Re: [Matplotlib-users] Matplotlib & Basemap / What is the Best Graphical Back-end for Raster Data Display (.png) ?
Dear colleagues, Yes, I've downloaded the latest stable image of Matplotlib source from the pypi repository matplotlib-1.5.1.tar.gz, running the commands: sudo python setup.py build and sudo python setup.py install. When executing larger plots, the Agg crashes with a segmentation fault message. My guess is that the c header files are not compiled with the correct platform setting (s390x). Is there a way to rebuild the c prerequisites used by the embedded Agg framework? Thanks in advance for your advice. Regards, Claude Falbriard Certified IT Specialist L2 - Middleware Phone: 55-13-99662-5703 | Mobile: 55-13-98117-3316 E-mail: clau...@br.ibm.com From: Benjamin Root <ben.v.r...@gmail.com> To: Claude Falbriard/Brazil/IBM@IBMBR Cc: Matplotlib Users <matplotlib-users@lists.sourceforge.net> Date: 03/03/2016 11:44 Subject:Re: [Matplotlib-users] Matplotlib & Basemap / What is the Best Graphical Back-end for Raster Data Display (.png) ? Matplotlib will not work at all without AGG. Even the AGG-less backends still use AGG for image handling (imshow() and such). We can not guarantee that matplotlib would work with agg 2.5, as that is the GPL'ed version. We develop against a patched 2.4 branch of AGG (which is BSD-licensed), which is distributed with our source, and is built as part of our build process. Have you tried building matplotlib directly from our source without a system install of AGG? Cheers Ben Root On Thu, Mar 3, 2016 at 6:34 AM, Claude Falbriard <clau...@br.ibm.com> wrote: Dear colleagues, I like to receive an advice about the best back-end choice for Matplotlib & Basemap to generate large .png images in a background processing mode. Having issues with the pre-compiled "Agg" package which does not work under my machine architecture. Also not able to recompile the Agg 2.5 package as its build throws an error at the build script autogen.sh. Error: ./configure: line 15546: syntax error near unexpected token `$SDL_VERSION,' ./configure: line 15546: `AM_PATH_SDL($SDL_VERSION,' When bypassing this line it runs into another dependency which is blocking the make install process. libtool: link: cannot find the library `../src/platform/X11/libaggplatformX11.la' or unhandled argument `../src/platform/X11/libaggplatformX11.la' Makefile:1166: recipe for target 'aa_demo' failed make[1]: *** [aa_demo] Error 1 make[1]: Leaving directory '/data/Downloads/agg/agg-2.5/examples' Makefile:481: recipe for target 'install-recursive' failed make: *** [install-recursive] Error 1 I do not plan to use any interactive access, so my guess is that excluding X11 libraries should work OK. My test showed that the "Cairo" package is working fine, but its quality (vector oriented) is not as good compared to the Agg raster display. Case the "Agg" is not able to install on my machine, is there an alternate graphical back-end available under SuSE environments? Regards, Claude Falbriard Certified IT Specialist L2 - Middleware Phone:55-13-99662-5703 | Mobile:55-13-98117-3316 E-mail: clau...@br.ibm.com -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Matplotlib & Basemap / What is the Best Graphical Back-end for Raster Data Display (.png) ?
Dear colleagues, I like to receive an advice about the best back-end choice for Matplotlib & Basemap to generate large .png images in a background processing mode. Having issues with the pre-compiled "Agg" package which does not work under my machine architecture. Also not able to recompile the Agg 2.5 package as its build throws an error at the build script autogen.sh. Error: ./configure: line 15546: syntax error near unexpected token `$SDL_VERSION,' ./configure: line 15546: `AM_PATH_SDL($SDL_VERSION,' When bypassing this line it runs into another dependency which is blocking the make install process. libtool: link: cannot find the library `../src/platform/X11/libaggplatformX11.la' or unhandled argument `../src/platform/X11/libaggplatformX11.la' Makefile:1166: recipe for target 'aa_demo' failed make[1]: *** [aa_demo] Error 1 make[1]: Leaving directory '/data/Downloads/agg/agg-2.5/examples' Makefile:481: recipe for target 'install-recursive' failed make: *** [install-recursive] Error 1 I do not plan to use any interactive access, so my guess is that excluding X11 libraries should work OK. My test showed that the "Cairo" package is working fine, but its quality (vector oriented) is not as good compared to the Agg raster display. Case the "Agg" is not able to install on my machine, is there an alternate graphical back-end available under SuSE environments? Regards, Claude Falbriard Certified IT Specialist L2 - Middleware Phone: 55-13-99662-5703 | Mobile: 55-13-98117-3316 E-mail: clau...@br.ibm.com -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Fw: Matplotlib 1.5.1 - Function pcolormesh throws Segmentation Fault / faulthandler traceback info / Error at Agg
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 0x03ffa45f7710 (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
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: clau...@br.ibm.com
From: Benjamin Root <ben.v.r...@gmail.com>
To: Claude Falbriard/Brazil/IBM@IBMBR
Cc: Matplotlib Users <matplotlib-users@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 <ben.v.r...@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 <clau...@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: clau...@br.ibm.com
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Re: [Matplotlib-users] Matplotlib 1.5.1 - Function pcolormesh throws Segmentation Fault / faulthandler traceback info
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 0x03ffa45f7710 (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 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: clau...@br.ibm.com From: Benjamin Root <ben.v.r...@gmail.com> To: Claude Falbriard/Brazil/IBM@IBMBR Cc: Matplotlib Users <matplotlib-users@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 <ben.v.r...@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 <clau...@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: clau...@br.ibm.com -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Matplotlib 1.5.1 - Function pcolormesh throws Segmentation Fault
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: clau...@br.ibm.com -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
