Re: [ESPResSo-users] Installation problem

[Shawn]

Hi  Jean-Noël and Kai,

I have used the script you uploaded, and it works. The espresso could be reinstalled successfully. Thanks a lot for your help.

Attached please find the output of the compilation process. I hope it will be helpful for your further investigation.

Jean-Noël Grad <address@hidden> 于2019年7月18日周四 上午5:06写道：

Hi,

Yes, as explained in a previous mail, this is an issue with CMake
because the io package is not supposed to be imported when you call
gen_code_info.py from the /build directory. The "ValueError: attempted
relative import beyond top-level package" is documented as an issue when
calling a script that imports a script located in the parent directory.
But the three-dots import statement is correct and should never cause an
issue. If Shawn's python version is indeed trying to import the standard
io module instead of espresso's io module, the three-dots import might
cause the observed issue. The experiment I proposed will rule out that
possibility, and if there's a new error message, we will be able to
narrow down the source of the error in our CMake's build strategy.

Hope this clarifies things,
JN

On 7/18/19 11:51 AM, Kai Szuttor wrote:
> Hi,
>
> the original error message:
>
> [ 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
>
> looks to me as the interpreter tries to import espressomd
> modules although there is no package information due to
> the fact that at that point a python script (gen_code_info.py) is called.
>
> I don’t see why this should be related to any arch. More probably would
> be an issue with the build system generator (cmake).
>
> Best,
>
> Kai
>
> 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
>> <mailto: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
>>> <mailto: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>
>>>>>> <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>
>

io-output.txt
Description: Text document