libMesh: A C++ Finite Element Library

Hi!

When I try to solve a problem with subdomains I receive the following error:

*** Solving time step 2, time = 200 ***
 Mesh Information:
  mesh_dimension()=3
  spatial_dimension()=3
  n_nodes()=1331
    n_local_nodes()=1331
  n_elem()=1000
    n_local_elem()=1000
    n_active_elem()=1000
  n_subdomains()=2
  n_partitions()=1
  n_processors()=1
  n_threads()=1
  processor_id()=0



*** Beginning solving Navier-Stokes problem
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal memory access
[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: likely location of problem given in stack below
[0]PETSC ERROR: ---------------------  Stack Frames ------------------------------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR:       INSTEAD the line number of the start of the function
[0]PETSC ERROR:       is given.
[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: run-dbg on a linux-gnu named MacBook-Pro-de-Daniel.local by root Fri Nov 23 01:33:51 2012
[0]PETSC ERROR: Libraries linked from /Users/daniel/Dev/petsc-3.2-p6/lib
[0]PETSC ERROR: Configure run at Tue Feb 28 22:00:36 2012
[0]PETSC ERROR: Configure options --prefix=/Users/daniel/Dev/petsc-3.2-p6 --with-cxx=mpicxx --with-cc=mpicc --with-fc=mpif90 --download-f-blas-lapack=1 --download-hypre=1 --with-shared-libraries=0
[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.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 3799 on
node MacBook-Pro-de-Daniel.local exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------

I have four equations at all and for each one I have a similar piece of code when I solve it:

                 if(time > dt ){
                      std::set<subdomain_id_type> id_list;
                      id_list.insert(1);
                      SystemSubsetBySubdomain::SubdomainSelectionByList selection(id_list);
                      SystemSubsetBySubdomain subset(navier_stokes_system, selection);
                      navier_stokes_system.restrict_solve_to(&subset, SUBSET_ZERO);
                  }
                  equation_systems.get_system("Navier-Stokes").solve();

I defined two subdomains.

Any idea of what is the cause of this error?

Best regards,

Daniel.

On Nov 22, 2012, at 8:34 PM, "Kirk, Benjamin (JSC-EG311)" <benjamin.kirk-1@...> wrote:

> I'll need a little more information than "it didn't work" - what are the error messages?
> 
> Another change is that we are strictly enforcing header prefixing, e.g. 
> 
> #include "libmesh/elem.h"
This was the problem. It's fixed now.

Thanks,
Ata


> 
> -Ben
> 
> 
> 
> On Nov 22, 2012, at 6:00 PM, "Ataollah Mesgarnejad" <amesga1@...> wrote:
> 
>> Thanks for the help, libMesh compiled nicely. However here is my dilemma: I used to include Make.common from libmesh_dir in my own code's Makefile and everything compiled easily however now I don't have any idea how to do this anymore? I tried Make.common in my install dir and it didn't work! Also I tried to compile several examples using the makefile in their folders and it didn't work.
>> 
>> Happy thanksgiving again,
>> Ata
>> 
>> On Nov 21, 2012, at 3:24 PM, "Kirk, Benjamin (JSC-EG311)" <benjamin.kirk-1@...> wrote:
>> 
>>> Quickstart from an svn up:
>>> 
>>> $ rm include/libmesh/*.h # in case there were any old symlinks - these are now generated by default.
>>> $ svn status # if this shows anything modified and you are not expecting it, do 'svn revert -R .'
>>> $ ./bootstrap
>>> $ ./configure --prefix=/my/path/to/libmesh
>>> $ make -jN # where N is your number of processors to speed up the build
>>> $ make check # run the examples to make sure everything is fine
>>> $ make install 
>>> $ make installcheck # optional, makes sure the install is behaving properly
>>> 
>>> then point your build system to the install directory.
>>> 
>>> That should work.  If it does not please repot the error message, but also try checking out a fresh copy of trunk - for example:
>>> 
>>> $ svn co https://libmesh.svn.sourceforge.net/svnroot/libmesh/trunk/libmesh libmesh.fresh
>>> 
>>> and try again and report the results.
>>> 
>>> 
>>> If you want to use multiple methods, they can be installed in the same place but need to be configured and built in separate directories.  The script ./contrib/bin/buildall.sh abstracts this, but the gist is
>>> 
>>> $ mkdir dbg devel opt
>>> $ cd dbg 
>>> $ ../configure --prefix=…  --with-method=dbg
>>> $ make && make install
>>> $ cd ../opt
>>> $ ../configure --prefix=… --with-method=opt
>>> $ ...
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Nov 21, 2012, at 1:34 PM, Ataollah Mesgarnejad <amesga1@...> wrote:
>>> 
>>>> Dear all,
>>>> 
>>>> I was wondering if someone can give me quick intro for the new make system ? I can't make heads nor tails of what's going on with autoconf.
>>>> 
>>>> Happy thanksgiving,
>>>> Ata
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