Ashwin,
That sounds entirely too painful. Given that, I'd say miniconda (using the
conda-forge channel as necessary for additional packages) is probably your
best bet. Personally, I'd much rather be focused on using Python rather
than figuring out a compiler.
Ryan
On Wed, Jun 15, 2016 at 8:47 PM, ashwinD12 <winash12@xxxxxxxxx> wrote:
> Ryan,
> I do have the hd5 installed yes. It is under /usr/local/lib
> and /usr/local/include. When I installed WRF two years ago these are
> required libraries. What I saw in this URL is
>
>
> http://bryanwweber.com/writing/personal/2014/01/11/installing-numpy-scipy-on-ubuntu-12.04.3-from-scratch-source-with-intel-compilers/
>
> I need to make changes to the intelcompiler.py file so that it reflects my
> environment. How I do not know yet.
>
>
>
> Regards,
> Ashwin.
>
> On Wed, Jun 15, 2016 at 8:45 PM, Ryan May <rmay@xxxxxxxx> wrote:
>
>> 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
>>
>
>
--
Ryan May, Ph.D.
Software Engineer
UCAR/Unidata
Boulder, CO
