Re: Compiling error(s)

[Rudolf Weeber]

Hi,


On Wed, Oct 14, 2020 at 04:47:01PM +0200, Zihan TAN wrote:
> I have been trying to run simulations with Espresso code in our
> super-computing center for this week. However, by far, I still haven't
> succeeded yet. It would be highly appreciated if you can help me with
> this issue.
> 
> It appears that Cmake can not find the correct python (version 3.6.8)
> headers. I post the error message below:
[...] 
> -- Found PythonInterp: /usr/bin/python3 (Required is at least version "3.3")
> -- Found Cython:
> /usr/local/software/jureca/Stages/2019a/software/Python/3.6.8-GCCcore-8.3.0/bin/cython
> (found suitable version "0.29.6", minimum required is "0.23")
> 
> /usr/bin/python3: symbol lookup error: /usr/bin/python3: undefined symbol:
> _Py_LegacyLocaleDetected
> 
> /usr/bin/python3: symbol lookup error: /usr/bin/python3: undefined symbol:
> _Py_LegacyLocaleDetected
> 
> CMake Error at
> /usr/local/software/jureca/Stages/2019a/software/CMake/3.14.0-GCCcore-8.3.0/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:137
> (message):
> 
>   Could NOT find PythonHeaders (missing: PYTHON_INCLUDE_DIRS PYTHON_INSTDIR)
> 
> Call Stack (most recent call first):
> 
>   
> /usr/local/software/jureca/Stages/2019a/software/CMake/3.14.0-GCCcore-8.3.0/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:378
> (_FPHSA_FAILURE_MESSAGE)
> 
>   cmake/FindPythonHeaders.cmake:37 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)

On supercomputers, Python is often loaded as package (eg. with module load ...)
However, CMake seems to select the system default python executable 
(/ur/bin/ppython) rather than one from a module.
However, a Cython binary is selected that comes froma module 
(/usr/local/software/jureca/Stages/2019a/software/Python/3.6.8-GCCcore-8.3.0/bin/cython)
A first step might be to use the Python interpreter from the module.
Likely, tis is under 
/usr/local/software/jureca/Stages/2019a/software/Python/3.6.8-GCCcore-8.3.0/bin/
Furthermore, Espresso needs Python header files (*.h) which are likely also 
somewhere under
/usr/local/software/jureca/Stages/2019a/software/Python/3.6.8-GCCcore-8.3.0/
The paths can be set in cmake, e.g., running ccmake . ain the build directory 
after running cmake.

Maybe, the support desk of the computing center can help.

Regards, Rudolf