Re: [ESPResSo-users] Installation problem

[Jean-Noël Grad]

Hi Kai,

To follow-up on our offline disccussion about Shawn's issue, I could 
only reproduce it when starting a python3.5.3 interpreter inside the 
/src/python/espressomd folder. Attached is a minimum non-working example 
reproducing the espressomd folder structure (bash command to get the 
error message: tar xfz MNWE.tar.gz; cd espressomd; python3).

A few observations:
- reproducible with python3.5.3 on my 32bit Debian laptop but not with 
64bit Debian in docker
- not reproducible with python3.5.2 and python3.6.8 on 64bit Ubuntu
- not reproducible with python2.7.13 on my 32bit Debian laptop
- Shawn has python3.6.x
- commenting out the import statement in 
espressomd/io/writer/__init__.py creates a different error message that 
suggests the real culprit is the "io" espressomd submodule overshadowing 
the standard "io" module

Best regards,
JN

On 7/17/19 7:44 PM, Jean-Noël Grad wrote:
> Hi Shawn,
>
> I am unable to reproduce the error message using your CMake command. 
> However, I am able to reproduce it by duplicating the structure of 
> /src/python/espressomd in a different folder and simply starting a 
> python3 interpreter inside of it:
>
> Fatal Python error: Py_Initialize: can't initialize sys standard streams
> Traceback (most recent call last):
>    File 
> "/home/grad/Documents/espresso-structure/src/python/espressomd/io/__init__.py", 
> line 17, in <module>
>    File 
> "/home/grad/Documents/espresso-structure/src/python/espressomd/io/writer/__init__.py", 
> line 1, in <module>
> ValueError: attempted relative import beyond top-level package
> Aborted
>
> This error shouldn't happen when using CMake because the target 
> "code_info.pyx" is generated via a python script located in the 
> top-level folder that is executed by a python interpreter running in the 
> /build folder.
>
> I'm currently investigating the issue with a coworker.
>
> Best regards,
> JN
>
> On 7/15/19 7:48 PM, Shawn wrote:
> > Hi Jean-Noël,
> > Thanks very much for helping me. Attached please find the script of my 
> > build and the cmake output. I just used the default myconfig.hpp file.
> >
> > Regards,
> > Shawn
> >
> > Jean-Noël Grad <address@hidden 
> > <mailto:address@hidden>> 于2019年7月15日周一 下午12:26写道：
> >
> >     Hi Shawn,
> >
> >     The 4.0.2 release is tested for both python versions. I'm not 
> > familiar
> >     with this error message. It could be due to your Cython version, 
> > or to
> >     an unclean build directory. To reproduce your issue, we will need the
> >     cmake command you used for this build and its output in the terminal.
> >     It's only 80 lines long and contains valuable information such as the
> >     Cython version and espresso dependencies. If you're using a custom
> >     myconfig.hpp file, please also post its content.
> >
> >     Best regards,
> >     JN
> >
> >     On 7/15/19 6:58 PM, Shawn wrote:
> >      > Hi everyone,
> >      > I am trying install espresso 4.0.2 with python 3. The cmake 
> > command
> >      > could be executed successfully, but when I tried to compile the
> >     source
> >      > code, I got errors below:
> >      >
> >      > [ 61%] Generating code_info.pyx
> >      > Fatal Python error: Py_Initialize: can't initialize sys standard
> >     streams
> >      > Traceback (most recent call last):
> >      >    File
> >      >
> >     
> > "/home/shawn/sourcecode/espresso/src/python/espressomd/io/__init__.py",
> >      > line 17, in <module>
> >      >    File
> >      >
> >     
> > "/home/shawn/sourcecode/espresso/src/python/espressomd/io/writer/__init__.py", 
> >
> >
> >      > line 17, in <module>
> >      > ValueError: attempted relative import beyond top-level package
> >      > /bin/sh: line 1: 15371 Aborted                 (core dumped)
> >      > /home/shawn/soft/python3/bin/python3 gen_code_info.py
> >      > /home/shawn/sourcecode/espresso/src/features.def
> >      >
> >     
> > /home/shawn/sourcecode/espresso/build4/src/python/espressomd/code_info.pyx 
> >
> >      > make[2]: *** [src/python/espressomd/code_info.pyx] Error 134
> >      > make[1]: *** [src/python/espressomd/CMakeFiles/code_info.dir/all]
> >     Error 2
> >      > make: *** [all] Error 2
> >      >
> >      > It's so confusing, because I can successfully install espresso 
> > with
> >      > python 2 on the same computer and I can also install espresso with
> >      > python 3 on another computer.
> >      >
> >      > Does anyone know how to fix this? Thank you very much.
> >      >
> >      > Regards,
> >      > Shawn

MNWE.tar.gz
Description: application/gzip