Problem at building LAMMPS through CMake

MehdiBgh · September 29, 2022, 12:03pm

I am trying to build LAMMPS through CMake, but encountered error as below:

~/Documents/lammps-29Sep2021/build$ cmake -C …/cmake/presets/basic.cmake
CMake Warning:
No source or binary directory provided. Both will be assumed to be the
same as the current working directory, but note that this warning will
become a fatal error in future CMake releases.

loading initial cache file …/cmake/presets/basic.cmake
CMake Error at CMakeLists.txt:62 (include) :
include could not find requested file:
LAMMPSUtils

Cake Error at CMakeLtsts.txt:64 (get lammps version) :
Unknown Cake command “get lamps version”.

–Configuring incomplete, errors occurred!
See also
“/home/mehdi/Documents/lammps-29Sep2021/build/CMakeFiles/CMakeOutput.log”

akohlmey · September 29, 2022, 12:09pm

That is because you are not using the correct command line. Please have another look at the instructions in the LAMMPS manual and/or the CMake documentation.

MehdiBgh · September 29, 2022, 12:21pm

Thanks. yes checked I missed another …/cmake at the end.

rookie · February 29, 2024, 6:30am

I encountered the following issue while compiling LAMMPS using the CMake method provided on the official website. I’m unsure how to resolve it. Seeking assistance, thank you.
In file included from /home/tongmj/software/lammps20240228/lammps-7Feb2024/src/pointers.h:33:0,
from …/lammps-7Feb2024/src/angle.h:17,
from …/lammps-7Feb2024/src/angle.cpp:14:
…/lammps-7Feb2024/src/fmt/format.h:1082:29: error: ‘std::runtime_error::runtime_error’ names constructor
…/lammps-7Feb2024/src/fmt/format.h: In function ‘OutputIt fmt::v10_lmp::detail::write_bytes(OutputIt, fmt::v10_lmp::string_view, const fmt::v10_lmp::format_specs&)’:
…/lammps-7Feb2024/src/fmt/format.h:1824:39: error: no default argument for ‘Char’
…/lammps-7Feb2024/src/fmt/format.h:1824:39: error: no default argument for ‘OutputIt’
…/lammps-7Feb2024/src/fmt/format.h: At global scope:
…/lammps-7Feb2024/src/fmt/format.h:2488:25: error: bit-field ‘format’ with non-integral type
…/lammps-7Feb2024/src/fmt/format.h: In function ‘fmt::v10_lmp::detail::float_specs fmt::v10_lmp::detail::parse_float_type_spec(const fmt::v10_lmp::format_specs&)’:
…/lammps-7Feb2024/src/fmt/format.h:2504:12: error: ‘struct fmt::v10_lmp::detail::float_specs’ has no member named ‘format’
…/lammps-7Feb2024/src/fmt/format.h:2510:12: error: ‘struct fmt::v10_lmp::detail::float_specs’ has no member named ‘format’
…/lammps-7Feb2024/src/fmt/format.h:2516:12: error: ‘struct fmt::v10_lmp::detail::float_specs’ has no member named ‘format’
…/lammps-7Feb2024/src/fmt/format.h:2523:12: error: ‘struct fmt::v10_lmp::detail::float_specs’ has no member named ‘format’
…/lammps-7Feb2024/src/fmt/format.h:2530:12: error: ‘struct fmt::v10_lmp::detail::float_specs’ has no member named ‘format’
…/lammps-7Feb2024/src/fmt/format.h: In lambda function:
…/lammps-7Feb2024/src/fmt/format.h:2680:16: error: ‘const struct fmt::v10_lmp::detail::float_specs’ has no member named ‘format’
…/lammps-7Feb2024/src/fmt/format.h:2681:16: error: ‘const struct fmt::v10_lmp::detail::float_specs’ has no member named ‘format’
…/lammps-7Feb2024/src/fmt/format.h: In function ‘OutputIt fmt::v10_lmp::detail::do_write_float(OutputIt, const DecimalFP&, const fmt::v10_lmp::format_specs&, fmt::v10_lmp::detail::float_specs, fmt::v10_lmp::detail::locale_ref)’:
…/lammps-7Feb2024/src/fmt/format.h:2724:36: error: ‘struct fmt::v10_lmp::detail::float_specs’ has no member named ‘format’
…/lammps-7Feb2024/src/fmt/format.h: In function ‘void fmt::v10_lmp::detail::adjust_precision(int&, int)’:
…/lammps-7Feb2024/src/fmt/format.h:2839:5: error: no matching function for call to ‘fmt::v10_lmp::format_error::format_error(const char [18])’
…/lammps-7Feb2024/src/fmt/format.h:2839:5: note: candidate is:
…/lammps-7Feb2024/src/fmt/format.h:1080:36: note: fmt::v10_lmp::format_error::format_error(const fmt::v10_lmp::format_error&)
…/lammps-7Feb2024/src/fmt/format.h:1080:36: note: no known conversion for argument 1 from ‘const char [18]’ to ‘const fmt::v10_lmp::format_error&’
…/lammps-7Feb2024/src/fmt/format.h: In function ‘int fmt::v10_lmp::detail::format_float(Float, int, fmt::v10_lmp::detail::float_specs, fmt::v10_lmp::detail::buffer&)’:
…/lammps-7Feb2024/src/fmt/format.h:3347:28: error: ‘struct fmt::v10_lmp::detail::float_specs’ has no member named ‘format’
…/lammps-7Feb2024/src/fmt/format.h: In function ‘OutputIt fmt::v10_lmp::detail::write_float(OutputIt, T, fmt::v10_lmp::format_specs, fmt::v10_lmp::detail::locale_ref)’:
…/lammps-7Feb2024/src/fmt/format.h:3673:14: error: ‘struct fmt::v10_lmp::detail::float_specs’ has no member named ‘format’
…/lammps-7Feb2024/src/fmt/format.h:3682:14: error: ‘struct fmt::v10_lmp::detail::float_specs’ has no member named ‘format’
…/lammps-7Feb2024/src/fmt/format.h:3687:21: error: ‘struct fmt::v10_lmp::detail::float_specs’ has no member named ‘format’
In file included from …/lammps-7Feb2024/src/angle.cpp:18:0:
…/lammps-7Feb2024/src/error.h: At global scope:
…/lammps-7Feb2024/src/error.h:26:3: error: expected unqualified-id before ‘[’ token
…/lammps-7Feb2024/src/error.h:27:3: error: expected unqualified-id before ‘[’ token
…/lammps-7Feb2024/src/error.h:30:3: error: expected unqualified-id before ‘[’ token
…/lammps-7Feb2024/src/error.h:37:3: error: expected unqualified-id before ‘[’ token
…/lammps-7Feb2024/src/error.h:57:3: error: expected unqualified-id before ‘[’ token
…/lammps-7Feb2024/src/error.h:75:3: error: expected unqualified-id before ‘[’ token
…/lammps-7Feb2024/src/error.h:76:3: error: expected unqualified-id before ‘[’ token
…/lammps-7Feb2024/src/angle.cpp:58:15: error: declaration of ‘virtual LAMMPS_NS::Angle::~Angle() noexcept (false)’ has a different exception specifier
In file included from …/lammps-7Feb2024/src/angle.cpp:14:0:
…/lammps-7Feb2024/src/angle.h:50:3: error: from previous declaration ‘virtual LAMMPS_NS::Angle::~Angle() noexcept (true)’
In file included from …/lammps-7Feb2024/src/angle.cpp:18:0:
…/lammps-7Feb2024/src/error.h: In instantiation of ‘void LAMMPS_NS::Error::all(const string&, int, const string&, Args&& …) [with Args = {}; std::string = std::basic_string]’:
…/lammps-7Feb2024/src/angle.cpp:73:84: required from here
…/lammps-7Feb2024/src/error.h:34:5: error: ‘_all’ was not declared in this scope
…/lammps-7Feb2024/src/error.h: In instantiation of ‘void LAMMPS_NS::Error::all(const string&, int, const string&, Args&& …) [with Args = {char*&, char*&}; std::string = std::basic_string]’:
…/lammps-7Feb2024/src/angle.cpp:87:89: required from here
…/lammps-7Feb2024/src/error.h:34:5: error: ‘_all’ was not declared in this scope
make[2]: *** [CMakeFiles/lammps.dir/build.make:63: CMakeFiles/lammps.dir/…/lammps-7Feb2024/src/angle.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:1029: CMakeFiles/lammps.dir/all] Error 2
make: *** [Makefile:130: all] Error 2

akohlmey · February 29, 2024, 10:37am

There is no enough information here to reproduce the error you are seeing and without the ability to reproduce it, there is no chance to give meaningful assistance.

Please provide:

the platform information (CPU, OS version etc.)
the information of which compiler and which version was used
the exact command line and output(!) from your CMake command

rookie · February 29, 2024, 11:57am

Dear Professor Kohlmeyer
I apologize for not providing detailed information.
1.（cmake …/cmake）
– Appending /opt/intel/oneapi/vpl/2023.0.0/lib:/opt/intel/oneapi/tbb/2021.8.0/env/…/lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/2021.10.0//libfabric/lib:/opt/intel/oneapi/mpi/2021.10.0//lib/release:/opt/intel/oneapi/mpi/2021.10.0//lib:/opt/intel/oneapi/mkl/2023.0.0/lib/intel64:/opt/intel/oneapi/ipp/2021.7.0/lib/intel64:/opt/intel/oneapi/ippcp/2021.6.3/lib/intel64:/opt/intel/oneapi/ipp/2021.7.0/lib/intel64:/opt/intel/oneapi/dnnl/2023.0.0/cpu_dpcpp_gpu_dpcpp/lib:/opt/intel/oneapi/dal/2023.0.0/lib/intel64:/opt/intel/oneapi/compiler/2023.0.0/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/compiler/2023.0.0/linux/lib:/opt/intel/oneapi/clck/2021.7.2/lib/intel64:/opt/intel/oneapi/ccl/2021.8.0/lib/cpu_gpu_dpcpp:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/mpi/intel64/libfabric/lib:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/ipp/lib/intel64:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/compiler/lib/intel64_lin:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/mkl/lib/intel64_lin:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/tbb/lib/intel64/gcc4.8:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/tbb/lib/intel64/gcc4.8:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/daal/lib/intel64_lin:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/daal/…/tbb/lib/intel64_lin/gcc4.4 to CMAKE_LIBRARY_PATH: /opt/intel/oneapi/vpl/2023.0.0/lib:/opt/intel/oneapi/tbb/2021.8.0/env/…/lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/2021.10.0//libfabric/lib:/opt/intel/oneapi/mpi/2021.10.0//lib/release:/opt/intel/oneapi/mpi/2021.10.0//lib:/opt/intel/oneapi/mkl/2023.0.0/lib/intel64:/opt/intel/oneapi/ipp/2021.7.0/lib/intel64:/opt/intel/oneapi/ippcp/2021.6.3/lib/intel64:/opt/intel/oneapi/ipp/2021.7.0/lib/intel64:/opt/intel/oneapi/dnnl/2023.0.0/cpu_dpcpp_gpu_dpcpp/lib:/opt/intel/oneapi/dal/2023.0.0/lib/intel64:/opt/intel/oneapi/compiler/2023.0.0/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/compiler/2023.0.0/linux/lib:/opt/intel/oneapi/clck/2021.7.2/lib/intel64:/opt/intel/oneapi/ccl/2021.8.0/lib/cpu_gpu_dpcpp:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/mpi/intel64/libfabric/lib:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/ipp/lib/intel64:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/compiler/lib/intel64_lin:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/mkl/lib/intel64_lin:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/tbb/lib/intel64/gcc4.8:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/tbb/lib/intel64/gcc4.8:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/daal/lib/intel64_lin:/home/lxl/intel/compilers_and_libraries_2020.0.139/linux/daal/…/tbb/lib/intel64_lin/gcc4.4
– <<< Build configuration >>>
LAMMPS Version: 20240207
Operating System: Linux Ubuntu" 20.04
CMake Version: 3.16.3
Build type: RelWithDebInfo
Install path: …/.local
Generator: Unix Makefiles using /usr/bin/make
– Enabled packages:
– <<< Compilers and Flags: >>>
– C++ Compiler: /usr/bin/c++
Type: GNU
Version: 4.7.4
C++ Flags: -O2 -g -DNDEBUG
Defines: LAMMPS_SMALLBIG;LAMMPS_MEMALIGN=64;LAMMPS_OMP_COMPAT=3;LAMMPS_GZIP;LAMMPS_FFMPEG
– <<< Linker flags: >>>
– Executable name: lmp
– Static library flags:
– <<< MPI flags >>>
– MPI_defines: MPICH_SKIP_MPICXX;OMPI_SKIP_MPICXX;_MPICC_H
– MPI includes: /opt/intel/oneapi/mpi/2021.10.0/include
– MPI libraries: /opt/intel/oneapi/mpi/2021.10.0/lib/libmpicxx.so;/opt/intel/oneapi/mpi/2021.10.0/lib/release/libmpi.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libdl.so;
– Configuring done
– Generating done
– Build files have been written to: …/lammps-7Feb2024/build
2.the commmand i use is (cmake --build .)
3.the whole output is
[ 0%] Generating includes/lammps/citeme.h
[ 0%] Built target citeme.h
[ 0%] Generating includes/lammps/neigh_list.h
[ 0%] Built target neigh_list.h
[ 0%] Generating includes/lammps/universe.h
[ 0%] Built target universe.h
[ 0%] Generating includes/lammps/kspace.h
[ 0%] Built target kspace.h
[ 0%] Generating includes/lammps/neighbor.h
[ 0%] Built target neighbor.h
[ 0%] Generating includes/lammps/memory.h
[ 0%] Built target memory.h
[ 1%] Generating includes/lammps/modify.h
[ 1%] Built target modify.h
[ 1%] Generating includes/lammps/lattice.h
[ 1%] Built target lattice.h
[ 1%] Generating includes/lammps/fmt/format.h
[ 1%] Built target fmt_format.h
[ 1%] Generating includes/lammps/lmppython.h
[ 1%] Built target lmppython.h
[ 1%] Generating includes/lammps/output.h
[ 1%] Built target output.h
[ 1%] Generating includes/lammps/domain.h
[ 1%] Built target domain.h
[ 1%] Generating includes/lammps/comm.h
[ 1%] Built target comm.h
[ 2%] Generating includes/lammps/lammps.h
[ 2%] Built target lammps.h
[ 3%] Generating includes/lammps/force.h
[ 3%] Built target force.h
[ 3%] Generating includes/lammps/compute.h
[ 3%] Built target compute.h
[ 3%] Generating includes/lammps/bond.h
[ 3%] Built target bond.h
[ 3%] Generating includes/lammps/exceptions.h
[ 3%] Built target exceptions.h
[ 3%] Generating includes/lammps/angle.h
[ 3%] Built target angle.h
[ 3%] Generating includes/lammps/improper.h
[ 3%] Built target improper.h
[ 3%] Generating includes/lammps/library.h
[ 3%] Built target library.h
[ 3%] Generating includes/lammps/lmptype.h
[ 3%] Built target lmptype.h
[ 3%] Generating includes/lammps/dihedral.h
[ 3%] Built target dihedral.h
[ 3%] Generating includes/lammps/atom.h
[ 3%] Built target atom.h
[ 4%] Generating includes/lammps/input.h
[ 4%] Built target input.h
[ 4%] Generating includes/lammps/update.h
[ 4%] Built target update.h
– Git Directory: …/lammps-7Feb2024/.git
– Generating lmpgitversion.h…
[ 4%] Built target gitversion
[ 5%] Generating includes/lammps/error.h
[ 5%] Built target error.h
[ 5%] Generating includes/lammps/group.h
[ 5%] Built target group.h
[ 6%] Generating includes/lammps/variable.h
[ 6%] Built target variable.h
[ 6%] Generating includes/lammps/fmt/core.h
[ 6%] Built target fmt_core.h
[ 6%] Generating includes/lammps/region.h
[ 6%] Built target region.h
[ 6%] Generating includes/lammps/utils.h
[ 6%] Built target utils.h
[ 7%] Generating includes/lammps/pair.h
[ 7%] Built target pair.h
[ 7%] Generating includes/lammps/pointers.h
[ 7%] Built target pointers.h
[ 8%] Generating includes/lammps/timer.h
[ 8%] Built target timer.h
[ 8%] Generating includes/lammps/info.h
[ 8%] Built target info.h
[ 8%] Generating includes/lammps/platform.h
[ 8%] Built target platform.h
[ 9%] Generating includes/lammps/command.h
[ 9%] Built target command.h
[ 9%] Generating includes/lammps/fix.h
[ 9%] Built target fix.h
[ 9%] Building CXX object CMakeFiles/lammps.dir/…/lammps-7Feb2024/src/angle.cpp.o
the rest of the output is the content I replied to earlier

akohlmey · February 29, 2024, 12:49pm

This is a very old C++ compiler and not suitable for compiling LAMMPS which requires full C++11 compatibility.

It is strange to see this version used, since your OS is Ubuntu 20.04 which ships with GNU 9.4.0 which is fully C++11 compliant (and more).

Bottom line. The problem is that you have a messed up Linux installation. This is not a problem of LAMMPS.

rookie · February 29, 2024, 2:35pm

Dear Professor Kohlmeyer
After following your advice, my QUIP package has been successfully installed. However, when running the in.gap file, I encountered the error code ‘SYSTEM ABORT: IPModel_GAP_Initialise_str: must be compiled with HAVE_GAP.’ What should I do next to resolve this issue? Thank you for your guidance."

akohlmey · February 29, 2024, 2:44pm

The error is self-explanatory. You didn’t follow my instructions about how to compile/install this and that is why your QUIP library is misconfigured.