A link error at the end of building LAMMPS with QUIP

LAMMPS LAMMPS Installation
1

Hello,

I have tried to compile a LAMMPS with QUIP but facing an issue regarding linking.

The version of LAMMPS is 23-Jun-2022.

I use cmake and QUIP is separated compiled aforehand, and the location of the library file of QUIP (libquip.a) is included in the cmake file (basic_w_quip.cmake) to build LAMMPS.

My linux server use modules and modules I am using are below

autotools, ohpc, libfabric, openmpi4, scalapack, prun, ucx, gnu9, openblas, cmake.

Below is the error message I encountered.

[ 97%] Building CXX object CMakeFiles/lammps.dir/home/yxj200002/_LAMMPS/lammps-23Jun2022_cmake/src/MANYBODY/pair_tersoff_zbl.cpp.o
[ 97%] Building CXX object CMakeFiles/lammps.dir/home/yxj200002/_LAMMPS/lammps-23Jun2022_cmake/src/MANYBODY/pair_threebody_table.cpp.o
[ 97%] Building CXX object CMakeFiles/lammps.dir/home/yxj200002/_LAMMPS/lammps-23Jun2022_cmake/src/MANYBODY/pair_vashishta.cpp.o
[ 97%] Building CXX object CMakeFiles/lammps.dir/home/yxj200002/_LAMMPS/lammps-23Jun2022_cmake/src/MANYBODY/pair_vashishta_table.cpp.o
[ 97%] Building CXX object CMakeFiles/lammps.dir/home/yxj200002/_LAMMPS/lammps-23Jun2022_cmake/src/ML-QUIP/pair_quip.cpp.o
[ 98%] Linking CXX shared library liblammps.so
[ 98%] Built target lammps
Scanning dependencies of target lmp
[ 98%] Building CXX object CMakeFiles/lmp.dir/home/yxj200002/_LAMMPS/lammps-23Jun2022_cmake/src/main.cpp.o
[100%] Linking CXX executable lmp
liblammps.so.0: undefined reference to `mpi_cart_shift_'
liblammps.so.0: undefined reference to `mpi_allgather_'
liblammps.so.0: undefined reference to `mpi_sendrecv_'
liblammps.so.0: undefined reference to `mpi_initialized_'
liblammps.so.0: undefined reference to `mpi_allgatherv_'
liblammps.so.0: undefined reference to `mpi_gatherv_'
liblammps.so.0: undefined reference to `mpi_comm_set_errhandler_'
liblammps.so.0: undefined reference to `mpi_comm_size_'
liblammps.so.0: undefined reference to `mpi_send_'
liblammps.so.0: undefined reference to `mpi_barrier_'
liblammps.so.0: undefined reference to `mpi_scatter_'
liblammps.so.0: undefined reference to `mpi_allreduce_'
liblammps.so.0: undefined reference to `mpi_wtime_'
liblammps.so.0: undefined reference to `mpi_get_count_'
liblammps.so.0: undefined reference to `mpi_comm_free_'
liblammps.so.0: undefined reference to `mpi_comm_split_'
liblammps.so.0: undefined reference to `mpi_cart_coords_'
liblammps.so.0: undefined reference to `mpi_abort_'
liblammps.so.0: undefined reference to `mpi_error_string_'
liblammps.so.0: undefined reference to `mpi_cart_create_'
liblammps.so.0: undefined reference to `mpi_comm_rank_'
liblammps.so.0: undefined reference to `mpi_recv_'
liblammps.so.0: undefined reference to `mpi_gather_'
liblammps.so.0: undefined reference to `mpi_bcast_'
liblammps.so.0: undefined reference to `mpi_get_processor_name_'
liblammps.so.0: undefined reference to `mpi_init_'
liblammps.so.0: undefined reference to `mpi_finalize_'
liblammps.so.0: undefined reference to `mpi_scatterv_'
collect2: error: ld returned 1 exit status
gmake[2]: *** [CMakeFiles/lmp.dir/build.make:89: lmp] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:669: CMakeFiles/lmp.dir/all] Error 2
gmake: *** [Makefile:130: all] Error 2
[[email protected] build_quip]$ module

Below is the cmake file I customized for LAMMPS.

# basic_w_quip.cmake

# NECESSARY OPTIONS FOR LAMMPS-python MODULES
set(BUILD_SHARED_LIBS "on" CACHE STRING "" FORCE)
set(LAMMPS_EXCEPTIONS "on" CACHE STRING "" FORCE)


# BUILD_MPI; default="yes"
set(BUILD_MPI "yes" CACHE STRING "" FORCE)


# LAMMPS_MACHINE; this string will be added at the rear tag of the executable.
set(LAMMPS_MACHINE "" CACHE STRING "" FORCE)


# DEFINE LAMMPS PACKAGES WHICH ARE INCLUDED. 
# 'set' command creates a variable with a given value.
#  set(<variable> <value> ... ) 
#set(ALL_PACKAGES KSPACE MANYBODY MOLECULE RIGID MEAM PHONON QEQ PYTHON ML-QUIP)
set(ALL_PACKAGES KSPACE MANYBODY ML-QUIP)

# Alternative way to include a LAMMPS package
#set(PKG_PYTHON "yes" CACHE STRING "" FORCE)


# 
foreach(PKG ${ALL_PACKAGES})
  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()


# ML-QUIP
set(QUIP_LIBRARY "/home/yxj200002/_QUIP/0.9.12/build/linux_x86_64_gfortran_openmpi/libquip.a" CACHE STRING "" FORCE)

Below is CMakeCache.txt.
CMakeCache.txt (37.5 KB)

I guess the cause of error might be trivial but because of my lack of experience, I cannot figure out how I can solve this issue and where I can start to look.

Could anyone who can help me with this issue?

Thank you.

2

The error message indicates that you have calls to the Fortran MPI interface, but are not linking to it. That suggests that you may have compiled the QUIP library with MPI support, but that would not be correct. As a simple test, try to compile LAMMPS without the ML-QUIP package and see if the compilation finishes without an error. If it does, then you should perhaps let LAMMPS download and compile the QUIP library for you automatically.

3

Thank you for letting me know that.

Sounds like that your guess is correct. I do not have a problem like this before without QUIP package.

I guess I should try both ways; compiling LAMMPS & QUIP simultaneously and fixing the separated QUIP library.