Re: [ESPResSo-users] Installation problem

Kai Szuttor

Institute for Computational Physics
Universität Stuttgart
Allmandring 3

Room 1.084
70569 Stuttgart, Germany
Phone: +49 711 685-67707

On 18. Jul 2019, at 11:39, Jean-Noël Grad <address@hidden> wrote:

Hi Shawn,

I can't reproduce the error message with python3.6.8 on 64bit CentOS 7 in docker. Only my 32bit Debian can reproduce the error, unfortunately espresso is not fully compatible with this specific 32bit architecture so I cannot look for a solution on it.

Let's do the following experiment: you'll rename the src/python/espressomd/io folder and try compiling again. To this end, please use the attached patch file and bash script (store both of them in /home/shawn/sourcecode/espresso). Run the bash script with "bash io-build.sh" and let me know if you still have an error message. Note that the source folder won't be cleaned up in case of error.

Best,
JN

On 2019-07-17 20:28, Shawn wrote:
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
<io.patch><io-build.sh>

From:	Kai Szuttor
Subject:	Re: [ESPResSo-users] Installation problem
Date:	Thu, 18 Jul 2019 11:51:06 +0200