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",
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. 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
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",
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. 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
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.
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",
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. 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?):
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",
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. 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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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: /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@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@gmail.com> wrote:
Hi,
I just installed YT and it's failing at the very start.
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",
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. 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
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
"/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/lib/__init__.py", there
a hint in there somewhere?):
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",
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. 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
Anybody come across this kind of error before. The code is built on a shared memory machine, using gcc. icc is actually
/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so: 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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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@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@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@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@gmail.com> wrote:
Hi,
I just installed YT and it's failing at the very start.
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",
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. 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
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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 <matthewturk@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@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@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 <matthewturk@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@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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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@gmail.com>wrote:
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 <matthewturk@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@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@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 <matthewturk@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@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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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@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@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@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@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@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@gmail.com>wrote:
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 <matthewturk@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@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@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
line 29, in <module> from yt.mods import *
File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/mods.py",
"/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/command_line.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 <matthewturk@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@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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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@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@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@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@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@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@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@gmail.com>wrote:
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 <matthewturk@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@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@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
line 29, in <module> from yt.mods import *
File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/mods.py",
"/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/command_line.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@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@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@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Glad you got that working. Perhaps we can incorporate this workaround into the install script as a special case for SUSE. If you have time, can you file an issue about this in our issue tracker? That way we will be sure to come back to it when we clear the issue backlog before the next release. https://bitbucket.org/yt_analysis/yt/issues/new On Thu, Jun 6, 2013 at 1:56 AM, John Regan <johnanthonyregan@gmail.com>wrote: > 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@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@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@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@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@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@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@gmail.com>wrote: >>> >>>> 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 <matthewturk@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@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@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@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@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@lists.spacepope.org >>>>> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>> >> > >>>>> >> _______________________________________________ >>>>> >> yt-users mailing list >>>>> >> yt-users@lists.spacepope.org >>>>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>> > >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > yt-users mailing list >>>>> > yt-users@lists.spacepope.org >>>>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>> > >>>>> _______________________________________________ >>>>> yt-users mailing list >>>>> yt-users@lists.spacepope.org >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>> >>>> >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users@lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >
will do. On 6 June 2013 09:59, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Glad you got that working. Perhaps we can incorporate this workaround into the install script as a special case for SUSE.
If you have time, can you file an issue about this in our issue tracker? That way we will be sure to come back to it when we clear the issue backlog before the next release.
https://bitbucket.org/yt_analysis/yt/issues/new
On Thu, Jun 6, 2013 at 1:56 AM, John Regan <johnanthonyregan@gmail.com>wrote:
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@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@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@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@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@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@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@gmail.com>wrote:
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 <matthewturk@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@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@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@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@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@lists.spacepope.org >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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participants (3)
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John Regan
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Matthew Turk
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Nathan Goldbaum