Re: [ESPResSo-users] Installation problem

[Shawn]

Hi Jean-Noël,

I really appreciate your help, and I also look forward to your investigation on this issue.

By the way,  currently my python version on 64-bit centos 7 is 3.6.5  but it seems like I have the same problem with python 3.7.2.

I hope these information is helpful for your investigation. Thanks very much.

Best,

Shawn

Jean-Noël Grad <address@hidden> 于2019年7月17日周三 下午1:09写道：

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
>>