Hi Nathan, I contacted the system admin about the dynamic linking issue. He suggested using the LD_PRELOAD env variable to override other linking variable and that worked. $ ldd /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so linux-vdso.so.1 => (0x00002aaaaaaab000) /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib64/libpng16.so.16 (0x00002aaaaacda000) libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00002aaaaaf6e000) libz.so.1 => /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/libz.so.1 (0x00002aaaab196000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002aaaab3ad000) libm.so.6 => /lib64/libm.so.6 (0x00002aaaab6b8000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002aaaab931000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aaaabb47000) libc.so.6 => /lib64/libc.so.6 (0x00002aaaabd65000) /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) $ pyyt Python 2.7.4 (default, Jun 4 2013, 11:02:31) [GCC 4.3.4 [gcc-4_3-branch revision 152973]] on linux2 Type "help", "copyright", "credits" or "license" for more information.
from yt.mods import *
So everything is now working nicely. I'm not sure if this is a YT issue or
a SUSE issue or maybe even something to do with the configuration of the
machine I am working on.
Likely YT's interaction with SUSE I suppose.
Cheers,
John
On 5 June 2013 08:41, John Regan
Hi Nathan,
Thanks for looking into this! OK so I reset the LD_LIBRARY_PATH env variable back to the default for my system. However, ldd then shows that libpng16.so.16 is not found.
jr347@universe:~/2013/YT> echo $LD_LIBRARY_PATH
/opt/intel/composer_xe_2013.2.146/tbb/lib/intel64:/opt/intel/composer_xe_2013.2.146/mkl/lib/intel64:/opt/intel/composer_xe_2013.2.146/ipp/lib/intel64:/opt/intel/composer_xe_2013.2.146/debugger/lib/intel64:/opt/intel/composer_xe_2013.2.146/debugger/gui/intel64:/opt/intel/composer_xe_2013.2.146/compiler/lib/intel64:/opt/intel/mic/myo/lib:/opt/intel/mic/coi/host-linux-release/lib:/home/cosmos/share/x86_64/pp8/lib:/opt/sgi/mpt/mpt-2.07/lib jr347@universe:~/2013/YT> ldd /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so linux-vdso.so.1 => (0x00007fffbfffe000) libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00007fffbfb57000) libz.so.1 => /lib64/libz.so.1 (0x00007fffbf940000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fffbf636000) libm.so.6 => /lib64/libm.so.6 (0x00007fffbf3bd000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fffbf1a6000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fffbef89000) libc.so.6 => /lib64/libc.so.6 (0x00007fffbec12000) /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) jr347@universe:~/2013/YT> ldd /home/cosmos/users/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/lib/png_writer.so linux-vdso.so.1 => (0x00007fffbfffe000) libm.so.6 => /lib64/libm.so.6 (0x00007fffbfb21000) libpng16.so.16 => not found libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fffbf903000) libc.so.6 => /lib64/libc.so.6 (0x00007fffbf58c000) /lib64/ld-linux-x86-64.so.2 (0x0000555555554000)
Rerunning the install script and sourcing the activation script updates LD_LIBRARY_PATH with the yt library path but this doesn't contain the libpng16.so.16 library so ldd still shows a problem. Running yt help gives an import error on libpng.so
(yt-x86_64)jr347@universe:~/2013/YT> yt help
Traceback (most recent call last): File "/home/cosmos/users/jr347/2013/YT/yt-x86_64/bin/yt", line 9, in <module> load_entry_point('yt==2.5.3', 'console_scripts', 'yt')() File "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py", line 337, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py", line 2311, in load_entry_point return ep.load() File "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py", line 2017, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 29, in <module> from yt.mods import * File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/mods.py", line 60, in <module>
from yt.data_objects.api import \ File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/api.py", line 31, in <module> from grid_patch import \ File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 35, in <module> from yt.data_objects.data_containers import YTFieldData File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 45, in <module> from yt.data_objects.derived_quantities import GridChildMaskWrapper File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 36, in <module> from yt.utilities.parallel_tools.parallel_analysis_interface import \ File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 39, in <module> from yt.utilities.lib import \ File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/lib/__init__.py", line 35, in <module> from .png_writer import * ImportError: libpng16.so.16: cannot open shared object file: No such file or directory
Cheers, John
On 4 June 2013 18:32, Nathan Goldbaum
wrote: Hi John,
So the issue is that matplotlib's png extension _png.so, is dynamically linking against /usr/lib65/libpng12.so.0. yt builds its own libpng, which lives in /yt-x86_64/lib64/libpng16.so.16. When things are working correctly, ldd should show that _png.so is pointing at yt's libpng.
You mentioned that you added libpng to your LD_LIBRARY_PATH in your first e-mail. First, I'd like you to delete that entry. After resetting LD_LIBRARY_PATH, ldd should show that _png.so is loading yt's libpng. Next, to make sure that everything is configured correctly, I'd like you to remove the 'done' file that lives in the matplotlib source directory in yt-x86_64/src/matplotlib-1.2.1, then rerun the install script. Do not rerun the install script in the yt environment (i.e. you should not see (yt-x86_64) in your prompt).
Please let us know if you run into any issues once you've done that. Also please feel free to stop by on our IRC channel (webchat is here: http://yt-project.org/irc.html) so we can help you out in real time.
Cheers,
Nathan
On Tue, Jun 4, 2013 at 9:41 AM, John Regan
wrote: Hi Matt,
(yt-x86_64)jr347@universe:~/2013/Stats/Halo1/DMonly/Enzo_Analysis/YT> ldd /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so linux-vdso.so.1 => (0x00007fffbfffe000) libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00007fffbfb56000) libz.so.1 => /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/libz.so.1 (0x00007fffbf93f000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fffbf635000) libm.so.6 => /lib64/libm.so.6 (0x00007fffbf3bb000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fffbf1a5000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fffbef88000) libc.so.6 => /lib64/libc.so.6 (0x00007fffbec10000) /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) (yt-x86_64)jr347@universe:~/2013/Stats/Halo1/DMonly/Enzo_Analysis/YT> (yt-x86_64)jr347@universe:~/2013/Stats/Halo1/DMonly/Enzo_Analysis/YT> ldd /home/cosmos/users/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/lib/png_writer.so linux-vdso.so.1 => (0x00007fffbfffe000) libm.so.6 => /lib64/libm.so.6 (0x00007fffbfb20000) libpng16.so.16 => /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib64/libpng16.so.16 (0x00007fffbf8de000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fffbf6c1000) libc.so.6 => /lib64/libc.so.6 (0x00007fffbf349000) libz.so.1 => /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/libz.so.1 (0x00007fffbf132000) /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) (yt-x86_64)jr347@universe:~/2013/Stats/Halo1/DMonly/Enzo_Analysis/YT>
Anything there look out of place?
John
On 4 June 2013 17:32, Matthew Turk
wrote: Hi John,
Ah, thanks. So png_set_longjmp_fn is something that we disable inside libpng when we build it, through the flag PNG_SETJMP_NOT_SUPPORTED (line 193 or so of yt/utilities/lib/setup.py) which leads me to believe that something is amiss with how _png.so is compiled. What's the output of:
ldd /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so ldd /home/cosmos/users/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/lib/png_writer.so
-Matt
On Tue, Jun 4, 2013 at 12:27 PM, John Regan
wrote: Hi Matt,
Yes first thing I did was source the activation script (prefix yt env shown below). yt help throws up similar errors:
(yt-x86_64)jr347@universe:~/2013/Stats/Halo1/DMonly/Enzo_Analysis/YT> yt help
Traceback (most recent call last): File "/home/cosmos/users/jr347/2013/YT/yt-x86_64/bin/yt", line 9, in <module> load_entry_point('yt==2.5.3', 'console_scripts', 'yt')() File
"/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py",
line 337, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File
"/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py",
line 2311, in load_entry_point return ep.load() File
"/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py",
line 2017, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File
line 29, in <module> from yt.mods import *
File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/mods.py",
"/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line
129, in <module> from yt.visualization.api import \ File
"/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/visualization/api.py",
line 34, in <module> from plot_collection import \ File
"/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py",
line 26, in <module> from matplotlib import figure File
"/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/figure.py",
line 32, in <module> from matplotlib.image import FigureImage File
"/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/image.py",
line 22, in <module> import matplotlib._png as _png ImportError:
/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so:
undefined symbol: png_set_longjmp_fn
Cheers, John
On 4 June 2013 17:19, Matthew Turk
wrote: Hi John,
Sorry to hear you're having trouble! When you first tried running, did you source the environment file that yt creates? I believe for your environment it would be something like this:
source /home/cosmos/users/jr347/2013/YT/yt-x86_64/bin/activate
which would set the various environment variables and so on. Then
you
can try doing something simple like "yt help" to see if it will import correctly.
Thanks,
-Matt
On Tue, Jun 4, 2013 at 12:10 PM, John Regan < johnanthonyregan@gmail.com> wrote: > Hi, > > I just installed YT and it's failing at the very start. > > Python 2.7.4 (default, Jun 4 2013, 11:02:31) > [GCC 4.3.4 [gcc-4_3-branch revision 152973]] on linux2 > Type "help", "copyright", "credits" or "license" for more information. >>>> from yt.mods import * > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/mods.py", line > 60, > in <module> > from yt.data_objects.api import \ > File > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/api.py", > line 31, in <module> > from grid_patch import \ > File > > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", > line 35, in <module> > from yt.data_objects.data_containers import YTFieldData > File > > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", > line 45, in <module> > from yt.data_objects.derived_quantities import GridChildMaskWrapper > File > > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", > line 36, in <module> > from yt.utilities.parallel_tools.parallel_analysis_interface import > \ > File > > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", > line 39, in <module> > from yt.utilities.lib import \ > File > > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/lib/__init__.py", > line 35, in <module> > from .png_writer import * > ImportError: libpng16.so.16: cannot open shared object file: No such > file or > directory >>>> > > Adding the path to the libpng16.so.16 library gets me to here (it also > seems > strange that the .so file was not already in the LD_LIBRARY_PATH - is > there > a hint in there somewhere?): > > Python 2.7.4 (default, Jun 4 2013, 11:02:31) > [GCC 4.3.4 [gcc-4_3-branch revision 152973]] on linux2 > Type "help", "copyright", "credits" or "license" for more information. >>>> from yt.mods import * > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/mods.py", line > 129, in <module> > from yt.visualization.api import \ > File > > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/visualization/api.py", > line 34, in <module> > from plot_collection import \ > File > > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", > line 26, in <module> > from matplotlib import figure > File > > "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/figure.py", > line 32, in <module> > from matplotlib.image import FigureImage > File > > "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/image.py", > line 22, in <module> > import matplotlib._png as _png > ImportError: > > /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so: > undefined symbol: png_set_longjmp_fn > > > Anybody come across this kind of error before. > The code is built on a shared memory machine, using gcc. icc is actually > the > default compiler but the YT script seems to pick up gcc by default and > it > builds (it doesn't build at all with icc). > > Install script attached in case it's helpful. > > Let me know if you need anymore info. Thanks in advance! > > John > > > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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