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 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 :
>
>> 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-linu
>> x-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
>> 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
>> 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 :
>>>
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
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 :
>
>> 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
>
sf@s
