CheckpointFile error with BDM

[TCYong123]

I have found an error when CheckpointFile is used to save a function with BDM finite element.

Example of code to reproduce error:
"""
import firedrake as fd

mesh = fd.IcosahedralSphereMesh(radius=6371220,
refinement_level=5, degree=1,
distribution_parameters = {"partition": True, "overlap_type": (fd.DistributedMeshOverlapType.VERTEX, 2)},
name="mesh")
degree = 1
V = fd.FunctionSpace(mesh, "BDM", degree+1)
f = fd.Function(V, name="f")
with fd.CheckpointFile("example.h5", 'w') as afile:
afile.save_mesh(mesh)
afile.save_function(f)
"""

Error message:
"""
Traceback (most recent call last):
File "/home/tcyong/sw_implicit/example.py", line 12, in
afile.save_function(f)
File "PETSc/Log.pyx", line 115, in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func
File "PETSc/Log.pyx", line 116, in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func
File "/home/tcyong/firedrake/src/firedrake/firedrake/checkpointing.py", line 805, in save_function
self._project_function_for_checkpointing(_f, f, method)
File "/home/tcyong/firedrake/src/firedrake/firedrake/checkpointing.py", line 1440, in _project_function_for_checkpointing
getattr(f, method)(_f)
File "PETSc/Log.pyx", line 115, in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func
File "PETSc/Log.pyx", line 116, in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func
File "/home/tcyong/firedrake/src/firedrake/firedrake/function.py", line 371, in interpolate
return interpolation.interpolate(expression, self, subset=subset, ad_block_tag=ad_block_tag)
File "PETSc/Log.pyx", line 115, in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func
File "PETSc/Log.pyx", line 116, in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func
File "/home/tcyong/firedrake/src/firedrake/firedrake/interpolation.py", line 61, in interpolate
return Interpolator(expr, V, subset=subset, access=access).interpolate(ad_block_tag=ad_block_tag)
File "/home/tcyong/firedrake/src/firedrake/firedrake/interpolation.py", line 87, in init
self.callable, arguments = make_interpolator(expr, V, subset, access)
File "PETSc/Log.pyx", line 115, in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func
File "PETSc/Log.pyx", line 116, in petsc4py.PETSc.Log.EventDecorator.decorator.wrapped_func
File "/home/tcyong/firedrake/src/firedrake/firedrake/interpolation.py", line 212, in make_interpolator
raise RuntimeError('Expression of length %d required, got length %d'
RuntimeError: Expression of length 2 required, got length 3
"""

[TCYong123]

A workaround suggested by Colin Cotter is to use fd.VectorFunctionSpace(mesh, "DG", degree+1) instead of fd.FunctionSpace(mesh, "BDM", degree+1)

[ksagiyam]

Thanks. This looks like an actual bug. I will attempt to fix this some time soon.

[tommbendall]

Not an answer, but I'm seeing a similar problem. I think it might be affecting all HDiv / HCurl spaces on meshes where the topological and geometric dimensions are not equal (e.g. the surface of a sphere). Here is a minimum failing example:

from firedrake import (CubedSphereMesh, FunctionSpace, Function, CheckpointFile)
import numpy as np

mesh_name = 'spherical_mesh'
mesh = CubedSphereMesh(10.0, 2, name=mesh_name)
V = FunctionSpace(mesh, 'RTCF', 1)
field = Function(V, name='f')
# Fill with some random data
field.dat.data[:] = np.random.randn(*np.shape(field.dat.data))

filename = 'spherical_mfe.h5'

# Store field
with CheckpointFile(filename, 'w') as chk:
    chk.save_mesh(mesh)
    chk.save_function(field, name='f')  # <-- failure here

# Pick up field
with CheckpointFile(filename, 'r') as chk:
    new_mesh = chk.load_mesh(mesh_name)
    new_field = chk.load_function(new_mesh, 'f')

# Compare original and picked up fields
denom = np.linalg.norm(field.dat.data_ro[:])
diff_array = new_field.dat.data_ro[:] - field.dat.data_ro[:]
assert np.linalg.norm(diff_array) / denom < 5e-16

which gives a very similar looking error:

  File "/home/thomas/firedrake/src/firedrake/firedrake/projection.py", line 272, in Projector
    raise ValueError("Shape mismatch between source %s and target %s in project" %
ValueError: Shape mismatch between source (3,) and target (2,) in project

Tracing back the error, the save function does a projection:

File "/home/thomas/firedrake/src/firedrake/firedrake/checkpointing.py", line 800, in save_function
    self._project_function_for_checkpointing(_f, f, method)
  File "/home/thomas/firedrake/src/firedrake/firedrake/checkpointing.py", line 1418, in _project_function_for_checkpointing

and we're not projecting into the right space. It looks like in embedding.py we select a 2D vector DG element when it should probably be 3D (as the geometric dimension is 3)

[ksagiyam]

Thanks. Yes, that is right. PR is now open: #2874.

[ksagiyam]

Merged to master.