Dear Nick,
I have uninstalled all the packages and installed them again.
Then I downloded sisl-0.8.3.tar.gz and installed it by
sudo python setup.py install
as you said. It seems that everything is installed properly because I
didn't recieve any error during installation.
But unfortunately, code dose not run as before.
I don't no where the log file has been saved. I copied what showed in
terminal during installation into a text file.
I attach this text file for you.
I would be pleased if you could help me to solve this problem.
Sincerely yours,
On Thu, Jun 1, 2017 at 10:29 PM, Nick Papior <[email protected]> wrote:
> It seems like you re-ran the installation script in the same directory as
> before.
>
> First remove the build directory, then do
> sudo python setup.py install
>
> and send me the installation log from that.
>
> PS. Do you have a fortran compiler? I.e. try and install gfortran:
> sudo apt-get install gfortran (for Debian style distros)
>
> 2017-05-29 15:36 GMT+02:00 maryam jamaati <[email protected]>:
>
>> Dear Nick,
>>
>> I have installed sisl manually by "$> python setup.py install" as you
>> said. But the mentioned error appeared again in the terminal. I attach the
>> installation log file.
>>
>> Best Regards,
>>
>>
>>
>>
>>
>> On Sun, May 28, 2017 at 12:41 AM, Nick Papior <[email protected]>
>> wrote:
>>
>>> It seems like you are installing using pip?
>>>
>>> As I mentioned in the previous mail, you should download the tarball and
>>> install sisl manually by using this command:
>>>
>>> $> python setup.py install
>>>
>>> If this is indeed what you did, could you please attach the entire
>>> installation log.
>>>
>>> 2017-05-27 7:54 GMT+02:00 maryam jamaati <[email protected]>:
>>>
>>>> Dear Nick,
>>>>
>>>> Thank you for your help.
>>>> I have installed sisl package. It was installed completely and
>>>> correctly as you can see in the below:
>>>>
>>>>
>>>> " Installed /usr/local/lib/python2.7/dist-
>>>> packages/sisl-0.8.3-py2.7-linux-i686.egg
>>>> Processing dependencies for sisl==0.8.3
>>>> Searching for netCDF4==1.2.7
>>>> Best match: netCDF4 1.2.7
>>>> Adding netCDF4 1.2.7 to easy-install.pth file
>>>> Installing ncinfo script to /usr/local/bin
>>>> Installing nc4tonc3 script to /usr/local/bin
>>>> Installing nc3tonc4 script to /usr/local/bin
>>>>
>>>> Using /usr/local/lib/python2.7/dist-packages
>>>> Searching for scipy==0.19.0
>>>> Best match: scipy 0.19.0
>>>> Adding scipy 0.19.0 to easy-install.pth file
>>>>
>>>> Using /usr/local/lib/python2.7/dist-packages
>>>> Searching for numpy==1.12.1
>>>> Best match: numpy 1.12.1
>>>> Adding numpy 1.12.1 to easy-install.pth file
>>>>
>>>> Using /usr/local/lib/python2.7/dist-packages
>>>> Searching for setuptools==3.3
>>>> Best match: setuptools 3.3
>>>> Adding setuptools 3.3 to easy-install.pth file
>>>> Installing easy_install script to /usr/local/bin
>>>> Installing easy_install-2.7 script to /usr/local/bin
>>>>
>>>> Using /usr/lib/python2.7/dist-packages
>>>> Searching for six==1.10.0
>>>> Best match: six 1.10.0
>>>> Adding six 1.10.0 to easy-install.pth file
>>>>
>>>> Using /home/sf/.local/lib/python2.7/site-packages
>>>> Finished processing dependencies for sisl==0.8.3"
>>>>
>>>> *But unfortunately*, when I run the code the *below error *appears:
>>>>
>>>> /usr/lib/python2.7/dist-packages/pkg_resources.py:1031: UserWarning:
>>>> /home/sf/.python-eggs is writable by group/others and vulnerable to attack
>>>> when used with get_resource_filename. Consider a more secure location (set
>>>> with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
>>>> warnings.warn(msg, UserWarning)
>>>> Traceback (most recent call last):
>>>> File "convert-tshs-nc.py", line 5, in <module>
>>>> H = sisl.get_sile(sys.argv[1]).read_es()
>>>> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 89,
>>>> in read_es
>>>> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 50,
>>>> in read_geom
>>>> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 35,
>>>> in read_sc
>>>> ValueError: failed to create intent(cache|hide)|optional array— must
>>>> have defined dimensions but got (3,0,)
>>>>
>>>> Best Regards,
>>>>
>>>> Maryam Jamaati
>>>>
>>>>
>>>> On Wed, May 24, 2017 at 11:21 AM, Nick Papior <[email protected]>
>>>> wrote:
>>>>
>>>>> I haven't tried the fortran extensions through pip.
>>>>>
>>>>> Could you please try and install sisl the manual way?
>>>>> Download the tar-ball and issue:
>>>>>
>>>>> python setup.py install
>>>>>
>>>>>
>>>>> 2017-05-23 10:09 GMT+02:00 maryam jamaati <[email protected]>:
>>>>>
>>>>>> Dear Nick,
>>>>>>
>>>>>> thanks for your attention.
>>>>>> I installed sisl via pip command. And it was successfully installed
>>>>>> without any errors.
>>>>>> Also i installed pre-requisite before installing sisl such as :
>>>>>> setuptools, numpy (>=1.9), scipy, netcdf4-python.
>>>>>>
>>>>>> Best Regards,
>>>>>>
>>>>>> On Mon, May 22, 2017 at 5:44 PM, Nick Papior <[email protected]>
>>>>>> wrote:
>>>>>>
>>>>>>> Could you tell us how you have installed sisl?
>>>>>>>
>>>>>>> Also, I think I made a mistake in the script, it should be:
>>>>>>>
>>>>>>> >>> script begin <<<
>>>>>>> #!/usr/bin/env python
>>>>>>> import sys
>>>>>>> import sisl
>>>>>>> # Read the electronic structure from the file
>>>>>>> H = sisl.get_sile(sys.argv[1]).read_es()
>>>>>>> H.write('output.nc')
>>>>>>> >>> script end <<<
>>>>>>>
>>>>>>> 2017-05-21 7:26 GMT+02:00 maryam jamaati <[email protected]>:
>>>>>>>
>>>>>>>> Dear siesta users,
>>>>>>>>
>>>>>>>> In order to convert from TSHS to nc we used this small script from (
>>>>>>>> https://answers.launchpad.net/siesta/+question/435947):
>>>>>>>>
>>>>>>>> #!/usr/bin/env python
>>>>>>>> import sys
>>>>>>>> import sisl
>>>>>>>> # Read the electronic structure from the file
>>>>>>>> H = get_sile(sys.argv[1]).read_es()
>>>>>>>> H.write('output.nc')
>>>>>>>> »> script end «<
>>>>>>>>
>>>>>>>> and then call it by:
>>>>>>>> python convert.py siesta.TSHS
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> But after running the code, the below error appears:
>>>>>>>> ValueError: failed to create intent(cache|hide)|optional array—
>>>>>>>> must have defined dimensions but got (3,0,)
>>>>>>>>
>>>>>>>> I would be pleased if anyone could help me to solve this problem.
>>>>>>>>
>>>>>>>> Best Regards,
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Kind regards Nick
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Kind regards Nick
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Kind regards Nick
>>>
>>
>>
>
>
> --
> Kind regards Nick
>
-2.7/sisl/shape
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'sisl.io.siesta._siesta' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g
-fwrapv -O2 -Wall -Wstrict-prototypes -fPIC
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/build
creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl
creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl/io
creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl/io/siesta
creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build
creating
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7
creating
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl
creating
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl/io
creating
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl/io/siesta
compile options:
'-Ibuild/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl/io/siesta
-I/usr/local/lib/python2.7/dist-packages/numpy/core/include
-I/usr/include/python2.7 -c'
x86_64-linux-gnu-gcc:
build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl/io/siesta/fortranobject.c
In file included from
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from
build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl/io/siesta/fortranobject.h:13,
from
build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl/io/siesta/fortranobject.c:2:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: #warning "Using deprecated NumPy API, disable it by " "#defining
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/sisl/io/siesta/_siestamodule.c
In file included from
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from
build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl/io/siesta/fortranobject.h:13,
from
build/src.linux-x86_64-2.7/sisl/io/siesta/_siestamodule.c:19:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: #warning "Using deprecated NumPy API, disable it by " "#defining
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
build/src.linux-x86_64-2.7/sisl/io/siesta/_siestamodule.c:145:12: warning:
‘f2py_size’ defined but not used [-Wunused-function]
static int f2py_size(PyArrayObject* var, ...)
^
compiling Fortran sources
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form
-fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC
-O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form
-fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
creating build/temp.linux-x86_64-2.7/sisl
creating build/temp.linux-x86_64-2.7/sisl/io
creating build/temp.linux-x86_64-2.7/sisl/io/siesta
creating build/temp.linux-x86_64-2.7/sisl/io/siesta/src
compile options:
'-Ibuild/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl/io/siesta
-I/usr/local/lib/python2.7/dist-packages/numpy/core/include
-I/usr/include/python2.7 -c'
gfortran:f90: sisl/io/siesta/src/free_unit.f90
gfortran:f90: sisl/io/siesta/src/write_hsx.f90
gfortran:f90: sisl/io/siesta/src/read_hsx_header.f90
gfortran:f90: sisl/io/siesta/src/read_hsx.f90
gfortran:f90: sisl/io/siesta/src/read_hs_header.f90
gfortran:f90: sisl/io/siesta/src/read_hs.f90
gfortran:f90: sisl/io/siesta/src/read_tshs_sizes.f90
gfortran:f90: sisl/io/siesta/src/read_tshs_geom.f90
gfortran:f90: sisl/io/siesta/src/read_tshs_cell.f90
gfortran:f90: sisl/io/siesta/src/read_tshs_es.f90
gfortran:f90: sisl/io/siesta/src/read_tshs_version.f90
/usr/bin/gfortran -Wall -g -Wall -g -shared
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl/io/siesta/_siestamodule.o
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/sisl/io/siesta/fortranobject.o
build/temp.linux-x86_64-2.7/sisl/io/siesta/src/free_unit.o
build/temp.linux-x86_64-2.7/sisl/io/siesta/src/write_hsx.o
build/temp.linux-x86_64-2.7/sisl/io/siesta/src/read_hsx_header.o
build/temp.linux-x86_64-2.7/sisl/io/siesta/src/read_hsx.o
build/temp.linux-x86_64-2.7/sisl/io/siesta/src/read_hs_header.o
build/temp.linux-x86_64-2.7/sisl/io/siesta/src/read_hs.o
build/temp.linux-x86_64-2.7/sisl/io/siesta/src/read_tshs_sizes.o
build/temp.linux-x86_64-2.7/sisl/io/siesta/src/read_tshs_geom.o
build/temp.linux-x86_64-2.7/sisl/io/siesta/src/read_tshs_cell.o
build/temp.linux-x86_64-2.7/sisl/io/siesta/src/read_tshs_es.o
build/temp.linux-x86_64-2.7/sisl/io/siesta/src/read_tshs_version.o -lgfortran
-o build/lib.linux-x86_64-2.7/sisl/io/siesta/_siesta.so
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/sisl
creating build/bdist.linux-x86_64/egg/sisl/geom
copying build/lib.linux-x86_64-2.7/sisl/geom/nanotube.py ->
build/bdist.linux-x86_64/egg/sisl/geom
copying build/lib.linux-x86_64-2.7/sisl/geom/__config__.py ->
build/bdist.linux-x86_64/egg/sisl/geom
copying build/lib.linux-x86_64-2.7/sisl/geom/flat.py ->
build/bdist.linux-x86_64/egg/sisl/geom
copying build/lib.linux-x86_64-2.7/sisl/geom/special.py ->
build/bdist.linux-x86_64/egg/sisl/geom
copying build/lib.linux-x86_64-2.7/sisl/geom/__init__.py ->
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copying build/lib.linux-x86_64-2.7/sisl/geom/setup.py ->
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copying build/lib.linux-x86_64-2.7/sisl/geom/basic.py ->
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copying build/lib.linux-x86_64-2.7/sisl/__config__.py ->
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creating build/bdist.linux-x86_64/egg/sisl/utils
copying build/lib.linux-x86_64-2.7/sisl/utils/__config__.py ->
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copying build/lib.linux-x86_64-2.7/sisl/utils/sdata.py ->
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copying build/lib.linux-x86_64-2.7/sisl/utils/misc.py ->
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copying build/lib.linux-x86_64-2.7/sisl/utils/ranges.py ->
build/bdist.linux-x86_64/egg/sisl/utils
copying build/lib.linux-x86_64-2.7/sisl/utils/c2f.py ->
build/bdist.linux-x86_64/egg/sisl/utils
copying build/lib.linux-x86_64-2.7/sisl/sparse.py ->
build/bdist.linux-x86_64/egg/sisl
creating build/bdist.linux-x86_64/egg/sisl/units
copying build/lib.linux-x86_64-2.7/sisl/units/__config__.py ->
build/bdist.linux-x86_64/egg/sisl/units
copying build/lib.linux-x86_64-2.7/sisl/units/__init__.py ->
build/bdist.linux-x86_64/egg/sisl/units
copying build/lib.linux-x86_64-2.7/sisl/units/setup.py ->
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copying build/lib.linux-x86_64-2.7/sisl/units/siesta.py ->
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creating build/bdist.linux-x86_64/egg/sisl/quantity
copying build/lib.linux-x86_64-2.7/sisl/quantity/__config__.py ->
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copying build/lib.linux-x86_64-2.7/sisl/quantity/dynmat.py ->
build/bdist.linux-x86_64/egg/sisl/quantity
copying build/lib.linux-x86_64-2.7/sisl/quantity/self_energy.py ->
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copying build/lib.linux-x86_64-2.7/sisl/quantity/__init__.py ->
build/bdist.linux-x86_64/egg/sisl/quantity
copying build/lib.linux-x86_64-2.7/sisl/quantity/setup.py ->
build/bdist.linux-x86_64/egg/sisl/quantity
copying build/lib.linux-x86_64-2.7/sisl/quantity/hamiltonian.py ->
build/bdist.linux-x86_64/egg/sisl/quantity
copying build/lib.linux-x86_64-2.7/sisl/__init__.py ->
build/bdist.linux-x86_64/egg/sisl
copying build/lib.linux-x86_64-2.7/sisl/quaternion.py ->
build/bdist.linux-x86_64/egg/sisl
copying build/lib.linux-x86_64-2.7/sisl/setup.py ->
build/bdist.linux-x86_64/egg/sisl
copying build/lib.linux-x86_64-2.7/sisl/_help.py ->
build/bdist.linux-x86_64/egg/sisl
creating build/bdist.linux-x86_64/egg/sisl/io
creating build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/xv.py ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/fdf.py ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/__config__.py ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/bands.py ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/tbtrans_proj.py ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/__init__.py ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/siesta_grid.py ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/setup.py ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/binaries.py ->
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copying build/lib.linux-x86_64-2.7/sisl/io/siesta/out.py ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/tbtrans.py ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/sile.py ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/_siesta.so ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/siesta.py ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/siesta/tbtrans_av.py ->
build/bdist.linux-x86_64/egg/sisl/io/siesta
copying build/lib.linux-x86_64-2.7/sisl/io/xsf.py ->
build/bdist.linux-x86_64/egg/sisl/io
copying build/lib.linux-x86_64-2.7/sisl/io/ham.py ->
build/bdist.linux-x86_64/egg/sisl/io
copying build/lib.linux-x86_64-2.7/sisl/io/__config__.py ->
build/bdist.linux-x86_64/egg/sisl/io
copying build/lib.linux-x86_64-2.7/sisl/io/xyz.py ->
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copying build/lib.linux-x86_64-2.7/sisl/io/gulp/__config__.py ->
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copying build/lib.linux-x86_64-2.7/sisl/io/gulp/setup.py ->
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copying build/lib.linux-x86_64-2.7/sisl/io/gulp/sile.py ->
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copying build/lib.linux-x86_64-2.7/sisl/io/gulp/hessian.py ->
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copying build/lib.linux-x86_64-2.7/sisl/io/cube.py ->
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copying build/lib.linux-x86_64-2.7/sisl/io/molden.py ->
build/bdist.linux-x86_64/egg/sisl/io
creating build/bdist.linux-x86_64/egg/sisl/io/wannier
copying build/lib.linux-x86_64-2.7/sisl/io/wannier/__config__.py ->
build/bdist.linux-x86_64/egg/sisl/io/wannier
copying build/lib.linux-x86_64-2.7/sisl/io/wannier/seedname.py ->
build/bdist.linux-x86_64/egg/sisl/io/wannier
copying build/lib.linux-x86_64-2.7/sisl/io/wannier/__init__.py ->
build/bdist.linux-x86_64/egg/sisl/io/wannier
copying build/lib.linux-x86_64-2.7/sisl/io/wannier/setup.py ->
build/bdist.linux-x86_64/egg/sisl/io/wannier
copying build/lib.linux-x86_64-2.7/sisl/io/wannier/sile.py ->
build/bdist.linux-x86_64/egg/sisl/io/wannier
copying build/lib.linux-x86_64-2.7/sisl/io/__init__.py ->
build/bdist.linux-x86_64/egg/sisl/io
copying build/lib.linux-x86_64-2.7/sisl/io/setup.py ->
build/bdist.linux-x86_64/egg/sisl/io
copying build/lib.linux-x86_64-2.7/sisl/io/_help.py ->
build/bdist.linux-x86_64/egg/sisl/io
creating build/bdist.linux-x86_64/egg/sisl/io/vasp
copying build/lib.linux-x86_64-2.7/sisl/io/vasp/__config__.py ->
build/bdist.linux-x86_64/egg/sisl/io/vasp
copying build/lib.linux-x86_64-2.7/sisl/io/vasp/__init__.py ->
build/bdist.linux-x86_64/egg/sisl/io/vasp
copying build/lib.linux-x86_64-2.7/sisl/io/vasp/setup.py ->
build/bdist.linux-x86_64/egg/sisl/io/vasp
copying build/lib.linux-x86_64-2.7/sisl/io/vasp/sile.py ->
build/bdist.linux-x86_64/egg/sisl/io/vasp
copying build/lib.linux-x86_64-2.7/sisl/io/vasp/car.py ->
build/bdist.linux-x86_64/egg/sisl/io/vasp
creating build/bdist.linux-x86_64/egg/sisl/io/bigdft
copying build/lib.linux-x86_64-2.7/sisl/io/bigdft/__config__.py ->
build/bdist.linux-x86_64/egg/sisl/io/bigdft
copying build/lib.linux-x86_64-2.7/sisl/io/bigdft/ascii.py ->
build/bdist.linux-x86_64/egg/sisl/io/bigdft
copying build/lib.linux-x86_64-2.7/sisl/io/bigdft/__init__.py ->
build/bdist.linux-x86_64/egg/sisl/io/bigdft
copying build/lib.linux-x86_64-2.7/sisl/io/bigdft/setup.py ->
build/bdist.linux-x86_64/egg/sisl/io/bigdft
copying build/lib.linux-x86_64-2.7/sisl/io/bigdft/sile.py ->
build/bdist.linux-x86_64/egg/sisl/io/bigdft
copying build/lib.linux-x86_64-2.7/sisl/io/sile.py ->
build/bdist.linux-x86_64/egg/sisl/io
copying build/lib.linux-x86_64-2.7/sisl/io/table.py ->
build/bdist.linux-x86_64/egg/sisl/io
copying build/lib.linux-x86_64-2.7/sisl/supercell.py ->
build/bdist.linux-x86_64/egg/sisl
copying build/lib.linux-x86_64-2.7/sisl/geometry.py ->
build/bdist.linux-x86_64/egg/sisl
copying build/lib.linux-x86_64-2.7/sisl/atom.py ->
build/bdist.linux-x86_64/egg/sisl
copying build/lib.linux-x86_64-2.7/sisl/info.py ->
build/bdist.linux-x86_64/egg/sisl
copying build/lib.linux-x86_64-2.7/sisl/grid.py ->
build/bdist.linux-x86_64/egg/sisl
creating build/bdist.linux-x86_64/egg/sisl/shape
copying build/lib.linux-x86_64-2.7/sisl/shape/__config__.py ->
build/bdist.linux-x86_64/egg/sisl/shape
copying build/lib.linux-x86_64-2.7/sisl/shape/__init__.py ->
build/bdist.linux-x86_64/egg/sisl/shape
copying build/lib.linux-x86_64-2.7/sisl/shape/setup.py ->
build/bdist.linux-x86_64/egg/sisl/shape
copying build/lib.linux-x86_64-2.7/sisl/shape/prism4.py ->
build/bdist.linux-x86_64/egg/sisl/shape
copying build/lib.linux-x86_64-2.7/sisl/shape/shape.py ->
build/bdist.linux-x86_64/egg/sisl/shape
copying build/lib.linux-x86_64-2.7/sisl/shape/ellipsoid.py ->
build/bdist.linux-x86_64/egg/sisl/shape
byte-compiling build/bdist.linux-x86_64/egg/sisl/geom/nanotube.py to
nanotube.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/geom/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/geom/flat.py to flat.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/geom/special.py to special.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/geom/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/geom/setup.py to setup.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/geom/basic.py to basic.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/__config__.py to __config__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/utils/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/utils/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/utils/setup.py to setup.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/utils/cmd.py to cmd.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/utils/sdata.py to sdata.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/utils/misc.py to misc.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/utils/ranges.py to ranges.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/utils/c2f.py to c2f.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/sparse.py to sparse.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/units/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/units/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/units/setup.py to setup.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/units/siesta.py to siesta.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/quantity/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/quantity/dynmat.py to
dynmat.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/quantity/self_energy.py to
self_energy.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/quantity/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/quantity/setup.py to setup.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/quantity/hamiltonian.py to
hamiltonian.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/quaternion.py to quaternion.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/setup.py to setup.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/_help.py to _help.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/xv.py to xv.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/fdf.py to fdf.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/bands.py to bands.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/tbtrans_proj.py to
tbtrans_proj.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/siesta_grid.py to
siesta_grid.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/setup.py to setup.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/binaries.py to
binaries.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/out.py to out.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/tbtrans.py to
tbtrans.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/sile.py to sile.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/siesta.py to
siesta.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/tbtrans_av.py to
tbtrans_av.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/xsf.py to xsf.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/ham.py to ham.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/xyz.py to xyz.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/gulp/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/gulp/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/gulp/setup.py to setup.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/gulp/sile.py to sile.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/gulp/got.py to got.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/gulp/hessian.py to
hessian.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/cube.py to cube.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/molden.py to molden.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/wannier/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/wannier/seedname.py to
seedname.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/wannier/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/wannier/setup.py to
setup.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/wannier/sile.py to sile.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/setup.py to setup.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/_help.py to _help.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/vasp/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/vasp/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/vasp/setup.py to setup.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/vasp/sile.py to sile.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/vasp/car.py to car.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/bigdft/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/bigdft/ascii.py to ascii.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/bigdft/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/bigdft/setup.py to setup.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/bigdft/sile.py to sile.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/sile.py to sile.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/table.py to table.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/supercell.py to supercell.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/geometry.py to geometry.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/atom.py to atom.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/info.py to info.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/grid.py to grid.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/shape/__config__.py to
__config__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/shape/__init__.py to
__init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/shape/setup.py to setup.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/shape/prism4.py to prism4.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/shape/shape.py to shape.pyc
byte-compiling build/bdist.linux-x86_64/egg/sisl/shape/ellipsoid.py to
ellipsoid.pyc
creating stub loader for sisl/io/siesta/_siesta.so
byte-compiling build/bdist.linux-x86_64/egg/sisl/io/siesta/_siesta.py to
_siesta.pyc
installing package data to build/bdist.linux-x86_64/egg
running install_data
creating build/bdist.linux-x86_64/egg/sisl/geom/tests
copying sisl/geom/tests/test_geom.py ->
build/bdist.linux-x86_64/egg/sisl/geom/tests/
creating build/bdist.linux-x86_64/egg/sisl/shape/tests
copying sisl/shape/tests/test_prism4.py ->
build/bdist.linux-x86_64/egg/sisl/shape/tests/
copying sisl/shape/tests/test_ellipsoid.py ->
build/bdist.linux-x86_64/egg/sisl/shape/tests/
creating build/bdist.linux-x86_64/egg/sisl/tests
copying sisl/tests/test_quaternion.py ->
build/bdist.linux-x86_64/egg/sisl/tests/
copying sisl/tests/test_atom.py -> build/bdist.linux-x86_64/egg/sisl/tests/
copying sisl/tests/test_geometry.py -> build/bdist.linux-x86_64/egg/sisl/tests/
copying sisl/tests/test_package.py -> build/bdist.linux-x86_64/egg/sisl/tests/
copying sisl/tests/test_sparse.py -> build/bdist.linux-x86_64/egg/sisl/tests/
copying sisl/tests/test_supercell.py -> build/bdist.linux-x86_64/egg/sisl/tests/
copying sisl/tests/test_sgeom.py -> build/bdist.linux-x86_64/egg/sisl/tests/
copying sisl/tests/test_grid.py -> build/bdist.linux-x86_64/egg/sisl/tests/
copying sisl/tests/test_geometry_return.py ->
build/bdist.linux-x86_64/egg/sisl/tests/
creating build/bdist.linux-x86_64/egg/sisl/units/tests
copying sisl/units/tests/test_siesta.py ->
build/bdist.linux-x86_64/egg/sisl/units/tests/
copying sisl/units/tests/test_units.py ->
build/bdist.linux-x86_64/egg/sisl/units/tests/
creating build/bdist.linux-x86_64/egg/sisl/quantity/tests
copying sisl/quantity/tests/test_self_energy.py ->
build/bdist.linux-x86_64/egg/sisl/quantity/tests/
copying sisl/quantity/tests/test_dynmat.py ->
build/bdist.linux-x86_64/egg/sisl/quantity/tests/
copying sisl/quantity/tests/test_hamiltonian.py ->
build/bdist.linux-x86_64/egg/sisl/quantity/tests/
creating build/bdist.linux-x86_64/egg/sisl/io/tests
copying sisl/io/tests/test_siesta.py ->
build/bdist.linux-x86_64/egg/sisl/io/tests/
copying sisl/io/tests/common.py -> build/bdist.linux-x86_64/egg/sisl/io/tests/
copying sisl/io/tests/test_fdf.py -> build/bdist.linux-x86_64/egg/sisl/io/tests/
copying sisl/io/tests/test_object.py ->
build/bdist.linux-x86_64/egg/sisl/io/tests/
copying sisl/io/tests/test_tb.py -> build/bdist.linux-x86_64/egg/sisl/io/tests/
copying sisl/io/tests/test_xyz.py -> build/bdist.linux-x86_64/egg/sisl/io/tests/
copying sisl/io/tests/test_xv.py -> build/bdist.linux-x86_64/egg/sisl/io/tests/
creating build/bdist.linux-x86_64/egg/sisl/utils/tests
copying sisl/utils/tests/test_ranges.py ->
build/bdist.linux-x86_64/egg/sisl/utils/tests/
copying sisl/utils/tests/test_c2f.py ->
build/bdist.linux-x86_64/egg/sisl/utils/tests/
copying sisl/utils/tests/test_misc.py ->
build/bdist.linux-x86_64/egg/sisl/utils/tests/
running install_clib
customize UnixCCompiler
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying sisl.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying sisl.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying sisl.egg-info/dependency_links.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying sisl.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying sisl.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying sisl.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...
creating dist
creating 'dist/sisl-0.8.3-py2.7-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 sisl-0.8.3-py2.7-linux-x86_64.egg
Copying sisl-0.8.3-py2.7-linux-x86_64.egg to
/usr/local/lib/python2.7/dist-packages
Adding sisl 0.8.3 to easy-install.pth file
Installing sgrid script to /usr/local/bin
Installing sgeom script to /usr/local/bin
Installing sdata script to /usr/local/bin
Installed
/usr/local/lib/python2.7/dist-packages/sisl-0.8.3-py2.7-linux-x86_64.egg
Processing dependencies for sisl==0.8.3
Searching for netCDF4==1.2.8
Best match: netCDF4 1.2.8
Adding netCDF4 1.2.8 to easy-install.pth file
Installing ncinfo script to /usr/local/bin
Installing nc4tonc3 script to /usr/local/bin
Installing nc3tonc4 script to /usr/local/bin
Using /usr/local/lib/python2.7/dist-packages
Searching for scipy==0.19.0
Best match: scipy 0.19.0
Adding scipy 0.19.0 to easy-install.pth file
Using /usr/local/lib/python2.7/dist-packages
Searching for numpy==1.13.0
Best match: numpy 1.13.0
Removing numpy 1.8.0 from easy-install.pth file
Adding numpy 1.13.0 to easy-install.pth file
Using /usr/local/lib/python2.7/dist-packages
Searching for setuptools==36.0.1
Best match: setuptools 36.0.1
Adding setuptools 36.0.1 to easy-install.pth file
Installing easy_install script to /usr/local/bin
Installing easy_install-3.6 script to /usr/local/bin
Using /usr/local/lib/python2.7/dist-packages
Searching for six==1.10.0
Best match: six 1.10.0
Adding six 1.10.0 to easy-install.pth file
Using /usr/local/lib/python2.7/dist-packages
Searching for Cython==0.25.2
Best match: Cython 0.25.2
Adding Cython 0.25.2 to easy-install.pth file
Installing cython script to /usr/local/bin
Installing cygdb script to /usr/local/bin
Installing cythonize script to /usr/local/bin
Using /usr/local/lib/python2.7/dist-packages
Finished processing dependencies for sisl==0.8.3
