Anaconda3 (conda 版本 4.7) 安装 Fenics 出现的错误

问题描述

很早之前用 Anaconda3 (conda 版本 4.6.8) 安装过一次 Fenics (conda create -n fenicsproject -c conda-forge fenics)，安装后可以成功运行算例。

这几天重新安装的 Anaconda3 (conda 版本 4.7.10) 然后重新安装 Fenics (conda create -n fenicsproject -c conda-forge fenics)，安装后运行到 from fenics import * 总是提示错误：

(fenicsproject) MacBookPro:~ xxx$ python
Python 3.7.3 | packaged by conda-forge | (default, Jul  1 2019, 14:38:56) 
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.

>>> from fenics import *
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Applications/anaconda3/envs/fenicsproject/lib/python3.7/site-packages/fenics/__init__.py", line 7, in <module>
    from dolfin import *
  File "/Applications/anaconda3/envs/fenicsproject/lib/python3.7/site-packages/dolfin/__init__.py", line 34, in <module>
    from .cpp import __version__
ImportError: dlopen(/Applications/anaconda3/envs/fenicsproject/lib/python3.7/site-packages/dolfin/cpp.cpython-37m-darwin.so, 2): Library not loaded: @rpath/libdmumps-5.1.2.dylib
  Referenced from: /Applications/anaconda3/envs/fenicsproject/lib/libpetsc.3.11.dylib
  Reason: image not found

然后卸载 Anaconda3，重装，仍然是这个错误，后来在 Fenics 论坛提问 Errors in calling `from fenics import *`，有人给出了解答

Try this:

conda create -n fenics2018 -c conda-forge fenics=2018

This worked for me (macOS Mojave 10.14.6), what did not work was fenics=2019. You can also try fenics=2017 but then I would suggest using

conda create -n fenics2017 -c conda-forge fenics=2017 scipy matplotlib=2.2.3 python=3.5 mpi4py sympy=1.1.1

Actually, I use:

conda create -n fenics2018 -c conda-forge fenics=2018 matplotlib scipy python=3.7 sympy spyder jupyter

and if you also want spyder and jupyter, then I had to reset spyder (the first time I opened spyder it crashed and said that I have to reset it. Then it worked). For jupyter I also had to install nb_conda:

conda install nb_conda

Hope this works for you.

edit: I also tried to launch Anaconda, changed the environment there and selected Spyder, this did not work for me. Uninstalled everything and installed miniconda

后面采取了 conda create -n fenics2018 -c conda-forge fenics=2018 matplotlib scipy python=3.7 sympy 这种重新建立了 fenics2018 的 virtual environment，安装完 fenics2018 后，调用 fenics2018 的 Python 解释器跑算例，可以运行了，但是总是 furture warning。

因为有 furture warning，所以最终还是想去掉这个 warning， 而从最开始提示的错误中可以看出可能与 mumps 有关，在 Anaconda 中的两个 virtual environment 中搜索 mumps 发现：
在 fenics2018 中有 mumps-mpi 和 mumps-include；
而 fenicsproject 中只有 mumps-mpi。

所以尝试在 fenicsproject 中安装 mumps-include(参考 https://anaconda.org/conda-forge/mumps-include): To install this package with conda run one of the following:

conda install -c conda-forge mumps-include
conda install -c conda-forge/label/gcc7 mumps-include
conda install -c conda-forge/label/cf201901 mumps-include

然后确实在 fenicsproject 安装上了 mumps-include，但是仍然不能运行算例，提示同样的错误。

解决方法

我在最开始提到了两次安装的 Anaconda 中 conda 的版本是不同的，其实在最新的 conda (4.7.10) 版本下安装 Fenics (conda create -n fenicsproject -c conda-forge fenics) 有个 warning:
Solving environment: failed with current_repodata.json, will retry with next repodata source.
后来参考 Solving environment: failed with current_repodata.json, will retry with next repodata source. 中将 conda 从 4.7 降级到 4.6 版本

conda config --set allow_conda_downgrades true
conda install conda=4.6.14

然后删掉了 Anaconda 中的 fenicsproject virtual environment 重新安装，conda create -n fenicsproject -c conda-forge fenics

最后可以用 fenicsproject 成功运行 Fenics 算例。

总结

可能是 conda 版本的问题，目前有的问题如下：

1. Solving environment: failed with current_repodata.json, will retry with next repodata source. UnsatisfiableError: #9004
2. Conda doesn´t work after update conda #8863