Re: [cctbxbb] error

22 Jun 2016

      Hi all,

I just checked in an update that should fix the gdk-pixbuf issue. I enabled
a flag called --enable-relocations in the configure step. I've created a
new installer on our CentOS 6 machine and a new installation does not
generate the error message. I'm running builds on the other Linux
distributions, but I don't expect any issues from this flag.

Let me know if the updated packages are causing any other issues. Thanks!

--
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 10:42 AM, Marcin Wojdyr  wrote:
...
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
...
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
file,
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
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