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

• To: Ryan May <rmay@xxxxxxxx>
• Subject: Re: [python-users] Python import error - undefined reference __intel_sse2_strcht
• From: ashwinD12 <winash12@xxxxxxxxx>
• Date: Thu, 16 Jun 2016 08:17:46 +0530

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
>

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  • [python-users] Python import error - undefined reference __intel_sse2_strcht
    • From: ashwinD12
  • Re: [python-users] Python import error - undefined reference __intel_sse2_strcht
    • From: Ryan May