Re: [python-users] Python import error - undefined reference __intel_sse2_strcht

  • To: ashwinD12 <winash12@xxxxxxxxx>
  • Subject: Re: [python-users] Python import error - undefined reference __intel_sse2_strcht
  • From: Julien Chastang <chastang@xxxxxxxx>
  • Date: Tue, 14 Jun 2016 23:36:10 -0600
Hi Ashwin,

Installing netCDF4-python via pip will not yield good results because of
the dependency problems you describe.

Instead, most or all users on this list will probably recommend you install
the conda package and environment management system which is available for
Linux.

To learn more about conda and how to install it see:
https://docs.continuum.io/anaconda/index

Once you have installed conda, you can run the following command on your
Linux system:

conda install netcdf4

Verify it is properly installed: python -c "import netCDF4"

As you become more familiar with conda, you'll also want to learn about
environments: http://conda.pydata.org/docs/using/envs.html.

-Julien

On Tue, Jun 14, 2016 at 10:21 PM, ashwinD12 <winash12@xxxxxxxxx> wrote:

> Hello,
>            I am trying to install netcdf4 package on Ubuntu 14.04 using
> the following command
>
> pip3 install netcdf4. This did install successfully but when I try to
> execute a script which had import netCDF4 I get the following error -
>
>
> My python is compiled with icc and not gcc !
>
> Traceback (most recent call last):
>  File "display.py", line 5, in <module>
> from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
> File "/usr/local/lib/python3.4/dist-packages/netCDF4/__init__.py", line 3, in 
> <module> from ._netCDF4 import *
> File "netCDF4/_netCDF4.pyx", line 942, in init netCDF4._netCDF4 
> (netCDF4/_netCDF4.c:76006)
> File "/usr/local/lib/python3.4/dist-packages/netcdftime/__init__.py", line 1, 
> in <module>
> from .netcdftime import utime, JulianDayFromDate, DateFromJulianDay
> File "/usr/local/lib/python3.4/dist-packages/netcdftime/netcdftime.py",   
> line 14, in <module>
> from ._datetime import datetime
>  ImportError: 
> /usr/local/lib/python3.4/dist-packages/netcdftime/_datetime.cpython-34m.so: 
> undefined symbol: __intel_sse2_strchr
>
>
> So it looks like this has a dependency on cython and hdf5.
>
> So I did install cython and that did install successfully.
>
> When I do a pip3 install h5py I get the following errors -
>
> Traceback (most recent call last):
>
>   File "<string>", line 1, in <module>
>
>   File "/tmp/pip_build_root/h5py/setup.py", line 149, in <module>
>
>     cmdclass = CMDCLASS,
>
>   File "/usr/lib/python3.4/distutils/core.py", line 148, in setup
>
>     dist.run_commands()
>
>   File "/usr/lib/python3.4/distutils/dist.py", line 955, in run_commands
>
>     self.run_command(cmd)
>
>   File "/usr/lib/python3.4/distutils/dist.py", line 974, in run_command
>
>     cmd_obj.run()
>
>   File "/usr/lib/python3/dist-packages/setuptools/command/install.py",
> line 53, in run
>
>     return _install.run(self)
>
>   File "/usr/lib/python3.4/distutils/command/install.py", line 583, in run
>
>     self.run_command('build')
>
>   File "/usr/lib/python3.4/distutils/cmd.py", line 313, in run_command
>
>     self.distribution.run_command(command)
>
>   File "/usr/lib/python3.4/distutils/dist.py", line 974, in run_command
>
>     cmd_obj.run()
>
>   File "/usr/lib/python3.4/distutils/command/build.py", line 126, in run
>
>     self.run_command(cmd_name)
>
>   File "/usr/lib/python3.4/distutils/cmd.py", line 313, in run_command
>
>     self.distribution.run_command(command)
>
>   File "/usr/lib/python3.4/distutils/dist.py", line 974, in run_command
>
>     cmd_obj.run()
>
>   File "/tmp/pip_build_root/h5py/setup_build.py", line 147, in run
>
>     from Cython.Build import cythonize
>
>   File "/usr/local/lib/python3.4/dist-packages/Cython/Build/__init__.py",
> line 1, in <module>
>
>     from .Dependencies import cythonize
>
>   File "/usr/local/lib/python3.4/dist-packages/Cython/Build/Dependencies.py",
> line 50, in <module>
>
>     from ..Compiler.Main import Context, CompilationOptions,
> default_options
>
>   File "/usr/local/lib/python3.4/dist-packages/Cython/Compiler/Main.py",
> line 28, in <module>
>
>     from .Scanning import PyrexScanner, FileSourceDescriptor
>
> ImportError: /usr/local/lib/python3.4/dist-packages/Cython/Compiler/
> Scanning.cpython-34m.so <http://scanning.cpython-34m.so/>: undefined
> symbol: __intel_sse2_strchr
>
> _______________________________________________
> NOTE: All exchanges posted to Unidata maintained email lists are
> recorded in the Unidata inquiry tracking system and made publicly
> available through the web.  Users who post to any of the lists we
> maintain are reminded to remove any personal information that they
> do not want to be made public.
>
>
> python-users mailing list
> python-users@xxxxxxxxxxxxxxxxxxxxxxxx
> For list information, to unsubscribe, or change your membership options,
> visit: http://www.unidata.ucar.edu/mailing_lists/
>



-- 
Julien Chastang
Scientific Software Developer
Unidata-UCAR
  • 2016 messages navigation, sorted by:
    1. Thread
    2. Subject
    3. Author
    4. Date
    5. ↑ Table Of Contents
  • Search the python-users archives: