<div dir="ltr"><div><div><div>Hi Nathan,<br><br></div><div>Thanks for looking into this!<br></div>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. <br>
<br>jr347@universe:~/2013/YT> echo $LD_LIBRARY_PATH<br>/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<br>
jr347@universe:~/2013/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 (0x00007fffbfb57000)<br>
libz.so.1 => /lib64/libz.so.1 (0x00007fffbf940000)<br> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fffbf636000)<br> libm.so.6 => /lib64/libm.so.6 (0x00007fffbf3bd000)<br> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fffbf1a6000)<br>
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fffbef89000)<br> libc.so.6 => /lib64/libc.so.6 (0x00007fffbec12000)<br> /lib64/ld-linux-x86-64.so.2 (0x0000555555554000)<br>jr347@universe:~/2013/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 (0x00007fffbfb21000)<br> libpng16.so.16 => not found<br> libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fffbf903000)<br>
libc.so.6 => /lib64/libc.so.6 (0x00007fffbf58c000)<br> /lib64/ld-linux-x86-64.so.2 (0x0000555555554000)<br><br></div>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<br>
<br>(yt-x86_64)jr347@universe:~/2013/YT> yt help<br>Traceback (most recent call last):<br> File "/home/cosmos/users/jr347/2013/YT/yt-x86_64/bin/yt", line 9, in <module><br> load_entry_point('yt==2.5.3', 'console_scripts', 'yt')()<br>
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<br> return get_distribution(dist).load_entry_point(group, name)<br>
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<br> return ep.load()<br> 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<br>
entry = __import__(self.module_name, globals(),globals(), ['__name__'])<br> File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 29, in <module><br> from yt.mods import *<br>
File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/mods.py", line 60, in <module><br> from yt.data_objects.api import \<br> File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/api.py", line 31, in <module><br>
from grid_patch import \<br> File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 35, in <module><br> from yt.data_objects.data_containers import YTFieldData<br>
File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 45, in <module><br> from yt.data_objects.derived_quantities import GridChildMaskWrapper<br> File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 36, in <module><br>
from yt.utilities.parallel_tools.parallel_analysis_interface import \<br> File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 39, in <module><br>
from yt.utilities.lib import \<br> File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/lib/__init__.py", line 35, in <module><br> from .png_writer import *<br>ImportError: libpng16.so.16: cannot open shared object file: No such file or directory<br>
<br><br></div>Cheers,<br>John<br><br><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 4 June 2013 18:32, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi John,<div><br></div><div>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.</div>
<div><br></div><div>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).</div>
<div><br></div><div>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: <a href="http://yt-project.org/irc.html" target="_blank">http://yt-project.org/irc.html</a>) so we can help you out in real time.</div>
<div><br></div><div>Cheers,</div><div><br></div><div>Nathan</div><div><br></div><div><br></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Jun 4, 2013 at 9:41 AM, John Regan <span dir="ltr"><<a href="mailto:johnanthonyregan@gmail.com" target="_blank">johnanthonyregan@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><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?<span><font color="#888888"><br>
<br></font></span></div><span><font color="#888888">John<br><div><div><br></div>
</div></font></span></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><div><br>
On Tue, Jun 4, 2013 at 12:27 PM, John Regan <<a href="mailto:johnanthonyregan@gmail.com" target="_blank">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" target="_blank">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" target="_blank">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>
>> > <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
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>> ><br>
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