmail.com> wrote:

> --------------Error detected during compile or
> link!-----------------------
> See
> http://www.mcs.anl.gov/petsc/petsc-2/documentation/troubleshooting.html
> /home/huyaoyu/Downloads/petsc-3.1-p8/linux-gnu-c-debug/bin/mpif90 -c
> -fPIC  -Wall -Wno-unused-variable -g
> -I/home/huyaoyu/Downloads/petsc-3.1-p8/linux-gnu-c-debug/include
> -I/home/huyaoyu/Downloads/petsc-3.1-p8/include
> -I/home/huyaoyu/Downloads/petsc-3.1-p8/linux-gnu-c-debug/include
> -I/usr/lib/openmpi/include -I/usr/lib/openmpi/lib
> -I/home/huyaoyu/Downloads/petsc-3.1-p8/linux-gnu-c-debug/include
> -I/home/huyaoyu/Downloads/petsc-3.1-p8/linux-gnu-c-debug/include
> -I/usr/lib/openmpi/include -I/usr/lib/openmpi/lib    -o ex5f.o ex5f.F
> ex5f.F:92.72:
>
>      call PetscOptionsGetReal(PETSC_NULL_CHARACTER,'-par',lambda,
>
> 1
> Warning: Line truncated at (1)
>

This is harmless, the Fortran compiler is creating a spurious warning. The
problem has been fixed in gcc-4.6.


> huyaoyu at ubuntu:~/Downloads/deal.II-non-threads/examples/step-17
> $ ./step-17
> [ubuntu:23497] *** Process received signal ***
> [ubuntu:23497] Signal: Segmentation fault (11)
> [ubuntu:23497] Signal code: Address not mapped (1)
> [ubuntu:23497] Failing at address: 0x44000098
> [ubuntu:23497] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfc60)
> [0x7f111b24ac60]
> [ubuntu:23497] [ 1] /usr/lib/libmpi.so.0(MPI_Comm_rank+0x5e)
> [0x7f111adbf3ce]
> [ubuntu:23497]
> [ 2]
> /home/huyaoyu/Downloads/petsc-3.1-p8/linux-gnu-c-debug/lib/libpetsc.so(PetscInitialize+0x5d1)
> [0x7f11190b97df]
> [ubuntu:23497] [ 3] ./step-17(main+0x3b) [0x42539f]
> [ubuntu:23497] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main
> +0xff) [0x7f1119793eff]
> [ubuntu:23497] [ 5] ./step-17() [0x4252a9]
> [ubuntu:23497] *** End of error message ***
> Segmentation fault
>
> After debug the deal.II program I found that it failed at the following
> line
>
> pinit.c line 578:
> ierr = MPI_Comm_rank(MPI_COMM_WORLD,&PetscGlobalRank);CHKERRQ(ierr);
>

Can you send the output of "ldd dealii-example"?

This normally happens when a different MPI is linked from that which is
compiled (or it's inconsistent between PETSc and deal.ii).
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110804/619215eb/attachment.htm>