[cctbxbb] error

Wed Jun 22 03:38:17 PDT 2016

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

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
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

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

-- 
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20160622/66e4cb5e/attachment.htm>