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
>
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--
Julien Chastang
Scientific Software Developer
Unidata-UCAR
