Building pair_allegro container

[namehta4]

Hi All,

I am trying to build pair_allegro with lammps 23.08 inside a docker container to support our users on our HPC center.
My docker recipe is as follows:

FROM docker.io/nvidia/cuda:12.1.1-devel-ubuntu22.04
WORKDIR /opt
ENV DEBIAN_FRONTEND noninteractive

RUN \
    apt-get update        &&   \
    apt-get install --yes      \
        build-essential        \
        autoconf               \
        cmake                  \
        flex                   \
        bison                  \
        zlib1g-dev             \
        fftw-dev               \
        fftw3                  \
        apbs                   \
        libicu-dev             \
        libbz2-dev             \
        libboost-all-dev       \
        libgmp-dev             \
        bc                     \
        libblas-dev            \
        liblapack-dev          \
        libfftw3-dev           \
        automake               \
        lsb-core               \
        libxc-dev              \
        git                    \
        unzip                  \
        gcc                    \
        g++                    \
        libgsl-dev             \
        libhdf5-serial-dev     \
        cmake                  \
        wget              &&   \
    apt-get clean all


#install miniconda
ENV installer=Miniconda3-py39_4.12.0-Linux-x86_64.sh

RUN wget https://repo.anaconda.com/miniconda/$installer && \
    /bin/bash $installer -b -p /opt/miniconda3          && \
    rm -rf $installer

ENV PATH=/opt/miniconda3/bin:$PATH
RUN conda install -y pip numpy scipy matplotlib setuptools mpi4py mkl-include


ARG mpich=4.1.1
ARG mpich_prefix=mpich-$mpich

RUN \
    wget https://www.mpich.org/static/downloads/$mpich/$mpich_prefix.tar.gz && \
    tar xvzf $mpich_prefix.tar.gz                                           && \
    cd $mpich_prefix                                                        && \
    ./configure FFLAGS=-fallow-argument-mismatch FCFLAGS=-fallow-argument-mismatch && \
    make -j 16                                                              && \
    make install                                                            && \
    make clean                                                              && \
    cd ..                                                                   && \
    rm -rf $mpich_prefix

RUN /sbin/ldconfig

#Installing lammps
WORKDIR /opt
RUN cd /opt
RUN git clone -b stable_2Aug2023 --recursive https://github.com/lammps/lammps.git lammps
#RUN git clone -b stable_29Sep2021_update2 --depth 1 https://github.com/lammps/lammps.git lammps 
RUN git clone https://github.com/mir-group/pair_allegro.git pair_allegro
RUN cd /opt/pair_allegro && \
    ./patch_lammps.sh /opt/lammps

RUN wget https://download.pytorch.org/libtorch/cu121/libtorch-cxx11-abi-shared-with-deps-2.1.0%2Bcu121.zip
RUN unzip libtorch-cxx11-abi-shared-with-deps-2.1.0+cu121.zip 
RUN rm -rf libtorch-cxx11-abi-shared-with-deps-2.1.0+cu121.zip
RUN mkdir ../include

RUN cd /opt/lammps
WORKDIR /opt/lammps
RUN mkdir build
RUN cd /opt/lammps/build
WORKDIR /opt/lammps/build
RUN cmake -DCMAKE_INSTALL_PREFIX=$PWD/../install -D CMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=/opt/libtorch \
          -DPKG_KOKKOS=ON -DKokkos_ARCH_AMPERE80=ON -DKokkos_ENABLE_CUDA=ON \
          -DMKL_INCLUDE_DIR="$CONDA_PREFIX/include" -DCMAKE_CXX_STANDARD=17 \
          -D BUILD_SHARED_LIBS=on -D LAMMPS_EXCEPTIONS=on -D PKG_MANYBODY=on -D PKG_MOLECULE=on \
          -D CMAKE_Fortran_COMPILER=mpif90 -D CMAKE_C_COMPILER=$(which mpicc) -D CMAKE_CXX_COMPILER=$(which mpicxx) \
          -D MPI_C_COMPILER=$(which mpicc) -D MPI_CXX_COMPILER=$(which mpicxx) -DCMAKE_CXX_STANDARD=17 \
          -D CMAKE_POSITION_INDEPENDENT_CODE=ON -D CMAKE_EXE_FLAGS="-dynamic" ../cmake
RUN make -j 4
RUN make install

# Setup entry point for production.
ENV PATH="$PATH:/opt/lammps/install/bin"
ENV PATH=/opt/lammps/install/bin:$PATH
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/lammps/install/lib

The build progresses to compiling lammps but fails with the following error:

712.4 /opt/lammps/src/pair_allegro.cpp(125): error: member "LAMMPS_NS::NeighRequest::half" (declared at line 54 of /opt/lammps/src/neigh_request.h) is inaccessible
712.4     neighbor->requests[irequest]->half = 0;
712.4                                   ^
712.4 
712.4 /opt/lammps/src/pair_allegro.cpp(126): error: member "LAMMPS_NS::NeighRequest::full" (declared at line 55 of /opt/lammps/src/neigh_request.h) is inaccessible
712.4     neighbor->requests[irequest]->full = 1;
712.4                                   ^
712.4 
712.4 /opt/lammps/src/pair_allegro.cpp(128): error: member "LAMMPS_NS::NeighRequest::ghost" (declared at line 68 of /opt/lammps/src/neigh_request.h) is inaccessible
712.4     neighbor->requests[irequest]->ghost = 1;
712.4                                   ^
712.4 
713.1 3 errors detected in the compilation of "/opt/lammps/src/pair_allegro.cpp".
713.2 [ 66%] Building CXX object CMakeFiles/lammps.dir/opt/lammps/src/pair_soft.cpp.o
713.3 make[2]: *** [CMakeFiles/lammps.dir/build.make:4822: CMakeFiles/lammps.dir/opt/lammps/src/pair_allegro.cpp.o] Error 2
713.3 make[2]: *** Waiting for unfinished jobs....
717.8 make[1]: *** [CMakeFiles/Makefile2:365: CMakeFiles/lammps.dir/all] Error 2
717.8 make: *** [Makefile:136: all] Error 2

May I please request your help?

Thank you!
Neil Mehta

[Tawfiq1448]

Same issue in my HPC center too. Is there any solution to this?

[Linux-cpp-lisp]

Hi @namehta4 , @Tawfiq1448 ,

Thanks for your (and your users') interest in our code!

This should be a version issue, see #30. Note also that for the moment we still recommend PyTorch 1.11 if possible.

[namehta4]

Hi Alby,

Thank you for your prompt response!
I was able to make the container image by changing the pair_allegro branch to multicut.

Thank you again!
Neil Mehta