> >> You'd either need to borrow a large memory machine for
> >> long enough to read in the Tetgen file and rewrite it
> as >> Nemesis, or you'd need to modify the TetGenIO to
> support >> reading a pre-parallelized ParallelMesh.
> >
> > I had a look at the class Nemesis_IO. There seem to be
> > some differences between the online documentation and
> > the class provided in version 0.7.1.
>
> You may need to use the SVN head; I forget how recent the
> latest ParallelMesh development was, but it's quite
> possible that it wasn't working yet in 0.7.1.
I have tried with the SVN version. The following code for
writing the nemesis file worked fine:
Mesh mesh;
TetGenIO TETGEN(mesh);
{ // read TETGEN file
OStringStream inmesh;
inmesh << mesh_dir << ReadMesh[actual_pulse]<<".ele";
TETGEN.read(inmesh.str().c_str());
}
mesh.prepare_for_use();
Nemesis_IO NEM (mesh);
NEM.write("out/nemmesh");
Afterwards, when I want to read it on one processor:
./tryRead-opt
Mesh mesh;
Nemesis_IO NEM (mesh);
NEM.read("nemmesh.1.0");
reading seems to work but, at the end of the program I get
the following error:
--------------------------------------------------------------------------------
Error flushing buffers to file.
[0] src/mesh/exodusII_io_helper.C, line 151, compiled Oct 30
2011 at 11:09:28
terminate called after throwing an instance of
'libMesh::LogicError'
what(): Error in libMesh internal logic
[tomo-PaineCalc:28510] *** Process received signal ***
[tomo-PaineCalc:28510] Signal: Aborted (6)
[tomo-PaineCalc:28510] Signal code: (-6)
[tomo-PaineCalc:28510] [ 0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xfc60)
[0x7f0606345c60]
[tomo-PaineCalc:28510] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35)
[0x7f0605115d05]
[tomo-PaineCalc:28510] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x186)
[0x7f0605119ab6]
[tomo-PaineCalc:28510] [ 3]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x11d)
[0x7f06055316dd]
[tomo-PaineCalc:28510] [ 4]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xb9926)
[0x7f060552f926]
[tomo-PaineCalc:28510] [ 5]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xb9953)
[0x7f060552f953]
[tomo-PaineCalc:28510] [ 6]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xb9a5e)
[0x7f060552fa5e]
[tomo-PaineCalc:28510] [ 7]
/home/ThermoPaine/libmesh_svn/lib/x86_64-unknown-linux-gnu_opt/libmesh.so(_ZN7libMesh18ExodusII_IO_Helper9check_errEiSs+0x1b3)
[0x7f060adbaa73]
[tomo-PaineCalc:28510] [ 8]
/home/ThermoPaine/libmesh_svn/lib/x86_64-unknown-linux-gnu_opt/libmesh.so(_ZN7libMesh17Nemesis_IO_HelperD1Ev+0x48)
[0x7f060ae88978]
[tomo-PaineCalc:28510] [ 9]
/home/ThermoPaine/libmesh_svn/lib/x86_64-unknown-linux-gnu_opt/libmesh.so(_ZN7libMesh17Nemesis_IO_HelperD0Ev+0x9)
[0x7f060ae89599]
[tomo-PaineCalc:28510] [10]
/home/ThermoPaine/libmesh_svn/lib/x86_64-unknown-linux-gnu_opt/libmesh.so(_ZN7libMesh10Nemesis_IOD1Ev+0x2d)
[0x7f060ae7c41d]
[tomo-PaineCalc:28510] [11] ./tryRead-opt(main+0x202)
[0x4589e2]
[tomo-PaineCalc:28510] [12]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff)
[0x7f0605100eff]
[tomo-PaineCalc:28510] [13] ./tryRead-opt() [0x458719]
[tomo-PaineCalc:28510] *** End of error message ***
Aborted
--------------------------------------------------------------------------------
However, if I want to read it when running with 'mpiexec -np
8 ./tryRead-opt'
I get a long error message - see at the end of the mail.
For configuring of libmesh I used the following options:
./configure --enable-slepc --enable-mpi --enable-parmesh
--enable-petsc
Do I maybe have to change something there?
thanks, Robert
--------------------------------------------------------------------------------
what(): Error in libMesh internal logic
[tomo-PaineCalc:28499] *** Process received signal ***
[tomo-PaineCalc:28499] Signal: Aborted (6)
[tomo-PaineCalc:28499] Signal code: (-6)
[tomo-PaineCalc:28500] [ 0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xfc60)
[0x7f9eac762c60]
[tomo-PaineCalc:28500] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35)
[0x7f9eab532d05]
[tomo-PaineCalc:28500] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x186)
[0x7f9eab536ab6]
[tomo-PaineCalc:28500] [ 3]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x11d)
[0x7f9eab94e6dd]
[tomo-PaineCalc:28500] [ 4]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xb9926)
[0x7f9eab94c926]
[tomo-PaineCalc:28500] [ 5]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xb9953)
[0x7f9eab94c953]
[tomo-PaineCalc:28500] [ 6]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xb9a5e)
[0x7f9eab94ca5e]
[tomo-PaineCalc:28500] [ 7]
/home/ThermoPaine/libmesh_svn/lib/x86_64-unknown-linux-gnu_opt/libmesh.so(_ZN7libMesh18ExodusII_IO_Helper9check_errEiSs+0x1b3)
[0x7f9eb11d7a73]
[tomo-PaineCalc:28500] [ 8]
/home/ThermoPaine/libmesh_svn/lib/x86_64-unknown-linux-gnu_opt/libmesh.so(_ZN7libMesh18ExodusII_IO_Helper4openEPKc+0x99)
[0x7f9eb11da299]
[tomo-PaineCalc:28500] [ 9]
/home/ThermoPaine/libmesh_svn/lib/x86_64-unknown-linux-gnu_opt/libmesh.so(_ZN7libMesh10Nemesis_IO4readERKSs+0xe5)
[0x7f9eb129a955]
[tomo-PaineCalc:28500] [10] ./tryRead-opt(main+0xe6)
[0x4588c6]
[tomo-PaineCalc:28500] [11]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff)
[0x7f9eab51deff]
[tomo-PaineCalc:28500] [12] ./tryRead-opt() [0x458719]
[tomo-PaineCalc:28503] [ 0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xfc60)
[0x7f497c5fbc60]
[tomo-PaineCalc:28503] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35)
[0x7f497b3cbd05]
[tomo-PaineCalc:28503] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x186)
[0x7f497b3cfab6]
[tomo-PaineCalc:28503] [ 3]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x11d)
[0x7f497b7e76dd]
[tomo-PaineCalc:28503] [ 4]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xb9926)
[0x7f497b7e5926]
[tomo-PaineCalc:28503] [ 5]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xb9953)
[0x7f497b7e5953]
[tomo-PaineCalc:28503] [ 6]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xb9a5e)
[0x7f497b7e5a5e]
[tomo-PaineCalc:28503] [ 7]
/home/ThermoPaine/libmesh_svn/lib/x86_64-unknown-linux-gnu_opt/libmesh.so(_ZN7libMesh18ExodusII_IO_Helper9check_errEiSs+0x1b3)
[0x7f4981070a73]
[tomo-PaineCalc:28503] [ 8]
/home/ThermoPaine/libmesh_svn/lib/x86_64-unknown-linux-gnu_opt/libmesh.so(_ZN7libMesh18ExodusII_IO_Helper4openEPKc+0x99)
[0x7f4981073299]
[tomo-PaineCalc:28503] [ 9]
/home/ThermoPaine/libmesh_svn/lib/x86_64-unknown-linux-gnu_opt/libmesh.so(_ZN7libMesh10Nemesis_IO4readERKSs+0xe5)
[0x7f4981133955]
[tomo-PaineCalc:28503] [10] ./tryRead-opt(main+0xe6)
[0x4588c6]
[tomo-PaineCalc:28503] [11]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff)
[0x7f497b3b6eff]
[tomo-PaineCalc:28503] [12] ./tryRead-opt() [0x458719]
[tomo-PaineCalc:28503] *** End of error message ***
[tomo-PaineCalc:28502] [ 0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xfc60)
[0x7fb12c0c9c60]
[tomo-PaineCalc:28502] [ 1]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35)
[0x7fb12ae99d05]
[tomo-PaineCalc:28502] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x186)
[0x7fb12ae9dab6]--------------------------------------------------------------------------
mpiexec noticed that process rank 3 with PID 28501 on node
tomo-PaineCalc exited on signal 6 (Aborted).
--------------------------------------------------------------------------
5 total processes killed (some possibly by mpiexec during
cleanup)
... and so on :-|
--------------------------------------------------------------------------------
------------------------------------------------------------------------------
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