[yt-users] Fwd: YT fails at start
John Regan
johnanthonyregan at gmail.com
Thu Jun 6 01:56:02 PDT 2013
Hi Nathan,
I contacted the system admin about the dynamic linking issue. He suggested
using the LD_PRELOAD env variable to override other linking variable and
that worked.
$ ldd
/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so
linux-vdso.so.1 => (0x00002aaaaaaab000)
/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib64/libpng16.so.16
(0x00002aaaaacda000)
libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00002aaaaaf6e000)
libz.so.1 =>
/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/libz.so.1
(0x00002aaaab196000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002aaaab3ad000)
libm.so.6 => /lib64/libm.so.6 (0x00002aaaab6b8000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002aaaab931000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aaaabb47000)
libc.so.6 => /lib64/libc.so.6 (0x00002aaaabd65000)
/lib64/ld-linux-x86-64.so.2 (0x0000555555554000)
$ pyyt
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 *
>>>
So everything is now working nicely. I'm not sure if this is a YT issue or
a SUSE issue or maybe even something to do with the configuration of the
machine I am working on.
Likely YT's interaction with SUSE I suppose.
Cheers,
John
On 5 June 2013 08:41, John Regan <johnanthonyregan at gmail.com> wrote:
> 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/20130606/b2d22721/attachment.html>
More information about the yt-users
mailing list