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

[huyaoyu]

Thanks to Satish Balay and Jed Brown. Your advices are pretty good!

I remove the petsc directory and deal.II directory. Re-build petsc and
deal.II with the mpi installed system wide. The configuration lines are
as follows:

For PETSc:
./config/configure.py --with-cc=/usr/bin/mpicc --with-fc=/usr/bin/mpif90
--download-f-blas-lapack=1 --with-shared

For deal.II:
./configure --enable-shared --disable-threads --with-petsc=$PETSC_DIR
--with-petsc-arch=$(PETSC_ARCH) --with-p4est=PATH-TO-P4EST --with-mpi

I will use p4est for grid distribution and I checked the configure
output of deal.II. The output says deal.II will use /usr/bin/mpicc for
CC variable and /usr/bin/mpiCC for CXX variable. And deal.II says: 
=================deal.II configure output=========================
checking for PETSc library
directory... /home/huyaoyu/Downloads/petsc-3.1-p8
checking for PETSc version... 3.1.0
checking for PETSc library architecture... linux-gnu-c-debug
checking for PETSc libmpiuni library... not found
checking for consistency of PETSc and deal.II MPI settings... yes
checking for PETSc scalar complex... no
================= end of deal.II configure output=================

After the compilation of PETSc and deal.II, I tried to compile the
specific example program of deal.II which will use PETSc. And everything
works well. No segmentation error any more! Great!

However, the test of PETSc trigger the same error while trying to
perform task in 2 process. Is it because I am using PETSc on a single
machine but not a cluster of computers?

Again, thanks to Satish Balay and Jed Brown, you are great!

HuYaoyu.

> > --------------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).