[cctbxbb] error

Thu Jun 23 01:58:04 PDT 2016

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 [bkpoon at lbl.gov]
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.html

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, <markus.gerstel at diamond.ac.uk<mailto:markus.gerstel at diamond.ac.uk>> wrote:
James followed up that once he installed libjpeg he got the same error message.

I ran one build with the current stable version of matplotlib 1.5.1, and that did not segfault. However I’m not going to change that dependency at this time with the phenix release looming.
Anyone have an idea for a less intrusive fix, or should we just wait until after phenix?

Markus Gerstel MBCS
Postdoctoral Research Associate
Tel: +44 1235 778698<tel:%2B44%201235%20778698>

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

From: Parkhurst, James (DLSLtd,RAL,LSCI)
Sent: 22 June 2016 10:37
To: Gerstel, Markus (DLSLtd,RAL,LSCI)

Cc: cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>
Subject: RE: error

Hi Markus,

I tried this on my machine and I think I needed to install numpy - it was picking up the system numpy. However, I then get the following message:

fc-list: symbol lookup error: fc-list: undefined symbol: FcPatternFormat
fc-list: symbol lookup error: fc-list: undefined symbol: FcPatternFormat
Plotting image failed: Matplotlib backend_wx and backend_wxagg require wxPython >=2.8

Presumably wxPython is distributed with DIALS, so do we need to have a newer version or something?

Thanks,

James
________________________________
From: Gerstel, Markus (DLSLtd,RAL,LSCI)
Sent: 22 June 2016 10:17
To: Parkhurst, James (DLSLtd,RAL,LSCI)
Cc: cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>
Subject: RE: error
Hi James,
CCing cctbxbb for further support

I can reproduce at least similar errors with both DIALS 1.2.5 and current nightly builds.
I think this may be a matplotlib 1.3.1 problem.
A minimal reproducer is:

$ dials.python
> 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 778698<tel:%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 at 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 at ws188 cctbx_introduction_1]$ which dials.python
/dls/science/users/sse87232/dials/dials-v1-2-4/build/bin/dials.python

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