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: [email protected] 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: [email protected]mailto:[email protected] 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@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

FWIW we also needed gdk-pixbuf in ccp4, because of coot. A few years ago I patched it to use $COOT_PREFIX to find loaders.cache: http://fg.oisin.rc-harwell.ac.uk/scm/loggerhead/devtools/trunk/view/head:/pa... I don't remember it well, but I think the second part of the patch is to make regeneration of the cache file not necessary. The only plugin that we have is for svg. Other formats can be included in the library, not as plugins. The configure command we use is: ./configure --prefix=$PREFIX \ --enable-shared --disable-static \ --disable-introspection --without-libtiff --disable-rpath \ --disable-glibtest --disable-nls --disable-gio-sniffing \ --with-included-loaders=png (some of this may not be necessary, the last line is to make png built-in rather than a plugin) Marcin On Wed, Jun 22, 2016 at 6:00 PM, Billy Poon wrote:

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, 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

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: [email protected] 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: [email protected] 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@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] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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, mailto:[email protected]> 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 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: 22 June 2016 10:37 To: Gerstel, Markus (DLSLtd,RAL,LSCI) Cc: [email protected]mailto:[email protected] 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: [email protected]mailto:[email protected] 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 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