Re: [Phonopy-users] importing and running problem "ImportError: libgomp.so.1: shared object cannot be dlopen()ed"

[Terence L. (Z. Liu) <ter...@gm...>]

After deletion and reinstallation, it works :D Thanks!

terencelz

On Feb 4, 2014, at 8:42 PM, Atsushi Togo <atz...@gm...> wrote:

> Hi,
> 
> Oh, I see that I unintentionally shipped version 1.8.1 with openmp
> support for GCC.
> So could you modify setup.py as follows?
> 
> extension = Extension('phonopy._phonopy',
> #                      extra_compile_args=['-fopenmp'],
> #                      extra_link_args=['-lgomp'],
>                      include_dirs=['c/harmonic_h'] + include_dirs_numpy,
>                      sources=['c/_phonopy.c',
>                               'c/harmonic/dynmat.c'])
> 
> extension_spglib = Extension(
>    'phonopy._spglib',
>    include_dirs=['c/spglib_h'] + include_dirs_numpy,
> #    extra_compile_args=['-fopenmp'],
> #    extra_link_args=['-lgomp'],
> 
> ....
> 
> 
> Togo
> 
> On Wed, Feb 5, 2014 at 6:41 AM, Terence Lewis <ter...@gm...> wrote:
>> Hi all, I was trying to install phonopy but there are some error messages
>> showing up.
>> 
>> I'm working on a supercomputer, not a desktop distribution, so I did a local
>> installation.
>> 
>> I "pip install" lxml and yaml locally with adding the site-packages to the
>> PYTHONPATH, which was successful because I could import them in python with
>> no problem. Then I followed the instructions from
>> http://phonopy.sourceforge.net/install.html. It had some "defined but not
>> used, used but not initiallized" warnings but no error. I added it to
>> PYTHONPATH as well and can find these all three packages in "pip freeze".
>> 
>> But when I use python to "import phonopy", or directly type in phonopy (in
>> my PATH), it generates an error.
>> 
>> 
>> Traceback (most recent call last):
>> 
>>  File "/nfs/02/asd/gab/local/phonopy-1.8.1/bin/phonopy", line 40, in
>> <module>
>> 
>>    from phonopy import *
>> 
>>  File "/nfs/02/asd/gab/local/phonopy-1.8.1/lib/python/phonopy/__init__.py",
>> line 38, in <module>
>> 
>>    from phonopy.structure.symmetry import Symmetry
>> 
>>  File
>> "/nfs/02/asd/gab/local/phonopy-1.8.1/lib/python/phonopy/structure/symmetry.py",
>> line 37, in <module>
>> 
>>    import phonopy.structure.spglib as spg
>> 
>>  File
>> "/nfs/02/asd/gab/local/phonopy-1.8.1/lib/python/phonopy/structure/spglib.py",
>> line 5, in <module>
>> 
>>    import phonopy._spglib as spg
>> 
>> ImportError: libgomp.so.1: shared object cannot be dlopen()ed
>> 
>> 
>> thanks,
>> 
>> terencelz
>> 
>> 
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> 
> 
> 
> -- 
> Atsushi Togo
> http://atztogo.github.com/
> atz...@gm...