jorgensd
commented
1 month ago Could you try with 0.8.1: https://github.com/jorgensd/dolfinx_mpc/tree/v0.8.1 and also give me the conda commands you ran to create your environment ?
Open bnherrerac opened 1 month ago
jorgensd
commented
1 month ago Could you try with 0.8.1: https://github.com/jorgensd/dolfinx_mpc/tree/v0.8.1 and also give me the conda commands you ran to create your environment ?
bnherrerac
commented
1 month ago Tried with 0.8.1 keeping dolfinx 0.8.0, the same error happened. I rerun these conda commands to create the env and install all the dependencies:
conda create -n fenicsx-env
conda activate fenicsx-env
conda install -c conda-forge fenics-dolfinx mpich pyvista
conda install conda-forge::dolfinx_mpc
conda install conda-forge::pytest
conda install scipywhich leaves me with dolfinx 0.8.0 and dolfinx-mpc 0.8.1. Here is a MWE that reproduces the error after this installation:
import numpy as np
from mpi4py import MPI
from dolfinx import fem, mesh
from dolfinx.common import Timer
from dolfinx_mpc import MultiPointConstraint
dolfinx_mesh = mesh.create_unit_cube(MPI.COMM_WORLD, 10, 10, 10)
V = fem.functionspace(dolfinx_mesh, ("Lagrange", 1, (dolfinx_mesh.geometry.dim, )))
def x_periodic_boundary(x):
return np.isclose(x[0], 1.0, atol=1e-8)
def x_periodic_relation(x):
out_x = np.zeros_like(x)
out_x[0] = 1 - x[0]
out_x[1] = x[1]
out_x[2] = x[2]
return out_x
with Timer("~PERIODIC: Initialize MPC"):
mpc = MultiPointConstraint(V)
mpc.create_periodic_constraint_geometrical(V, x_periodic_boundary, x_periodic_relation, bcs=[])
mpc.finalize()Thank you for your help!
jorgensd
commented
1 month ago I can reproduce this. I think this is an issue with an incompatibility with nanobind versions. I will ask @minrk for guidance as he is a wizard at this!
minrk
commented
1 month ago This is almost certainly an incompatibility in nanobind (likely a compiler version mismatch) that should be pinned but apparently isn't. Can you share the output of conda env export?
minrk
commented
1 month ago Yup, it's the same nanobind abi pinning issue that I believe I've fixed in dolfinx itself, but didn't realize it extended to mpc as well. The quickest workaround is to add gxx=12 to your list of packages, and it should pick the right compatible version of everything.
When this PR is merged, the latest builds of everything should work together again.
bnherrerac
commented
1 month ago Thank you both for looking into this. The command conda install gxx=12 worked well as a workaround. I am having a similar issue in scifem too, the exact same as here.
This is the output of conda env export:
Hello, I am unable to run the periodic demos using dolfinx 0.8.0 and dolfinx_mpc 0.8.0, with Python 3.12.6. The demos I can't run are the following:
In both cases I get a similar error, here's the error for
demo_periodic_geometrical.py:And the error for
demo_periodic3d_topological.py:I installed dolfinx and dolfinx_mpc via conda install, and made sure that both versions are 0.8.0. I am trying to run a similar code, where I impose periodic boundary conditions in opposite faces of an unit cell, but I get stuck when calling
create_periodic_constraint_geometrical, as in the demo. If you have any idea how I could get around this, it would be very helpful. Thanks in advance!