[yt-users] Fwd: YT fails at start
John Regan
johnanthonyregan at gmail.com
Wed Jun 5 00:41:08 PDT 2013
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 at 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 at 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 at 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 at 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 <nathan12343 at gmail.com> 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 <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
>>> >> >
>>> >> _______________________________________________
>>> >> yt-users mailing list
>>> >> yt-users at lists.spacepope.org
>>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>> >
>>> >
>>> >
>>> > _______________________________________________
>>> > yt-users mailing list
>>> > yt-users at lists.spacepope.org
>>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>> >
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20130605/c10f5d62/attachment.html>
More information about the yt-users
mailing list