assign values to function in parallel

Question

I know this questioned might be asked and answered in several different ways. I have gone through all of them but still can't figure out a way. I guess my problem is slightly different than theirs. I have been struggling for quite a few days on this issue. Hopefully someone could shed some light.

Simply speaking, I import an xml format 2D mesh which has 72 vertices. Also, from a file I import a numpy vector which has the size of 144, i.e. 2 DOFs per vertex. I order the values in the file as

DOF1@Vertex1
DOF2@Vertex1
DOF1@Vertex2
DOF2@Vertex2
...
...

My code works fine in serial. But in parallel (>1 processor), I can't get it right. Below is a minimal working code snippet. You can see the output g looks different in serial and parallel when visualizing the .pvd file. The correct g looks like this.

from dolfin import *
import numpy as np

mesh = Mesh("xmlmesh.xml")

V = VectorFunctionSpace(mesh, "CG", 1) 

g_np = np.loadtxt("measuredDisp_1col.txt")   # Order: 1st node: x, y; 2nd node: x, y ...
g = Function(V)

dofs_local = dof_to_vertex_map(V)
my_first, my_last = V.dofmap().ownership_range() # get range of local process
dofs = filter(lambda dof: dof in range(my_last-my_first), dofs_local) #filter ghost dofs

g_np = g_np[dofs]

g.vector().set_local( g_np )

File("output/g.pvd") << g

If you want to run the code snippet, you may want to download the two files I'm using, the mesh and the numpy vector.

Thanks in advance!

By the way, I'm using fenics 2016.1.0.

Answer 1

A simple solution is to

1) Run your code in serial and save g using the HDF5File class.

fid = HDF5File(mpi_comm, "g.h5", "w")
fid.write(g, "g")
fid.close()

2) Run your code in parallel and read g from the HDF5File

g = Function(V)
fid =HDF5File(mpi_comm, "g.h5", "r")
fid.read(g,"g")
fid.close()

Comments

It works like a charm. Nice work-around! Thanks!

Though I'm not sure if it will take too long if I have more than a million entries in g. If there's no one providing a neater solution in a couple of days, I'll select yours as the best answer.