Save MeshFunction in parallel with parameters['ghost_mode'] = 'shared_facet'

I/O
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1

When I try to save a MeshFunction with MPI with parameters['ghost_mode'] = 'shared_facet' it gives me some error. May I know how to solve this? and what is the problem here?

I am using dolfin 2018.2.0.

from dolfin import *
from os import path
parameters['ghost_mode'] = 'shared_facet'
# Create a mesh
mesh = UnitSquareMesh(32, 32)

class rectangle(SubDomain):
    def inside(self,x, on_boundary):
        return between(x[0],(0.25,0.75)) and between(x[1],(0.25,0.75))
Rec = rectangle()

# Define domain indicator function
domainindicator = MeshFunction('size_t', mesh, mesh.topology().dim())
domainindicator.set_all(1)
Rec.mark(domainindicator,0)

my_filed = XDMFFile(MPI.comm_world, "domainindicator.xdmf")
my_filed.write(domainindicator)

Above is the MWE and it gives this error:

HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) MPI-process 1:
  #000: ../../../src/H5Dio.c line 263 in H5Dwrite(): file selection+offset not within extent
    major: Dataspace
    minor: Out of range
2

Can’t replicate with my local installation. I have a newer HDF5 version in the same series (1.10.10, while you have 1.10.0). You may also want to upgrade to the latest dolfin version.

3

Hi

Do you get this error when using the newer version?

4

no, everything is working correctly, and I can open the xdmf file in paraview and visualize the two subdomains.

5

Sorry for double check, but did you try it with more than 1 core (mpirun -n 2), serial run also works for me

6

Works in parallel as well. If it works for you in serial, but not in parallel, it’s possible that your hdf5 installation isn’t configured properly to work in parallel.