Error in PVD file writing associated with projection

I/O
1

Hi everyone,
I experienced a wierd issue with PVD writing using legacy FEniCS. Running multiple simulations in a for cycle, I noticed that pvd files are not saved correctly after the first iteration (i.e., the first simulation). Surprisingly, the cause seems to be a projection operation. Indeed, the error disappear when such line is removed from the code.

Here’s a minimal script reproducing the issue:

import fenics
from pathlib import Path

def fake_sim(iteration: int):
    msh = fenics.UnitSquareMesh(10, 10)  # generate mesh
    V = fenics.FunctionSpace(msh, "Lagrange", 1)  # generate function space

    # generate a function
    foo_exp = fenics.Expression("x[0] < 0.5 ? 1. : 0", degree=1)
    foo = fenics.interpolate(foo_exp, V)

    # do random projection (originally, I was computing grad(foo))
    foo_projection = fenics.project(2 * foo, V)   # REMOVING THIS EVERYTHING WORKS

    # generate output folder
    out_folder = Path(f"out/iteration_n{iteration}")
    out_folder.mkdir(exist_ok=True, parents=True)

    # generate pvd file
    foo_pvd = fenics.File(str(out_folder / Path(f"foo.pvd")))

    # write on file at t 0
    foo_pvd.write(foo, 0)

def main():
    # run sequence of "simulations"
    for i in range(3):
        print(f"Started iteration {i}")
        fake_sim(i)

if __name__ == "__main__":
    main()

Here are some additional details:

  • I am using FEniCS 2019.1.0 in a Singularity container
  • I am using Paraview 5.13
  • I know that it is recommended to use xdmf files instead of pvd files. Indeed, I do not encounter the same problem using xdmf. Nevertheless, I need to use pvd files for saving the functions I compute on multiple nodes of my cluster.
  • Below, I attach the pictures of the foo function I visualize in Paraview on iteration 0 and 1.

Can anyone illuminate me on the reason why project should mess up with the writing of a pvd file?

The result on the first iteration:

debug_pvd_it0
debug_pvd_it01482×765 12.5 KB

The result on the second iteration:

debug_pvd_it1
debug_pvd_it11482×765 21.1 KB

2

Can’t reproduce this locally. I have out/iteration_n0/foo.pvd, out/iteration_n1/foo.pvd and out/iteration_n2/foo.pvd, and they all look like in your first picture.

1 Like
3

Dear Francesco,
Thanks for your kind answer. Apparently, it is an issue related to the latest version of Paraview (5.13). Using an older version (5.9) everything works fine.

4

That would align with the setup I tested when I answered, where I have paraview 5.12.1.