Background
I am installing DOLFINx v0.9.0 from source on Ubuntu 24.04 LTS with the goal of enabling MPI parallel support. I have successfully installed all dependencies, including PETSc 3.21.5 and petsc4py 3.21.5. However, when importing DOLFINx, I encounter an AssertionError because dolfinx.common.has_petsc4py returns False. I have tried multiple approaches, including recompiling the C++ core and Python interface, but the issue persists. I would appreciate the community’s help in diagnosing and resolving this problem.
System Environment
- Operating System: Ubuntu 24.04 LTS
- Python Version: 3.12.3 (in a virtual environment named
fenicsx-env) - DOLFINx Version: v0.9.0 (built from GitHub source)
- PETSc Version: 3.21.5 (built from source, installed at
/usr/local/petsc) - petsc4py Version: 3.21.5 (installed via pip)
- MPI Implementation: MPICH 4.1 (installed via
sudo apt install mpich) - HDF5: System version (
/usr/lib/x86_64-linux-gnu/hdf5/mpich, installed viasudo apt install libhdf5-mpich-dev, supports parallel) - CMake Version: 3.29.6 (built from source)
Installation Steps
-
Installed PETSc:
git clone -b v3.21.5 PETSc / petsc · GitLab petsc
cd petsc
./configure --with-mpi=1 --with-hdf5=1 --with-hdf5-dir=/usr/lib/x86_64-linux-gnu/hdf5/mpich --prefix=/usr/local/petsc
make PETSC_DIR=(pwd) PETSC_ARCH=arch-linux-c-opt all -j(nproc)
sudo make PETSC_DIR=$(pwd) PETSC_ARCH=arch-linux-c-opt install
export PETSC_DIR=/usr/local/petsc
export PETSC_ARCH=arch-linux-c-opt -
Installed petsc4py:
source ~/fenicsx-env/bin/activate
PETSC_DIR=/usr/local/petsc PETSC_ARCH=arch-linux-c-opt pip install petsc4py==3.21.5 -
Installed DOLFINx C++ Core:
cd ~/Downloads/dolfinx/cpp/build
cmake -DCMAKE_BUILD_TYPE=Release
-DCMAKE_PREFIX_PATH=“/usr/local;/usr/local/petsc;/usr/lib/x86_64-linux-gnu/hdf5/mpich”
-DPython3_EXECUTABLE=$(which python3)
-DHDF5_ROOT=/usr/lib/x86_64-linux-gnu/hdf5/mpich
-DPETSC_DIR=/usr/local/petsc
-DPETSC_ARCH=arch-linux-c-opt
..
make -j$(nproc)
sudo make install
-
Installed DOLFINx Python Interface:
cd ~/Downloads/dolfinx/python
PETSC_DIR=/usr/local/petsc PETSC_ARCH=arch-linux-c-opt pip install . -
Environment Variables:
export LD_LIBRARY_PATH=/usr/local/petsc/lib:/usr/lib/x86_64-linux-gnu/hdf5/mpich:$LD_LIBRARY_PATH
Issue Description
When importing DOLFINx, I get the following error:
python -c “import dolfinx; print(dolfinx.version)”
Traceback (most recent call last):
File “”, line 1, in
File “/home/asus/fenicsx-env/lib/python3.12/site-packages/dolfinx/init.py”, line 20, in
assert dolfinx.common.has_petsc4py
^^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError
The same error occurs with parallel execution:
mpirun -np 4 python -c “import dolfinx; print(dolfinx.version)”
Debugging Information
- petsc4py Verification:
python -c “import petsc4py; print(petsc4py.version)”
Output:
3.21.5
python -c “import petsc4py; petsc4py.init(); from petsc4py import PETSc; print(PETSc.Sys.getVersion())”
Output:
(3, 21, 5)
petsc4pycan initialize PETSc correctly.
- Debugging
dolfinx/__init__.py:
Modified to include:
import petsc4py
print(“petsc4py version:”, petsc4py.version)
from dolfinx import cpp
print(“cpp module loaded:”, cpp)
print(“has_petsc4py before assert:”, dolfinx.common.has_petsc4py)
assert dolfinx.common.has_petsc4py, “petsc4py not detected”
Output:
petsc4py version: 3.21.5
cpp module loaded: <module ‘dolfinx.cpp’ from ‘/home/asus/fenicsx-env/lib/python3.12/site-packages/dolfinx/cpp.cpython-312-x86_64-linux-gnu.so’>
has_petsc4py before assert: False
Traceback (most recent call last):
…
AssertionError: petsc4py not detected
The dolfinx.cpp module loads successfully, but has_petsc4py is False.
- Debugging dolfinx/common.py:
Modified to include:
from dolfinx import cpp as _cpp
import petsc4py
petsc4py.init()
from petsc4py import PETSc
print(“PETSc version from petsc4py:”, PETSc.Sys.getVersion())
print(“has_petsc4py from cpp:”, _cpp.common.has_petsc4py())
Output:
PETSc version from petsc4py: (3, 21, 5)
has_petsc4py from cpp: False - CMake Output (Partial):
– Found PETSc version 3.21.5, prefix: /usr/local/petsc
– Found MPI_C: /usr/lib/x86_64-linux-gnu/mpich/lib/libmpich.so (found suitable version “4.1”, minimum required is “3”)
– Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/mpich/libhdf5.so … - Library Files:
ls /usr/local/petsc/lib | grep libpetsc
Output:
libpetsc.so libpetsc.so.3.21 libpetsc.so.3.21.5
ls /usr/local/lib | grep libdolfinx
Output:
libdolfinx.so libdolfinx.so.0.9 libdolfinx.so.0.9.0
Problem Analysis
Both petsc4py and PETSc work correctly, and the dolfinx.cpp module loads without issues.
However, dolfinx.common.has_petsc4py (exposed via dolfinx.cpp) always returns False, indicating that the DOLFINx C++ core does not detect or enable PETSc.
The CMake output confirms that PETSc is found, but it’s unclear if it is fully enabled (e.g., whether the HAS_PETSC macro is defined).
Steps Tried
Verified PETSC_DIR and PETSC_ARCH environment variables.
Added /usr/local/petsc/lib to LD_LIBRARY_PATH.
Recompiled the DOLFINx C++ core and Python interface multiple times.
Added -DENABLE_PETSC=ON to CMake, but no change.
Debugged dolfinx/init.py and dolfinx/common.py to confirm petsc4py and dolfinx.cpp behavior.
Request for Help
Can someone clarify how DOLFINx v0.9.0’s C++ core detects and enables PETSc during the build process?
What could cause dolfinx.common.has_petsc4py to return False even though PETSc and petsc4py are functional?
Are there specific CMake options or patches needed to ensure PETSc is fully enabled?
If this is a compatibility issue, which PETSc version is recommended for DOLFINx v0.9.0?
Thank you for your assistance!