[Dune] Problem with GmshReader

[Oliver Sander]

Hi Mladek,
I've tried again, this time with dune 2.2.1 from the Debian packages,
and hand-compiled dune-grid-2.2.1 for the UGGrid support.  Still,
I don't get any crashes.  Can you try if it runs if you configure without MPI?
Can you post a backtrace?
--
Oliver

Am 08.11.2013 12:48, schrieb Mladen Jurak:
> Hi Oliver,
> I use version 2.2.1 of dune with openmpi. Here is the linker line:
> 
> /bin/bash ../libtool  --tag=CXX   --mode=link mpiCC -std=c++0x -Wmissing-include-dirs -Wcast-align -Wno-sign-compare -Wno-packed-bitfield-compat -Wno-unused-parameter -fno-strict-aliasing
> -fstrict-overflow -g          -o code code-code.o -L/home/jurak/Code/Dune/release-2.2.1-dbg/dune-grid-2.2.1/lib -ldunegrid -L/home/jurak/Code/Dune/release-2.2.1-dbg/dune-geometry-2.2.1/lib
> -ldunegeometry -L/home/jurak/Code/Dune/release-2.2.1-dbg/dune-common-2.2.1/lib -ldunecommon   -L/usr/local/ALUGrid/lib -lalugrid -pthread -L/usr/lib/openmpi/lib -lmpi -lopen-rte -lopen-pal -ldl
> -Wl,--export-dynamic -lnsl -lutil -lm -ldl -L/usr/local/UG/lib   -lugS2 -lugS3 -ldevS -pthread -L/usr/lib/openmpi/lib -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
> -pthread -L/usr/lib/openmpi/lib -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl -L/home/jurak/Code/Dune/release-2.2.1-dbg/dune-grid-2.2.1/lib -ldunegrid
> -L/home/jurak/Code/Dune/release-2.2.1-dbg/dune-geometry-2.2.1/lib -ldunegeometry -L/home/jurak/Code/Dune/release-2.2.1-dbg/dune-common-2.2.1/lib -ldunecommon
> libtool: link: mpiCC -std=c++0x -Wmissing-include-dirs -Wcast-align -Wno-sign-compare -Wno-packed-bitfield-compat -Wno-unused-parameter -fno-strict-aliasing -fstrict-overflow -g -o code code-code.o
> -pthread -Wl,--export-dynamic -pthread -Wl,--export-dynamic -pthread -Wl,--export-dynamic -L/home/jurak/Code/Dune/release-2.2.1-dbg/dune-grid-2.2.1/lib
> -L/home/jurak/Code/Dune/release-2.2.1-dbg/dune-geometry-2.2.1/lib -L/home/jurak/Code/Dune/release-2.2.1-dbg/dune-common-2.2.1/lib -L/usr/local/ALUGrid/lib -L/usr/lib -L/usr/lib/openmpi/lib
> -L/usr/local/UG/lib -lnsl -lutil -lm -ldl /home/jurak/Code/Dune/release-2.2.1-dbg/dune-grid-2.2.1/lib/.libs/libdunegrid.a /usr/local/ALUGrid/lib/libalugrid.a -lmetis /usr/local/UG/lib/libugS2.a
> /usr/local/UG/lib/libugS3.a /usr/local/UG/lib/libdevS.a /home/jurak/Code/Dune/release-2.2.1-dbg/dune-geometry-2.2.1/lib/.libs/libdunegeometry.a
> /home/jurak/Code/Dune/release-2.2.1-dbg/dune-common-2.2.1/lib/.libs/libdunecommon.a -llapack -lblas -lgfortran -lquadmath /usr/lib/openmpi/lib/libmpi_cxx.so /usr/lib/openmpi/lib/libmpi.so
> /usr/lib/openmpi/lib/libopen-rte.so /usr/lib/openmpi/lib/libopen-pal.so -pthread -Wl,-rpath -Wl,/usr/lib/openmpi/lib -Wl,-rpath -Wl,/usr/lib/openmpi/lib
> 
> Mladen
> 
>  On 11/08/2013 12:47 PM, Oliver Sander wrote:
>> Hi Mladen,
>> I ran your code using dune from git master, and there are no errors.
>> What version do you use?  Do you have built Dune with mpi installed?
>> -- 
>> Oliver
>>
>> Am 08.11.2013 12:18, schrieb Mladen Jurak:
>>> Hi,
>>> here is the mesh.
>>> Mladen
>>>
>>> On 11/08/2013 10:52 AM, Oliver Sander wrote:
>>>> Hi Mladen,
>>>> the code looks okay to me.  Can you please send the simple.msh file you test with?
>>>> Thanks,
>>>> Oliver
>>>>
>>>> Am 08.11.2013 10:37, schrieb Mladen Jurak:
>>>>> Dear Dune,
>>>>>
>>>>> I found a strange problem with GmshReader<>::read() function.
>>>>> Sample code that I send you constructs well a UGGrid grid from "simple.msh" file.
>>>>> But, if I uncomment the code that iterates over all vertices the
>>>>> GmshReader<>::read() functions finishes with a segmentation fault.
>>>>> In the other hand, iteration over elements does not affect the mesh reading.
>>>>> Can you reproduce this error?
>>>>>
>>>>> Best regards,
>>>>> Mladen
>>>>>
>>>>>
>>>>> #ifdef HAVE_CONFIG_H
>>>>> # include "config.h"
>>>>> #endif
>>>>> #include <iostream>
>>>>> #include <vector>
>>>>>
>>>>> #include <dune/common/mpihelper.hh>
>>>>> #include <dune/grid/uggrid.hh>
>>>>> #include <dune/grid/io/file/gmshreader.hh>
>>>>>
>>>>> int main(int argc, char** argv)
>>>>> {
>>>>>       Dune::MPIHelper& helper = Dune::MPIHelper::instance(argc, argv);
>>>>>       // read grid
>>>>>       const int dim =2;
>>>>>       typedef Dune::UGGrid<dim> GridType;
>>>>>       GridType * p_grid = Dune::GmshReader<GridType>::read("simple.msh");
>>>>>
>>>>>       // iterate over all vertices
>>>>> //    typedef typename GridType::LeafGridView LeafGridView;
>>>>> //    LeafGridView leafView = p_grid->leafView();
>>>>> //
>>>>> //    typedef typename LeafGridView::template Codim<dim>::Iterator VertexLeafIterator;
>>>>> //    for (VertexLeafIterator it  = leafView.template begin<dim>();
>>>>> //                            it != leafView.template end<dim>(); ++it) {
>>>>> //      //
>>>>> //
>>>>> //    }
>>>>>       return 0;
>>>>> }
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>> Dune at dune-project.org
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>>>>>
>>>
>>>
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> 


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