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Re: [ESPResSo-users] Installation problem

From: Jean-Noël Grad
Subject: Re: [ESPResSo-users] Installation problem
Date: Wed, 17 Jul 2019 20:09:20 +0200
User-agent: Mozilla/5.0 (X11; Linux i686; rv:60.0) Gecko/20100101 Thunderbird/60.7.2

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/ creates a different error message that suggests the real culprit is the "io" espressomd submodule overshadowing the standard "io" module

Best regards,

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/", line 17, in <module>   File "/home/grad/Documents/espresso-structure/src/python/espressomd/io/writer/", line 1, in <module>
ValueError: attempted relative import beyond top-level package

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,

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.


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,

    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
     > code, I got errors below:
     > [ 61%] Generating code_info.pyx
     > Fatal Python error: Py_Initialize: can't initialize sys standard
     > Traceback (most recent call last):
     >    File
     > line 17, in <module>
     >    File

     > 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
     > /home/shawn/sourcecode/espresso/src/features.def
     > 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

Attachment: MNWE.tar.gz
Description: application/gzip

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