PotNet enviroment set up about airs HOT 8 CLOSED

I create another folder and use it as TARGET_PATH to install again and success. Here is my output

:/home/hongshuh/PotNet/functions/gsl/lib/

Thanks for your reply!

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Thanks for the issue. I think this is an installation issue of torch-geometric. I rewrote the README and decoupled the torch-geometric installation from the yml file. Could you please try it out again? And let me know if you have any questions.

from airs.

Thanks for your reply, now I am able to set up the enviroment, but there is another error when run
python setup.py build_ext --inplace

running build_ext
building 'series' extension
gcc -pthread -B /home/hongshuh/anaconda3/envs/potnet/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/hongshuh/anaconda3/envs/potnet/include -fPIC -O2 -isystem /home/hongshuh/anaconda3/envs/potnet/include -fPIC -I/home/hongshuh/anaconda3/envs/potnet/lib/python3.9/site-packages/numpy/core/include -Igsl/include -I/home/hongshuh/anaconda3/envs/potnet/include/python3.9 -c bessel.c -o build/temp.linux-x86_64-3.9/bessel.o -std=c++11 -I./gsl/include
cc1: warning: command-line option ‘-std=c++11’ is valid for C++/ObjC++ but not for C
bessel.c:3:10: fatal error: gsl/gsl_sf_bessel.h: No such file or directory
    3 | #include <gsl/gsl_sf_bessel.h>
      |          ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: command '/usr/bin/gcc' failed with exit code 1```

from airs.

Hi, could you please show me your ~/.bashrc about LD_LIBRARY_PATH? I want to see if it is correctly exported.

from airs.

Hi, could you please show me your ~/.bashrc about LD_LIBRARY_PATH?

I was adding export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/hongshuh/PotNet/lib/ to ~/.bashrc. Did I make a mistake?

from airs.

Should it be like lib/lib since lib is a gsl subdirectory? I mean, during configuration we output the gsl into the prefix TARGET_PATH and lib is a subdirectory of TARGET_PATH. I doubt if the path is correct or if you are directly using the network directory as TARGET_PATH. It works fine on my server, so I need to identify what the cause is first.

from airs.

What is your output when run echo $$LD_LIBRARY_PATH, I think it is because my path did not set up correctly.

from airs.

It is :/home/grads/k/kruskallin/potnet/functions/gsl/lib/ when I echo $LD_LIBRARY_PATH. Here, /home/grads/k/kruskallin/potnet/functions/gsl/ is an empty directory made by myself and is my TARGET_PATH and the directory gsl after c++ compilation looks like

May I ask what is your output when you run echo $LD_LIBRARY_PATH?

from airs.