Hi Billy,
Thanks for looking into this. The error message I'm getting is copied below. However, I can verify that setting the GDK_PIXBUF_MODULE_FILE environment variable removed the PixBuf warnings. But I still get the segfault.
James
(cctbx_introduction_1.py:22529): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory
(cctbx_introduction_1.py:22529): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory
(cctbx_introduction_1.py:22529): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory
(cctbx_introduction_1.py:22529): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory
(cctbx_introduction_1.py:22529): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory
(cctbx_introduction_1.py:22529): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory
(cctbx_introduction_1.py:22529): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory
Segmentation fault (core dumped)
________________________________
From: Billy Poon [[email protected]]
Sent: 22 June 2016 18:00
To: cctbx mailing list
Cc: Parkhurst, James (DLSLtd,RAL,LSCI)
Subject: Re: [cctbxbb] error
Hi all,
I haven't found the place where the loaders.cache directory is hard-coded, but I'll keep looking. In the meantime, there is a workaround for the GTK message. You can export the GDK_PIXBUF_MODULE_FILE environment variable to point to <installation directory>/base/lib. That will tell gdk-pixbuf where to look for the loaders.cache file.
https://developer.gnome.org/gdk-pixbuf/unstable//gdk-pixbuf-query-loaders.ht...
The loaders.cache file is updated during the installation. It's a text file, so if you look at it, the directories for the loaders should be updated with the installation directory. But for some reason, the directory for the loaders.cache file is hard-coded somewhere.
I was planning on updating the rest of the packages (numpy, matplotlib, PIL -> Pillow, etc.) after the Phenix release, so the segmentation fault issue should go away if a newer version matplotlib works.
Hi James,
What is the error message that you're getting?
--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org
On Wed, Jun 22, 2016 at 3:38 AM,
import matplotlib.pyplot as plt plt.imshow([[1]]) Gtk-Message… (press ctrl+D) Segmentation fault
When compiled on the same machine I do not get the Gtk-Messages, but I do get the segmentation fault. Markus Gerstel MBCS Postdoctoral Research Associate Tel: +44 1235 778698tel:%2B44%201235%20778698 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE From: Parkhurst, James (DLSLtd,RAL,LSCI) Sent: 21 June 2016 16:58 To: Gerstel, Markus (DLSLtd,RAL,LSCI) Subject: FW: error Hi Markus, I've been getting my summer student to do the cctbx_introduction tutorials in dials_scratch. He's using a version of dials downloaded from the website and when he runs the introduction script he gets errors about gdk-pixbuf giving paths to /scratch/jenkins_slave/workspace/. This seems like there is a jenkins path being set in the distributed installers. Would you have any idea how I can fix this? I'm downloading the linux installer of DIALS now so I can test this myself. Thanks, James ________________________________ [sse87232@ws188 cctbx_introduction_1]$ dials.python cctbx_introduction_1_test.py ximg2701_00001.cbf (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory Segmentation fault (core dumped) [sse87232@ws188 cctbx_introduction_1]$ which dials.python /dls/science/users/sse87232/dials/dials-v1-2-4/build/bin/dials.python -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb