[Dune] GMSH reader fails in parallel case

Mon Jul 14 23:07:22 CEST 2014

There is a utility in dune-grid that will load a gmsh file, distribute it, and
write it as a set of files in alugrid format:
http://cgit.dune-project.org/repositories/dune-grid/tree/src/gmsh-to-alu
The reading part should be exactly what your want.  Note that you need to
configure dune-grid with --enable-extra-utilities (or similar) to actually
compile those programs.  Note also that you can attach data to (physical entity
number) to entities in gmsh, and that program can redistribute that kind of
data too, which should explain some complications in the code.

Hope that get you started,
Jö.

Am Mon, 14. Jul 2014, 16:13:54 +0000 schrieb Sacconi, Andrea:
> Hi all,
> 
> following Andreas's suggestions, I added these lines of code:
> 
>    HostGridType* gridPtr(nullptr);
>     if(rank==0)
> 	gridPtr=Dune::GmshReader<HostGridType>::read(FileName);
>     else gridPtr = new HostGridType();
> 
> so only the process with rank 0 reads the file, while the others initialise an empty grid.
> Then I call:
> 
> grid.loadBalance();
> 
> but unfortunately this error message appears:
> 
> as7211 at macomp000:~/dune-2.3.1/dune-bulk/src$ mpirun -n 2 dune_bulk
> Reading 3d Gmsh grid...
> version 2.2 Gmsh file detected
> file contains 3323 nodes
> file contains 19216 elements
> number of real vertices = 3322
> number of boundary elements = 3036
> number of elements = 15981
> 
> Created parallel ALUGrid<3,3,simplex,nonconforming> from macro grid file ''. 
> 
> [macomp000:5707] *** An error occurred in MPI_Allgather
> [macomp000:5707] *** on communicator MPI COMMUNICATOR 3 DUP FROM 0
> [macomp000:5707] *** MPI_ERR_TRUNCATE: message truncated
> [macomp000:5707] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
> --------------------------------------------------------------------------
> mpirun noticed that the job aborted, but has no info as to the process
> that caused that situation.
> 
> So, it appears that the file has been read (by the process 0) and the grid initialised correctly. The problem is, process 0 freezes at the end of the reading bit. If you comment the line with load balancing, nothing appears on the screen, because the process 0 is frozen.
> Any ideas about this issue? I'm very confused.
> 
> Thanks again!
> Andrea
> __________________________________________________________
> 
> Andrea Sacconi
> PhD student, Applied Mathematics
> AMMP Section, Department of Mathematics, Imperial College London,
> London SW7 2AZ, UK
> a.sacconi11 at imperial.ac.uk
> 
> ________________________________________
> From: dune-bounces+a.sacconi11=imperial.ac.uk at dune-project.org [dune-bounces+a.sacconi11=imperial.ac.uk at dune-project.org] on behalf of Oliver Sander [sander at igpm.rwth-aachen.de]
> Sent: 14 July 2014 15:37
> To: dune at dune-project.org
> Subject: Re: [Dune] GMSH reader fails in parallel case
> 
> Am 14.07.2014 14:54, schrieb Andreas Dedner:
> > There has never been a clear decision I think on how the grid readers should work in the
> > case that the macro grid is not pre distributed. In ALU the idea is that the grid is distributed
> > but in a way that one process has all the elements and the others are empty. Consequently
> > only process zero should read the gmsh file and the others should generate an empty grid.
> > Now I remember that UG does it differently (requiring) that all process read the full macro grid.
> > As I said a place were we need to fix the semantics. DGF does it the ALU way that is why that works
> > and gmshreader does in the UG way...
> >
> > The simplest way to avoid the issue is to surround the call to the gmshreader by if (rank==0)
> > and to construct empty ALUGrids in the else part - but then I assume UG would not be happy....
> >
> 
> I don't think so.  UGGrid contains extra code to handle that case.  I don't really know how much
> testing it got, though.
> --
> Oliver
> 
> > Andreas
> >
> > PS: it would help if you could open a flyspray task with a report, a test program, I could then add
> > my 5 cent from above. This would increase the chances that we would actually discuss this
> > at the developer meeting in September.
> >
> >
> > On 14/07/14 13:00, Sacconi, Andrea wrote:
> >> Hi DUNErs,
> >>
> >> I would like to ask you a question about the GMSH reader for parallel computation (with open-MPI 1.6.5). I am using AlugridSimplex <3,3> for a standard Poisson problem.
> >> Everything is fine in the sequential case, while in the parallel case I get the error reported below.
> >>
> >> as7211 at macomp01:~/dune-2.3.1/dune-bulk/src$ mpirun -n 2 dune_bulk
> >> Reading 3d Gmsh grid...
> >> Reading 3d Gmsh grid...
> >> version 2.2 Gmsh file detected
> >> version 2.2 Gmsh file detected
> >> file contains 3323 nodes
> >> file contains 3323 nodes
> >> file contains 19216 elements
> >> file contains 19216 elements
> >> terminate called after throwing an instance of 'Dune::GridError'
> >> [macomp01:03890] *** Process received signal ***
> >> [macomp01:03890] Signal: Aborted (6)
> >> [macomp01:03890] Signal code:  (-6)
> >> [macomp01:03890] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7ff363b7b340]
> >> [macomp01:03890] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x39) [0x7ff3637dbf79]
> >> [macomp01:03890] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x148) [0x7ff3637df388]
> >> [macomp01:03890] [ 3] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x155) [0x7ff3643056b5]
> >> [macomp01:03890] [ 4] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e836) [0x7ff364303836]
> >> [macomp01:03890] [ 5] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e863) [0x7ff364303863]
> >> [macomp01:03890] [ 6] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5eaa2) [0x7ff364303aa2]
> >> [macomp01:03890] [ 7]
> >> dune_bulk(_ZN4Dune16ALU3dGridFactoryINS_7ALUGridILi3ELi3ELNS_18ALUGridElementTypeE0ELNS_21ALUGridRefinementTypeE1EP19ompi_communicator_tEEE12insertVertexERKNS_11FieldVectorIdLi3EEE+0x1b2) [0x616c82]
> >>
> >> Any idea about how to use make only the master process read the grid, and not all the processes? In any case, how can the issue be fixed?
> >> By the way, if I use DGF reader everything runs fine, both in the sequential and parallel case.
> >>
> >> Thanks in advance!
> >> Andrea
> >> __________________________________________________________
> >>
> >> Andrea Sacconi
> >> PhD student, Applied Mathematics
> >> AMMP Section, Department of Mathematics, Imperial College London,
> >> London SW7 2AZ, UK
> >> a.sacconi11 at imperial.ac.uk
> >> _______________________________________________
> >> Dune mailing list
> >> Dune at dune-project.org
> >> http://lists.dune-project.org/mailman/listinfo/dune
> >
> >
> > _______________________________________________
> > Dune mailing list
> > Dune at dune-project.org
> > http://lists.dune-project.org/mailman/listinfo/dune
> 
> 
> 
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-- 
Jorrit (Jö) Fahlke, Institute for Computational und Applied Mathematics,
University of Münster, Orleans-Ring 10, D-48149 Münster
Tel: +49 251 83 35146 Fax: +49 251 83 32729

Of all the things I've lost, I miss my mind the most.
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