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tfrederiksen / inelastica

Python package for eigenchannels, vibrations and inelastic electron transport based on SIESTA/TranSIESTA DFT
https://tfrederiksen.github.io/inelastica
GNU Lesser General Public License v3.0
33 stars 16 forks source link

Inelastica installation issue with python3 #60

Closed el-abed closed 4 years ago

el-abed commented 4 years ago

Good evening all, I installed inelastica using python3 and it seems successful. I found two folders inelastica 1.3.6 and Inelastica.

I wanted to test it and I got the following error: _Problems encountered with F90helpers.so Falling back on a pure python (slower) implementation Try compiling manually following these steps: $ cd Inelastica/fortran $ source compile.bat (or compilealternative.bat) $ cp F90helpers.so /site-packages/Inelastica/fortran

So i did that and thought it would work but still got the same error. Then i used: EigenChannels -M 1 FOLDER/ >update5.txt to track every second within the txt file and I got the following:

Traceback (most recent call last): File "/home/562/eh8122/.local/lib/python3.7/site-packages/inelastica-1.3.6/bin/EigenChannels", line 11, in Module.main(options) File "/home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/EigenChannels.py", line 135, in main VC.OptionsCheck(options) File "/home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/misc/valuecheck.py", line 217, in OptionsCheck opts.buffer, L, R = SIO.GetBufferAtomsList(opts.TSHS, opts.fn) File "/home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/io/siesta.py", line 1884, in GetBufferAtomsList d = ReadTSHS(fn, nua=True) File "/home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/io/siesta.py", line 1874, in ReadTSHS nou, nos, nspin, nua, maxnh = F90.readtshs.read_size(fn) NameError: name 'F90' is not defined

So I am not sure what went wrong and hope i could get assistance with such issue. Thank you and looking forward to your replies. EL-abed

zerothi commented 4 years ago

Could you please do a regular installation using python3 setup.py install, and give the full output.

el-abed commented 4 years ago

I have been told to use python3 setup.py install --user which got me the following:

system_info:
  NOT AVAILABLE

lapack_opt_info:
lapack_mkl_info:
customize UnixCCompiler
  FOUND:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/apps/intel-ct/2019.3.199/mkl/lib/intel64/']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    include_dirs = ['/apps/intel-ct/2019.3.199/mkl', '/apps/intel-ct/2019.3.199/mkl/include', '/apps/intel-ct/2019.3.199/mkl/lib']

  FOUND:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/apps/intel-ct/2019.3.199/mkl/lib/intel64/']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    include_dirs = ['/apps/intel-ct/2019.3.199/mkl', '/apps/intel-ct/2019.3.199/mkl/include', '/apps/intel-ct/2019.3.199/mkl/lib']

running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building py_modules sources
building extension "Inelastica.fortran.F90helpers" sources
f2py options: []
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran' to include_dirs.
  adding 'build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90' to sources.
building extension "Inelastica.fortran.F90_lapack" sources
f2py options: []
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran' to include_dirs.
build_src: building npy-pkg config files
running build_py
copying Inelastica/info.py -> build/lib.linux-x86_64-3.7/Inelastica
copying build/src.linux-x86_64-3.7/Inelastica/__config__.py -> build/lib.linux-x86_64-3.7/Inelastica
copying build/src.linux-x86_64-3.7/Inelastica/fortran/__config__.py -> build/lib.linux-x86_64-3.7/Inelastica/fortran
copying build/src.linux-x86_64-3.7/Inelastica/io/__config__.py -> build/lib.linux-x86_64-3.7/Inelastica/io
copying build/src.linux-x86_64-3.7/Inelastica/physics/__config__.py -> build/lib.linux-x86_64-3.7/Inelastica/physics
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /opt/nci/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
running build_scripts
running install_lib
copying build/lib.linux-x86_64-3.7/Inelastica/fortran/__config__.py -> /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/fortran
copying build/lib.linux-x86_64-3.7/Inelastica/io/__config__.py -> /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/io
copying build/lib.linux-x86_64-3.7/Inelastica/__config__.py -> /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica
copying build/lib.linux-x86_64-3.7/Inelastica/info.py -> /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica
copying build/lib.linux-x86_64-3.7/Inelastica/physics/__config__.py -> /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/physics
byte-compiling /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/fortran/__config__.py to __config__.cpython-37.pyc
byte-compiling /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/SupercellPhonons.py to SupercellPhonons.cpython-37.pyc
  File "/home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/SupercellPhonons.py", line 406
    ge.SetYaxis(vmin=-20, vmax=20, label='E-E\sF\N (eV)', majorUnit=5.0)
                                        ^
SyntaxError: (unicode error) 'unicodeescape' codec can't decode bytes in position 6-7: malformed \N character escape

byte-compiling /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/pyTBT.py to pyTBT.cpython-37.pyc
  File "/home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/pyTBT.py", line 384
    g.SetXaxis(label='E-E\sF\N (eV)', autoscale=True)
                    ^
SyntaxError: (unicode error) 'unicodeescape' codec can't decode bytes in position 6-7: malformed \N character escape

byte-compiling /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/io/__config__.py to __config__.cpython-37.pyc
byte-compiling /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/__config__.py to __config__.cpython-37.pyc
byte-compiling /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/info.py to info.cpython-37.pyc
byte-compiling /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica/physics/__config__.py to __config__.cpython-37.pyc
running install_scripts
changing mode of /home/562/eh8122/.local/bin/agr2pdf to 755
changing mode of /home/562/eh8122/.local/bin/Inelastica to 755
changing mode of /home/562/eh8122/.local/bin/Vasp2Siesta to 755
changing mode of /home/562/eh8122/.local/bin/Phonons to 755
changing mode of /home/562/eh8122/.local/bin/geom2zmat to 755
changing mode of /home/562/eh8122/.local/bin/geom2geom to 755
changing mode of /home/562/eh8122/.local/bin/bands2xmgr to 755
changing mode of /home/562/eh8122/.local/bin/ComputeDOS to 755
changing mode of /home/562/eh8122/.local/bin/WriteWavefunctions to 755
changing mode of /home/562/eh8122/.local/bin/kaverage-TBT to 755
changing mode of /home/562/eh8122/.local/bin/grid2grid to 755
changing mode of /home/562/eh8122/.local/bin/setupFCrun to 755
changing mode of /home/562/eh8122/.local/bin/siesta_cleanup to 755
changing mode of /home/562/eh8122/.local/bin/STM to 755
changing mode of /home/562/eh8122/.local/bin/EigenChannels to 755
changing mode of /home/562/eh8122/.local/bin/pyTBT to 755
changing mode of /home/562/eh8122/.local/bin/Bandstructures to 755
changing mode of /home/562/eh8122/.local/bin/NEB to 755
changing mode of /home/562/eh8122/.local/bin/setupOSrun to 755
changing mode of /home/562/eh8122/.local/bin/kaverage-IETS to 755
changing mode of /home/562/eh8122/.local/bin/average-gridfunc to 755
running install_egg_info
Removing /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica-0.0.0-py3.7.egg-info
Writing /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica-0.0.0-py3.7.egg-info
running install_clib
customize UnixCCompiler
el-abed commented 4 years ago

If i use only python3 setup.py install i get the following not sure if it would help:

system_info:
  NOT AVAILABLE

lapack_opt_info:
lapack_mkl_info:
customize UnixCCompiler
  FOUND:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/apps/intel-ct/2019.3.199/mkl/lib/intel64/']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    include_dirs = ['/apps/intel-ct/2019.3.199/mkl', '/apps/intel-ct/2019.3.199/mkl/include', '/apps/intel-ct/2019.3.199/mkl/lib']

  FOUND:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/apps/intel-ct/2019.3.199/mkl/lib/intel64/']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    include_dirs = ['/apps/intel-ct/2019.3.199/mkl', '/apps/intel-ct/2019.3.199/mkl/include', '/apps/intel-ct/2019.3.199/mkl/lib']

running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building py_modules sources
building extension "Inelastica.fortran.F90helpers" sources
f2py options: []
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran' to include_dirs.
  adding 'build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90' to sources.
building extension "Inelastica.fortran.F90_lapack" sources
f2py options: []
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran' to include_dirs.
build_src: building npy-pkg config files
running build_py
copying Inelastica/info.py -> build/lib.linux-x86_64-3.7/Inelastica
copying build/src.linux-x86_64-3.7/Inelastica/__config__.py -> build/lib.linux-x86_64-3.7/Inelastica
copying build/src.linux-x86_64-3.7/Inelastica/fortran/__config__.py -> build/lib.linux-x86_64-3.7/Inelastica/fortran
copying build/src.linux-x86_64-3.7/Inelastica/io/__config__.py -> build/lib.linux-x86_64-3.7/Inelastica/io
copying build/src.linux-x86_64-3.7/Inelastica/physics/__config__.py -> build/lib.linux-x86_64-3.7/Inelastica/physics
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /opt/nci/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
running build_scripts
running install_lib
creating /apps/python3/3.7.4/lib/python3.7/site-packages/Inelastica
error: could not create '/apps/python3/3.7.4/lib/python3.7/site-packages/Inelastica': Read-only file system
zerothi commented 4 years ago

Yeah, these bugs have already been fixed. Could you please download the latest commit (git clone) and install the development version. Please report back if it works!

@tfrederiksen if this fixes the installation procedure; a new release should be done to fix these Py3 errors.

el-abed commented 4 years ago

I got much more warnings than before to be honest: system_info: NOT AVAILABLE

lapack_opt_info: lapack_mkl_info: customize UnixCCompiler FOUND: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/apps/intel-ct/2019.3.199/mkl/lib/intel64/'] define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)] include_dirs = ['/apps/intel-ct/2019.3.199/mkl', '/apps/intel-ct/2019.3.199/mkl/include', '/apps/intel-ct/2019.3.199/mkl/lib']

FOUND: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/apps/intel-ct/2019.3.199/mkl/lib/intel64/'] define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)] include_dirs = ['/apps/intel-ct/2019.3.199/mkl', '/apps/intel-ct/2019.3.199/mkl/include', '/apps/intel-ct/2019.3.199/mkl/lib']

running install running bdist_egg running egg_info running build_src build_src building py_modules sources creating build creating build/src.linux-x86_64-3.7 creating build/src.linux-x86_64-3.7/Inelastica creating build/src.linux-x86_64-3.7/Inelastica/fortran creating build/src.linux-x86_64-3.7/Inelastica/io creating build/src.linux-x86_64-3.7/Inelastica/physics building extension "Inelastica.fortran.F90helpers" sources f2py options: [] f2py:> build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c Reading fortran codes... Reading file 'Inelastica/fortran/expansion_SE.f90' (format:free) Reading file 'Inelastica/fortran/readTSHS.f90' (format:free) Reading file 'Inelastica/fortran/removeUnitCellXij.f90' (format:free) Reading file 'Inelastica/fortran/setkpointhelper.f90' (format:free) Post-processing... Block: F90helpers Block: expansion_se Block: readtshs Block: deallocate Block: read_size Block: read Block: remove_atoms Block: tshs_version Block: ucorb Block: removeunitcellxij Block: setkpointhelper Post-processing (stage 2)... Block: F90helpers Block: unknown_interface Block: expansion_se Block: readtshs Block: deallocate Block: read_size Block: read Block: remove_atoms Block: tshs_version Block: ucorb Block: removeunitcellxij Block: setkpointhelper Building modules... Building module "F90helpers"... Constructing wrapper function "expansion_se"... oesh,sgf = expansion_se(no_s,na1,na2,kpt,lasto,esh,g0,[no_u,na_u]) Constructing wrapper function "removeunitcellxij"... xij = removeunitcellxij(numh,xij,xa,listh,atomindx,[nnzs,no_u,na_u]) Constructing wrapper function "setkpointhelper"... full = setkpointhelper(sparse,kpoint,numh,rcell,xij,listhptr,listh,[nnzs,no_u]) Constructing F90 module support for "readtshs"... Variables: version s h xij xa listhptr numh listh lasto getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' Constructing wrapper function "readtshs.deallocate"... deallocate() Constructing wrapper function "readtshs.read_size"... no_u,no_s,nspin,na_u,maxnh = read_size(fname) Constructing wrapper function "readtshs.read"... gamma,onlys,no_u,no_s,nspin,maxnh,qtot,temp,na_u,ef,ucell,ts_kscell,ts_kdispl,ts_gamma_scf,istep,ia1 = read(fname) Creating wrapper for Fortran subroutine "remove_atoms"("remove_atoms")... Constructing wrapper function "readtshs.remove_atoms"... na_u,no_u,maxnh = remove_atoms(list) Creating wrapper for Fortran function "tshs_version"("tshs_version")... Constructing wrapper function "readtshs.tshs_version"... version = tshs_version(fname) Creating wrapper for Fortran function "ucorb"("ucorb")... Constructing wrapper function "readtshs.ucorb"... modp = ucorb(a,p) Wrote C/API module "F90helpers" to file "build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c" Fortran 90 wrappers are saved to "build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90" adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran' to include_dirs. creating build/src.linux-x86_64-3.7/build creating build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7 creating build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica creating build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran copying /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/f2py/src/fortranobject.c -> build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran copying /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/f2py/src/fortranobject.h -> build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran adding 'build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90' to sources. building extension "Inelastica.fortran.F90_lapack" sources f2py options: [] f2py:> build/src.linux-x86_64-3.7/Inelastica/fortran/F90_lapackmodule.c Reading fortran codes... Reading file 'Inelastica/fortran/surfaceGreen.f90' (format:free) Post-processing... Block: F90_lapack Block: surfacegreen In: :F90_lapack:Inelastica/fortran/surfaceGreen.f90:surfacegreen get_parameters: got "name 'dcmplx' is not defined" on 'dcmplx(1.,0.)' In: :F90_lapack:Inelastica/fortran/surfaceGreen.f90:surfacegreen get_parameters: got "name 'dcmplx' is not defined" on 'dcmplx(-1.,0.)' In: :F90_lapack:Inelastica/fortran/surfaceGreen.f90:surfacegreen get_parameters: got "name 'dcmplx' is not defined" on 'dcmplx(0.,0.)' Post-processing (stage 2)... Building modules... Building module "F90_lapack"... Constructing wrapper function "surfacegreen"... gs = surfacegreen(no,ze,h00,s00,h01,s01,accur,is_left) Wrote C/API module "F90_lapack" to file "build/src.linux-x86_64-3.7/Inelastica/fortran/F90_lapackmodule.c" adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran' to include_dirs. build_src: building npy-pkg config files creating Inelastica.egg-info writing Inelastica.egg-info/PKG-INFO writing dependency_links to Inelastica.egg-info/dependency_links.txt writing top-level names to Inelastica.egg-info/top_level.txt writing manifest file 'Inelastica.egg-info/SOURCES.txt' reading manifest file 'Inelastica.egg-info/SOURCES.txt' writing manifest file 'Inelastica.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/SupercellPhonons.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/BandStruct.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/iets.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/pyTBT.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/NEGF.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/EigenChannels.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/NEB.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/SetupRuns.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/STMFD.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/STM.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/info.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/setup.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/MakeGeom.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/Symmetry.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/Phonons.py -> build/lib.linux-x86_64-3.7/Inelastica copying Inelastica/init.py -> build/lib.linux-x86_64-3.7/Inelastica copying build/src.linux-x86_64-3.7/Inelastica/config.py -> build/lib.linux-x86_64-3.7/Inelastica creating build/lib.linux-x86_64-3.7/Inelastica/fortran copying Inelastica/fortran/setup.py -> build/lib.linux-x86_64-3.7/Inelastica/fortran copying Inelastica/fortran/init.py -> build/lib.linux-x86_64-3.7/Inelastica/fortran copying build/src.linux-x86_64-3.7/Inelastica/fortran/config.py -> build/lib.linux-x86_64-3.7/Inelastica/fortran creating build/lib.linux-x86_64-3.7/Inelastica/math copying Inelastica/math/gausskronrod.py -> build/lib.linux-x86_64-3.7/Inelastica/math copying Inelastica/math/spectral.py -> build/lib.linux-x86_64-3.7/Inelastica/math copying Inelastica/math/misc.py -> build/lib.linux-x86_64-3.7/Inelastica/math copying Inelastica/math/sphericalharmonics.py -> build/lib.linux-x86_64-3.7/Inelastica/math copying Inelastica/math/hilbert.py -> build/lib.linux-x86_64-3.7/Inelastica/math copying Inelastica/math/init.py -> build/lib.linux-x86_64-3.7/Inelastica/math creating build/lib.linux-x86_64-3.7/Inelastica/io copying Inelastica/io/netcdf.py -> build/lib.linux-x86_64-3.7/Inelastica/io copying Inelastica/io/siesta.py -> build/lib.linux-x86_64-3.7/Inelastica/io copying Inelastica/io/setup.py -> build/lib.linux-x86_64-3.7/Inelastica/io copying Inelastica/io/vasp.py -> build/lib.linux-x86_64-3.7/Inelastica/io copying Inelastica/io/log.py -> build/lib.linux-x86_64-3.7/Inelastica/io copying Inelastica/io/xmgrace.py -> build/lib.linux-x86_64-3.7/Inelastica/io copying Inelastica/io/init.py -> build/lib.linux-x86_64-3.7/Inelastica/io copying build/src.linux-x86_64-3.7/Inelastica/io/config.py -> build/lib.linux-x86_64-3.7/Inelastica/io creating build/lib.linux-x86_64-3.7/Inelastica/misc copying Inelastica/misc/valuecheck.py -> build/lib.linux-x86_64-3.7/Inelastica/misc copying Inelastica/misc/multiproc.py -> build/lib.linux-x86_64-3.7/Inelastica/misc copying Inelastica/misc/init.py -> build/lib.linux-x86_64-3.7/Inelastica/misc creating build/lib.linux-x86_64-3.7/Inelastica/physics copying Inelastica/physics/constants.py -> build/lib.linux-x86_64-3.7/Inelastica/physics copying Inelastica/physics/mesh.py -> build/lib.linux-x86_64-3.7/Inelastica/physics copying Inelastica/physics/setup.py -> build/lib.linux-x86_64-3.7/Inelastica/physics copying Inelastica/physics/init.py -> build/lib.linux-x86_64-3.7/Inelastica/physics copying build/src.linux-x86_64-3.7/Inelastica/physics/config.py -> build/lib.linux-x86_64-3.7/Inelastica/physics running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']' customize Gnu95FCompiler Found executable /opt/nci/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using build_ext building 'Inelastica.fortran.F90helpers' extension compiling C sources C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

creating build/temp.linux-x86_64-3.7/build creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran -I/apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include -I/apps/python3/3.7.4/include/python3.7m -c' gcc: build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c gcc: build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.c In file included from /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1830, from /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:12, from /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/arrayobject.h:4, from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.h:13, from build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c:16: /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

warning "Using deprecated NumPy API, disable it with " \

^~~ In file included from /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1830, from /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:12, from /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/arrayobject.h:4, from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.h:13, from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.c:2: /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

warning "Using deprecated NumPy API, disable it with " \

^~~ build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c: In function ‘f2py_setup_readtshs’: build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c:1572:36: warning: assignment to ‘f2py_init_func’ {aka ‘void ()(int , long int , void ()(char , long int ), int )’} from incompatible pointer type ‘void ()(int , int , void ()(char , int ), int )’ [-Wincompatible-pointer-types] f2py_readtshs_def[i_f2py++].func = s; ^ build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c:1573:36: warning: assignment to ‘f2py_init_func’ {aka ‘void ()(int , long int , void ()(char , long int ), int )’} from incompatible pointer type ‘void ()(int , int , void ()(char , int ), int )’ [-Wincompatible-pointer-types] f2py_readtshs_def[i_f2py++].func = h; ^ build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c:1574:36: warning: assignment to ‘f2py_init_func’ {aka ‘void ()(int , long int , void ()(char , long int ), int )’} from incompatible pointer type ‘void ()(int , int , void ()(char , int ), int )’ [-Wincompatible-pointer-types] f2py_readtshs_def[i_f2py++].func = xij; ^ build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c:1575:36: warning: assignment to ‘f2py_init_func’ {aka ‘void ()(int , long int , void ()(char , long int ), int )’} from incompatible pointer type ‘void ()(int , int , void ()(char , int ), int )’ [-Wincompatible-pointer-types] f2py_readtshs_def[i_f2py++].func = xa; ^ build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c:1576:36: warning: assignment to ‘f2py_init_func’ {aka ‘void ()(int , long int , void ()(char , long int ), int )’} from incompatible pointer type ‘void ()(int , int , void ()(char , int ), int )’ [-Wincompatible-pointer-types] f2py_readtshs_def[i_f2py++].func = listhptr; ^ build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c:1577:36: warning: assignment to ‘f2py_init_func’ {aka ‘void ()(int , long int , void ()(char , long int ), int )’} from incompatible pointer type ‘void ()(int , int , void ()(char , int ), int )’ [-Wincompatible-pointer-types] f2py_readtshs_def[i_f2py++].func = numh; ^ build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c:1578:36: warning: assignment to ‘f2py_init_func’ {aka ‘void ()(int , long int , void ()(char , long int ), int )’} from incompatible pointer type ‘void ()(int , int , void ()(char , int ), int )’ [-Wincompatible-pointer-types] f2py_readtshs_def[i_f2py++].func = listh; ^ build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c:1579:36: warning: assignment to ‘f2py_init_func’ {aka ‘void ()(int , long int , void ()(char , long int ), int )’} from incompatible pointer type ‘void ()(int , int , void ()(char , int ), int )’ [-Wincompatible-pointer-types] f2py_readtshs_def[i_f2py++].func = lasto; ^ At top level: build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c:143:12: warning: ‘f2py_size’ defined but not used [-Wunused-function] static int f2py_size(PyArrayObject* var, ...) ^~~~~ compiling Fortran 90 module sources creating build/temp.linux-x86_64-3.7/Inelastica creating build/temp.linux-x86_64-3.7/Inelastica/fortran Fortran f77 compiler: /opt/nci/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /opt/nci/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops Fortran fix compiler: /opt/nci/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran -I/apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include -I/apps/python3/3.7.4/include/python3.7m -c' extra options: '-Jbuild/temp.linux-x86_64-3.7/Inelastica/fortran -Ibuild/temp.linux-x86_64-3.7/Inelastica/fortran' gfortran:f90: Inelastica/fortran/readTSHS.f90 Inelastica/fortran/readTSHS.f90:307:0:

 real(kind=8), allocatable :: nH(:,:)

Warning: ‘nh.dim[1].ubound’ may be used uninitialized in this function [-Wmaybe-uninitialized] Inelastica/fortran/readTSHS.f90:307:0: Warning: ‘nh.dim[1].stride’ may be used uninitialized in this function [-Wmaybe-uninitialized] Inelastica/fortran/readTSHS.f90:451:0:

    H = nH

Warning: ‘nh.dim[0].ubound’ may be used uninitialized in this function [-Wmaybe-uninitialized] Inelastica/fortran/readTSHS.f90:420:0:

          nH(nind,:) = H(ind,:)

Warning: ‘nh.offset’ may be used uninitialized in this function [-Wmaybe-uninitialized] compiling Fortran sources Fortran f77 compiler: /opt/nci/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /opt/nci/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops Fortran fix compiler: /opt/nci/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran -I/apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include -I/apps/python3/3.7.4/include/python3.7m -c' extra options: '-Jbuild/temp.linux-x86_64-3.7/Inelastica/fortran -Ibuild/temp.linux-x86_64-3.7/Inelastica/fortran' gfortran:f90: Inelastica/fortran/expansion_SE.f90 gfortran:f90: Inelastica/fortran/removeUnitCellXij.f90 gfortran:f90: Inelastica/fortran/setkpointhelper.f90 gfortran:f90: build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90 build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90:271:10:

   use readtshs, only : version
      1

Warning: Unused module variable ‘h’ which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90:271:10:

   use readtshs, only : version
      1

Warning: Unused module variable ‘lasto’ which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90:271:10:

   use readtshs, only : version
      1

Warning: Unused module variable ‘listh’ which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90:271:10:

   use readtshs, only : version
      1

Warning: Unused module variable ‘listhptr’ which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90:271:10:

   use readtshs, only : version
      1

Warning: Unused module variable ‘numh’ which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90:271:10:

   use readtshs, only : version
      1

Warning: Unused module variable ‘s’ which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90:271:10:

   use readtshs, only : version
      1

Warning: Unused module variable ‘xa’ which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90:271:10:

   use readtshs, only : version
      1

Warning: Unused module variable ‘xij’ which has been explicitly imported at (1) [-Wunused-variable] /opt/nci/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.o build/temp.linux-x86_64-3.7/Inelastica/fortran/readTSHS.o build/temp.linux-x86_64-3.7/Inelastica/fortran/expansion_SE.o build/temp.linux-x86_64-3.7/Inelastica/fortran/removeUnitCellXij.o build/temp.linux-x86_64-3.7/Inelastica/fortran/setkpointhelper.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.o -L/half-root/usr/bin/../lib/gcc/x86_64-redhat-linux/8 -L/half-root/usr/bin/../lib/gcc/x86_64-redhat-linux/8 -L/apps/python3/3.7.4/lib -lpython3.7m -lgfortran -o build/lib.linux-x86_64-3.7/Inelastica/fortran/F90helpers.cpython-37m-x86_64-linux-gnu.so building 'Inelastica.fortran.F90_lapack' extension compiling C sources C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

compile options: '-DSCIPY_MKL_H -DHAVE_CBLAS -I/apps/intel-ct/2019.3.199/mkl -I/apps/intel-ct/2019.3.199/mkl/include -I/apps/intel-ct/2019.3.199/mkl/lib -Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran -I/apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include -I/apps/python3/3.7.4/include/python3.7m -c' gcc: build/src.linux-x86_64-3.7/Inelastica/fortran/F90_lapackmodule.c gcc: build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.c In file included from /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1830, from /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:12, from /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/arrayobject.h:4, from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.h:13, from build/src.linux-x86_64-3.7/Inelastica/fortran/F90_lapackmodule.c:16: /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

warning "Using deprecated NumPy API, disable it with " \

^~~ In file included from /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1830, from /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:12, from /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/arrayobject.h:4, from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.h:13, from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.c:2: /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

warning "Using deprecated NumPy API, disable it with " \

^~~ build/src.linux-x86_64-3.7/Inelastica/fortran/F90_lapackmodule.c:103:12: warning: ‘f2py_size’ defined but not used [-Wunused-function] static int f2py_size(PyArrayObject* var, ...) ^~~~~ compiling Fortran sources Fortran f77 compiler: /opt/nci/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /opt/nci/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops Fortran fix compiler: /opt/nci/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops compile options: '-DSCIPY_MKL_H -DHAVE_CBLAS -I/apps/intel-ct/2019.3.199/mkl -I/apps/intel-ct/2019.3.199/mkl/include -I/apps/intel-ct/2019.3.199/mkl/lib -Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran -I/apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/core/include -I/apps/python3/3.7.4/include/python3.7m -c' gfortran:f90: Inelastica/fortran/surfaceGreen.f90 /opt/nci/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/F90_lapackmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.o build/temp.linux-x86_64-3.7/Inelastica/fortran/surfaceGreen.o -L/apps/intel-ct/2019.3.199/mkl/lib/intel64/ -L/half-root/usr/bin/../lib/gcc/x86_64-redhat-linux/8 -L/half-root/usr/bin/../lib/gcc/x86_64-redhat-linux/8 -L/apps/python3/3.7.4/lib -lmkl_rt -lpthread -lpython3.7m -lgfortran -o build/lib.linux-x86_64-3.7/Inelastica/fortran/F90_lapack.cpython-37m-x86_64-linux-gnu.so creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/Inelastica creating build/bdist.linux-x86_64/egg/Inelastica/fortran copying build/lib.linux-x86_64-3.7/Inelastica/fortran/F90_lapack.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/egg/Inelastica/fortran copying build/lib.linux-x86_64-3.7/Inelastica/fortran/config.py -> build/bdist.linux-x86_64/egg/Inelastica/fortran copying build/lib.linux-x86_64-3.7/Inelastica/fortran/F90helpers.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/egg/Inelastica/fortran copying build/lib.linux-x86_64-3.7/Inelastica/fortran/setup.py -> build/bdist.linux-x86_64/egg/Inelastica/fortran copying build/lib.linux-x86_64-3.7/Inelastica/fortran/init.py -> build/bdist.linux-x86_64/egg/Inelastica/fortran copying build/lib.linux-x86_64-3.7/Inelastica/SupercellPhonons.py -> build/bdist.linux-x86_64/egg/Inelastica copying build/lib.linux-x86_64-3.7/Inelastica/BandStruct.py -> build/bdist.linux-x86_64/egg/Inelastica copying build/lib.linux-x86_64-3.7/Inelastica/iets.py -> build/bdist.linux-x86_64/egg/Inelastica copying build/lib.linux-x86_64-3.7/Inelastica/pyTBT.py -> build/bdist.linux-x86_64/egg/Inelastica creating build/bdist.linux-x86_64/egg/Inelastica/math copying build/lib.linux-x86_64-3.7/Inelastica/math/gausskronrod.py -> build/bdist.linux-x86_64/egg/Inelastica/math copying build/lib.linux-x86_64-3.7/Inelastica/math/spectral.py -> build/bdist.linux-x86_64/egg/Inelastica/math copying build/lib.linux-x86_64-3.7/Inelastica/math/misc.py -> build/bdist.linux-x86_64/egg/Inelastica/math copying build/lib.linux-x86_64-3.7/Inelastica/math/sphericalharmonics.py -> build/bdist.linux-x86_64/egg/Inelastica/math copying build/lib.linux-x86_64-3.7/Inelastica/math/hilbert.py -> build/bdist.linux-x86_64/egg/Inelastica/math copying build/lib.linux-x86_64-3.7/Inelastica/math/init.py -> build/bdist.linux-x86_64/egg/Inelastica/math copying build/lib.linux-x86_64-3.7/Inelastica/NEGF.py -> build/bdist.linux-x86_64/egg/Inelastica creating build/bdist.linux-x86_64/egg/Inelastica/io copying build/lib.linux-x86_64-3.7/Inelastica/io/netcdf.py -> build/bdist.linux-x86_64/egg/Inelastica/io copying build/lib.linux-x86_64-3.7/Inelastica/io/siesta.py -> build/bdist.linux-x86_64/egg/Inelastica/io copying build/lib.linux-x86_64-3.7/Inelastica/io/config.py -> build/bdist.linux-x86_64/egg/Inelastica/io copying build/lib.linux-x86_64-3.7/Inelastica/io/setup.py -> build/bdist.linux-x86_64/egg/Inelastica/io copying build/lib.linux-x86_64-3.7/Inelastica/io/vasp.py -> build/bdist.linux-x86_64/egg/Inelastica/io copying build/lib.linux-x86_64-3.7/Inelastica/io/log.py -> build/bdist.linux-x86_64/egg/Inelastica/io copying build/lib.linux-x86_64-3.7/Inelastica/io/xmgrace.py -> build/bdist.linux-x86_64/egg/Inelastica/io copying build/lib.linux-x86_64-3.7/Inelastica/io/init.py -> build/bdist.linux-x86_64/egg/Inelastica/io copying build/lib.linux-x86_64-3.7/Inelastica/config.py -> build/bdist.linux-x86_64/egg/Inelastica copying build/lib.linux-x86_64-3.7/Inelastica/EigenChannels.py -> build/bdist.linux-x86_64/egg/Inelastica creating build/bdist.linux-x86_64/egg/Inelastica/misc copying build/lib.linux-x86_64-3.7/Inelastica/misc/valuecheck.py -> build/bdist.linux-x86_64/egg/Inelastica/misc copying build/lib.linux-x86_64-3.7/Inelastica/misc/multiproc.py -> build/bdist.linux-x86_64/egg/Inelastica/misc copying build/lib.linux-x86_64-3.7/Inelastica/misc/init.py -> build/bdist.linux-x86_64/egg/Inelastica/misc copying build/lib.linux-x86_64-3.7/Inelastica/NEB.py -> build/bdist.linux-x86_64/egg/Inelastica copying build/lib.linux-x86_64-3.7/Inelastica/SetupRuns.py -> build/bdist.linux-x86_64/egg/Inelastica copying build/lib.linux-x86_64-3.7/Inelastica/STMFD.py -> build/bdist.linux-x86_64/egg/Inelastica copying build/lib.linux-x86_64-3.7/Inelastica/STM.py -> build/bdist.linux-x86_64/egg/Inelastica copying build/lib.linux-x86_64-3.7/Inelastica/info.py -> build/bdist.linux-x86_64/egg/Inelastica copying build/lib.linux-x86_64-3.7/Inelastica/setup.py -> build/bdist.linux-x86_64/egg/Inelastica copying build/lib.linux-x86_64-3.7/Inelastica/MakeGeom.py -> build/bdist.linux-x86_64/egg/Inelastica creating build/bdist.linux-x86_64/egg/Inelastica/physics copying build/lib.linux-x86_64-3.7/Inelastica/physics/constants.py -> build/bdist.linux-x86_64/egg/Inelastica/physics copying build/lib.linux-x86_64-3.7/Inelastica/physics/config.py -> build/bdist.linux-x86_64/egg/Inelastica/physics copying build/lib.linux-x86_64-3.7/Inelastica/physics/mesh.py -> build/bdist.linux-x86_64/egg/Inelastica/physics copying build/lib.linux-x86_64-3.7/Inelastica/physics/setup.py -> build/bdist.linux-x86_64/egg/Inelastica/physics copying build/lib.linux-x86_64-3.7/Inelastica/physics/init.py -> build/bdist.linux-x86_64/egg/Inelastica/physics copying build/lib.linux-x86_64-3.7/Inelastica/Symmetry.py -> build/bdist.linux-x86_64/egg/Inelastica copying build/lib.linux-x86_64-3.7/Inelastica/Phonons.py -> build/bdist.linux-x86_64/egg/Inelastica copying build/lib.linux-x86_64-3.7/Inelastica/init.py -> build/bdist.linux-x86_64/egg/Inelastica byte-compiling build/bdist.linux-x86_64/egg/Inelastica/fortran/config.py to config.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/fortran/setup.py to setup.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/fortran/init.py to init.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/SupercellPhonons.py to SupercellPhonons.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/BandStruct.py to BandStruct.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/iets.py to iets.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/pyTBT.py to pyTBT.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/math/gausskronrod.py to gausskronrod.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/math/spectral.py to spectral.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/math/misc.py to misc.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/math/sphericalharmonics.py to sphericalharmonics.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/math/hilbert.py to hilbert.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/math/init.py to init.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/NEGF.py to NEGF.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/io/netcdf.py to netcdf.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/io/siesta.py to siesta.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/io/config.py to config.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/io/setup.py to setup.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/io/vasp.py to vasp.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/io/log.py to log.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/io/xmgrace.py to xmgrace.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/io/init.py to init.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/config.py to config.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/EigenChannels.py to EigenChannels.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/misc/valuecheck.py to valuecheck.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/misc/multiproc.py to multiproc.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/misc/init.py to init.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/NEB.py to NEB.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/SetupRuns.py to SetupRuns.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/STMFD.py to STMFD.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/STM.py to STM.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/info.py to info.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/setup.py to setup.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/MakeGeom.py to MakeGeom.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/physics/constants.py to constants.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/physics/config.py to config.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/physics/mesh.py to mesh.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/physics/setup.py to setup.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/physics/init.py to init.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/Symmetry.py to Symmetry.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/Phonons.py to Phonons.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/init.py to init.cpython-37.pyc creating stub loader for Inelastica/fortran/F90helpers.cpython-37m-x86_64-linux-gnu.so creating stub loader for Inelastica/fortran/F90_lapack.cpython-37m-x86_64-linux-gnu.so byte-compiling build/bdist.linux-x86_64/egg/Inelastica/fortran/F90helpers.py to F90helpers.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/Inelastica/fortran/F90_lapack.py to F90_lapack.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts running install_scripts running build_scripts creating build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/Inelastica -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/EigenChannels -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/pyTBT -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/geom2geom -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/geom2zmat -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/Bandstructures -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/ComputeDOS -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/Vasp2Siesta -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/Phonons -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/NEB -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/grid2grid -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/setupFCrun -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/setupOSrun -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/kaverage-TBT -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/STM -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/kaverage-IETS -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/average-gridfunc -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/scripts/WriteWavefunctions -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/utils/agr2pdf -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/utils/bands2xmgr -> build/scripts.linux-x86_64-3.7 copying and adjusting Inelastica/utils/siesta_cleanup -> build/scripts.linux-x86_64-3.7 changing mode of build/scripts.linux-x86_64-3.7/Inelastica from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/EigenChannels from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/pyTBT from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/geom2geom from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/geom2zmat from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/Bandstructures from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/ComputeDOS from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/Vasp2Siesta from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/Phonons from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/NEB from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/grid2grid from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/setupFCrun from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/setupOSrun from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/kaverage-TBT from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/STM from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/kaverage-IETS from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/average-gridfunc from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/WriteWavefunctions from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/agr2pdf from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/bands2xmgr from 644 to 755 changing mode of build/scripts.linux-x86_64-3.7/siesta_cleanup from 644 to 755 creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/agr2pdf -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/Inelastica -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/Vasp2Siesta -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/Phonons -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/geom2zmat -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/geom2geom -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/bands2xmgr -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/ComputeDOS -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/WriteWavefunctions -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/kaverage-TBT -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/grid2grid -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/setupFCrun -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/siesta_cleanup -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/STM -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/EigenChannels -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/pyTBT -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/Bandstructures -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/NEB -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/setupOSrun -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/kaverage-IETS -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts.linux-x86_64-3.7/average-gridfunc -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/agr2pdf to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/Inelastica to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/Vasp2Siesta to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/Phonons to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/geom2zmat to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/geom2geom to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/bands2xmgr to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/ComputeDOS to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/WriteWavefunctions to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/kaverage-TBT to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/grid2grid to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/setupFCrun to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/siesta_cleanup to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/STM to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/EigenChannels to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/pyTBT to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/Bandstructures to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/NEB to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/setupOSrun to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/kaverage-IETS to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/average-gridfunc to 755 copying Inelastica.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying Inelastica.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying Inelastica.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying Inelastica.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt zip_safe flag not set; analyzing archive contents... Inelastica.pycache.SetupRuns.cpython-37: module references file Inelastica.pycache.config.cpython-37: module references file Inelastica.fortran.pycache.F90_lapack.cpython-37: module references file Inelastica.fortran.pycache.F90helpers.cpython-37: module references file Inelastica.fortran.pycache.config.cpython-37: module references file Inelastica.io.pycache.config.cpython-37: module references file Inelastica.physics.pycache.config.cpython-37: module references file creating dist creating 'dist/Inelastica-0.0.0-py3.7-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing Inelastica-0.0.0-py3.7-linux-x86_64.egg creating /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica-0.0.0-py3.7-linux-x86_64.egg Extracting Inelastica-0.0.0-py3.7-linux-x86_64.egg to /home/562/eh8122/.local/lib/python3.7/site-packages Adding Inelastica 0.0.0 to easy-install.pth file Installing Bandstructures script to /home/562/eh8122/.local/bin Installing ComputeDOS script to /home/562/eh8122/.local/bin Installing EigenChannels script to /home/562/eh8122/.local/bin Installing Inelastica script to /home/562/eh8122/.local/bin Installing NEB script to /home/562/eh8122/.local/bin Installing Phonons script to /home/562/eh8122/.local/bin Installing STM script to /home/562/eh8122/.local/bin Installing Vasp2Siesta script to /home/562/eh8122/.local/bin Installing WriteWavefunctions script to /home/562/eh8122/.local/bin Installing agr2pdf script to /home/562/eh8122/.local/bin Installing average-gridfunc script to /home/562/eh8122/.local/bin Installing bands2xmgr script to /home/562/eh8122/.local/bin Installing geom2geom script to /home/562/eh8122/.local/bin Installing geom2zmat script to /home/562/eh8122/.local/bin Installing grid2grid script to /home/562/eh8122/.local/bin Installing kaverage-IETS script to /home/562/eh8122/.local/bin Installing kaverage-TBT script to /home/562/eh8122/.local/bin Installing pyTBT script to /home/562/eh8122/.local/bin Installing setupFCrun script to /home/562/eh8122/.local/bin Installing setupOSrun script to /home/562/eh8122/.local/bin Installing siesta_cleanup script to /home/562/eh8122/.local/bin

Installed /home/562/eh8122/.local/lib/python3.7/site-packages/Inelastica-0.0.0-py3.7-linux-x86_64.egg Processing dependencies for Inelastica==0.0.0 Finished processing dependencies for Inelastica==0.0.0

el-abed commented 4 years ago

And when i tried /home/562/eh8122/.local/bin/EigenChannels the error i got: Traceback (most recent call last): File "/home/562/eh8122/.local/bin/EigenChannels", line 4, in import('pkg_resources').run_script('Inelastica==0.0.0', 'EigenChannels') File "/apps/python3/3.7.4/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/apps/python3/3.7.4/lib/python3.7/site-packages/pkg_resources/init.py", line 1453, in run_script .format(**locals()), pkg_resources.ResolutionError: Script 'scripts/EigenChannels' not found in metadata at None

el-abed commented 4 years ago

UPDATE: I tried the following steps: [eh8122@gadi-login-04 ~]$ module load python3/3.7.4 [eh8122@gadi-login-04 ~]$ module load hdf5/1.10.5 [eh8122@gadi-login-04 ~]$ module load netcdf/4.7.1 [eh8122@gadi-login-04 ~]$ pip3 install -v --no-binary :all: --user git+https://github.com/tfrederiksen/inelastica.git Created temporary directory: /scratch/g46/eh8122/tmp/pip-ephem-wheel-cache-m8z05zca Created temporary directory: /scratch/g46/eh8122/tmp/pip-req-tracker-k0p_njk5 Created requirements tracker '/scratch/g46/eh8122/tmp/pip-req-tracker-k0pnjk5' Created temporary directory: /scratch/g46/eh8122/tmp/pip-install-59hsnfj Collecting git+https://github.com/tfrederiksen/inelastica.git Created temporary directory: /scratch/g46/eh8122/tmp/pip-req-build-1h0oiwqv Cloning https://github.com/tfrederiksen/inelastica.git to /scratch/g46/eh8122/tmp/pip-req-build-1h0oiwqv Running command git clone -q https://github.com/tfrederiksen/inelastica.git /scratch/g46/eh8122/tmp/pip-req-build-1h0oiwqv Added git+https://github.com/tfrederiksen/inelastica.git to build tracker '/scratch/g46/eh8122/tmp/pip-req-tracker-k0p_njk5' Running setup.py (path:/scratch/g46/eh8122/tmp/pip-req-build-1h0oiwqv/setup.py) egg_info for package from git+https://github.com/tfrederiksen/inelastica.git Running command python setup.py egg_info system_info: NOT AVAILABLE

lapack_opt_info:
lapack_mkl_info:
customize UnixCCompiler
  FOUND:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/apps/intel-ct/2019.3.199/mkl/lib/intel64/']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    include_dirs = ['/apps/intel-ct/2019.3.199/mkl', '/apps/intel-ct/2019.3.199/mkl/include', '/apps/intel-ct/2019.3.199/mkl/lib']

  FOUND:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/apps/intel-ct/2019.3.199/mkl/lib/intel64/']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    include_dirs = ['/apps/intel-ct/2019.3.199/mkl', '/apps/intel-ct/2019.3.199/mkl/include', '/apps/intel-ct/2019.3.199/mkl/lib']

running egg_info
running build_src
build_src
building py_modules sources
creating build
creating build/src.linux-x86_64-3.7
creating build/src.linux-x86_64-3.7/Inelastica
creating build/src.linux-x86_64-3.7/Inelastica/fortran
creating build/src.linux-x86_64-3.7/Inelastica/io
creating build/src.linux-x86_64-3.7/Inelastica/physics
building extension "Inelastica.fortran.F90helpers" sources
f2py options: []
f2py:> build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c
Reading fortran codes...
    Reading file 'Inelastica/fortran/expansion_SE.f90' (format:free)
    Reading file 'Inelastica/fortran/readTSHS.f90' (format:free)
    Reading file 'Inelastica/fortran/removeUnitCellXij.f90' (format:free)
    Reading file 'Inelastica/fortran/setkpointhelper.f90' (format:free)
Post-processing...
    Block: F90helpers
                    Block: expansion_se
                    Block: readtshs
                            Block: deallocate
                            Block: read_size
                            Block: read
                            Block: remove_atoms
                            Block: tshs_version
                            Block: ucorb
                    Block: removeunitcellxij
                    Block: setkpointhelper
Post-processing (stage 2)...
    Block: F90helpers
            Block: unknown_interface
                    Block: expansion_se
                    Block: readtshs
                            Block: deallocate
                            Block: read_size
                            Block: read
                            Block: remove_atoms
                            Block: tshs_version
                            Block: ucorb
                    Block: removeunitcellxij
                    Block: setkpointhelper
Building modules...
    Building module "F90helpers"...
            Constructing wrapper function "expansion_se"...
              oesh,sgf = expansion_se(no_s,na1,na2,kpt,lasto,esh,g0,[no_u,na_u])
            Constructing wrapper function "removeunitcellxij"...
              xij = removeunitcellxij(numh,xij,xa,listh,atomindx,[nnzs,no_u,na_u])
            Constructing wrapper function "setkpointhelper"...
              full = setkpointhelper(sparse,kpoint,numh,rcell,xij,listhptr,listh,[nnzs,no_u])
            Constructing F90 module support for "readtshs"...
              Variables: version s h xij xa listhptr numh listh lasto
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
                    Constructing wrapper function "readtshs.deallocate"...
                      deallocate()
                    Constructing wrapper function "readtshs.read_size"...
                      no_u,no_s,nspin,na_u,maxnh = read_size(fname)
                    Constructing wrapper function "readtshs.read"...
                      gamma,onlys,no_u,no_s,nspin,maxnh,qtot,temp,na_u,ef,ucell,ts_kscell,ts_kdispl,ts_gamma_scf,istep,ia1 = read(fname)
            Creating wrapper for Fortran subroutine "remove_atoms"("remove_atoms")...
                    Constructing wrapper function "readtshs.remove_atoms"...
                      na_u,no_u,maxnh = remove_atoms(list)
            Creating wrapper for Fortran function "tshs_version"("tshs_version")...
                    Constructing wrapper function "readtshs.tshs_version"...
                      version = tshs_version(fname)
            Creating wrapper for Fortran function "ucorb"("ucorb")...
                    Constructing wrapper function "readtshs.ucorb"...
                      modp = ucorb(a,p)
    Wrote C/API module "F90helpers" to file "build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpersmodule.c"
    Fortran 90 wrappers are saved to "build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90"
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran' to include_dirs.
creating build/src.linux-x86_64-3.7/build
creating build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7
creating build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica
creating build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran
copying /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/f2py/src/fortranobject.c -> build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran
copying /apps/python3/3.7.4/lib/python3.7/site-packages/numpy-1.17.2-py3.7-linux-x86_64.egg/numpy/f2py/src/fortranobject.h -> build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran
  adding 'build/src.linux-x86_64-3.7/Inelastica/fortran/F90helpers-f2pywrappers2.f90' to sources.
building extension "Inelastica.fortran.F90_lapack" sources
f2py options: []
f2py:> build/src.linux-x86_64-3.7/Inelastica/fortran/F90_lapackmodule.c
Reading fortran codes...
    Reading file 'Inelastica/fortran/surfaceGreen.f90' (format:free)
Post-processing...
    Block: F90_lapack
                    Block: surfacegreen
In: :F90_lapack:Inelastica/fortran/surfaceGreen.f90:surfacegreen
get_parameters: got "name 'dcmplx' is not defined" on 'dcmplx(1.,0.)'
In: :F90_lapack:Inelastica/fortran/surfaceGreen.f90:surfacegreen
get_parameters: got "name 'dcmplx' is not defined" on 'dcmplx(-1.,0.)'
In: :F90_lapack:Inelastica/fortran/surfaceGreen.f90:surfacegreen
get_parameters: got "name 'dcmplx' is not defined" on 'dcmplx(0.,0.)'
Post-processing (stage 2)...
Building modules...
    Building module "F90_lapack"...
            Constructing wrapper function "surfacegreen"...
              gs = surfacegreen(no,ze,h00,s00,h01,s01,accur,is_left)
    Wrote C/API module "F90_lapack" to file "build/src.linux-x86_64-3.7/Inelastica/fortran/F90_lapackmodule.c"
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/Inelastica/fortran' to include_dirs.
build_src: building npy-pkg config files
creating /scratch/g46/eh8122/tmp/pip-req-build-1h0oiwqv/pip-egg-info/Inelastica.egg-info
writing /scratch/g46/eh8122/tmp/pip-req-build-1h0oiwqv/pip-egg-info/Inelastica.egg-info/PKG-INFO
writing dependency_links to /scratch/g46/eh8122/tmp/pip-req-build-1h0oiwqv/pip-egg-info/Inelastica.egg-info/dependency_links.txt
writing top-level names to /scratch/g46/eh8122/tmp/pip-req-build-1h0oiwqv/pip-egg-info/Inelastica.egg-info/top_level.txt
writing manifest file '/scratch/g46/eh8122/tmp/pip-req-build-1h0oiwqv/pip-egg-info/Inelastica.egg-info/SOURCES.txt'
reading manifest file '/scratch/g46/eh8122/tmp/pip-req-build-1h0oiwqv/pip-egg-info/Inelastica.egg-info/SOURCES.txt'
writing manifest file '/scratch/g46/eh8122/tmp/pip-req-build-1h0oiwqv/pip-egg-info/Inelastica.egg-info/SOURCES.txt'

Source in /scratch/g46/eh8122/tmp/pip-req-build-1h0oiwqv has version 0.0.0, which satisfies requirement Inelastica==0.0.0 from git+https://github.com/tfrederiksen/inelastica.git Removed Inelastica==0.0.0 from git+https://github.com/tfrederiksen/inelastica.git from build tracker '/scratch/g46/eh8122/tmp/pip-req-tracker-k0p_njk5' Requirement already satisfied (use --upgrade to upgrade): Inelastica==0.0.0 from git+https://github.com/tfrederiksen/inelastica.git in ./.local/lib/python3.7/site-packages Cleaning up... Removing source in /scratch/g46/eh8122/tmp/pip-req-build-1h0oiwqv Removed build tracker '/scratch/g46/eh8122/tmp/pip-req-tracker-k0p_njk5'

el-abed commented 4 years ago

I tested using module load python3/3.7.4 module load hdf5/1.10.5 module load netcdf/4.7.1 pip3 install -v --no-binary :all: --user git+https://github.com/tfrederiksen/inelastica.git

It worked! :)

el-abed commented 4 years ago

I am trying now to run it in parallel here is my script: `#!/bin/bash

PBS -P g46

PBS -q normal

PBS -l walltime=42:00:00

PBS -l mem=280gb

PBS -l ncpus=48

PBS -l wd

PBS -l storage=scratch/g46

module load openmpi/4.0.1 module load intel-mkl/2019.3.199 module load python3/3.7.4 module load hdf5/1.10.5 module load netcdf/4.7.1

mpirun /home/562/eh8122/.local/bin/EigenChannels -M 0.3 96NEW > UPDATE.txt`

It seems in the UPDATE.txt that if i want 48 cores to run for this job, it is as if the job is running 48 times as shown below:

el-abed commented 4 years ago

Sorry pressed the wrong button: UPDATE.txt

Why is that? Unlike with python2 inelastica version which i had before, this would happen. Any way to fix this?

zerothi commented 4 years ago

Inelastica isn't parallelized with mpi. So don't do what you are doing :)

el-abed commented 4 years ago

Would that be something to be considered for the future to be submitting a parallel job?

zerothi commented 4 years ago

It would be nice, but don't suspect this anytime soon. However, if your LAPACK/BLAS are threaded you can simply use threaded LAPACK/BLAS and still use several threads/processors. Please ask your local IT administration for instructions.

tfrederiksen commented 4 years ago

Thanks, I released the latest code as v1.3.7 in 4d97902da34b27902471d1fc90275d1f53206dbb .

zerothi commented 4 years ago

@tfrederiksen great! :)

el-abed commented 4 years ago

@zerothi sorry for reopening the other thread. Just because it was directly related. Thanks a lot for the help! @tfrederiksen One question before closing this thread: Would the latest version work with mpi?

zerothi commented 4 years ago

@el-abed no still no MPI.

el-abed commented 4 years ago

All good. Thank you again!