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

[huyaoyu]

Hi everyone,

I am new to PETSc. The reason I should use PETSc is because another
package named deal.II will get help from PETSc. The computer has ubuntu
11.04 64bit installed. deal.II version is 7.0

So I downloaded the PETSc source code (3.1-p8) and do the configuration
(after setting the environment variables correctly) like this:
./conf/configure.py --with-cc=gcc --with-fc=gfortran
-download-f-blas-lapack=1 -download-mpich=1 --with-shared

The configuration went well I supposed.

Then I invoked the command:
make all test

But the test log (that appeared on the shell) showed that the test had
failed when it was trying to perform a task in 2 processes.
=========================================
Running test examples to verify correct installation
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1
MPI process
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2
MPI processes
--------------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)

WITH SOME OTHER WARNINGS LIKE THE ABOVE
...
THEN

/home/huyaoyu/Downloads/petsc-3.1-p8/linux-gnu-c-debug/bin/mpif90 -fPIC
-Wall -Wno-unused-variable -g  -o ex5f ex5f.o
-Wl,-rpath,/home/huyaoyu/Downloads/petsc-3.1-p8/linux-gnu-c-debug/lib
-L/home/huyaoyu/Downloads/petsc-3.1-p8/linux-gnu-c-debug/lib -lpetsc
-lX11
-Wl,-rpath,/home/huyaoyu/Downloads/petsc-3.1-p8/linux-gnu-c-debug/lib
-L/home/huyaoyu/Downloads/petsc-3.1-p8/linux-gnu-c-debug/lib -lflapack
-lfblas -lnsl -lrt
-Wl,-rpath,/home/huyaoyu/Downloads/petsc-3.1-p8/linux-gnu-c-debug/lib
-L/home/huyaoyu/Downloads/petsc-3.1-p8/linux-gnu-c-debug/lib
-Wl,-rpath,/usr/lib/openmpi/lib -L/usr/lib/openmpi/lib
-Wl,-rpath,/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2
-L/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2
-Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ldl
-lmpich -lrt -lmpi -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s -lpthread
-lmpichf90 -lmpi_f90 -lmpi_f77 -lgfortran -lm -lm -lm -lm -ldl -lmpich
-lrt -lmpi -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s -lpthread -ldl 
/bin/rm -f ex5f.o
Fortran example src/snes/examples/tutorials/ex5f run successfully with 1
MPI process
Completed test examples
==================================================================

I just ignore it because I think if PETSc succeeds on 1 process and that
is all I want for now. 1 process is enough for deal.II to work on my
computer. (deal.II may work on cluster, but I only have on computer
right now. And I just want to see some particular tutorial programs of
deal.II that only work on cluster).Then after I re-build deal.II this
PETSc support, I triggered the deal.II program that will use PETSc
library. And I got the following segmentation fault:

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);

gdb tells me that: 
MPI_COMM_WORLD  = 1140850688 (0x44000000)
PetscGlobalRank = -1
And MPI_Comm_rank failed at some where the disassembly code is
"testb $0x90,0x98(%rbx)"

The deal.II program triggers the same error every time it runs.

Then I remove the whole PETSc directory and extract the source files
again. Configure PETSc use the following line

--with-cc=mpicc --with-fc=mpif90 --download-f-blas-lapack=1
--download-mpich=1 --with-shared

Again, the PETSc test failed on 2 processes exactly the same with
before. And the deal.II program gave the segmentation error at the
identical place(pinit.c, ierr =
MPI_Comm_rank(MPI_COMM_WORLD,&PetscGlobalRank);CHKERRQ(ierr);).

I searched the mailing list and got this
https://lists.mcs.anl.gov/mailman/htdig/petsc-users/2008-July/003194.html
The guys were talking about a problem just likes mine. They said that a
fresh re-installation of PETSc will solve the problem. But the solution
they got dose not work for me.

How can I fix it? It seems that the installation of PETSc may be wrong.
I have mpich2 installed on the system, it that matter? And I tried to
configure PETSc without the argument "-download-mpich=1" then compile,
but the same test error and segmentation error appeared.

Does it have some thing to do with the 64bit issue? Or, do I have to
post an email to petsc-maint at mcs.anl.gov along with the configure.log
file attached?

Any help, thanks!

Best,

HuYaoyu