Re: [Phonopy-users] install phono3py on MacOS
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Re: [Phonopy-users] install phono3py on MacOS
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From: Hui W. <hu...@uc...> - 2017-07-22 15:27:54
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Dear Togo,
I really appreciate your help on installing phono3py. I reinstalled the latest phonopy and latest phono3py exactly as you suggested, and they have all been successfully as shown below:
==============
Using /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
Finished processing dependencies for phonopy==1.11.12
==============
Installed /Users/Hui_DFT/Library/Python/2.7/lib/python/site-packages/phono3py-1.11.13-py2.7-macosx-10.12-x86_64.egg
Processing dependencies for phono3py==1.11.13
Finished processing dependencies for phono3py==1.11.13
==============
However, when i tried to test the Si_LDA in the example directory by using the phono3py in the script directory:
phono3py --dim="2 2 2" --sym_fc3r --sym_fc2 --tsym -c POSCAR-unitcell
it still failed the same as before (as follows):
==============
~/Software/Conda/phono3py/example/Si-LDA$ phono3py --dim="2 2 2" --sym_fc3r --sym_fc2 --tsy
Traceback (most recent call last):
File "/usr/local/bin/phono3py", line 42, in <module>
from phonopy.interface import read_crystal_structure, get_force_sets
ImportError: cannot import name get_force_sets
==============
I feel sorry to bother you, but since i am new learner of phono3py, and have very little experience on it, so please help to see what could be the problem causing this error? Many many thanks.
Best.
Hui
> On Jul 22, 2017, at 10:16 PM, Atsushi Togo <atz...@gm...> wrote:
>
> Please use the combination of the latest phono3py and latest phonopy.
> I wrote the procedure. I did my best to help you. Please do your best.
>
> % git clone https://github.com/atztogo/phonopy.git
> % cd phonopy
> % python setup.py install --user
> % cd ..
> % git clone https://github.com/atztogo/phono3py.git
> % cd phono3py
> % python setup.py install --user
> % cd ..
>
> Togo
>
> On Sat, Jul 22, 2017 at 11:10 PM, Hui Wang <hu...@uc...> wrote:
>> Thanks for you reply, Togo. It seems work with gcc,
>> ==============
>> Installing phono3py script to /Users/Hui_DFT/Library/Python/2.7/bin
>> Installing kaccum script to /Users/Hui_DFT/Library/Python/2.7/bin
>> Installing kdeplot script to /Users/Hui_DFT/Library/Python/2.7/bin
>>
>> Installed /Users/Hui_DFT/Library/Python/2.7/lib/python/site-packages/phono3py-1.11.13-py2.7-macosx-10.12-x86_64.egg
>> Processing dependencies for phono3py==1.11.13
>> Finished processing dependencies for phono3py==1.11.13
>> ==============
>> But, when i try to test the Si_PBE in the example by using the phono3py in the script directory:
>> phono3py --dim="2 2 2" --sym_fc3r --sym_fc2 --tsym -c POSCAR-unitcell
>> it failed as follows
>> ==============
>> Traceback (most recent call last):
>> File "/usr/local/bin/phono3py", line 42, in <module>
>> from phonopy.interface import read_crystal_structure, get_force_sets
>> ImportError: cannot import name get_force_sets
>> ==============
>>
>> Is this because my previous phonopy is out of date (version 1.10.0)? Or what’s the possible reason causing the error? Thanks for your help, looking forward to your reply.
>>
>> Best.
>> Hui
>>
>>
>>> On Jul 22, 2017, at 9:39 PM, Atsushi Togo <atz...@gm...> wrote:
>>>
>>> How about
>>>
>>> export CC=gcc
>>>
>>> Togo
>>>
>>> On Sat, Jul 22, 2017 at 10:37 PM, Hui Wang <hu...@uc...> wrote:
>>>> Dear Phonopy developer:
>>>> Thanks for your suggestions. I installed the miniconda and wget as
>>>> you suggest, while i failed when i try to install gcc7 as shown below,
>>>> ===============
>>>> ---> Computing dependencies for gcc7
>>>> Error: Can't install libgcc-devel because conflicting ports are active:
>>>> libgcc
>>>> Error: Follow https://guide.macports.org/#project.tickets to report a bug.
>>>> Error: Processing of port gcc7 failed
>>>> ===============
>>>> I continue anyway to install numpy scipy h5py pyyaml matplotlib
>>>> openblas as suggested, then I try to install phono3py by command python
>>>> setup.py install --user, which failed as shown below,
>>>> ===============
>>>> copying phono3py/phonon3/reciprocal_to_normal.py ->
>>>> build/lib.macosx-10.12-x86_64-2.7/phono3py/phonon3
>>>> copying phono3py/phonon3/triplets.py ->
>>>> build/lib.macosx-10.12-x86_64-2.7/phono3py/phonon3
>>>> running build_ext
>>>> building 'phono3py._lapackepy' extension
>>>> creating build/temp.macosx-10.12-x86_64-2.7
>>>> creating build/temp.macosx-10.12-x86_64-2.7/c
>>>> creating build/temp.macosx-10.12-x86_64-2.7/c/harmonic
>>>> /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -pipe -Os -fwrapv
>>>> -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ic/harmonic_h
>>>> -Ic/anharmonic_h -Ic/spglib_h -Ic/kspclib_h
>>>> -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include
>>>> -I/opt/local/include
>>>> -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
>>>> -c c/_lapackepy.c -o build/temp.macosx-10.12-x86_64-2.7/c/_lapackepy.o
>>>> -fopenmp
>>>> clang: error: unsupported option '-fopenmp'
>>>> error: command '/usr/bin/clang' failed with exit status 1
>>>> ================
>>>> It seems like MacBook’s compiler clang doesn’t support ‘-fopenmp’,
>>>> is this because gcc7 doesn’t install successfully, is gcc7 necessary? Do you
>>>> have any ideas on how to solve this issue, thanks a lot in advance.
>>>>
>>>> Best.
>>>> Hui
>>>>
>>>>
>>>>
>>>> On Jul 21, 2017, at 5:15 PM, Atsushi Togo <atz...@gm...> wrote:
>>>>
>>>> Hi,
>>>>
>>>> One way with conda, I will explain roughly.
>>>>
>>>> I suppose you have this environment variable.
>>>> export PATH=~/.miniconda3/bin:$PATH
>>>> I also asume you have gcc compiler on your system. I install it by
>>>> using MacPort, e.g.,
>>>> % sudo port install gcc7
>>>> (maybe also wget because I am familiar with it than curl.)
>>>> % sudo port install wget
>>>>
>>>> Download miniconda at https://conda.io/miniconda.html.
>>>> % wget
>>>> https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
>>>>
>>>> Install conda
>>>> % bash miniconda.sh -b -p $HOME/.miniconda3
>>>>
>>>> Package install
>>>> % conda update conda
>>>> % conda install numpy scipy h5py pyyaml matplotlib openblas
>>>>
>>>> Install phonopy and phono3py
>>>> % git clone https://github.com/atztogo/phonopy.git
>>>> % cd phonopy
>>>> % python setup.py install --user
>>>> % cd ..
>>>> % git clone https://github.com/atztogo/phono3py.git
>>>> % cd phono3py
>>>> % python setup.py install --user
>>>> % cd ..
>>>>
>>>> Togo
>>>>
>>>> On Fri, Jul 21, 2017 at 6:01 PM, Hui Wang <hu...@uc...> wrote:
>>>>
>>>> Dear Phonopy developer:
>>>> I have successfully installed phonopy on my Macbook, which works
>>>> normally. Now i want to install phono3y on my MacBook, I checked the website
>>>> of phono3py, it said use conda or pip, or from source code. Is there any
>>>> instructions on how to install phono3py on MacBook OS? Thanks.
>>>>
>>>> Best.
>>>> Hui
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> Phonopy-users mailing list
>>>> Pho...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Atsushi Togo
>>>> Elements Strategy Initiative for Structural Materials, Kyoto university
>>>> E-mail: atz...@gm...
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> Phonopy-users mailing list
>>>> Pho...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> Phonopy-users mailing list
>>>> Pho...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
>>>>
>>>
>>>
>>>
>>> --
>>> Atsushi Togo
>>> Elements Strategy Initiative for Structural Materials, Kyoto university
>>> E-mail: atz...@gm...
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> Phonopy-users mailing list
>>> Pho...@li...
>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Phonopy-users mailing list
>> Pho...@li...
>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
>
>
>
> --
> Atsushi Togo
> Elements Strategy Initiative for Structural Materials, Kyoto university
> E-mail: atz...@gm...
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Phonopy-users mailing list
> Pho...@li...
> https://lists.sourceforge.net/lists/listinfo/phonopy-users
>
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