Python numpy/scipy version incompatibilities when installing DOLFIN v. 2019.1.0

[moravveji]

Hi,

I tried to install DOLFIN/2019.1.0.post1-foss-2018a-Python-3.6.4, by adapting from the similar module from 2018.1.0. However, the build fails with the following message

== 2019-12-20 14:36:20,765 run.py:173 DEBUG run_cmd: running cmd pip install --prefix /myApps/software/DOLFIN/2019.1.0.post1-foss-2018a-Python-3.6.4 . (in myShm/DOLFIN/2019.1.0.post1/foss-2018a-Python-3.6.4/dolfin-2019.1.0.post0/python)
== 2019-12-20 14:36:20,765 run.py:192 INFO running cmd: pip install --prefix /myApps/software/DOLFIN/2019.1.0.post1-foss-2018a-Python-3.6.4 .
== 2019-12-20 14:36:25,181 build_log.py:163 ERROR EasyBuild crashed with an error (at ?:124 in __init__): cmd "pip install --prefix /myApps/software/DOLFIN/2019.1.0.post1-foss-2018a-Python-3.6.4 ." exited with exit code 1 and output:
Processing myShm/DOLFIN/2019.1.0.post1/foss-2018a-Python-3.6.4/dolfin-2019.1.0.post0/python
Requirement already satisfied: numpy in /myApps/software/Python/3.6.4-foss-2018a/lib/python3.6/site-packages/numpy-1.14.0-py3.6-linux-x86_64.egg (from fenics-dolfin==2019.1.0) (1.14.0)
Collecting pkgconfig (from fenics-dolfin==2019.1.0)
  Using cached https://files.pythonhosted.org/packages/b4/2c/bf434cb5a6590417e1d4468050ec317ea17fd6231c2a256df4646c11e588/pkgconfig-1.5.1-py2.py3-none-any.whl
Collecting pybind11==2.2.4 (from fenics-dolfin==2019.1.0)
  Using cached https://files.pythonhosted.org/packages/f2/7c/e71995e59e108799800cb0fce6c4b4927914d7eada0723dd20bae3b51786/pybind11-2.2.4-py2.py3-none-any.whl
Collecting fenics-ffc<2019.2,>=2019.1.0 (from fenics-dolfin==2019.1.0)
  Using cached https://files.pythonhosted.org/packages/74/b6/0c3743a5b9fecaf3b7fe7b0c6526e7c635bd1bb6f9bc4a177bababc79131/fenics_ffc-2019.1.0.post0-py3-none-any.whl
Collecting fenics-ufl<2019.2,>=2019.1.0 (from fenics-dolfin==2019.1.0)
  Using cached https://files.pythonhosted.org/packages/59/cd/e102c234b8be3bcff5395c555182caf2d1662e24e0417b0005e5f05ec33c/fenics_ufl-2019.1.0-py3-none-any.whl
Collecting fenics-dijitso<2019.2,>=2019.1.0 (from fenics-dolfin==2019.1.0)
  Using cached https://files.pythonhosted.org/packages/f2/62/c061cb9f8f5547915804cdf8046fe2989c5b7317445fb1246ac77a9bad7f/fenics_dijitso-2019.1.0-py3-none-any.whl
Collecting fenics-fiat<2019.2,>=2019.1.0 (from fenics-ffc<2019.2,>=2019.1.0->fenics-dolfin==2019.1.0)
  Using cached https://files.pythonhosted.org/packages/05/54/e463570ef224ca199c2baf0b77f10b8de44ce9b40374c0fc229d108e6c26/fenics_fiat-2019.1.0-py3-none-any.whl
Requirement already satisfied: sympy in /myApps/software/FIAT/2018.1.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages (from fenics-fiat<2019.2,>=2019.1.0->fenics-ffc<2019.2,>=2019.1.0->fenics-dolfin==2019.1.0) (1.2)
Requirement already satisfied: mpmath>=0.19 in /myApps/software/Python/3.6.4-foss-2018a/lib/python3.6/site-packages (from sympy->fenics-fiat<2019.2,>=2019.1.0->fenics-ffc<2019.2,>=2019.1.0->fenics-dolfin==2019.1.0) (1.0.0)
Installing collected packages: pkgconfig, pybind11, fenics-ufl, fenics-fiat, fenics-dijitso, fenics-ffc, fenics-dolfin
  Found existing installation: fenics-ufl 2018.1.0
    Uninstalling fenics-ufl-2018.1.0:
ERROR: Could not install packages due to an EnvironmentError: [Errno 13] Permission denied: 'ufl-analyse'
Consider using the `--user` option or check the permissions.

WARNING: You are using pip version 19.1.1, however version 19.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
 (at easybuild/tools/run.py:501 in parse_cmd_output)
== 2019-12-20 14:36:25,182 easyblock.py:3050 WARNING build failed (first 300 chars): cmd "pip install --prefix /myApps/software/DOLFIN/2019.1.0.post1-foss-2018a-Python-3.6.4 ." exited with exit code 1 and output:
Processing myShm/DOLFIN/2019.1.0.post1/foss-2018a-Python-3.6.4/dolfin-2019.1.0.post0/python
Requirement already satisfied: numpy in /vsc-hard
== 2019-12-20 14:36:25,192 easyblock.py:294 INFO Closing log for application name DOLFIN version 2019.1.0.post1

Indeed, I checked the permissions on the installation folder, and all was OK, and a lot of files already existed in the lib, bin folders etc. The same with the Python dependency folder.

So, I wonder how I can fix this issue.

Kind regards
Ehsan
dolfin.logs.tar.gz

[boegel]

@moravveji Is fenics-ufl also installed system-wide, or with pip install --user?

It looks like pip is trying to uninstall another version of fenics-ufl...

[moravveji]

In fact, the two following modules are installed systemwide, which are also dependencies of the DOLFIN:
FIAT/2018.1.0-foss-2018a-Python-3.6.4 and UFL/2018.1.0-foss-2018a-Python-3.6.4.

Normally, we have a g+w permissions on apps folders; would that mean that one application might modify another application installed by another colleague? If so, we have to restrict the permissions.

[boegel]

The culprit seems to be that DOLFIN requires fenics-ufl<2019.2,>=2019.1.0, which is not met by the UFL 2018.1.0` module you're using as dependency.

So, pip install tries to get rid of fenics-ufl 2018.1.0 before install a matching fenics-ufl version itself, which is where it's blowing up...

[boegel]

@moravveji Based on https://bugs.python.org/issue31710, the issue could be that pkg-config is missing on your system, can you check that, and see if adding pkg-config as a build dependency in your Tkinter easyconfig fixes the problem you're seeing?

[moravveji]

Nice idea Kenneth.
However, adding pkg-config/0.29.2-GCCcore-6.4.0 as a build dependency still does not resolve the issue, and gives the same error message. I have attached the new debug logs.
Tkinter-logs.tar.gz

[boegel]

The last two comments actually belong in #9517, they're not relevant for the DOLFIN problems being discussed here, so I copied them there...