[Dune] How to use parallel UGGrid?]
Oliver Sander
sander at mi.fu-berlin.de
Tue Jun 22 21:17:01 CEST 2010
Hi Wolfgang!
I can reproduce your crash now. I'll have a look.
best,
Oliver
Am 2010-06-21 11:06, schrieb giese at mathematik.hu-berlin.de:
> Hi Oliver,
>
> I forgot to send you the UG Version that is installed:
> UG-2008-11-13.tar.gz was used and patched with
> ug-dune-patches-2009-12-01.diff . Does this cause any problems with Dune
> 2.0?
>
> Best regards,
> Wolfgang
>
>
> ----
> Hi Oliver,
>
> thanks for your mail. UG and Dune are compiled with --enable-parallel. I
> am using the latest Revisions: dune-commen rev. 6048, dune-grid rev. 6832,
> dune-istl rev. 1226, dune-localfunctions rev. 882, dune-pdelab rev. 529
>
> The following Components are installed.
>
> dune-common.............: version 2.1-svn
> ALBERTA.................: version 2.0
> ALUGrid.................: version 1.22
> AlgLib for DUNE.........: no
> AmiraMesh...............: no
> GMP.....................: yes
> Grape...................: yes
> MPI.....................: yes (OpenMPI)
> OpenGL..................: yes
> UG......................: yes (parallel)
> psurface................: yes
>
> You can find the file cube.msh attached.
>
> Best regards,
> Wolfgang
>
> I am also sending you code and error message.
>
> Code:
>
> #ifdef HAVE_CONFIG_H
> #include "config.h"
> #endif
> #include<iostream>
> #include<vector>
> #include<string>
>
> #include<dune/common/mpihelper.hh>
> #include<dune/common/exceptions.hh>
> #include<dune/grid/io/file/vtk/vtkwriter.hh>
> #include<dune/grid/io/file/gmshreader.hh> // New: Dune::GmshReader
> #if HAVE_UG // New: Use UG here
> #include<dune/grid/uggrid.hh>
> #endif
>
> int main(int argc, char** argv)
> {
> try{
> //Maybe initialize Mpi
> Dune::MPIHelper& helper = Dune::MPIHelper::instance(argc, argv);
> if(Dune::MPIHelper::isFake)
> std::cout<< "This is a sequential program."<< std::endl;
> else
> {
> if(helper.rank()==0)
> std::cout<< "parallel run on "<< helper.size()<< "
> process(es)"<< std::endl;
> }
>
> // check arguments
> if (argc!=3)
> {
> std::cout<< "usage: "<< argv[0]<< "<gridName> <level>"<< std::endl;
> return 1;
> }
>
> // refinement level
> int level = 0;
> sscanf(argv[2], "%d",&level);
>
> // instanciate ug grid object (xxx MB heap)
> typedef Dune::UGGrid<3> GridType;
> GridType grid(400);
>
> // read a gmsh file
> std::string gridName = argv[1];
> if(helper.rank()==0) {
> Dune::GmshReader<GridType> gmshreader;
> gmshreader.read(grid, gridName);
> grid.globalRefine(level);
> }
>
> // edit gridName
> gridName.erase(0, gridName.rfind("/")+1);
> gridName.erase(gridName.find(".",0), gridName.length());
>
> if(!Dune::MPIHelper::isFake)
> grid.loadBalance();
>
> // get a grid view
> typedef GridType::LeafGridView GV;
> const GV& gv = grid.leafView();
>
> // plot celldata
> std::vector<int> a(gv.size(0), 1);
>
> // output
> Dune::VTKWriter<GV> vtkwriter(gv);
> vtkwriter.addCellData(a, "celldata");
> vtkwriter.write(gridName.c_str(), Dune::VTKOptions::ascii);
>
> // done
> return 0;
> }
> catch (Dune::Exception&e){
> std::cerr<< "Dune reported error: "<< e<< std::endl;
> return 1;
> }
> catch (...){
> std::cerr<< "Unknown exception thrown!"<< std::endl;
> return 1;
> }
>
> }
>
> Error Message:
>
> parallel run on 3 process(es)
> DimX=3, DimY=1, DimZ=1
> Reading 3d Gmsh grid...
> Dune reported error: GridError: The grid has not been properly initialized!
> Dune reported error: GridError: The grid has not been properly initialized!
> version 2 Gmsh file detected
> file contains 14 nodes
> file contains 48 elements
> number of real vertices = 14
> number of boundary elements = 24
> number of elements = 24
>
> Then the process stops and does not finish...
>
>
>
>> Hi Wolfgang!
>> I tried your code, but cannot reproduce the problem. Can I have your
>> grid? Does is load in a sequential setting? What is your dune version?
>> What kind of UG do you have? How many processes did you try?
>> What is your MPI?
>>
>> --
>> Oliver
>>
>> Am 2010-06-18 11:02, schrieb giese at mathematik.hu-berlin.de:
>>
>>> Dear Dune-Developers,
>>>
>>> I have a question regarding the usage of the parallel UGGrid in
>>> combination
>>> with the gmshreader. I tried an easy example in DUNE, where the
>>> programme
>>> just reads a grid using the gmshreader and produces an output of the
>>> distributed grid using the vtkwriter. The crucial part of the code looks
>>> as follows:
>>>
>>> .
>>> .
>>> .
>>>
>>> typedef Dune::UGGrid<3> GridType;
>>> GridType grid(400);
>>>
>>> // read a gmsh file
>>> Dune::GmshReader<GridType> gmshreader;
>>> gmshreader.read(grid, "cube.msh");
>>>
>>> // refine grid
>>> grid.globalRefine(level);
>>>
>>> if(!Dune::MPIHelper::isFake)
>>> grid.loadBalance();
>>>
>>> // get a grid view
>>> typedef GridType::LeafGridView GV;
>>> const GV& gv = grid.leafView();
>>>
>>> // plot celldata
>>> std::vector<int> a(gv.size(0), 1);
>>>
>>> // output
>>> Dune::VTKWriter<GV> vtkwriter(gv);
>>> vtkwriter.addCellData(a, "celldata");
>>> vtkwriter.write("TestGrid", Dune::VTKOptions::ascii);
>>>
>>> .
>>> .
>>> .
>>>
>>> This code produces an error message, which you can be seen below. It
>>> seems
>>> that UGGrid starts in parallel. It is actually configured with
>>> "--enable-parallel". But somehow in the end something is going wrong.
>>> What
>>> do I have to change? Do I have to add some code? Maybe you have an easy
>>> example that works in parallel? I would be very grateful if you could
>>> help
>>> me!
>>>
>>> Best regards,
>>> Wolfgang Giese
>>>
>>> ---Error Message---
>>> The programme "gridtest" started on three nodes produces the
>>> following error Message:
>>>
>>> parallel run on 3 process(es)
>>> DimX=3, DimY=1, DimZ=1
>>> Reading 3d Gmsh grid...
>>> Reading 3d Gmsh grid...
>>> Reading 3d Gmsh grid...
>>> version 2 Gmsh file detected
>>> file contains 14 nodes
>>> number of real vertices = 14
>>> number of boundary elements = 24
>>> number of elements = 24
>>> number of real vertices = 14
>>> number of boundary elements = 24
>>> number of elements = 24
>>> file contains 48 elements
>>> number of real vertices = 14
>>> number of boundary elements = 24
>>> number of elements = 24
>>> [node18:11171] *** Process received signal ***
>>> [node18:11171] Signal: Segmentation fault (11)
>>> [node18:11171] Signal code: Address not mapped (1)
>>> [node18:11171] Failing at address: 0x7359e3588
>>> [node18:11170] *** Process received signal ***
>>> [node18:11170] Signal: Segmentation fault (11)
>>> [node18:11170] Signal code: Address not mapped (1)
>>> [node18:11170] Failing at address: 0x1655035c8
>>> [node18:11170] [ 0] /lib64/libpthread.so.0 [0x2b402c690a90]
>>> [node18:11170] [ 1]
>>> ./gridtest(_ZN4Dune6UGGridILi3EE12globalRefineEi+0xdb)
>>> [0x60c78b]
>>> [node18:11170] [ 2] ./gridtest(main+0x233) [0x597213]
>>> [node18:11170] [ 3] /lib64/libc.so.6(__libc_start_main+0xe6)
>>> [0x2b402c8bd586]
>>> [node18:11170] [ 4] ./gridtest [0x596b79]
>>> [node18:11170] *** End of error message ***
>>> [node18:11171] [ 0] /lib64/libpthread.so.0 [0x2ac5e672ca90]
>>> [node18:11171] [ 1]
>>> ./gridtest(_ZN4Dune6UGGridILi3EE12globalRefineEi+0xdb)
>>> [0x60c78b]
>>> [node18:11171] [ 2] ./gridtest(main+0x233) [0x597213]
>>> [node18:11171] [ 3] /lib64/libc.so.6(__libc_start_main+0xe6)
>>> [0x2ac5e6959586]
>>> [node18:11171] [ 4] ./gridtest [0x596b79]
>>> [node18:11171] *** End of error message ***
>>> --------------------------------------------------------------------------
>>> mpirun noticed that process rank 2 with PID 11171 on node node18 exited
>>> on
>>> signal 11 (Segmentation fault).
>>> --------------------------------------------------------------------------
>>>
>>>
>>> _______________________________________________
>>> Dune mailing list
>>> Dune at dune-project.org
>>> http://lists.dune-project.org/mailman/listinfo/dune
>>>
>>>
>>
>> --
>> ************************************************************************
>> * Oliver Sander ** email: sander at mi.fu-berlin.de *
>> * Freie Universität Berlin ** phone: + 49 (30) 838 75348 *
>> * Institut für Mathematik ** URL : page.mi.fu-berlin.de/~sander *
>> * Arnimallee 6 ** -------------------------------------*
>> * 14195 Berlin, Germany ** Member of MATHEON (www.matheon.de) *
>> ************************************************************************
>>
>>
--
************************************************************************
* Oliver Sander ** email: sander at mi.fu-berlin.de *
* Freie Universität Berlin ** phone: + 49 (30) 838 75348 *
* Institut für Mathematik ** URL : page.mi.fu-berlin.de/~sander *
* Arnimallee 6 ** -------------------------------------*
* 14195 Berlin, Germany ** Member of MATHEON (www.matheon.de) *
************************************************************************
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