Build fails with kokkos error

[namehta4]

HI,

I am trying to build LAMMPS Allegro in a container with the following build script:

FROM nvcr.io/nvidia/cuda:11.8.0-cudnn8-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 libgmp-dev \
        libboost-all-dev bc libblas-dev liblapack-dev git    \   
        libfftw3-dev automake lsb-core libxc-dev libgsl-dev  \
        unzip libhdf5-serial-dev ffmpeg libcurl4-openssl-dev \
        libboost-dev libboost-system-dev libtool swig        \   
        libboost-filesystem-dev libboost-graph-dev uuid-dev  \
        libboost-regex-dev libedit-dev libyaml-cpp-dev make  \
        python3-yaml automake pkg-config libc6-dev libzmq3-dev \
        libjansson-dev liblz4-dev libarchive-dev python3-pip \
        libsqlite3-dev lua5.1 liblua5.1-dev lua-posix jq     \   
        python3-dev python3-cffi python3-ply python3-sphinx  \
        aspell aspell-en valgrind libyaml-cpp-dev wget vim   \   
        libquadmath0 \
        make libzmq3-dev python3-yaml time valgrind  libeigen3-dev \
        mlocate python3-jsonschema python-is-python3       &&\ 
    apt-get clean all 

RUN apt-get update && apt-get install --yes gpg-agent wget
RUN wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
RUN echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list
RUN apt-get update 
RUN apt-get install --yes intel-oneapi-mkl intel-oneapi-mkl-devel && \
    apt-get clean all 


WORKDIR /opt
ARG mpich=4.2.2
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 \
    --prefix=/opt/mpich/install                                             && \
    make -j 16                                                              && \
    make install                                                            && \
    make clean                                                              && \
    cd ..                                                                   && \
    rm -rf $mpich_prefix.tar.gz
ENV PATH=$PATH:/opt/mpich/install/bin
ENV PATH=$PATH:/opt/mpich/install/include
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/mpich/install/lib
RUN /sbin/ldconfig

ENV PATH=$PATH:/usr/local/cuda/lib64/stubs
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64/stubs
ENV PATH=$PATH:/usr/local/cuda-11.8/targets/x86_64-linux/lib/stubs
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.8/targets/x86_64-linux/lib/stubs

RUN ln -s /usr/local/cuda-11.8/targets/x86_64-linux/lib/stubs/libnvidia-ml.so /usr/local/cuda-11.8/targets/x86_64-linux/lib/stubs/libnvidia-ml.so.1 

RUN python -m pip install cffi numpy meson ninja
RUN python -m pip install setuptools
RUN python -m pip install mpi4py -i https://pypi.anaconda.org/mpi4py/simple
RUN python -m pip install numpy scipy matplotlib
RUN python -m pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
RUN python -m pip install clang-format
ENV TORCH_CUDA_ARCH_LIST="8.0 8.6 8.9 9.0"

#Installing lammps
WORKDIR /opt
RUN cd /opt
RUN git clone -b stable_29Aug2024_update1 https://github.com/lammps/lammps  
RUN git clone -b multicut https://github.com/mir-group/pair_allegro.git pair_allegro
RUN cd /opt/pair_allegro && \
    ./patch_lammps.sh /opt/lammps
RUN git clone https://github.com/mir-group/pair_nequip
RUN cd /opt/pair_nequip && \
    cp /opt/pair_nequip/pair_nequip.cpp /opt/lammps/src  && \
    cp /opt/pair_nequip/pair_nequip.h /opt/lammps/src

RUN apt-get install --yes clang-format xxd
RUN wget https://download.pytorch.org/libtorch/cu118/libtorch-shared-with-deps-2.5.1%2Bcu118.zip && \
    unzip libtorch-shared-with-deps-2.5.1+cu118.zip                         && \
    rm -r libtorch-shared-with-deps-2.5.1+cu118.zip                         && \
    mv libtorch libtorch-gpu                                                
ENV PATH=$PATH:/opt/libtorch-gpu/bin
ENV PATH=$PATH:/opt/libtorch-gpu/include
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/libtorch-gpu/lib


ENV PATH=$PATH:/opt/lammps/build/plumed_build-prefix/bin
ENV PATH=$PATH:/opt/lammps/build/plumed_build-prefix/include
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/lammps/build/plumed_build-prefix/lib
ENV PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/opt/lammps/build/plumed_build-prefix/lib/pkgconfig
ENV PLUMED_KERNEL=/opt/lammps/build/plumed_build-prefix/lib/libplumedKernel.so
WORKDIR /opt/lammps
RUN mkdir build
WORKDIR /opt/lammps/build
RUN cmake -DMKL_INCLUDE_DIR=/opt/intel/oneapi/mkl/2025.0/include -DMKL_LIBRARY=/opt/intel/oneapi/mkl/2025.0/lib \
          -D CMAKE_BUILD_TYPE=Release -D CMAKE_PREFIX_PATH=/opt/libtorch-gpu \
          -D CMAKE_INSTALL_PREFIX=/opt/lammps/install -D CMAKE_CXX_STANDARD=17 -D CMAKE_CXX_STANDARD_REQUIRED=ON \
          -D BUILD_MPI=ON -D CMAKE_CXX_COMPILER=/opt/lammps/lib/kokkos/bin/nvcc_wrapper -D BUILD_SHARED_LIBS=ON \
          -D PKG_MANYBODY=ON -D PKG_MOLECULE=ON -D PKG_KSPACE=ON -D PKG_REPLICA=ON -D PKG_REAXFF=ON -D PKG_QEQ=ON \
          -D PKG_PHONON=ON -D PKG_ELECTRODE=yes -D PKG_PLUMED=yes -D DOWNLOAD_PLUMED=yes -D PLUMED_MODE=shared \
          -D PKG_KOKKOS=yes -D Kokkos_ARCH_AMPERE80=ON -D Kokkos_ENABLE_CUDA=yes \
          -D BUILD_SHARED_LIBS=ON \
          -D CMAKE_PREFIX_PATH="/opt/libtorch-gpu;/usr/local/cuda-11.8/compat;/opt/intel/oneapi/mkl/2025.0" ../cmake
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.8/compat
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/oneapi/mkl/2025.0/lib
RUN make verbose=1 -j 16
RUN make install
ENV PATH=/opt/lammps/install/bin:$PATH
ENV PATH=/opt/lammps/install/lib:$PATH
ENV PATH=/opt/lammps/install/include:$PATH
ENV LD_LIBRARY_PATH=/opt/lammps/install/lib:$LD_LIBRARY_PATH

However, my build fails with the following error:

[100%] Built target lammps
[100%] Building CXX object CMakeFiles/lmp.dir/opt/lammps/src/main.cpp.o
[100%] Linking CXX executable lmp
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Cuda::fence(std::string const&) const'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Impl::fill_host_accessible_header_info(Kokkos::Impl::SharedAllocationRecord<void, void>*, Kokkos::Impl::SharedAllocationHeader&, std::string const&)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Impl::log_warning(std::string const&)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Impl::throw_runtime_exception(std::string const&)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::fence(std::string const&)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Tools::beginParallelFor(std::string const&, unsigned int, unsigned long*)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Profiling::beginDeepCopy(Kokkos_Profiling_SpaceHandle, std::string, void const*, Kokkos_Profiling_SpaceHandle, std::string, void const*, unsigned long)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Impl::safe_throw_allocation_with_header_failure(std::string const&, std::string const&, Kokkos::Experimental::RawMemoryAllocationFailure const&)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Impl::SharedAllocationRecordCommon<Kokkos::HostSpace>::SharedAllocationRecordCommon(Kokkos::HostSpace const&, std::string const&, unsigned long, void (*)(Kokkos::Impl::SharedAllocationRecord<void, void>*))'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Tools::modifyDualView(std::string const&, void const*, bool)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Tools::beginFence(std::string, unsigned int, unsigned long*)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Tools::beginParallelScan(std::string const&, unsigned int, unsigned long*)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Impl::SharedAllocationRecord<void, void>::SharedAllocationRecord(Kokkos::Impl::SharedAllocationHeader*, unsigned long, void (*)(Kokkos::Impl::SharedAllocationRecord<void, void>*), std::string const&)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Tools::beginParallelReduce(std::string const&, unsigned int, unsigned long*)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Impl::SharedAllocationRecordCommon<Kokkos::CudaHostPinnedSpace>::allocate_tracked(Kokkos::CudaHostPinnedSpace const&, std::string const&, unsigned long)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Impl::HostInaccessibleSharedAllocationRecordCommon<Kokkos::CudaSpace>::get_label() const'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Impl::HostInaccessibleSharedAllocationRecordCommon<Kokkos::CudaSpace>::HostInaccessibleSharedAllocationRecordCommon(Kokkos::CudaSpace const&, std::string const&, unsigned long, void (*)(Kokkos::Impl::SharedAllocationRecord<void, void>*))'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Impl::SharedAllocationRecordCommon<Kokkos::HostSpace>::get_label() const'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Tools::syncDualView(std::string const&, void const*, bool)'
/usr/bin/ld: liblammps.so.0: undefined reference to `Kokkos::Profiling::beginParallelFor(std::string const&, unsigned int, unsigned long*)'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/lmp.dir/build.make:110: lmp] Error 1
make[1]: *** [CMakeFiles/Makefile2:416: CMakeFiles/lmp.dir/all] Error 2
make: *** [Makefile:136: all] Error 2
Error: building at STEP "RUN make verbose=1 -j 16": while running runtime: exit status 2

May I please request your help with this?

Thanks!
Neil