Скачать ZIP-архив

rmc_lammps_build_notes.md · 3.2 KiB · Markdown Исходник

Build LAMMPS with RMCProfile === 1. We first need to compile `LAMMPS` separately to obtain the library file `liblammps.so.0`, together with a soft link file `liblammps.so` pointing to the library file. Once we have the compiled `liblammps.so.0` library file, creating the soft link is as simple as running, ``` ln -s liblammps.so.0 liblammps.so ``` - The `LAMMPS` source codes are hosted on [GitHub](https://github.com/lammps/lammps) and the building instructions can be found [here](https://docs.lammps.org/Build_cmake.html) > Starting from the `Stable release candidate 2 August 2023` (see the pull request [here](https://github.com/lammps/lammps/pull/3825)), `LAMMPS` changed the Fortran interface. I haven't checked how we can work with the new interface. The following compiling therefore will only work seamlessly with the version of `LAMMPS` before the aforementioned release. I am not sure whether or not the old wrapper will work with the newer version of `LAMMPS`. In case not, we then have to spend some time checking how to make the new wrapper working with RMCProfile. - Here follows is a bare minimum example for building `LAMMPS`, ``` source /home/y8z/intel/oneapi/setvars.sh cmake ../cmake -D CMAKE_CXX_COMPILER=icx-cc cmake ../cmake -D BUILD_MPI=no -D BUILD_OMP=yes -D PKG_OPENMP=yes -D BUILD_SHARED_LIBS=yes -D PKG_REAXFF=yes -D PKG_EXTRA-PAIR=yes ``` > Here I am using the intel `oneapi` installed into my own area on Big Bird. It seems that intel changes the compiler name for C++ to `icx-cc` instead of the old `icc`. > The `-D BUILD_SHARED_LIBS=yes` flags tell the compiler to create the shared library file we need. > The implementation of `LAMMPS` in RMCProfile is serial so we don't need the MPI build for `LAMMPS`. > The `-D PKG_REAXFF=yes` worries about enabling the `ReaxFF` potential. It is through this kind of flags that `LAMMPS` build controls what potentials to compile. 2. Next we need to build the `LAMMPS` wrapper -- source codes for the wrapper were provided with the `LAMMPS` source codes. > Starting from the `Stable release candidate 2 August 2023` (see the pull request [here](https://github.com/lammps/lammps/pull/3825)), `LAMMPS` changed the Fortran interface. I haven't checked how we can work with the new interface. The following compiling therefore will only work seamlessly with the version of `LAMMPS` before the aforementioned release. I am not sure whether or not the old wrapper will work with the newer version of `LAMMPS`. In case not, we then have to spend some time checking how to make the new wrapper working with RMCProfile. In the `RMCProfile` repo (the `lammps_rmc_ready` branch), under the `ubuntu1804-cuda-intel` directory, we have a `Makefile_lammps_wrapper_oneAPI` file for building the `LAMMPS` wrapper, creating the library file `liblammps_fortran.so`. 3. Then we just need to link the library when compiling the RMCProfile executable, including the link to both the `liblammps.so` and `liblammps_fortran.so` libraries. The `Makefile_mpi_oneAPI` file can be used as the reference about the library linking and the bash script `build_rmcprofile_lammps.sh` combines the step 2 & 3.

Build LAMMPS with RMCProfile

We first need to compile LAMMPS separately to obtain the library file liblammps.so.0, together with a soft link file liblammps.so pointing to the library file. Once we have the compiled liblammps.so.0 library file, creating the soft link is as simple as running,
```
ln -s liblammps.so.0 liblammps.so
```
- The LAMMPS source codes are hosted on GitHub and the building instructions can be found here
  
  Starting from the Stable release candidate 2 August 2023 (see the pull request here), LAMMPS changed the Fortran interface. I haven't checked how we can work with the new interface. The following compiling therefore will only work seamlessly with the version of LAMMPS before the aforementioned release. I am not sure whether or not the old wrapper will work with the newer version of LAMMPS. In case not, we then have to spend some time checking how to make the new wrapper working with RMCProfile.
- Here follows is a bare minimum example for building LAMMPS,
```
source /home/y8z/intel/oneapi/setvars.sh
cmake ../cmake -D CMAKE_CXX_COMPILER=icx-cc
cmake ../cmake -D BUILD_MPI=no -D BUILD_OMP=yes -D PKG_OPENMP=yes -D BUILD_SHARED_LIBS=yes -D PKG_REAXFF=yes -D PKG_EXTRA-PAIR=yes
```
  Here I am using the intel oneapi installed into my own area on Big Bird. It seems that intel changes the compiler name for C++ to icx-cc instead of the old icc.
  
  The -D BUILD_SHARED_LIBS=yes flags tell the compiler to create the shared library file we need.
  
  The implementation of LAMMPS in RMCProfile is serial so we don't need the MPI build for LAMMPS.
  
  The -D PKG_REAXFF=yes worries about enabling the ReaxFF potential. It is through this kind of flags that LAMMPS build controls what potentials to compile.
Next we need to build the LAMMPS wrapper -- source codes for the wrapper were provided with the LAMMPS source codes.

Starting from the Stable release candidate 2 August 2023 (see the pull request here), LAMMPS changed the Fortran interface. I haven't checked how we can work with the new interface. The following compiling therefore will only work seamlessly with the version of LAMMPS before the aforementioned release. I am not sure whether or not the old wrapper will work with the newer version of LAMMPS. In case not, we then have to spend some time checking how to make the new wrapper working with RMCProfile.

In the RMCProfile repo (the lammps_rmc_ready branch), under the ubuntu1804-cuda-intel directory, we have a Makefile_lammps_wrapper_oneAPI file for building the LAMMPS wrapper, creating the library file liblammps_fortran.so.
Then we just need to link the library when compiling the RMCProfile executable, including the link to both the liblammps.so and liblammps_fortran.so libraries. The Makefile_mpi_oneAPI file can be used as the reference about the library linking and the bash script build_rmcprofile_lammps.sh combines the step 2 & 3.