[Dune] How to use parallel UGGrid?
Oliver Sander
sander at mi.fu-berlin.de
Fri Jun 25 07:47:34 CEST 2010
Hi Wolfgang!
I just committed a bugfix in dune-grid. Please update your installation,
and the crash should be gone now.
Unfortunately, the program now stalls in the UGGrid destructor.
I don't really know what this is, yet. However, since it is only the
destructor, you may still be able to do your computations, and
then have the program abort before the destructor call.
best,
Oliver
Am 2010-06-20 23:59, schrieb giese at mathematik.hu-berlin.de:
> 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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