[yt-users] Fwd: YT fails at start
Nathan Goldbaum
nathan12343 at gmail.com
Tue Jun 4 10:32:30 PDT 2013
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 at gmail.com>wrote:
> 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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