I hit this as well and as best I can tell, this is due to a known (?) issue with shared libraries on os x. All other examples should run fine. Note that this doesn't occur on the automake branch.
On Sep 18, 2012, at 12:43 AM, Paul Hui Sun <huiprobable@...> wrote:
> Without specifying any options, the problem I had didn't occur any more, the examples seem to be built all fine, until this one below. I think it might be because that I have run ./configure with some certain environmental variables before, and they were recalled somehow.
>
>
> ***************************************************************
> * Running Example ./miscellaneous_ex6-opt
> ***************************************************************
>
> Triangulating an L-shaped domain with holes
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 6, Wed Jan 11 09:28:45 CST 2012
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: ./miscellaneous_ex6-opt on a darwin-op named new-host-2.home by Paul Mon Sep 17 22:37:13 2012
> [0]PETSC ERROR: Libraries linked from /Users/Paul/sfw/petsc/3.2-p6/darwin-opt/lib
> [0]PETSC ERROR: Configure run at Fri Sep 14 12:20:58 2012
> [0]PETSC ERROR: Configure options --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --CC=/Users/Paul/sfw/darwin/openmpi/1.4.3/bin/mpicc --CXX=/Users/Paul/sfw/darwin/openmpi/1.4.3/bin/mpicxx --FC=/Users/Paul/sfw/darwin/openmpi/1.4.3/bin/mpif90 --LDFLAGS="-L/Users/Paul/sfw/darwin/openmpi/1.4.3/lib -Wl,-rpath,/Users/Paul/sfw/darwin/openmpi/1.4.3/lib" --with-shared-libraries=0 --with-dynamic-libraries=0 --with-default-arch=0 --PETSC_ARCH=darwin-opt --with-debugging=0 --with-c++-support=1 --with-hypre=1 --download-hypre=1
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0
> with errorcode 59.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> make[2]: *** [run] Error 59
> make[1]: *** [run] Error 1
> make: *** [run_examples] Error 2
>
>
> On Sep 17, 2012, at 10:27 PM, "Paul T. Bauman" <ptbauman@...> wrote:
>
>> On Tue, Sep 18, 2012 at 12:22 AM, Paul Hui Sun <huiprobable@...> wrote:
>> CC=/usr/local/gfortran/bin/gcc CXX=/usr/local/gfortran/bin/g++ FC=gfortran F77=gfortran METHOD=opt
>>
>> libMesh doesn't need fortran. Try just doing: ./configure and see if you can build and run the examples. If you aren't setting CC/CXX, you should be using the native CLang compiler that comes with XCode.
>
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