Error raised when compiling lammps with Cmake

[Cloudac7]

I just used Cmake to compile Lammps as well as DeePMD-kit interface (USER-DEEPMD module).

Some environment:

• Intel MPI 2017.5.239
• GCC 9.3.0
• CUDA 11.3
• HDF5 1.12.2
• DeePMD-kit 2.1.3
• Lammps 20220623 Update1
• Plumed 2.8.0
• GSL 2.7
• CMake 3.24

I have modified CMakeLists.txt to add USER-DEEPMD into it (Ref) and the command I used is this:

cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake \
-D BUILD_MPI=yes -D BUILD_OMP=yes -D LAMMPS_MACHINE=mpi \
-D PKG_PLUMED=yes -D PKG_H5MD=yes -D PKG_COLVARS=yes \
-D PKG_USER-DEEPMD=ON -D CMAKE_CXX_FLAGS="-DHIGH_PREC" \
-D CMAKE_CXX_FLAGS="-I${deepmd_root}/include -I${tensorflow_root}/include -L${deepmd_root}/lib -L${tensorflow_root}/lib -Wl,--no-as-needed -lrt -ldeepmd_op -ldeepmd_op_cuda -ldeepmd -ltensorflow_cc -ltensorflow_framework -Wl,-rpath=${deepmd_root}/lib -Wl,-rpath=${tensorflow_root}/lib" \
-D CMAKE_INSTALL_PREFIX=${tensorflow_root} ../cmake

However, I finally ran into the very issue as the error log shown here:

[ 23%] Building CXX object CMakeFiles/lammps.dir/data/share/soft/deepmd/2.1.3/lammps-stable_23Jun2022_update1/src/force.cpp.o
/data/share/soft/deepmd/2.1.3/lammps-stable_23Jun2022_update1/src/force.cpp: In instantiation of ‘S* style_creator(LAMMPS_NS::LAMMPS*) [with S = LAMMPS_NS::KSpace; T = LAMMPS_NS::PPPMDPLR]’:
/data/share/soft/deepmd/2.1.3/lammps-stable_23Jun2022_update1/src/USER-DEEPMD/pppm_dplr.h:3:1:   required from here
/data/share/soft/deepmd/2.1.3/lammps-stable_23Jun2022_update1/src/force.cpp:43:10: error: no matching function for call to ‘LAMMPS_NS::PPPMDPLR::PPPMDPLR(LAMMPS_NS::LAMMPS*&)’
   43 |   return new T(lmp);
      |          ^~~~~~~~~~
In file included from /data/share/soft/deepmd/2.1.3/lammps-stable_23Jun2022_update1/build/styles/style_kspace.h:23,
                 from /data/share/soft/deepmd/2.1.3/lammps-stable_23Jun2022_update1/src/force.cpp:20:
/data/share/soft/deepmd/2.1.3/lammps-stable_23Jun2022_update1/src/USER-DEEPMD/pppm_dplr.h:26:5: note: candidate: ‘LAMMPS_NS::PPPMDPLR::PPPMDPLR(LAMMPS_NS::LAMMPS*, int, char**)’
   26 |     PPPMDPLR(class LAMMPS *, int, char **);
      |     ^~~~~~~~
/data/share/soft/deepmd/2.1.3/lammps-stable_23Jun2022_update1/src/USER-DEEPMD/pppm_dplr.h:26:5: note:   candidate expects 3 arguments, 1 provided
/data/share/soft/deepmd/2.1.3/lammps-stable_23Jun2022_update1/src/USER-DEEPMD/pppm_dplr.h:22:9: note: candidate: ‘LAMMPS_NS::PPPMDPLR::PPPMDPLR(const LAMMPS_NS::PPPMDPLR&)’
   22 |   class PPPMDPLR : public PPPM {
      |         ^~~~~~~~
/data/share/soft/deepmd/2.1.3/lammps-stable_23Jun2022_update1/src/USER-DEEPMD/pppm_dplr.h:22:9: note:   no known conversion for argument 1 from ‘LAMMPS_NS::LAMMPS*’ to ‘const LAMMPS_NS::PPPMDPLR&’
make[2]: *** [CMakeFiles/lammps.dir/data/share/soft/deepmd/2.1.3/lammps-stable_23Jun2022_update1/src/force.cpp.o] Error 1
make[1]: *** [CMakeFiles/lammps.dir/all] Error 2
make: *** [all] Error 2

How could I move on if using cmake?

[Yi-FanLi]

You should add -DLAMMPS_VERSION_NUMBER=20220623 in your CMAKE_CXX_FLAGS.

[Cloudac7]

After all the steps, I finally get this error:

[100%] Linking CXX executable lmp_mpi
plumed_build-prefix/lib/libplumed.a(kernel.o): In function `PLMD::PlumedMain::readInputLines(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
(.text+0x11823c): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/bin/ld: warning: libjpeg.so.9, needed by /data/share/apps/deepmd/2.1/lib/libtensorflow_cc.so, may conflict with libjpeg.so.62
liblammps_mpi.a(compute_deeptensor_atom.cpp.o): In function `LAMMPS_NS::ComputeDeeptensorAtom::ComputeDeeptensorAtom(LAMMPS_NS::LAMMPS*, int, char**)':
compute_deeptensor_atom.cpp:(.text+0xa2): undefined reference to `deepmd::DeepTensor::DeepTensor()'
compute_deeptensor_atom.cpp:(.text+0x1ea): undefined reference to `deepmd::DeepTensor::init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
liblammps_mpi.a(compute_deeptensor_atom.cpp.o): In function `LAMMPS_NS::ComputeDeeptensorAtom::compute_peratom()':
compute_deeptensor_atom.cpp:(.text+0xb01): undefined reference to `deepmd::DeepTensor::compute(std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> > const&, std::vector<int, std::allocator<int> > const&, std::vector<float, std::allocator<float> > const&, int, deepmd::InputNlist const&)'
liblammps_mpi.a(fix_dplr.cpp.o): In function `LAMMPS_NS::FixDPLR::FixDPLR(LAMMPS_NS::LAMMPS*, int, char**)':
fix_dplr.cpp:(.text+0x328): undefined reference to `deepmd::DeepTensor::DeepTensor()'
fix_dplr.cpp:(.text+0x33d): undefined reference to `deepmd::DipoleChargeModifier::DipoleChargeModifier()'
fix_dplr.cpp:(.text+0x108d): undefined reference to `deepmd::DeepTensor::init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
fix_dplr.cpp:(.text+0x1119): undefined reference to `deepmd::DipoleChargeModifier::init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
liblammps_mpi.a(fix_dplr.cpp.o): In function `LAMMPS_NS::FixDPLR::pre_force(int)':
fix_dplr.cpp:(.text+0x2477): undefined reference to `deepmd::DeepTensor::compute(std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> > const&, std::vector<int, std::allocator<int> > const&, std::vector<float, std::allocator<float> > const&, int, deepmd::InputNlist const&)'
fix_dplr.cpp:(.text+0x256d): undefined reference to `deepmd::select_by_type(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, int&, std::vector<float, std::allocator<float> > const&, std::vector<int, std::allocator<int> > const&, int const&, std::vector<int, std::allocator<int> > const&)'
fix_dplr.cpp:(.text+0x25fb): undefined reference to `void deepmd::select_map<int>(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> > const&, std::vector<int, std::allocator<int> > const&, int const&)'
liblammps_mpi.a(fix_dplr.cpp.o): In function `LAMMPS_NS::FixDPLR::post_force(int)':
fix_dplr.cpp:(.text+0x3599): undefined reference to `deepmd::DipoleChargeModifier::compute(std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> > const&, std::vector<int, std::allocator<int> > const&, std::vector<float, std::allocator<float> > const&, std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > > const&, std::vector<float, std::allocator<float> > const&, int, deepmd::InputNlist const&)'
liblammps_mpi.a(pair_deepmd.cpp.o): In function `LAMMPS_NS::PairDeepMD::get_file_content(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
pair_deepmd.cpp:(.text+0x33b): undefined reference to `deepmd::read_file_to_string(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'
liblammps_mpi.a(pair_deepmd.cpp.o): In function `LAMMPS_NS::PairDeepMD::PairDeepMD(LAMMPS_NS::LAMMPS*)':
pair_deepmd.cpp:(.text+0x7e3): undefined reference to `deepmd::DeepPot::DeepPot()'
pair_deepmd.cpp:(.text+0x7f8): undefined reference to `deepmd::DeepPotModelDevi::DeepPotModelDevi()'
pair_deepmd.cpp:(.text+0xc28): undefined reference to `deepmd::DeepPotModelDevi::~DeepPotModelDevi()'
pair_deepmd.cpp:(.text+0xc42): undefined reference to `deepmd::DeepPot::~DeepPot()'
liblammps_mpi.a(pair_deepmd.cpp.o): In function `LAMMPS_NS::PairDeepMD::print_summary(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) const':
pair_deepmd.cpp:(.text+0xd6f): undefined reference to `deepmd::DeepPot::print_summary(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
liblammps_mpi.a(pair_deepmd.cpp.o): In function `LAMMPS_NS::PairDeepMD::~PairDeepMD()':
pair_deepmd.cpp:(.text+0x11b7): undefined reference to `deepmd::DeepPotModelDevi::~DeepPotModelDevi()'
pair_deepmd.cpp:(.text+0x11c9): undefined reference to `deepmd::DeepPot::~DeepPot()'
liblammps_mpi.a(pair_deepmd.cpp.o): In function `LAMMPS_NS::PairDeepMD::compute(int, int)':
pair_deepmd.cpp:(.text+0x1c83): undefined reference to `deepmd::DeepPot::compute(double&, std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> > const&, std::vector<int, std::allocator<int> > const&, std::vector<float, std::allocator<float> > const&, int, deepmd::InputNlist const&, int const&, std::vector<float, std::allocator<float> > const&, std::vector<float, std::allocator<float> > const&)'
pair_deepmd.cpp:(.text+0x21ab): undefined reference to `deepmd::DeepPot::compute(double&, std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> > const&, std::vector<int, std::allocator<int> > const&, std::vector<float, std::allocator<float> > const&, int, deepmd::InputNlist const&, int const&, std::vector<float, std::allocator<float> > const&, std::vector<float, std::allocator<float> > const&)'
pair_deepmd.cpp:(.text+0x2d96): undefined reference to `deepmd::DeepPotModelDevi::compute(std::vector<double, std::allocator<double> >&, std::vector<std::vector<float, std::allocator<float> >, std::allocator<std::vector<float, std::allocator<float> > > >&, std::vector<std::vector<float, std::allocator<float> >, std::allocator<std::vector<float, std::allocator<float> > > >&, std::vector<std::vector<float, std::allocator<float> >, std::allocator<std::vector<float, std::allocator<float> > > >&, std::vector<std::vector<float, std::allocator<float> >, std::allocator<std::vector<float, std::allocator<float> > > >&, std::vector<float, std::allocator<float> > const&, std::vector<int, std::allocator<int> > const&, std::vector<float, std::allocator<float> > const&, int, deepmd::InputNlist const&, int const&, std::vector<float, std::allocator<float> > const&, std::vector<float, std::allocator<float> > const&)'
pair_deepmd.cpp:(.text+0x3a68): undefined reference to `deepmd::DeepPotModelDevi::compute_avg(std::vector<float, std::allocator<float> >&, std::vector<std::vector<float, std::allocator<float> >, std::allocator<std::vector<float, std::allocator<float> > > > const&)'
pair_deepmd.cpp:(.text+0x3a93): undefined reference to `deepmd::DeepPotModelDevi::compute_std_f(std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> > const&, std::vector<std::vector<float, std::allocator<float> >, std::allocator<std::vector<float, std::allocator<float> > > > const&)'
pair_deepmd.cpp:(.text+0x3afe): undefined reference to `deepmd::DeepPotModelDevi::compute_relative_std_f(std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> > const&, float)'
pair_deepmd.cpp:(.text+0x3d8b): undefined reference to `deepmd::DeepPotModelDevi::compute_avg(std::vector<float, std::allocator<float> >&, std::vector<std::vector<float, std::allocator<float> >, std::allocator<std::vector<float, std::allocator<float> > > > const&)'
pair_deepmd.cpp:(.text+0x3db6): undefined reference to `deepmd::DeepPotModelDevi::compute_std_e(std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> > const&, std::vector<std::vector<float, std::allocator<float> >, std::allocator<std::vector<float, std::allocator<float> > > > const&)'
pair_deepmd.cpp:(.text+0x4375): undefined reference to `deepmd::DeepPotModelDevi::compute_avg(std::vector<float, std::allocator<float> >&, std::vector<std::vector<float, std::allocator<float> >, std::allocator<std::vector<float, std::allocator<float> > > > const&)'
pair_deepmd.cpp:(.text+0x43b4): undefined reference to `deepmd::DeepPotModelDevi::compute_std(std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> > const&, std::vector<std::vector<float, std::allocator<float> >, std::allocator<std::vector<float, std::allocator<float> > > > const&, int const&)'
pair_deepmd.cpp:(.text+0x440c): undefined reference to `deepmd::DeepPotModelDevi::compute_relative_std(std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> > const&, float, int const&)'
pair_deepmd.cpp:(.text+0x509f): undefined reference to `deepmd::DeepPot::compute(double&, std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> >&, std::vector<float, std::allocator<float> > const&, std::vector<int, std::allocator<int> > const&, std::vector<float, std::allocator<float> > const&, std::vector<float, std::allocator<float> > const&, std::vector<float, std::allocator<float> > const&)'
liblammps_mpi.a(pair_deepmd.cpp.o): In function `LAMMPS_NS::PairDeepMD::settings(int, char**)':
pair_deepmd.cpp:(.text+0x6a7d): undefined reference to `deepmd::DeepPot::init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
pair_deepmd.cpp:(.text+0x6c22): undefined reference to `deepmd::DeepPot::init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
pair_deepmd.cpp:(.text+0x6cd0): undefined reference to `deepmd::DeepPotModelDevi::init(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
/data/share/apps/deepmd/2.1/lib/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9'
collect2: error: ld returned 1 exit status
make[2]: *** [lmp_mpi] Error 1
make[1]: *** [CMakeFiles/lmp.dir/all] Error 2
make: *** [all] Error 2

It seems that the include was not correctly recogonized.

[njzjz]

I think you should follow the flags defined in env.sh.

[Cloudac7]

I think you should follow the flags defined in env.sh.

Sorry for misleading in my description above, I just changed the flags to the same as which found in env.sh, however, issue not solved.

Now the command of cmake is:

cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake \
-D BUILD_MPI=yes -D BUILD_OMP=yes -D LAMMPS_MACHINE=mpi \
-D PKG_PLUMED=yes -D PKG_H5MD=yes -D PKG_COLVARS=yes \
-D PKG_USER-DEEPMD=ON -D CMAKE_CXX_FLAGS="-DHIGH_PREC" \
-D CMAKE_CXX_FLAGS="-I${deepmd_root}/include -I${tensorflow_root}/include -L${deepmd_root}/lib -L${tensorflow_root}/lib -Wl,--no-as-needed -ldeepmd_cc -ltensorflow_cc -ltensorflow_framework -Wl,-rpath=${deepmd_root}/lib -Wl,-rpath=${tensorflow_root}/lib -DLAMMPS_VERSION_NUMBER=20220623 -std=c++14" \
-D CMAKE_INSTALL_PREFIX=${tensorflow_root} ../cmake

And env.sh:

DEEPMD_ROOT=/data/share/apps/deepmd/2.1/deepmd_root
TENSORFLOW_INCLUDE_DIRS="/data/share/apps/deepmd/2.1/include;/data/share/apps/deepmd/2.1/include"
TENSORFLOW_LIBRARY_PATH="/data/share/apps/deepmd/2.1/lib;/data/share/apps/deepmd/2.1/lib"

TF_INCLUDE_DIRS=`echo $TENSORFLOW_INCLUDE_DIRS | sed "s/;/ -I/g"`
TF_LIBRARY_PATH=`echo $TENSORFLOW_LIBRARY_PATH | sed "s/;/ -L/g"`
TF_RPATH=`echo $TENSORFLOW_LIBRARY_PATH | sed "s/;/ -Wl,-rpath=/g"`

NNP_INC=" -std=c++14 -DHIGH_PREC  -DLAMMPS_VERSION_NUMBER=20220623 -I$DEEPMD_ROOT/include/ "
NNP_PATH=" -L$TF_LIBRARY_PATH -L$DEEPMD_ROOT/lib"
NNP_LIB=" -Wl,--no-as-needed -ldeepmd_cc -ltensorflow_cc -ltensorflow_framework -Wl,-rpath=$TF_RPATH -Wl,-rpath=$DEEPMD_ROOT/lib"

[njzjz]

-D CMAKE_CXX_FLAGS="-DHIGH_PREC" \
-D CMAKE_CXX_FLAGS="-I${deepmd_root}/include -I${tensorflow_root}/include -L${deepmd_root}/lib -L${tensorflow_root}/lib -Wl,--no-as-needed -ldeepmd_cc -ltensorflow_cc -ltensorflow_framework -Wl,-rpath=${deepmd_root}/lib -Wl,-rpath=${tensorflow_root}/lib -DLAMMPS_VERSION_NUMBER=20220623 -std=c++14" \

You defined CMAKE_CXX_FLAGS twice, so the latter one would override the former one.

[Cloudac7]

-D CMAKE_CXX_FLAGS="-DHIGH_PREC" \
-D CMAKE_CXX_FLAGS="-I${deepmd_root}/include -I${tensorflow_root}/include -L${deepmd_root}/lib -L${tensorflow_root}/lib -Wl,--no-as-needed -ldeepmd_cc -ltensorflow_cc -ltensorflow_framework -Wl,-rpath=${deepmd_root}/lib -Wl,-rpath=${tensorflow_root}/lib -DLAMMPS_VERSION_NUMBER=20220623 -std=c++14" \

You defined CMAKE_CXX_FLAGS twice, so the latter one would override the former one.

Seems to be the solution. I just rewrote the command and thus got the success info.