Installation Error

[kimiaGF]

I am attempting to build LAMMPS (built-in mode) from source following the instructions give here. Under section 1.4.1 of the instructions, when I run make mpi -j4 I get the following error:

In file included from ../compute_deeptensor_atom.h:12:0,
                 from ../style_compute.h:17,
                 from ../modify.cpp:15:
../pair_deepmd.h:27:10: fatal error: deepmd/deepmd.hpp: No such file or directory
 #include "deepmd/deepmd.hpp"
          ^~~~~~~~~~~~~~~~~~~
compilation terminated.
make[1]: *** [modify.o] Error 1

I cannot find where deepmd.hpp is located anywhere in the USER-DEEPMD or lammps src directories. Has anyone else had this issue?

LAMMPS install: /lammps-stable_2Aug2023
Deepmd-kit version: DeePMD-kit v2.2.3

[njzjz]

deepmd/deepmd.hpp is located in $deepmd_root/include. Does Makefile.package contain the correct path?

[kimiaGF]

I believe I did not build deepmd with the Lammps root keyword defined and that was the issue. However, now I am getting a new error:

/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: warning: libtensorflow_cc.so.2, needed by /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so, not found (try using -rpath or -rpath-link)
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: warning: libtensorflow_framework.so.2, needed by /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so, not found (try using -rpath or -rpath-link)
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::Tensor::CheckTypeAndIsAligned(tensorflow::DataType) const'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tsl::Status::~Status()@tensorflow'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::GraphDef::GraphDef(google::protobuf::Arena*, bool)'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::TensorShape::CheckDimsEqual(int) const@tensorflow'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::ConfigProto::~ConfigProto()'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::GraphDef::~GraphDef()'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::TensorShapeBase<tensorflow::TensorShape>::TensorShapeBase()@tensorflow'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tsl::ReadBinaryProto(tsl::Env*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, google::protobuf::MessageLite*)@tensorflow'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::TensorShapeRep::SlowCopyFrom(tensorflow::TensorShapeRep const&)@tensorflow'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::NewSession(tensorflow::SessionOptions const&, tensorflow::Session**)'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tsl::Status::ToString[abi:cxx11]() const@tensorflow'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `google::protobuf::TextFormat::Parse(google::protobuf::io::ZeroCopyInputStream*, google::protobuf::Message*)'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tsl::Env::Default()'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::TensorShapeBase<tensorflow::TensorShape>::dim_size(int) const@tensorflow'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::TensorShapeRep::DestructorOutOfLine()@tensorflow'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::TensorShapeBase<tensorflow::TensorShape>::AddDim(long)@tensorflow'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::Tensor::Tensor(tensorflow::DataType, tensorflow::TensorShape const&)'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::Tensor::~Tensor()'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `google::protobuf::io::FileInputStream::FileInputStream(int, int)'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::SessionOptions::SessionOptions()@tensorflow'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::GPUOptions* google::protobuf::Arena::CreateMaybeMessage<tensorflow::GPUOptions>(google::protobuf::Arena*)'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tsl::ReadFileToString(tsl::Env*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*)@tensorflow'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `google::protobuf::MessageLite::ParseFromString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `google::protobuf::internal::ArenaStringPtr::Set(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, google::protobuf::Arena*)'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `tensorflow::GraphDef::~GraphDef()'
/blue/subhash/kimia.gh/envs/lammps/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /blue/subhash/kimia.gh/envs/lammps/lib/libdeepmd_cc.so: undefined reference to `google::protobuf::MessageLite::SerializeToOstream(std::ostream*) const'
collect2: error: ld returned 1 exit status
make[1]: *** [../lmp_mpi] Error 1

this is again after running make mpi -j4 in section 1.4.1 of the LAMMPS installation.

[Taixi-Feng]

Looks like questions about GNU packages

[njzjz]

The reason might be that you didn't give the TensorFlow path in the build options. Usually, it should be set automatically by make yes-user-deepmd, but I am wondering if you did some steps that are different from the documentation.