Dear all, I tried to create a simple mesh in gmsh with a hole in it and would like to import this into firedrake. When I try to use this mesh with mymesh = Mesh("test1.msh") elt = FiniteElement("CG", "triangle", 1) CG1 = FunctionSpace(mymesh, elt) I get the error below. Any ideas why? I attached the mesh. Thank you! Henrik Traceback (most recent call last): File "charge.py", line 25, in <module> CG1 = FunctionSpace(mymesh, elt) File "/home/hb111949/.local/lib/python2.7/site-packages/PyOP2-0.11.0_425_g64db689-py2.7-linux-x86_64.egg/pyop2/caching.py", line 161, in __new__ obj = make_obj() File "/home/hb111949/.local/lib/python2.7/site-packages/PyOP2-0.11.0_425_g64db689-py2.7-linux-x86_64.egg/pyop2/caching.py", line 142, in make_obj obj.__init__(*args, **kwargs) File "/home/hb111949/Code/firedrake/firedrake/functionspace.py", line 578, in __init__ mesh.init() File "/home/hb111949/Code/firedrake/firedrake/mesh.py", line 480, in init self._callback(self) File "/home/hb111949/Code/firedrake/firedrake/mesh.py", line 404, in callback old_to_new = self._plex.getOrdering(PETSc.Mat.OrderingType.RCM).indices File "PETSc/DMPlex.pyx", line 601, in petsc4py.PETSc.DMPlex.getOrdering (src/petsc4py.PETSc.c:224945) petsc4py.PETSc.Error: error code 77 [0] DMPlexGetOrdering() line 136 in /rwthfs/rz/cluster/home/hb111949/Code/petsc/src/dm/impls/plex/plexreorder.c [0] DMPlexCreateOrderingClosure_Static() line 43 in /rwthfs/rz/cluster/home/hb111949/Code/petsc/src/dm/impls/plex/plexreorder.c [0] Petsc has generated inconsistent data [0] Number of depth 1 faces 40 does not match permuted nubmer 38 -- Dipl.-Math. Henrik Büsing Institute for Applied Geophysics and Geothermal Energy E.ON Energy Research Center RWTH Aachen University ------------------------------------------------------ Mathieustr. 10 | Tel +49 (0)241 80 49907 52074 Aachen, Germany | Fax +49 (0)241 80 49889 ------------------------------------------------------ http://www.eonerc.rwth-aachen.de/GGE hbuesing@eonerc.rwth-aachen.de ------------------------------------------------------
Dear Henrik, On 14/12/15 14:24, Buesing, Henrik wrote:
Dear all,
I tried to create a simple mesh in gmsh with a hole in it and would like to import this into firedrake. When I try to use this mesh with
mymesh = Mesh("test1.msh")
elt = FiniteElement("CG", "triangle", 1)
CG1 = FunctionSpace(mymesh, elt)
I get the error below.
Any ideas why? I attached the mesh. Thank you!
This looks like a bug, either in our mesh reading, or somewhere a bit further down the line. Could you please file a github issue for the problem so we can track it sensibly. Thanks, Lawrence
I tried to create a simple mesh in gmsh with a hole in it and would like to import this into firedrake. When I try to use this mesh with
mymesh = Mesh("test1.msh")
elt = FiniteElement("CG", "triangle", 1)
CG1 = FunctionSpace(mymesh, elt)
I get the error below.
Any ideas why? I attached the mesh. Thank you!
This looks like a bug, either in our mesh reading, or somewhere a bit further down the line.
Could you please file a github issue for the problem so we can track it sensibly.
On 14/12/15 14:40, Lawrence Mitchell wrote:
Dear Henrik,
On 14/12/15 14:24, Buesing, Henrik wrote:
Dear all,
I tried to create a simple mesh in gmsh with a hole in it and would like to import this into firedrake. When I try to use this mesh with
mymesh = Mesh("test1.msh")
elt = FiniteElement("CG", "triangle", 1)
CG1 = FunctionSpace(mymesh, elt)
I get the error below.
Any ideas why? I attached the mesh. Thank you!
This looks like a bug, either in our mesh reading, or somewhere a bit further down the line.
Could you please file a github issue for the problem so we can track it sensibly.
Hmm, on closer inspection it looks like you have two "rogue" points in your mesh file that are not part of any cell (at the center of the mesh in the hole). If I remove those points then I can read the mesh successfully. What happens is that we compute a numbering of vertices (and edges) in the mesh by traversing the cells in order and numbering all the vertices we see attached to each cell. But your mesh has some vertices not attached to any cells, so we didn't number them, and then you get a nasty error later on. We could handle this case more gracefully, so if you can still report the issue, that would be great. Cheers, Lawrence
Hmm, on closer inspection it looks like you have two "rogue" points in your mesh file that are not part of any cell (at the center of the mesh in the hole).
[Buesing, Henrik] Yes. Right. I used these to create to the circle. I will just delete them. Henrik https://github.com/firedrakeproject/firedrake/issues/664
participants (2)
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Buesing, Henrik
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Lawrence Mitchell