matplotlib warning - how to change figure.max_open_warning setting?

[Andrew Krohn]

Hi Everyone,

I wrote myself a little script to help expedite some otu table processing (https://github.com/alk224/Cdiv_2d_and_stats).  Maybe it helps people, maybe not.  What it does is take input from the user and run:

1) core diversity (parallel)

2) anosim and permanova stats (parallel)

3) make 2d plots (parallel)

The output is great.  However, during the process of making 2D plots, it throws a bunch of errors (I assume dependent on # fields in mapping file) from matplotlib.  Not errors, per se, but warnings about opening so many figures.  There is a setting that can be changed to silence this obnoxious output.  I tried changing it in the script with the following line:

python -c "import matplotlib; matplotlib.rcParams['figure.max_open_warning'] = 0"

But that doesn't seem to do anything.  Can anyone who speaks better python help out with this?

[Daniel McDonald]

Hi Andrew,

Thanks for that! 

Can you send on an example of the errors/warnings your getting?

Best,

Daniel

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[Andrew Krohn]

/usr/local/lib/python2.7/dist-packages/matplotlib/pyplot.py:412: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_num_figures`).

  max_open_warning, RuntimeWarning)

[Daniel McDonald]

The make_2d_plots.py script likely isn't being as aggressive as it should with closing figures, but I don't expect anything negative to result.

Best,

Daniel

On Sun Dec 14 2014 at 5:00:34 PM Andrew Krohn <andrew...@gmail.com> wrote:

/usr/local/lib/python2.7/dist-packages/matplotlib/pyplot.py:412: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_num_figures`).

  max_open_warning, RuntimeWarning)

[Andrew Krohn]

I had a problem with the organization of the anosim and permanova output.  I updated the git repository and these stats are now run on a single core.  Might help people who try this on a virtual machine.

[Andrew Krohn]

Yea, it doesn't hurt anything, but it makes the output full of garbage.  Can anyone see why my python command isn't doing what I think it should?  

[Daniel McDonald]

That command would need to be executed within make_2d_plots.py as the state is not persistent across processes.

Best,

Daniel

[Andrew Krohn]

OK.  I was hoping for an answer that would set this globally.  I even tried modifying the rcparam file manually and rebooted and nothing persists.  Help, matplotlib is annoying and I can't do anything about it!!

[Daniel McDonald]

matplotlib can be challenging to work with at times. You can always redirect stderr if that helps

-Daniel

[Jorge Cañardo Alastuey]

Hi Andrew,

Do the matplotlib instructions to set a global rc parameters file work for you?

Best,
Jorge

[Andrew Krohn]

Hi Jorge,

I have set that and rebooted and verified that it was still changed after a reboot.  I set it zero first as that is supposed to disable the warning, then to 10000 thinking that would be far more than the number of plots I every open and still the same behavior.  I checked via the python command line that I am modifying the correct file.  I posted a question to stackoverflow tagged with matplotlib in the hopes that a matplotlib person might be able to help.