[yt-users] Fwd: YT fails at start

John Regan johnanthonyregan at gmail.com
Tue Jun 4 09:41:11 PDT 2013


Hi Matt,

(yt-x86_64)jr347 at 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 at universe:~/2013/Stats/Halo1/DMonly/Enzo_Analysis/YT>
(yt-x86_64)jr347 at 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 at universe:~/2013/Stats/Halo1/DMonly/Enzo_Analysis/YT>


Anything there look out of place?

John



On 4 June 2013 17:32, Matthew Turk <matthewturk at gmail.com> 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 <johnanthonyregan at gmail.com>
> 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 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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> >
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