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phonopy / phono3py

A simulation package of phonon-phonon interaction related properties
http://phonopy.github.io/phono3py/
BSD 3-Clause "New" or "Revised" License
117 stars 54 forks source link

working phono3py raises error: Symbol not found: __gfortran_concat_string #3

Closed glensk closed 7 years ago

glensk commented 7 years ago

Dear Atz Togo,

I installed phono3py successfully and tried the example/Si-PBE (in the exaples folder). I obtained the FORCES_FC3 file also successfully. In the next step however (for the calculation of the lattice thermal conductivity) I get an error when running

phono3py --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="11 11 11" --fc3 --fc2 --br

(see full output at bottom of this message)

"... ImportError: dlopen(/Users/glensk/Library/Caches/Python-Eggs/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg-tmp/phono3py/_lapackepy.so, 2): Symbol not found: __gfortran_concat_string Referenced from: /Users/glensk/Library/Caches/Python-Eggs/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg-tmp/phono3py/_lapackepy.so Expected in: flat namespace in /Users/glensk/Library/Caches/Python-Eggs/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg-tmp/phono3py/_lapackepy.so "

This problem seems to be related to gfortran (?). Any help and or hints how to proceed would be appreciated.

System: OS X 10.12.4

Thanks, Albert

Full output of the skript: % phono3py --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="11 11 11" --fc3 --fc2 --br

_ | | | / _ | ' | ' \ / | ' \ / \ | | ' | | | | | |) | | | | () | | | | () |) | |) | || | | ./|| ||_/|| ||_/__/| ./ _, | || || |/ 1.11.11

Run mode: conductivity-RTA Spacegroup: Fd-3m (227) ------------------------------ primitive cell ------------------------------ Lattice vectors: a 0.000000000000000 2.733131445000000 2.733131445000000 b 2.733131445000000 0.000000000000000 2.733131445000000 c 2.733131445000000 2.733131445000000 0.000000000000000 Atomic positions (fractional): 1 Si 0.87500000000000 0.87500000000000 0.87500000000000 28.085 2 Si 0.12500000000000 0.12500000000000 0.12500000000000 28.085 -------------------------------- super cell -------------------------------- Lattice vectors: a 10.932525780000001 0.000000000000000 0.000000000000000 b 0.000000000000000 10.932525780000001 0.000000000000000 c 0.000000000000000 0.000000000000000 10.932525780000001 Atomic positions (fractional): 1 Si 0.43750000000000 0.43750000000000 0.43750000000000 28.085 > 1 2 Si 0.93750000000000 0.43750000000000 0.43750000000000 28.085 > 1 3 Si 0.43750000000000 0.93750000000000 0.43750000000000 28.085 > 1 4 Si 0.93750000000000 0.93750000000000 0.43750000000000 28.085 > 1 5 Si 0.43750000000000 0.43750000000000 0.93750000000000 28.085 > 1 6 Si 0.93750000000000 0.43750000000000 0.93750000000000 28.085 > 1 7 Si 0.43750000000000 0.93750000000000 0.93750000000000 28.085 > 1 8 Si 0.93750000000000 0.93750000000000 0.93750000000000 28.085 > 1 9 Si 0.43750000000000 0.18750000000000 0.18750000000000 28.085 > 1 10 Si 0.93750000000000 0.18750000000000 0.18750000000000 28.085 > 1 11 Si 0.43750000000000 0.68750000000000 0.18750000000000 28.085 > 1 12 Si 0.93750000000000 0.68750000000000 0.18750000000000 28.085 > 1 13 Si 0.43750000000000 0.18750000000000 0.68750000000000 28.085 > 1 14 Si 0.93750000000000 0.18750000000000 0.68750000000000 28.085 > 1 15 Si 0.43750000000000 0.68750000000000 0.68750000000000 28.085 > 1 16 Si 0.93750000000000 0.68750000000000 0.68750000000000 28.085 > 1 17 Si 0.18750000000000 0.43750000000000 0.18750000000000 28.085 > 1 18 Si 0.68750000000000 0.43750000000000 0.18750000000000 28.085 > 1 19 Si 0.18750000000000 0.93750000000000 0.18750000000000 28.085 > 1 20 Si 0.68750000000000 0.93750000000000 0.18750000000000 28.085 > 1 21 Si 0.18750000000000 0.43750000000000 0.68750000000000 28.085 > 1 22 Si 0.68750000000000 0.43750000000000 0.68750000000000 28.085 > 1 23 Si 0.18750000000000 0.93750000000000 0.68750000000000 28.085 > 1 24 Si 0.68750000000000 0.93750000000000 0.68750000000000 28.085 > 1 25 Si 0.18750000000000 0.18750000000000 0.43750000000000 28.085 > 1 26 Si 0.68750000000000 0.18750000000000 0.43750000000000 28.085 > 1 27 Si 0.18750000000000 0.68750000000000 0.43750000000000 28.085 > 1 28 Si 0.68750000000000 0.68750000000000 0.43750000000000 28.085 > 1 29 Si 0.18750000000000 0.18750000000000 0.93750000000000 28.085 > 1 30 Si 0.68750000000000 0.18750000000000 0.93750000000000 28.085 > 1 31 Si 0.18750000000000 0.68750000000000 0.93750000000000 28.085 > 1 32 Si 0.68750000000000 0.68750000000000 0.93750000000000 28.085 > 1 33 Si 0.06250000000000 0.06250000000000 0.06250000000000 28.085 > 33 34 Si 0.56250000000000 0.06250000000000 0.06250000000000 28.085 > 33 35 Si 0.06250000000000 0.56250000000000 0.06250000000000 28.085 > 33 36 Si 0.56250000000000 0.56250000000000 0.06250000000000 28.085 > 33 37 Si 0.06250000000000 0.06250000000000 0.56250000000000 28.085 > 33 38 Si 0.56250000000000 0.06250000000000 0.56250000000000 28.085 > 33 39 Si 0.06250000000000 0.56250000000000 0.56250000000000 28.085 > 33 40 Si 0.56250000000000 0.56250000000000 0.56250000000000 28.085 > 33 41 Si 0.06250000000000 0.31250000000000 0.31250000000000 28.085 > 33 42 Si 0.56250000000000 0.31250000000000 0.31250000000000 28.085 > 33 43 Si 0.06250000000000 0.81250000000000 0.31250000000000 28.085 > 33 44 Si 0.56250000000000 0.81250000000000 0.31250000000000 28.085 > 33 45 Si 0.06250000000000 0.31250000000000 0.81250000000000 28.085 > 33 46 Si 0.56250000000000 0.31250000000000 0.81250000000000 28.085 > 33 47 Si 0.06250000000000 0.81250000000000 0.81250000000000 28.085 > 33 48 Si 0.56250000000000 0.81250000000000 0.81250000000000 28.085 > 33 49 Si 0.31250000000000 0.06250000000000 0.31250000000000 28.085 > 33 50 Si 0.81250000000000 0.06250000000000 0.31250000000000 28.085 > 33 51 Si 0.31250000000000 0.56250000000000 0.31250000000000 28.085 > 33 52 Si 0.81250000000000 0.56250000000000 0.31250000000000 28.085 > 33 53 Si 0.31250000000000 0.06250000000000 0.81250000000000 28.085 > 33 54 Si 0.81250000000000 0.06250000000000 0.81250000000000 28.085 > 33 55 Si 0.31250000000000 0.56250000000000 0.81250000000000 28.085 > 33 56 Si 0.81250000000000 0.56250000000000 0.81250000000000 28.085 > 33 57 Si 0.31250000000000 0.31250000000000 0.06250000000000 28.085 > 33 58 Si 0.81250000000000 0.31250000000000 0.06250000000000 28.085 > 33 59 Si 0.31250000000000 0.81250000000000 0.06250000000000 28.085 > 33 60 Si 0.81250000000000 0.81250000000000 0.06250000000000 28.085 > 33 61 Si 0.31250000000000 0.31250000000000 0.56250000000000 28.085 > 33 62 Si 0.81250000000000 0.31250000000000 0.56250000000000 28.085 > 33 63 Si 0.31250000000000 0.81250000000000 0.56250000000000 28.085 > 33 64 Si 0.81250000000000 0.81250000000000 0.56250000000000 28.085 > 33 ------------------- ratio (supercell for fc)/(primitive) ------------------- -2.00 2.00 2.00 2.00-2.00 2.00 2.00 2.00-2.00 ----------------------------- Force constants ------------------------------ Reading fc3 from fc3.hdf5 max drift of fc3: -0.000000 (xxx) -0.000000 (xxx) -0.000000 (xxx) Reading fc2 from fc2.hdf5 max drift of fc2: 0.000000 (yy) 0.000000 (xx) --------------------------------- Settings --------------------------------- Mesh sampling: [ 11 11 11 ] BZ integration: Tetrahedron-method Temperature: 0.0 10.0 20.0 30.0 40.0 ... 1000.0 Cutoff frequency: 0.01 Traceback (most recent call last): File "/Users/glensk/.local/bin/phono3py", line 4, in import('pkg_resources').run_script('phono3py==1.11.11', 'phono3py') File "/Users/glensk/anaconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 744, in run_script

File "/Users/glensk/anaconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 1506, in run_script

File "/Users/glensk/.local/lib/python2.7/site-packages/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg/EGG-INFO/scripts/phono3py", line 627, in

File "build/bdist.macosx-10.7-x86_64/egg/phono3py/phonon3/init.py", line 155, in set_phph_interaction

File "build/bdist.macosx-10.7-x86_64/egg/phono3py/phonon3/interaction.py", line 262, in set_dynamical_matrix File "build/bdist.macosx-10.7-x86_64/egg/phono3py/phonon3/interaction.py", line 292, in set_phonons File "build/bdist.macosx-10.7-x86_64/egg/phono3py/phonon3/interaction.py", line 343, in _set_phonon_c File "build/bdist.macosx-10.7-x86_64/egg/phono3py/phonon/solver.py", line 48, in set_phonon_c File "build/bdist.macosx-10.7-x86_64/egg/phono3py/_lapackepy.py", line 7, in File "build/bdist.macosx-10.7-x86_64/egg/phono3py/_lapackepy.py", line 6, in bootstrap ImportError: dlopen(/Users/glensk/Library/Caches/Python-Eggs/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg-tmp/phono3py/_lapackepy.so, 2): Symbol not found: __gfortran_concat_string Referenced from: /Users/glensk/Library/Caches/Python-Eggs/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg-tmp/phono3py/_lapackepy.so Expected in: flat namespace in /Users/glensk/Library/Caches/Python-Eggs/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg-tmp/phono3py/_lapackepy.so

15:07:25 glensk@mac /Users/glensk/Dropbox/scripts/phonons/phono3py/example/Si-PBE/redo_phono3py_redo_as_in_README

%ls FORCES_FC3 POSCAR-unitcell SPOSCAR disp_fc3.yaml fc2.hdf5 fc3.hdf5 phono3py.yaml phono3py_disp.yaml 15:42:12 glensk@mac /Users/glensk/Dropbox/scripts/phonons/phono3py/example/Si-PBE/redo_phono3py_redo_as_in_README %

atztogo commented 7 years ago

I guess linking lapacke, lapack or blas didn't go well or you need to set LD_LIBRARY_PATH to those directories where those libraries exist.

glensk commented 7 years ago

Dear Atz Togo,

My LD_LIBRARY_PATH contains /usr/local/opt/lapack/lib:/usr/local/opt/openblas/lib and

%ls /usr/local/opt/lapack/lib cmake/ libblas.dylib@ libblas.3.7.0.dylib liblapacke.dylib liblapack.3.7.0.dylib pkgconfig/ libblas.3.dylib@ liblapack.dylib@ liblapack.3.dylib@ libtmglib.dylib

%ls /usr/local/opt/openblas/lib cmake/ liblapack.dylib@ libopenblas.dylib@ libopenblas_haswellp-r0.2.19.dylib libblas.dylib@ libopenblas.a@ libopenblas_haswellp-r0.2.19.a

in setup.py i have included: include_dirs += ['/usr/local/opt/lapack/include'] include_dirs += ['/usr/local/opt/openblas/include'] extra_link_args_lapacke = ['/usr/local/opt/openblas/lib/libopenblas.a']

where %ls /usr/local/opt/lapack/include lapacke.h lapacke_config.h lapacke_mangling.h lapacke_utils.h

%ls /usr/local/opt/openblas/include cblas.h f77blas.h lapacke.h lapacke_config.h lapacke_mangling.h lapacke_utils.h openblas_config.h

and I also have tried to include in "include_dirs" not both ---lapack and openblas--- but only one of them at a time.

However, there is no lib/python folder which was created during the setup.py process therefore I don't have anything included in the PYTHONPATH. (I also tried to bind /Users/$USERNAME/.local/lib/python2.7 into PYTHONPATH which raises the same problem: """ ImportError: dlopen(/Users/glensk/Library/Caches/Python-Eggs/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg-tmp/phono3py/_lapackepy.so, 2): Symbol not found: __gfortran_concat_string Referenced from: /Users/glensk/Library/Caches/Python-Eggs/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg-tmp/phono3py/_lapackepy.so Expected in: flat namespace in /Users/glensk/Library/Caches/Python-Eggs/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg-tmp/phono3py/_lapackepy.so ) """

With respect to the linking: Since there was no error in the setup.py process, how can I check whether the linking of lapacke, lapack or blas did go well? At least phono3py is working until i execute: phono3py --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="11 11 11" --fc3 --fc2 --br

Any help is warmly welcome,

albert

atztogo commented 7 years ago

Hi,

On my mac, close to the end of setup.py message, it is shown below,

gcc -bundle -undefined dynamic_lookup -L/opt/local/lib -Wl,-headerpad_max_install_names -L/opt/local/lib/db48 build/temp.macosx-10.12-x86_64-2.7/c/_phono3py.o build/temp.macosx-10.12-x86_64-2.7/c/harmonic/dynmat.o build/temp.macosx-10.12-x86_64-2.7/c/harmonic/lapack_wrapper.o build/temp.macosx-10.12-x86_64-2.7/c/harmonic/phonoc_array.o build/temp.macosx-10.12-x86_64-2.7/c/harmonic/phonoc_utils.o build/temp.macosx-10.12-x86_64-2.7/c/anharmonic/phonon3/fc3.o build/temp.macosx-10.12-x86_64-2.7/c/anharmonic/phonon3/frequency_shift.o build/temp.macosx-10.12-x86_64-2.7/c/anharmonic/phonon3/interaction.o build/temp.macosx-10.12-x86_64-2.7/c/anharmonic/phonon3/real_to_reciprocal.o build/temp.macosx-10.12-x86_64-2.7/c/anharmonic/phonon3/reciprocal_to_normal.o build/temp.macosx-10.12-x86_64-2.7/c/anharmonic/phonon3/imag_self_energy_with_g.o build/temp.macosx-10.12-x86_64-2.7/c/anharmonic/phonon3/pp_collision.o build/temp.macosx-10.12-x86_64-2.7/c/anharmonic/phonon3/collision_matrix.o build/temp.macosx-10.12-x86_64-2.7/c/anharmonic/other/isotope.o build/temp.macosx-10.12-x86_64-2.7/c/anharmonic/triplet/triplet.o build/temp.macosx-10.12-x86_64-2.7/c/anharmonic/triplet/triplet_kpoint.o build/temp.macosx-10.12-x86_64-2.7/c/anharmonic/triplet/triplet_iw.o build/temp.macosx-10.12-x86_64-2.7/c/spglib/mathfunc.o build/temp.macosx-10.12-x86_64-2.7/c/spglib/kpoint.o build/temp.macosx-10.12-x86_64-2.7/c/kspclib/kgrid.o build/temp.macosx-10.12-x86_64-2.7/c/kspclib/tetrahedron_method.o -o build/lib.macosx-10.12-x86_64-2.7/phono3py/_phono3py.so -lgomp /opt/local/lib/libopenblas.a ...

If you use static link library of openblas, /opt/local/lib/libopenblas.a must be here. But openblas is not always containing lapacke in it. How did you install openblas. In my case, I use macport. If your environment is similar to me, you don't need to modify setup.py.

Togo

On Mon, Apr 24, 2017 at 4:05 PM, Albert notifications@github.com wrote:

Dear Atz Togo,

My LD_LIBRARY_PATH contains /usr/local/opt/lapack/lib:/usr/local/opt/openblas/lib and

%ls /usr/local/opt/lapack/lib cmake/ libblas.dylib@ libblas.3.7.0.dylib liblapacke.dylib liblapack.3.7.0.dylib pkgconfig/ libblas.3.dylib@ liblapack.dylib@ liblapack.3.dylib@ libtmglib.dylib

%ls /usr/local/opt/openblas/lib cmake/ liblapack.dylib@ libopenblas.dylib@ libopenblas_haswellp-r0.2.19. dylib libblas.dylib@ libopenblas.a@ libopenblas_haswellp-r0.2.19.a

in setup.py i have included: include_dirs += ['/usr/local/opt/lapack/include'] include_dirs += ['/usr/local/opt/openblas/include'] extra_link_args_lapacke = ['/usr/local/opt/openblas/lib/libopenblas.a']

where %ls /usr/local/opt/lapack/include lapacke.h lapacke_config.h lapacke_mangling.h lapacke_utils.h

%ls /usr/local/opt/openblas/include cblas.h f77blas.h lapacke.h lapacke_config.h lapacke_mangling.h lapacke_utils.h openblas_config.h

and I also have tried to include in "include_dirs" not both ---lapack and openblas--- but only one of them at a time.

However, there is no lib/python folder which was created during the setup.py process therefore I don't have anything included in the PYTHONPATH. (I also tried to bind /Users/$USERNAME/.local/lib/python2.7 into PYTHONPATH which raises the same problem: """ ImportError: dlopen(/Users/glensk/Library/Caches/Python-Eggs/phono3py-1. 11.11-py2.7-macosx-10.7-x86_64.egg-tmp/phono3py/_lapackepy.so, 2): Symbol not found: __gfortran_concat_string Referenced from: /Users/glensk/Library/Caches/ Python-Eggs/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg- tmp/phono3py/_lapackepy.so Expected in: flat namespace in /Users/glensk/Library/Caches/Python-Eggs/phono3py-1.11.11- py2.7-macosx-10.7-x86_64.egg-tmp/phono3py/_lapackepy.so ) """

With respect to the linking: Since there was no error in the setup.py process, how can I check whether the linking of lapacke, lapack or blas did go well? At least phono3py is working until i execute: phono3py --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="11 11 11" --fc3 --fc2 --br

Any help is warmly welcome,

albert

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/atztogo/phono3py/issues/3#issuecomment-296548669, or mute the thread https://github.com/notifications/unsubscribe-auth/AA6MPKrjck0G9Q_cy2yW3bgqrvc9LicDks5rzEmpgaJpZM4NEVlI .

-- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz.togo@gmail.com

glensk commented 7 years ago

Dear Atz Togo,

the output in my case is very similar to yours:

gcc-6 -bundle -undefined dynamic_lookup -L/Users/glensk/anaconda2/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.7-x86_64-2.7/c/_phono3py.o build/temp.macosx-10.7-x86_64-2.7/c/harmonic/dynmat.o build/temp.macosx-10.7-x86_64-2.7/c/harmonic/lapack_wrapper.o build/temp.macosx-10.7-x86_64-2.7/c/harmonic/phonoc_array.o build/temp.macosx-10.7-x86_64-2.7/c/harmonic/phonoc_utils.o build/temp.macosx-10.7-x86_64-2.7/c/anharmonic/phonon3/fc3.o build/temp.macosx-10.7-x86_64-2.7/c/anharmonic/phonon3/frequency_shift.o build/temp.macosx-10.7-x86_64-2.7/c/anharmonic/phonon3/interaction.o build/temp.macosx-10.7-x86_64-2.7/c/anharmonic/phonon3/real_to_reciprocal.o build/temp.macosx-10.7-x86_64-2.7/c/anharmonic/phonon3/reciprocal_to_normal.o build/temp.macosx-10.7-x86_64-2.7/c/anharmonic/phonon3/imag_self_energy_with_g.o build/temp.macosx-10.7-x86_64-2.7/c/anharmonic/phonon3/pp_collision.o build/temp.macosx-10.7-x86_64-2.7/c/anharmonic/phonon3/collision_matrix.o build/temp.macosx-10.7-x86_64-2.7/c/anharmonic/other/isotope.o build/temp.macosx-10.7-x86_64-2.7/c/anharmonic/triplet/triplet.o build/temp.macosx-10.7-x86_64-2.7/c/anharmonic/triplet/ triplet_kpoint.o build/temp.macosx-10.7-x86_64-2.7/c/anharmonic/triplet/triplet_iw.o build/temp.macosx-10.7-x86_64-2.7/c/spglib/mathfunc.o build/temp.macosx-10.7-x86_64-2.7/c/spglib/kpoint.o build/temp.macosx-10.7-x86_64-2.7/c/kspclib/kgrid.o build/temp.macosx-10.7-x86_64-2.7/c/kspclib/tetrahedron_method.o -L/Users/glensk/anaconda2/lib -o build/lib.macosx-10.7-x86_64-2.7/phono3py/_phono3py.so -lgomp /usr/local/opt/openblas/lib/libopenblas.a

I use static link library of penblas and included extra_link_args_lapacke = ['/usr/local/opt/openblas/lib/libopenblas.a'] to setup.py

Just for completeness: %ls /usr/local/opt/openblas/lib cmake/ libblas.dylib@ liblapack.dylib@ libopenblas.a@ libopenblas.dylib@ libopenblas_haswellp-r0.2.19.a libopenblas_haswellp-r0.2.19.dylib

in my case, openblas include lapacke: %ls /usr/local/opt/openblas/include cblas.h f77blas.h lapacke.h lapacke_config.h lapacke_mangling.h lapacke_utils.h openblas_config.h

I installed openblas using homebrew on my mac: %brew install openblas --with-openmp

Since I have the openblas and lapack in different folder, I only adjusted this in setup.py. So I changed: 

include_dirs += ['/opt/local/include']
extra_link_args_lapacke = ['/opt/local/lib/libopenblas.a']

to include_dirs += ['/usr/local/opt/openblas/include'] extra_link_args_lapacke = ['/usr/local/opt/openblas/lib/libopenblas.a']

and the installation run smoothly:

"""" ... reating 'dist/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg' and adding 'build/bdist.macosx-10.7-x86_64/egg' to it removing 'build/bdist.macosx-10.7-x86_64/egg' (and everything under it) Processing phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg Removing /Users/glensk/.local/lib/python2.7/site-packages/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg Copying phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg to /Users/glensk/.local/lib/python2.7/site-packages phono3py 1.11.11 is already the active version in easy-install.pth Installing phono3py script to /Users/glensk/.local/bin Installing kaccum script to /Users/glensk/.local/bin Installing kdeplot script to /Users/glensk/.local/bin

Installed /Users/glensk/.local/lib/python2.7/site-packages/phono3py-1.11.11-py2.7-macosx-10.7-x86_64.egg Processing dependencies for phono3py==1.11.11 Finished processing dependencies for phono3py==1.11.11 """"

However, as mentioned, I dont obtain a lib/python folder to include to PYTHONPATH

Thank you for your quick response, albert

atztogo commented 7 years ago

Have you installed libgfortran?

Togo

atztogo commented 7 years ago

I have no idea about homebrew. So as another choice, I have tried to set-up with conda. For the combination of conda & Mac, I have updated setup.py of phono3py, and this is found in the develop branch thought the change is small.

To set-up conda, the environment variables are set for example:

export PATH=~/.miniconda2/bin:~/.local/bin:$PATH
export C_INCLUDE_PATH=~/.miniconda2/include

Then

% wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh
% bash miniconda.sh -b -p $HOME/.miniconda2
% conda update --yes conda
% conda install --yes python=2 numpy scipy h5py pyyaml matplotlib openblas
(I use gcc6 from MacPort.)
% export CC=gcc
(If phonopy is not installed, then under the directory where phonopy setup.py exists)
% python setup.py install --user
(under the directory where phono3py setup.py exists)
% echo "extra_link_args_lapacke = ['-lopenblas']" |tee libopenblas.py
% python setup.py install --user

This worked on my Mac after removing conflicting packages from MacPort. But finally you will need more powerful computer.

glensk commented 7 years ago

Dear Atz Togo!

so great! Thank you very much! With your latest change it is now easily possible to use phono3py on my mac (where I dont use MacPorts but rather Homebrew).

For my mac however I had to download Miniconda (from here and install by

bash Miniconda2-latest-MacOSX-x86_64.sh -b -p $HOME/.miniconda2

(the wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh was not working in my case)

I also used export CC=gcc-6 installed by homebrew (brew reinstall gcc --without-multilib)

Thank you very much! Your Help is sincerely appreciated,

albert

PS: is it possible to include this in the "normal" phonopy rather than just in the develop branch? What were the changes?

With this, I think, you can set this issue as settled :)

atztogo commented 7 years ago

I merged the change into the master branch of phono3py, which means the change is released. The change is this, 32de7f51578ab7753dc12dcf79114a4f83d72665. I just make setup.py on Mac to use extra_link_args_lapacke = ['-lopenblas'] (the content in libopenblas.py) instead of extra_link_args_lapacke = ['-llapacke', '-llapack', '-lblas'] when libopenblas.py exists.