[Matplotlib-users] Matplotlib 1.5.1 - Function pcolormesh throws Segmentation Fault

Discussion:

Claude Falbriard

2016-02-24 20:04:43 UTC

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: ***@br.ibm.com

Benjamin Root

2016-02-24 20:33:28 UTC

Permalink

Could you try using faulthandler and post the traceback please? That'll
help us isolate the problem better.

Ben Root

Post by Claude Falbriard
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*.
*http://polar.ncep.noaa.gov/waves/examples/usingpython.shtml*
<http://polar.ncep.noaa.gov/waves/examples/usingpython.shtml>*]*
The following line is causing a *Segmentation fault* error even when
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
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Benjamin Root

2016-02-24 20:34:35 UTC

Permalink

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

Post by Benjamin Root
Could you try using faulthandler and post the traceback please? That'll
help us isolate the problem better.
Ben Root

Claude Falbriard

2016-02-24 21:10:13 UTC

Permalink

Dear colleagues,

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: ***@br.ibm.com

From: Benjamin Root <***@gmail.com>
To: Claude Falbriard/Brazil/***@IBMBR
Cc: Matplotlib Users <matplotlib-***@lists.sourceforge.net>
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 <***@gmail.com>
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 <***@br.ibm.com>
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: ***@br.ibm.com