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 <johnanthonyregan@gmail.com> 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 <matthewturk@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@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@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@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@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
>> >
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