[Matplotlib-users] Fw: Matplotlib 1.5.1 - Function pcolormesh throws Segmentation Fault / faulthandler traceback info / Error at Agg

[Claude F. <cl...@br...>]

Dear colleagues, 

Complementing this topic: 

. The segmentation fault error relates to the use of the "Agg" graphical 
back-end which crashes with larger plots when using the command pyplot 
savefig.
  Case I switch to the .use("Cairo") package, the processing completes OK 
although the image is not matching the color scheme.
  This machine, a z13, does not have an interactive X display, its a cpu 
in a cloud, a back-end machine with web access. 

My question 1: 
Is it possible to recompile the failing "Agg" framework from its source in 
"c" and make it compatible with the hardware. Any hints how to run the 
make 
build and install and add it to the Matplotlib pyplot services? 

My question 2: 
Is there an alternate back-end solution available for .png or .tif, 
preferably in a Python space, that is accepted by the matplotlib pyplot 
tool as 
a valid choice and does not require a display configuration? Worst case, 
is there a bypass solution available? 

Thanks advance for your guidance. 

Regards, 
Claude 

History: 
----------

Thanks for the quick feedback. 

I've installed the "faulthandler" package, added it to the import and 
enabled it with faulthandler.enable(). 
Below the console trace of the test using the pcolormesh function and the 
traceback information: 

python test3.py

Fatal Python error: Segmentation fault

Current thread 0x000003ffa45f7710 (most recent call first):
  File "/usr/lib64/python2.7/site-packages/matplotlib/collections.py", 
line 1877 in draw
  File "/usr/lib64/python2.7/site-packages/matplotlib/artist.py", line 61 
in draw_wrapper
  File "/usr/lib64/python2.7/site-packages/matplotlib/axes/_base.py", line 
2324 in draw
  File "/usr/lib64/python2.7/site-packages/matplotlib/artist.py", line 61 
in draw_wrapper
  File "/usr/lib64/python2.7/site-packages/matplotlib/figure.py", line 
1159 in draw
  File "/usr/lib64/python2.7/site-packages/matplotlib/artist.py", line 61 
in draw_wrapper
  File 
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py", 
line 474 in draw
  File 
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py", 
line 527 in print_png
  File "/usr/lib64/python2.7/site-packages/matplotlib/backend_bases.py", 
line 2232 in print_figure
  File "/usr/lib64/python2.7/site-packages/matplotlib/figure.py", line 
1565 in savefig
  File "/usr/lib64/python2.7/site-packages/matplotlib/pyplot.py", line 688 
in savefig
  File "test3.py", line 47 in <module>
Segmentation fault

Hope this information helps to circle the issue. 


Regards,

Claude Falbriard
Certified IT Specialist L2 - Middleware


Phone: 55-13-99662-5703 | Mobile: 55-13-98117-3316
E-mail: cl...@br...




From:   Benjamin Root <ben...@gm...>
To:     Claude Falbriard/Brazil/IBM@IBMBR
Cc:     Matplotlib Users <mat...@li...>
Date:   24/02/2016 17:35
Subject:        Re: [Matplotlib-users] Matplotlib 1.5.1 - Function 
pcolormesh throws Segmentation Fault



Sorry, forgot to post the link: https://pypi.python.org/pypi/faulthandler/

On Wed, Feb 24, 2016 at 3:33 PM, Benjamin Root <ben...@gm...> 
wrote:
Could you try using faulthandler and post the traceback please? That'll 
help us isolate the problem better.

Ben Root

On Wed, Feb 24, 2016 at 3:04 PM, Claude Falbriard <cl...@br...> 
wrote:
Dear colleagues,

 I've done a build from source of latest Matplotlib package and deployed 
it at our IBM z13 machine (s390x). It uses the current release 1.5.1. 
During the unit tests I found an issue with a test case from NOAA which 
uses a pcolormesh draw function with basemap. 

Example 2: Plot data from an NWW3 GRiB2 file - [ here:  
http://polar.ncep.noaa.gov/waves/examples/usingpython.shtml]  

The following line is causing a Segmentation fault error even when adding 
an 8GB swap memory to the process: 

cs = m.pcolormesh(x,y,data,shading='flat',cmap=plt.cm.jet)

I also tryed to execute other, similar samples that use pcolormesh, but 
receiving the same error. Is this a known issue or might it be be related 
to the memory environment ? Any hints how to debug this error? 

Regards,

Claude Falbriard
Certified IT Specialist L2 - Middleware


Phone:55-13-99662-5703 | Mobile:55-13-98117-3316
E-mail: cl...@br...



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