Ashwin,
I echo that conda is a good solution in general, but I want to clarify
something. Your original problem was missing the C HDF5 library--your
installing h5py does nothing to solve this. Instead, you should install the
hdf5 libs on Ubuntu (not using pip, but apt-get).
Ryan
On Tue, Jun 14, 2016 at 11:21 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
>
--
Ryan May, Ph.D.
Software Engineer
UCAR/Unidata
Boulder, CO
