LAMMPS Python package not being detected if source files are removed, but LAMMPS still works

LAMMPS LAMMPS Beginners
1

I’ve been recently given access to a computer cluster at my university. However, it’s outdate regarding the LAMMPS and Python versions and I had to install them in my personal directory without sudo privileges. I used a lot of help from ChatGPT since I don’t know too much about building from source. Here I attach the LAMMPS part, Python has been installed through pyenv:

git clone -b stable https://github.com/lammps/lammps.git
cd lammps
mkdir build
cd build
cmake \
  -D BUILD  _MPI=on \
  -D BUILD_LIB=on \
  -D PKG_PYTHON=on \
  -D PKG_MANYBODY=on \
  -D PKG_EXTRA-FIX=on \
  -D PKG_EXTRA-DUMP=on \
  -D PKG_EXTRA-COMPUTE=on \
  -D PKG_EXTRA-COMMAND=on \
  -D PYTHON_EXECUTABLE=$(pyenv which python3.13) \
  -D CMAKE_INSTALL_PREFIX=$HOME/.lammps \
  ../cmake
export CC=mpicc
export CXX=mpicxx
make -j8
make install

And I have to add this to .bashrc to make it work:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/.pyenv/versions/3.13.0/lib
alias lmp=".lammps/build/lmp"
export PATH=$HOME/.lammps/bin:$PATH
export PYTHONPATH=$HOME/.lammps/lib/lammps:$PYTHONPATH
export LD_LIBRARY_PATH=$HOME/.lammps/lib:$LD_LIBRARY_PATH
export LIBSTDCPP_PATH=$(mpicxx -print-file-name=libstdc++.so)
export LD_LIBRARY_PATH=$(dirname $LIBSTDCPP_PATH):$LD_LIBRARY_PATH
export OMP_NUM_THREADS=2

I want to install LAMMPS in .lammps and remove all source files at lammps to keep the home directory clean. If I remove lammps, the new aliased command lmp works (overwrites original command at the cluster) fine, but import lammps in Python fails. It doesn’t fail if I don’t remove that folder though.

Is there any other way of doing this apart from having all files in .lammps directly?

2

The information you followed was wrong.
Please read the manual.

3

A fairly standard directory structure for such installs is:

$HOME
  |- .local
      |- src
          |- lammps // source dir
               |- ...
      |- [lib]
      |- [bin]

where directories in square brackets are created by CMake.

This lets you complete your usual installation, not have to delete any files, and still have a clean home directory.

4

This has nothing to do with the problem at hand.
The “make install” from CMake simply does not install the LAMMPS python module.
There is a special “make install-python” step for that, which builds a proper python wheel first and then installs it with python -m pip into the proper location; either into the current virtual environment, or system-wide, or when failing permissions for a system installation into the designated folder in the user home directory.

The problem here is that @acgc99 is trusting ChatGPT too much. It mixed different chunks of the LAMMPS manual in inconsistent ways and that resulted in a mess.

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