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
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
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
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:
undefined symbol: png_set_longjmp_fn
Cheers, John
On 4 June 2013 17:19, Matthew Turk
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",
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",
/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so: line 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
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