[Dune] Problem with GmshReader

[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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>>>>
>>
>>
>> _______________________________________________
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>>
>

-- 
Mladen Jurak
Department of Mathematics
Faculty of Science
University of Zagreb
Bijenicka 30
10000 Zagreb
Croatia

Tel: +385 (0)1 460 5738
Fax: +385 (0)1 468 0335
E-mail: jurak at math.hr <mailto:jurak at math.hr>
Web: http://web.math.hr/~jurak <http://web.math.hr/%7Ejurak>
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