<div dir="ltr"><div><div>Hi Matt, <br><br>(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<br> linux-vdso.so.1 => (0x00007fffbfffe000)<br>
libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00007fffbfb56000)<br> libz.so.1 => /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/libz.so.1 (0x00007fffbf93f000)<br> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fffbf635000)<br>
libm.so.6 => /lib64/libm.so.6 (0x00007fffbf3bb000)<br> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fffbf1a5000)<br> libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fffbef88000)<br> libc.so.6 => /lib64/libc.so.6 (0x00007fffbec10000)<br>
/lib64/ld-linux-x86-64.so.2 (0x0000555555554000)<br>(yt-x86_64)jr347@universe:~/2013/Stats/Halo1/DMonly/Enzo_Analysis/YT> <br>(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<br>
linux-vdso.so.1 => (0x00007fffbfffe000)<br> libm.so.6 => /lib64/libm.so.6 (0x00007fffbfb20000)<br> libpng16.so.16 => /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib64/libpng16.so.16 (0x00007fffbf8de000)<br>
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fffbf6c1000)<br> libc.so.6 => /lib64/libc.so.6 (0x00007fffbf349000)<br> libz.so.1 => /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/libz.so.1 (0x00007fffbf132000)<br>
/lib64/ld-linux-x86-64.so.2 (0x0000555555554000)<br>(yt-x86_64)jr347@universe:~/2013/Stats/Halo1/DMonly/Enzo_Analysis/YT> <br><br><br></div>Anything there look out of place?<br><br></div>John<br><div><div><br></div>
</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 4 June 2013 17:32, Matthew Turk <span dir="ltr"><<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi John,<br>
<br>
Ah, thanks. So png_set_longjmp_fn is something that we disable inside<br>
libpng when we build it, through the flag PNG_SETJMP_NOT_SUPPORTED<br>
(line 193 or so of yt/utilities/lib/setup.py) which leads me to<br>
believe that something is amiss with how _png.so is compiled. What's<br>
the output of:<br>
<br>
ldd /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so<br>
ldd /home/cosmos/users/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/lib/png_writer.so<br>
<br>
-Matt<br>
<div class="HOEnZb"><div class="h5"><br>
On Tue, Jun 4, 2013 at 12:27 PM, John Regan <<a href="mailto:johnanthonyregan@gmail.com">johnanthonyregan@gmail.com</a>> wrote:<br>
> Hi Matt,<br>
><br>
> Yes first thing I did was source the activation script (prefix yt env shown<br>
> below).<br>
> yt help throws up similar errors:<br>
><br>
> (yt-x86_64)jr347@universe:~/2013/Stats/Halo1/DMonly/Enzo_Analysis/YT> yt<br>
> help<br>
><br>
> Traceback (most recent call last):<br>
> File "/home/cosmos/users/jr347/2013/YT/yt-x86_64/bin/yt", line 9, in<br>
> <module><br>
> load_entry_point('yt==2.5.3', 'console_scripts', 'yt')()<br>
> File<br>
> "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py",<br>
> line 337, in load_entry_point<br>
> return get_distribution(dist).load_entry_point(group, name)<br>
> File<br>
> "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py",<br>
> line 2311, in load_entry_point<br>
> return ep.load()<br>
> File<br>
> "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py",<br>
> line 2017, in load<br>
> entry = __import__(self.module_name, globals(),globals(), ['__name__'])<br>
> File<br>
> "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/command_line.py",<br>
> line 29, in <module><br>
> from yt.mods import *<br>
><br>
> File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/mods.py", line<br>
> 129, in <module><br>
> from yt.visualization.api import \<br>
> File<br>
> "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/visualization/api.py",<br>
> line 34, in <module><br>
> from plot_collection import \<br>
> File<br>
> "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py",<br>
> line 26, in <module><br>
> from matplotlib import figure<br>
> File<br>
> "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/figure.py",<br>
> line 32, in <module><br>
> from matplotlib.image import FigureImage<br>
> File<br>
> "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/image.py",<br>
> line 22, in <module><br>
> import matplotlib._png as _png<br>
> ImportError:<br>
> /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so:<br>
> undefined symbol: png_set_longjmp_fn<br>
><br>
> Cheers,<br>
> John<br>
><br>
><br>
> On 4 June 2013 17:19, Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>> wrote:<br>
>><br>
>> Hi John,<br>
>><br>
>> Sorry to hear you're having trouble! When you first tried running,<br>
>> did you source the environment file that yt creates? I believe for<br>
>> your environment it would be something like this:<br>
>><br>
>> source /home/cosmos/users/jr347/2013/YT/yt-x86_64/bin/activate<br>
>><br>
>> which would set the various environment variables and so on. Then you<br>
>> can try doing something simple like "yt help" to see if it will import<br>
>> correctly.<br>
>><br>
>> Thanks,<br>
>><br>
>> -Matt<br>
>><br>
>> On Tue, Jun 4, 2013 at 12:10 PM, John Regan <<a href="mailto:johnanthonyregan@gmail.com">johnanthonyregan@gmail.com</a>><br>
>> wrote:<br>
>> > Hi,<br>
>> ><br>
>> > I just installed YT and it's failing at the very start.<br>
>> ><br>
>> > Python 2.7.4 (default, Jun 4 2013, 11:02:31)<br>
>> > [GCC 4.3.4 [gcc-4_3-branch revision 152973]] on linux2<br>
>> > Type "help", "copyright", "credits" or "license" for more information.<br>
>> >>>> from yt.mods import *<br>
>> > Traceback (most recent call last):<br>
>> > File "<stdin>", line 1, in <module><br>
>> > File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/mods.py", line<br>
>> > 60,<br>
>> > in <module><br>
>> > from yt.data_objects.api import \<br>
>> > File<br>
>> > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/api.py",<br>
>> > line 31, in <module><br>
>> > from grid_patch import \<br>
>> > File<br>
>> ><br>
>> > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py",<br>
>> > line 35, in <module><br>
>> > from yt.data_objects.data_containers import YTFieldData<br>
>> > File<br>
>> ><br>
>> > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",<br>
>> > line 45, in <module><br>
>> > from yt.data_objects.derived_quantities import GridChildMaskWrapper<br>
>> > File<br>
>> ><br>
>> > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py",<br>
>> > line 36, in <module><br>
>> > from yt.utilities.parallel_tools.parallel_analysis_interface import<br>
>> > \<br>
>> > File<br>
>> ><br>
>> > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",<br>
>> > line 39, in <module><br>
>> > from yt.utilities.lib import \<br>
>> > File<br>
>> ><br>
>> > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/lib/__init__.py",<br>
>> > line 35, in <module><br>
>> > from .png_writer import *<br>
>> > ImportError: libpng16.so.16: cannot open shared object file: No such<br>
>> > file or<br>
>> > directory<br>
>> >>>><br>
>> ><br>
>> > Adding the path to the libpng16.so.16 library gets me to here (it also<br>
>> > seems<br>
>> > strange that the .so file was not already in the LD_LIBRARY_PATH - is<br>
>> > there<br>
>> > a hint in there somewhere?):<br>
>> ><br>
>> > Python 2.7.4 (default, Jun 4 2013, 11:02:31)<br>
>> > [GCC 4.3.4 [gcc-4_3-branch revision 152973]] on linux2<br>
>> > Type "help", "copyright", "credits" or "license" for more information.<br>
>> >>>> from yt.mods import *<br>
>> > Traceback (most recent call last):<br>
>> > File "<stdin>", line 1, in <module><br>
>> > File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/mods.py", line<br>
>> > 129, in <module><br>
>> > from yt.visualization.api import \<br>
>> > File<br>
>> ><br>
>> > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/visualization/api.py",<br>
>> > line 34, in <module><br>
>> > from plot_collection import \<br>
>> > File<br>
>> ><br>
>> > "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py",<br>
>> > line 26, in <module><br>
>> > from matplotlib import figure<br>
>> > File<br>
>> ><br>
>> > "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/figure.py",<br>
>> > line 32, in <module><br>
>> > from matplotlib.image import FigureImage<br>
>> > File<br>
>> ><br>
>> > "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/image.py",<br>
>> > line 22, in <module><br>
>> > import matplotlib._png as _png<br>
>> > ImportError:<br>
>> ><br>
>> > /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so:<br>
>> > undefined symbol: png_set_longjmp_fn<br>
>> ><br>
>> ><br>
>> > Anybody come across this kind of error before.<br>
>> > The code is built on a shared memory machine, using gcc. icc is actually<br>
>> > the<br>
>> > default compiler but the YT script seems to pick up gcc by default and<br>
>> > it<br>
>> > builds (it doesn't build at all with icc).<br>
>> ><br>
>> > Install script attached in case it's helpful.<br>
>> ><br>
>> > Let me know if you need anymore info. Thanks in advance!<br>
>> ><br>
>> > John<br>
>> ><br>
>> ><br>
>> ><br>
>> ><br>
>> > _______________________________________________<br>
>> > yt-users mailing list<br>
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>> ><br>
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</div></div></blockquote></div><br></div>