FeniCs on Apple silicon M1

jcarlmz · March 30, 2021, 2:35pm

Greetings community, I wish to know if FeniCs (or FeniCS-X) can be installed to run natively on the new Apple silicon M1 processor based on the arm64 architecture. Thanks.

IgorBaratta · March 30, 2021, 8:46pm

I don’t think that should be any issue with FeniCS-X.
But I’m not sure if it’s currently being tested in this architecture.

Tomaubier · April 16, 2021, 6:01am

Did you manage to make it work yet?

dparsons · April 16, 2021, 10:07am

arm64 in general is known to work. The Debian and Ubuntu linux packages build for arm64.

Tomaubier · April 17, 2021, 2:41pm

Ok I’ve just been able to test it, the docker version of dolphinx does seem to work flawlessly.

Tomaubier · April 17, 2021, 3:34pm

Actually I might have spoken a bit too quickly… Trying to import dolfinx using the dolfinx/lab docker image available on docker hub on a MacBook Air M1 causes the kernel to crash and restart.
Is there any way to fix this?
Note that non-X version of Fenics (quay.io/fenicsproject/stable:latest) is working properly.

jcarlmz · April 18, 2021, 12:35am

Are you using the docker version for apple silicon m1 ?

jackhale · April 21, 2021, 3:04pm

I am a developer of FEniCS. Today we introduced experimental native ARM64 builds of our Docker images.

From the end users point of view nothing changes, i.e.:

docker run -ti dolfinx/dolfinx

The lab image should also work.

Feedback here or on our Slack in #fenicsx would be much appreciated from Mac M1 users.

jcarlmz · April 21, 2021, 5:23pm

Is there a native ARM64 build for FeniCS 2019.1.0 to test on a Mac M1 ? I am still using that version. Thanks.

jackhale · April 22, 2021, 3:46pm

No… You are welcome to try building from the original Dockerfiles on ARM. You will certainly need to modify/adapt them but it will put you on the right path.

https://bitbucket.org/fenics-project/docker/src/master/dockerfiles/

I can’t really provide support, FEniCS 2019.1.0 is ‘legacy’ now.

jcarlmz · April 23, 2021, 4:15am

I installed the ARM build of FenicsX on a Mac M1 using

docker run -ti dolfinx/dolfinx

However, I see that some demos are not working since this docker image does not include packages such as PyVista, PyVistaqt and Gmsh. Can I install them inside the docker container ?

dokken · April 23, 2021, 5:53am

You can install both packages.
Gmsh is installed on amd systems by unzipping a binary: dolfinx/Dockerfile at main · FEniCS/dolfinx · GitHub
so you might have to install gmsh from source (gmsh is pip installable, but does not always work out of the box). For more info on gmsh see: Gmsh: a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities

For pyvista, see: Plot functions in dolfinx - #5 by dokken

Pyvistaqt requires some extra packages:

apt-get install -y --no-install-recommends python3-pyqt5 libgl1-mesa-glx  # pyvistaqt
pip3 install pyvista pyvistaqt

jcarlmz · April 24, 2021, 4:44am

I tried to install PyVista on a Mac M1 by using your suggestions in

However I get the errors:

ERROR: Could not find a version that satisfies the requirement vtk (from pyvista) (from versions: none)

ERROR: No matching distribution found for vtk (from pyvista)

Is there any way to fix this ?

dokken · April 24, 2021, 5:10am

Unfortunately VTK has not published wheels for python 3.9 yet, see:

You might have to install VTK manually

jcarlmz · April 24, 2021, 6:04am

Can Matplotlib still be used with FeniCX ?

Tomaubier · April 24, 2021, 10:19am

Sorry for the delay but yes I’m using the latest Apple Silicon version.

Tomaubier · April 24, 2021, 10:22am

I tried running the newly updated Jupyter Lab dolfinx environment and faced this error:

~ % docker run -ti dolfinx/lab:latest 
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-lab", line 5, in <module>
    from jupyterlab.labapp import main
  File "/usr/local/lib/python3.8/dist-packages/jupyterlab/__init__.py", line 7, in <module>
    from .labapp import LabApp
  File "/usr/local/lib/python3.8/dist-packages/jupyterlab/labapp.py", line 15, in <module>
    from jupyterlab_server import slugify, WORKSPACE_EXTENSION
  File "/usr/local/lib/python3.8/dist-packages/jupyterlab_server/__init__.py", line 4, in <module>
    from .app import LabServerApp
  File "/usr/local/lib/python3.8/dist-packages/jupyterlab_server/app.py", line 7, in <module>
    from jupyter_server.extension.application import ExtensionApp, ExtensionAppJinjaMixin
  File "/usr/local/lib/python3.8/dist-packages/jupyter_server/__init__.py", line 15, in <module>
    from ._version import version_info, __version__
  File "/usr/local/lib/python3.8/dist-packages/jupyter_server/_version.py", line 5, in <module>
    from jupyter_packaging import get_version_info
  File "/usr/local/lib/python3.8/dist-packages/jupyter_packaging/__init__.py", line 7, in <module>
    from .setupbase import *
  File "/usr/local/lib/python3.8/dist-packages/jupyter_packaging/setupbase.py", line 38, in <module>
    from setuptools.config import StaticModule
ImportError: cannot import name 'StaticModule' from 'setuptools.config' (/usr/lib/python3/dist-packages/setuptools/config.py)
~ %

Tomaubier · April 26, 2021, 9:49am

This issue seem to have been fixed in the latest release.

Tomaubier · April 27, 2021, 1:47pm

Did anyone manage to install gmsh? I tried installing it using pip on the latest build of dolfinx/lab (18b29689a687) without any success (see Can't start gmsh after installing via pip (#1023) · Issues · gmsh / gmsh · GitLab).
Additionally the procedure for the installation from source detailed here Gmsh compilation · Wiki · gmsh / gmsh · GitLab led me to the following error when running the make command:

root@fad3fabceb5c:~/gmsh/build# make
Scanning dependencies of target gmsh
[  0%] Building CXX object CMakeFiles/gmsh.dir/Common/Main.cpp.o
[  0%] Building CXX object CMakeFiles/gmsh.dir/Common/GmshGlobal.cpp.o

...

[ 13%] Building CXX object CMakeFiles/gmsh.dir/Geo/GVertex.cpp.o
[ 13%] Building CXX object CMakeFiles/gmsh.dir/Geo/GEdge.cpp.o
[ 13%] Building CXX object CMakeFiles/gmsh.dir/Geo/GFace.cpp.o
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [CMakeFiles/gmsh.dir/build.make:1194: CMakeFiles/gmsh.dir/Geo/GFace.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:1355: CMakeFiles/gmsh.dir/all] Error 2
make: *** [Makefile:163: all] Error 2

Am I doing anything wrong? Any help would be appreciated.

jackhale · April 27, 2021, 2:37pm

The gmsh and vtk developers are not yet publishing binary packages for ARM. You can see that we skip these on ARM in the Dockerfile:

github.com

FEniCS/dolfinx/blob/main/docker/Dockerfile#L196


RUN wget -nc --quiet https://github.com/ornladios/ADIOS2/archive/v${ADIOS2_VERSION}.tar.gz -O adios2-v${ADIOS2_VERSION}.tar.gz && \
    mkdir -p adios2-v${ADIOS2_VERSION} && \
    tar -xf adios2-v${ADIOS2_VERSION}.tar.gz -C adios2-v${ADIOS2_VERSION} --strip-components 1 && \
    cmake -DADIOS2_USE_Fortran=Off -DBUILD_TESTING=Off -DADIOS2_BUILD_EXAMPLES=Off -DADIOS2_USE_ZeroMQ=Off  -B build-dir -S ./adios2-v${ADIOS2_VERSION} && \
    cmake --build build-dir && \
    cmake --install build-dir && \
    rm -rf /tmp/*


# Download Install gmsh SDK
# Only compatible with x86-64 (amd64)
RUN dpkgArch="$(dpkg --print-architecture)"; \
    case "$dpkgArch" in amd64) \
      cd /usr/local && \
      wget -nc --quiet http://gmsh.info/bin/Linux/gmsh-${GMSH_VERSION}-Linux64-sdk.tgz && \
      tar -xf gmsh-${GMSH_VERSION}-Linux64-sdk.tgz && \
      rm gmsh-${GMSH_VERSION}-Linux64-sdk.tgz ;; \
    esac;


ENV PATH=/usr/local/gmsh-${GMSH_VERSION}-Linux64-sdk/bin:$PATH \
    PYTHONPATH=/usr/local/gmsh-${GMSH_VERSION}-Linux64-sdk/lib:$PYTHONPATH

github.com

FEniCS/dolfinx/blob/main/docker/Dockerfile#L446


RUN pip3 install --upgrade --no-cache-dir jupyter jupyterlab


# pyvista dependencies from apt
RUN apt-get -qq update && \
    apt-get -y install libgl1-mesa-dev xvfb && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*


# pyvista dependencies from pip. Only compatible with x86-64 (amd64).
# matplotlib improves plotting quality with better color maps and properly rendering colorbars.
RUN dpkgArch="$(dpkg --print-architecture)"; \
    case "$dpkgArch" in amd64) \
      pip3 install --no-cache-dir pyvista ;; \
    esac; \
    pip3 install --no-cache-dir matplotlib


EXPOSE 8888/tcp
ENV SHELL /bin/bash
ENTRYPOINT ["jupyter", "lab", "--ip", "0.0.0.0", "--no-browser", "--allow-root"]

I think it is only a matter of time before this is fixed upstream, so I’d rather not manually compile gmsh/vtk etc. for now. If the situation hasn’t improved in three months then we can revisit the decision.

@Tomaubier Your error looks typical of a compiler being killed due by the kernel due to using all of the available memory. Try increasing the amount of memory allocated to Docker?

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