Running PDE error with 'TimeSeries'

Question

Hello , I have successfully installed and run fenics by the means of conda - forge. Docker however didn't work for me . I am using OS X El Captain. The problem I haven't solved so far is when I am running an example of reaction - diffusion PDE system.
https://fenicsproject.org/pub/tutorial/python/vol1/ft09_reaction_system.py

The error message:

NameError                                 Traceback (most recent call last)
<ipython-input-4-809c858e3c6f> in <module>()
     59 
     60 # Create time series for reading velocity data
---> 61 timeseries_w = TimeSeries('navier_stokes_cylinder/velocity_series')
     62 
     63 # Create VTK files for visualization output

NameError: name 'TimeSeries' is not defined

I could find one answer on stack overflow that it has to do with hdf5 for OS X systems. I am wondering if the solution was found for that.

I would also like to describe the problem I am striving to solve with fenics:
I have series of PDE describing reaction diffusion mechanism in the living cell. These are non-homogenous parabolic equations with a little bit complex function f. Before I wrote a script for matlab which worked fine with pdex4pde. However I would really like to move to python as it gives much more opportunities for system extension. My question is: can Fenics be suitable for that? Or maybe its too much for the simple problem I am trying to solve?

chris_richardson · Answer 1 · Apr 21, 2017

You are right that TimeSeries has been replaced with a HDF5 equivalent, TimeSeriesHDF5.
It should be possible to use on OSX, provided it is installed correctly, though I appreciate that can be tricky. If you don't need a velocity field, and only want to look at reaction-diffusion, then you can probably just remove it anyway.

You should be able to solve simple problems with FEniCS, maybe start with something very simple and work upwards. It is also worthwhile looking at the "demos" which are included with FEniCS, rather than the tutorial, as the demos are maintained up-to-date with the package.

answered Apr 21, 2017 by chris_richardson FEniCS Expert (31,740 points)

I just want to add that the reason why the FEniCS package in conda-forge is built without HDF5 is because the HDF5 package in conda-forge is built without parallel support. AFAIK, the next release of FEniCS will not require a parallel-enabled HDF5. Also, there will be a HDF5 package with parallel support in conda-forge in the not-so-distant future.

commented Apr 24, 2017 by johannr FEniCS Expert (17,350 points)

So how should we replace TimeSeries on a conda-forge installation ? Neither TimeSeries nor TimeSeriesHDF5 work on the Navier-Stockes tutorial 09 from the Github repo.

commented May 25, 2017 by aurelienpierre FEniCS Novice (100 points)

Running PDE error with 'TimeSeries'

1 Answer