Error installing Fenics for python

General
1

Hello,
I am on OSX 14.1 and I am trying to install Fenics for python. I follow these instructions. I did succesfully the steps in Installation → From Source section. However, when I get to the next section I get the error when I get to the line

 % git clone --branch=$FENICS_VERSION https://bitbucket.org/fenics-project/mshr

Cloning into 'mshr'...
fatal: Remote branch 2019.1.0.post0 not found in upstream origin

note that

 % echo $FENICS_VERSION
2019.1.0.post0

May you please help ?
Thanks

2

Please note that mshr (Bitbucket) is long deprecated.
Anyhow, to get your code to work replace $FENICS_VERSION with 2019.1.0.

3

I see, I will try it. What should I use instead of the deprecated version ?

4

Hello,
I followed your instruction, and now I no longer get an error to the line above. However, if I proceed with the installations steps shown here, I get an error at

% mkdir dolfin/build && cd dolfin/build && cmake ..
-- The C compiler identification is AppleClang 15.0.0.15000100
-- The CXX compiler identification is AppleClang 15.0.0.15000100
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test HAVE_PIPE
-- Performing Test HAVE_PIPE - Success
-- Performing Test HAVE_PEDANTIC
-- Performing Test HAVE_PEDANTIC - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_OPTIMISATION
-- Performing Test HAVE_O2_OPTIMISATION - Success
CMake Warning (dev) at /usr/local/share/cmake-3.29/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args` (MPI_C) does
  not match the name of the calling package (MPI).  This can lead to problems
  in calling code that expects `find_package` result variables (e.g.,
  `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/modules/FindMPI.cmake:611 (find_package_handle_standard_args)
  CMakeLists.txt:227 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found MPI_C: /opt/homebrew/Cellar/open-mpi/5.0.1/lib/libmpi.dylib
CMake Warning (dev) at /usr/local/share/cmake-3.29/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args` (MPI_CXX)
  does not match the name of the calling package (MPI).  This can lead to
  problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/modules/FindMPI.cmake:611 (find_package_handle_standard_args)
  CMakeLists.txt:227 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found MPI_CXX: /opt/homebrew/Cellar/open-mpi/5.0.1/lib/libmpi.dylib
-- Found Boost: /opt/homebrew/include (found version "1.84.0") found components: timer filesystem program_options iostreams regex
CMake Error at /usr/local/share/cmake-3.29/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
  Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)
  (Required is at least version "3.2.90")
Call Stack (most recent call first):
  /usr/local/share/cmake-3.29/Modules/FindPackageHandleStandardArgs.cmake:600 (_FPHSA_FAILURE_MESSAGE)
  cmake/modules/FindEigen3.cmake:97 (find_package_handle_standard_args)
  CMakeLists.txt:276 (find_package)


-- Configuring incomplete, errors occurred!

Do you know why?
Thanks

5

I am not sure why you want to install DOLFIN from source, when it is available as docker images, on conda, through apt-get (ubuntu) and various other ways (including spack).

If you want to install from source, you need to install all other dependencies as well, including Eigen3, petsc etc.

Please also note that DOLFIN is not recommended for new users, see; The new DOLFINx solver is now recommended over DOLFIN for details

6

I cannot install the docker image because I plan to use fenics on a remote computer, where they do not allow docker.
The conda installation (I followed these instructions) crashes too:

 % conda create -n fenicsproject -c conda-forge fenics

Retrieving notices: ...working... Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)'))': /conda-forge/notices.json

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)'))': /conda-forge/notices.json

Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)'))': /conda-forge/notices.json

ERROR conda.notices.fetch:get_channel_notice_response(68): Request error <HTTPSConnectionPool(host='conda.anaconda.org', port=443): Max retries exceeded with url: /conda-forge/notices.json (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)')))> for channel: conda-forge url: https://conda.anaconda.org/conda-forge/notices.json
done
Channels:
 - conda-forge
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): / Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)'))': /conda-forge/osx-arm64/repodata.json.zst

Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)'))': /conda-forge/noarch/repodata.json.zst

- Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)'))': /conda-forge/osx-arm64/repodata.json.zst

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)'))': /conda-forge/noarch/repodata.json.zst

/ Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)'))': /conda-forge/osx-arm64/repodata.json.zst

Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)'))': /conda-forge/noarch/repodata.json.zst

failed

CondaSSLError: Encountered an SSL error. Most likely a certificate verification issue.

Exception: HTTPSConnectionPool(host='conda.anaconda.org', port=443): Max retries exceeded with url: /conda-forge/osx-arm64/repodata.json.zst (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)')))


michele@Micheles-MacBook-Pro /Applications % conda create -n fenicsproject -c conda-forge fenics

Channels:
 - conda-forge
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): / Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, '[SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1006)'))': /conda-forge/noarch/repodata.json.zst

Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, '[SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1006)'))': /conda-forge/osx-arm64/repodata.json.zst

\ Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, '[SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1006)'))': /conda-forge/noarch/repodata.json.zst

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, '[SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1006)'))': /conda-forge/osx-arm64/repodata.json.zst

done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - fenics

Current channels:

  - https://conda.anaconda.org/conda-forge
  - defaults

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.