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<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">James followed up that once he installed libjpeg he got the same error message.<o:p></o:p></span></a></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Anyone have an idea for a less intrusive fix, or should we just wait until after phenix?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Markus Gerstel MBCS<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Postdoctoral Research Associate<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Tel: +44 1235 778698<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Diamond Light Source Ltd.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Diamond House<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Harwell Science & Innovation Campus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Didcot<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Oxfordshire<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">OX11 0DE<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Parkhurst, James (DLSLtd,RAL,LSCI)
<br>
<b>Sent:</b> 22 June 2016 10:37<br>
<b>To:</b> Gerstel, Markus (DLSLtd,RAL,LSCI)<br>
<b>Cc:</b> cctbxbb@phenix-online.org<br>
<b>Subject:</b> RE: error<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Hi Markus,<br>
<br>
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:<br>
<br>
fc-list: symbol lookup error: fc-list: undefined symbol: FcPatternFormat<br>
fc-list: symbol lookup error: fc-list: undefined symbol: FcPatternFormat<br>
Plotting image failed: Matplotlib backend_wx and backend_wxagg require wxPython >=2.8<br>
<br>
Presumably wxPython is distributed with DIALS, so do we need to have a newer version or something?<br>
<br>
Thanks,<br>
<br>
James<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> Gerstel, Markus (DLSLtd,RAL,LSCI)<br>
<b>Sent:</b> 22 June 2016 10:17<br>
<b>To:</b> Parkhurst, James (DLSLtd,RAL,LSCI)<br>
<b>Cc:</b> <a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br>
<b>Subject:</b> RE: error</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi James,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">CCing cctbxbb for further support</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I can reproduce at least similar errors with both DIALS 1.2.5 and current nightly builds.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I think this may be a matplotlib 1.3.1 problem.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">A minimal reproducer is:</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">$ dials.python</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">> import matplotlib.pyplot as plt</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">> plt.imshow([[1]])</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Gtk-Message…</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">> (press ctrl+D)</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Segmentation fault</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">When compiled on the same machine I do not get the Gtk-Messages, but I do get the segmentation fault.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Markus Gerstel MBCS</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Postdoctoral Research Associate</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Tel: +44 1235 778698</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Diamond Light Source Ltd.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Diamond House</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Harwell Science & Innovation Campus</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Didcot</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Oxfordshire</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">OX11 0DE</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> Parkhurst, James (DLSLtd,RAL,LSCI)
<br>
<b>Sent:</b> 21 June 2016 16:58<br>
<b>To:</b> Gerstel, Markus (DLSLtd,RAL,LSCI)<br>
<b>Subject:</b> FW: error</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Hi Markus,<br>
<br>
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.<br>
<br>
Thanks,<br>
<br>
James</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">[sse87232@ws188 cctbx_introduction_1]$ dials.python cctbx_introduction_1_test.py ximg2701_00001.cbf
<br>
<br>
(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<br>
<br>
(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<br>
<br>
(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<br>
<br>
(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<br>
<br>
(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<br>
<br>
(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<br>
<br>
(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<br>
Segmentation fault (core dumped)<br>
[sse87232@ws188 cctbx_introduction_1]$ which dials.python<br>
/dls/science/users/sse87232/dials/dials-v1-2-4/build/bin/dials.python</span><span style="color:black"><o:p></o:p></span></p>
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