The full anaconda download is very large, but you get just about every
scipy-related package with it. You can also go with "miniconda" which is
the minimal install and then you can pick and choose what to install from
there.
As for having an existing install of those libraries, one of the genius
ideas of conda is that most of the dynamic linkages are done up in the
user-space level, and furthermore, it is all self-contained. Installing
libnetcdf via conda will not interfere with anything outside of conda, and
things outside conda are very unlikely to interfere with the packages
managed via conda.
By the way, you will likely want to utilize the "conda-forge" channel for
those hard-to-install packages, but you should be fine for the most part
with just the default channel.
Cheers!
Ben Root
On Wed, Jun 15, 2016 at 9:56 AM, ashwinD12 <winash12@xxxxxxxxx> wrote:
> Hi Julien,
> Thanks for your prompt response. I can go ahead with
> installing conda but I have two follow up concerns
>
> 1) size of the download seems fairly large - 3g and I got a slow network.
> Hope it won't be a problem
>
> 2) I already have an existing netcdf fortran and c installation as ell as
> hdf5 installation. I won't this wont interfere with that.
>
>
> Regards,
> Ashwin.
>
> On Wed, Jun 15, 2016 at 11:06 AM, Julien Chastang <chastang@xxxxxxxx>
> wrote:
>
>> 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
>>
>
>
> _______________________________________________
> 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/
>
