Analysis stage of "mdpow-pow benzene" failing

[Ntr9999]

Final stage of the benzene tutorial outputs errors (after output of values and files). Originally mentioned here: #126

To fully reproduce:
conda create -c conda-forge -n mdpow python=2.7 numpy scipy 'matplotlib<3.3' 'mdanalysis<2' 'mdanalysistests<2' pyyaml
conda activate mdpow
pip install gromacswrapper
git clone https://github.com/Becksteinlab/MDPOW.git
pip install ./MDPOW

I copied the benzene.itp,pdb&yml files into a desktop/benzene/benzene and then:

cd desktop/benzene
conda activate mdpow
source /usr/local/opt/gromacs/bin/GMXRC
mdpow-equilibrium --solvent water benzene/benzene.yml
mdpow-equilibrium --solvent octanol benzene/benzene.yml
mdpow-fep --solvent water benzene/benzene.yml
mdpow-fep --solvent octanol benzene/benzene.yml
mdpow-pow benzene

Note: I set maxthreads =1 for mdpow-fep --solvent octanol benzene/benzene.yml, I don't believe this is relevant though.

All steps are fine until the final step mdpow-pow benzene, where files are outputted correctly I believe (apart from only 1 graph on DeltaA.png maybe?) but there is some errors shown relating to matplotlib.

The output (from when it starts failing):

mdpow.fep   : INFO     [BNZ] Octanol solvation free energy (Gibbs) -20.0205 (2.40) kJ/mol
mdpow.fep   : INFO     [BNZ] Octanol solvation free energy (coulomb) 1.52674 (0.27) kJ/mol
mdpow.fep   : INFO     [BNZ] Octanol solvation free energy (vdw) 18.4938 (2.38) kJ/mol
mdpow.fep   : INFO     [BNZ] Values at T = 300 K
mdpow.fep   : INFO     [BNZ] Free energy of transfer water --> octanol: -12.260 (3.707) kJ/mol
mdpow.fep   : INFO     [BNZ] log P_ow: 2.135 (0.645)
mdpow       : INFO     Wrote results to '/Users/mark/Desktop/benzene/pow.txt'
mdpow       : INFO     Wrote solvation energy terms to '/Users/mark/Desktop/benzene/energies.txt'
/Users/mark/opt/anaconda3/envs/mdpow/bin/mdpow-pow:131: UserWarning: 
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

The backend was *originally* set to 'MacOSX' by the following code:
  File "/Users/mark/opt/anaconda3/envs/mdpow/bin/mdpow-pow", line 39, in <module>
    import mdpow.fep
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/mdpow/fep.py", line 137, in <module>
    import gromacs, gromacs.utilities
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/__init__.py", line 183, in <module>
    from . import fileformats
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/fileformats/__init__.py", line 10, in <module>
    from .xvg import XVG
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/fileformats/xvg.py", line 203, in <module>
    from matplotlib import pyplot as plt
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/matplotlib/pyplot.py", line 71, in <module>
    from matplotlib.backends import pylab_setup
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/matplotlib/backends/__init__.py", line 17, in <module>
    line for line in traceback.format_stack()


  matplotlib.use('agg')  # quick non-interactive plotting
mdpow       : CRITICAL Running analysis in directory 'benzene' failed
mdpow       : ERROR    Catastrophic problem occurred, see the stack trace for hints.
Traceback (most recent call last):
  File "/Users/mark/opt/anaconda3/envs/mdpow/bin/mdpow-pow", line 233, in <module>
    force=opts.force, stride=opts.stride, permissive=opts.permissive)
  File "/Users/mark/opt/anaconda3/envs/mdpow/bin/mdpow-pow", line 136, in run_pow
    activate_subplot(1)
  File "/Users/mark/opt/anaconda3/envs/mdpow/bin/mdpow-pow", line 163, in activate_subplot
    return axes(gcf().get_axes()[numPlot])
IndexError: list index out of range
Traceback (most recent call last):
  File "/Users/mark/opt/anaconda3/envs/mdpow/bin/mdpow-pow", line 233, in <module>
    force=opts.force, stride=opts.stride, permissive=opts.permissive)
  File "/Users/mark/opt/anaconda3/envs/mdpow/bin/mdpow-pow", line 136, in run_pow
    activate_subplot(1)
  File "/Users/mark/opt/anaconda3/envs/mdpow/bin/mdpow-pow", line 163, in activate_subplot
    return axes(gcf().get_axes()[numPlot])
IndexError: list index out of range

mdpow.log

Many thanks.

[orbeckst]

The matplotlib backend thing should not be a problem.

I am not sure what failed in the plots. It looks as if one plot is missing (maybe no data??). Sorry, I know, not very helpful.

[orbeckst]

@VOD555 are you able to reproduce the error above?

[VOD555]

@orbeckst I met another error about the plot function. I'm running the tutorial to see whether we can reproduce thiserror.

[VOD555]

I'm doubting whether it's caused by pylab, I'm trying to rewrite the plot functions without pylab.

[VOD555]

This first error was caused by the use of matplotlib in gromacswrapper.
We should import matplotlib before importing gromacswrapper and fixed this.

[VOD555]

The second error is due to plt.close() at line 1189 in fep.py. As the plot window is closed, we can't activate it again with gcf().get_axes() which generates a empty list.