Pysharc undefined symbol: get_grad_ shared object file

[MatthijsHak]

Dear developers,

I have a problem using pysharc via the shared object file. After compiling sharc with pysharc I try to import pysharc, but I receive the following message:

sharc.cpython-39-x86_64-linux-gnu.so: undefined symbol: getgrad

I found that this function is defined in the /pysharc/include/interface.h file, and that the order of compiling should be correct as specified in the Makefile (I did not change anything in this file). Also when I look at the sharc_setup dir, the directory /pysharc/include should be included during compilation. So I do not know what the problem is here.

Could you help me out?

[markusoppel]

Hi, we have never seen this error. But anyway, the pathes you give the sharc_setup dir and the path to the definition are not correct. In Linux, these pathes should either contain the full path of the installation directory, e.g. something like: /work/homdirs/myhomedir/myharcinstallation/sharc/pysharc/include/...

or be relativ path names, which never begin with a "/" but rather a directory name or something líke ".."

It looks like you have not defined an enviroment variable which is used within the Makefile. Please have a closer look. If you cannot figure it out, please send a copy of your Makefile and the a detailed error message (command you are trying to execute, environment etc.)

Cheers, Markus

[MatthijsHak]

Hi Markus,

Thanks for the quick response. Sorry for confusing you, but I gave the full path. I have installed and used sharc multiple times, but now I want to use schnarc, for which I require pysharc. I followed these instructions to install sharc with pysharc:

Repository: https://github.com/schnarc/SchNarc

However, after the installation process, I encountered an issue with the shared object file. It seems that several variables are not defined properly. As a result, I encountered an error when trying to use the pysharc module:

mhakkennes@int5:~/software/ml_aimd/sharc/pysharc/bin(main)$ python pysharc_lvc.py 
Traceback (most recent call last):
  File "/gpfs/home6/mhakkennes/software/ml_aimd/sharc/pysharc/bin/pysharc_lvc.py", line 45, in <module>
    from sharc.pysharc.interface import SHARC_INTERFACE
ImportError: /home/mhakkennes/software/ml_aimd/sharc/pysharc/sharc/sharc.cpython-39-x86_64-linux-gnu.so: undefined symbol: get_grad_

To provide you with more context, my PYTHONPATH is set as follows:

/home/mhakkennes/software/ml_aimd/sharc/pysharc/sharc:/home/mhakkennes/software/ml_aimd/sharc/lib

For your reference, I have attached a zip file containing the files from the pysharc directory and a directory source for the sharc source, along with the build_info.inc and Makefile. Additionally, I included a file displaying a list of symbols from the shared object file using the nm command. Lastly, I provided the output of the "make install" command for both pysharc and sharc.

I would appreciate your assistance in resolving this issue. Please let me know if you require any further information.

sharc_compile_files.zip

Thank you for your help.

Regards, Matthijs

[MatthijsHak]

I managed to compile it correctly. Problem was that when I specified the full path to my python env, as specified in the instructions in schnarc, then I would get this error. However, when I used $CONDA_PREFIX it was fine. Thanks for the help!