[yt-users] Fwd: YT fails at start
John Regan
johnanthonyregan at gmail.com
Tue Jun 4 09:27:29 PDT 2013
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 at 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
"/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
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 <matthewturk at gmail.com> 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 at 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 at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
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