My answer isn't related to your error message, but I'd just like to remind you that Firedrake doesn't support unstructured hexahedral meshes. You can read in an unstructured quadrilateral mesh, and then extrude it, and you can manipulate the coordinates as you wish. But the only hexahedral elements we have are extruded quadrilaterals.

From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Tomasz Salwa [RPG] <mmtjs@leeds.ac.uk>
Sent: 09 May 2016 17:04:59
To: firedrake
Subject: [firedrake] firedrake & gmsh 3d hexahedron mesh

Dear all,

Can anybody familiar with gmsh tell me why firedrake protests when loading the attached mesh? How can it be corrected?

Thank you,

Tomasz

Error listing:

...

File "/home/tommy/work/programs/lin_coupled_3d/lib/coupled_system.py", line 23, in __init__
    self.mesh = fd.Mesh("L_domain.msh")
File "<decorator-gen-275>", line 2, in Mesh
File "/home/tommy/programs/firedrake/local/lib/python2.7/site-packages/pyop2/profiling.py", line 203, in wrapper
    return f(*args, **kwargs)
File "/home/tommy/programs/firedrake/local/lib/python2.7/site-packages/firedrake/mesh.py", line 1075, in Mesh
    plex = _from_gmsh(meshfile)
File "/home/tommy/programs/firedrake/local/lib/python2.7/site-packages/firedrake/mesh.py", line 159, in _from_gmsh
    gmsh_plex = PETSc.DMPlex().createGmsh(gmsh_viewer)
File "PETSc/DMPlex.pyx", line 109, in petsc4py.PETSc.DMPlex.createGmsh (src/petsc4py.PETSc.c:222051)
petsc4py.PETSc.Error: error code 62
[0] DMPlexCreateGmsh() line 247 in /tmp/pip-5Zhs5M-build/src/dm/impls/plex/plexgmsh.c
[0] Invalid argument
[0] Could not determine Plex facet for element 913