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phoebe-team / phoebe

A high-performance framework for solving phonon and electron Boltzmann equations
https://phoebe-team.github.io/phoebe/
MIT License
89 stars 19 forks source link

building phoebe on supercomputer, HPC and Ubuntu #217

Closed DI20028 closed 4 months ago

DI20028 commented 4 months ago

I am trying to build phoebe in supercomputer, HPC and Ubuntu but it gives -- Configuring incomplete, errors occurred! It shows: I have also attached the error file for your refrence. error.txt

CMake Error at CMakeLists.txt:11 (cmake_policy): Policy "CMP0144" is not known to this version of CMake.

-- The C compiler identification is GNU 4.8.5 -- The CXX compiler identification is GNU 4.8.5 -- The Fortran compiler identification is GNU 4.8.5 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/gfortran - skipped /home/DDD/wd/program/zip/phoebe-develop /home/DDD/wd/program/zip/phoebe-develop/src/algebra/Matrix.cpp/home/DDD/wd/program/zip/phoebe-develop/src/algebra/PMatrix.cpp/home/DDD/wd/program/zip/phoebe-develop/src/algebra/SMatrix.cpp/home/DDD/wd/program/zip/phoebe-develop/src/apps/app.cpp/home/DDD/wd/program/zip/phoebe-develop/src/apps/bands_app.cpp/home/DDD/wd/program/zip/phoebe-develop/src/apps/dos_app.cpp/home/DDD/wd/program/zip/phoebe-develop/src/apps/electron_wannier_transport_app.cpp/home/DDD/wd/program/zip/phoebe-develop/src/apps/elph_plot_app.cpp/home/DDD/wd/program/zip/phoebe-develop/src/apps/elph_qe_to_phoebe_app.cpp/home/DDD/wd/program/zip/phoebe-develop/src/apps/lifetimes_app.cpp/home/DDD/wd/program/zip/phoebe-develop/src/apps/ph_el_lifetimes.cpp/home/DDD/wd/program/zip/phoebe-develop/src/apps/phonon_transport_app.cpp/home/DDD/wd/program/zip/phoebe-develop/src/apps/qe_to_phoebe_epa.cpp/home/DDD/wd/program/zip/phoebe-develop/src/apps/qe_to_phoebe_utils.cpp/home/DDD/wd/program/zip/phoebe-develop/src/apps/qe_to_phoebe_wannier.cpp/home/DDD/wd/program/zip/phoebe-develop/src/apps/transport_epa_app.cpp/home/DDD/wd/program/zip/phoebe-develop/src/bands/active_bandstructure.cpp/home/DDD/wd/program/zip/phoebe-develop/src/bands/bandstructure.cpp/home/DDD/wd/program/zip/phoebe-develop/src/bands/window.cpp/home/DDD/wd/program/zip/phoebe-develop/src/bte/drift.cpp/home/DDD/wd/program/zip/phoebe-develop/src/bte/el_scattering.cpp/home/DDD/wd/program/zip/phoebe-develop/src/bte/helper_3rd_state.cpp/home/DDD/wd/program/zip/phoebe-develop/src/bte/helper_el_scattering.cpp/home/DDD/wd/program/zip/phoebe-develop/src/bte/ph_scattering.cpp/home/DDD/wd/program/zip/phoebe-develop/src/bte/phel_scattering.cpp/home/DDD/wd/program/zip/phoebe-develop/src/bte/scattering.cpp/home/DDD/wd/program/zip/phoebe-develop/src/bte/vector_bte.cpp/home/DDD/wd/program/zip/phoebe-develop/src/bte/vector_epa.cpp/home/DDD/wd/program/zip/phoebe-develop/src/common_kokkos.cpp/home/DDD/wd/program/zip/phoebe-develop/src/constants/periodic_table.cpp/home/DDD/wd/program/zip/phoebe-develop/src/context.cpp/home/DDD/wd/program/zip/phoebe-develop/src/crystal.cpp/home/DDD/wd/program/zip/phoebe-develop/src/delta_function.cpp/home/DDD/wd/program/zip/phoebe-develop/src/exceptions.cpp/home/DDD/wd/program/zip/phoebe-develop/src/harmonic/electron_h0_fourier.cpp/home/DDD/wd/program/zip/phoebe-develop/src/harmonic/electron_h0_wannier.cpp/home/DDD/wd/program/zip/phoebe-develop/src/harmonic/harmonic.cpp/home/DDD/wd/program/zip/phoebe-develop/src/harmonic/phonon_h0.cpp/home/DDD/wd/program/zip/phoebe-develop/src/harmonic/phonon_h0_kokkos.cpp/home/DDD/wd/program/zip/phoebe-develop/src/harmonic/phonon_h0_sum_rule.cpp/home/DDD/wd/program/zip/phoebe-develop/src/interaction/interaction_3ph.cpp/home/DDD/wd/program/zip/phoebe-develop/src/interaction/interaction_elph.cpp/home/DDD/wd/program/zip/phoebe-develop/src/interaction/interaction_elph_parsing.cpp/home/DDD/wd/program/zip/phoebe-develop/src/interaction/interaction_epa.cpp/home/DDD/wd/program/zip/phoebe-develop/src/io.cpp/home/DDD/wd/program/zip/phoebe-develop/src/mpi/mpiController.cpp/home/DDD/wd/program/zip/phoebe-develop/src/mpi/mpiHelper.cpp/home/DDD/wd/program/zip/phoebe-develop/src/observable/electron_viscosity.cpp/home/DDD/wd/program/zip/phoebe-develop/src/observable/observable.cpp/home/DDD/wd/program/zip/phoebe-develop/src/observable/onsager.cpp/home/DDD/wd/program/zip/phoebe-develop/src/observable/phonon_thermal_cond.cpp/home/DDD/wd/program/zip/phoebe-develop/src/observable/phonon_viscosity.cpp/home/DDD/wd/program/zip/phoebe-develop/src/observable/specific_heat.cpp/home/DDD/wd/program/zip/phoebe-develop/src/observable/viscosity_io.cpp/home/DDD/wd/program/zip/phoebe-develop/src/observable/wigner_electron.cpp/home/DDD/wd/program/zip/phoebe-develop/src/observable/wigner_phonon_thermal_cond.cpp/home/DDD/wd/program/zip/phoebe-develop/src/parser/ifc3_parser.cpp/home/DDD/wd/program/zip/phoebe-develop/src/parser/parser.cpp/home/DDD/wd/program/zip/phoebe-develop/src/parser/phonopy_input_parser.cpp/home/DDD/wd/program/zip/phoebe-develop/src/parser/qe_input_parser.cpp/home/DDD/wd/program/zip/phoebe-develop/src/particle.cpp/home/DDD/wd/program/zip/phoebe-develop/src/points.cpp/home/DDD/wd/program/zip/phoebe-develop/src/statistics_sweep.cpp/home/DDD/wd/program/zip/phoebe-develop/src/utilities.cpp CMake Error at lib/CMakeLists.txt:1 (add_subdirectory): The source directory

/home/DDD/wd/program/zip/phoebe-develop/lib/kokkos

does not contain a CMakeLists.txt file. Call Stack (most recent call first): CMakeLists.txt:57 (include)

CMake Error at lib/CMakeLists.txt:2 (add_subdirectory): The source directory

/home/DDD/wd/program/zip/phoebe-develop/lib/kokkos-kernels

does not contain a CMakeLists.txt file. Call Stack (most recent call first): CMakeLists.txt:57 (include)

-- Found Python: /home/DDD/anaconda3/bin/python3.9 (found version "3.9.13") found components: Interpreter -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE
-- Using the multi-header code from /home/DDD/wd/program/zip/phoebe-develop/build/json_src/include/ -- Found CUDAToolkit: /opt/ohpc/pub/compiler/cuda/cuda-10.1/include (found version "10.1.243") -- Found MPI_C: /home/pub/compiler/intel/2018_4/compilers_and_libraries_2018.5.274/linux/mpi/intel64/lib/release_mt/libmpi.so (found version "3.1") -- Found MPI_CXX: /home/pub/compiler/intel/2018_4/compilers_and_libraries_2018.5.274/linux/mpi/intel64/lib/libmpicxx.so (found version "3.1") -- Found MPI_Fortran: /home/pub/compiler/intel/2018_4/compilers_and_libraries_2018.5.274/linux/mpi/intel64/lib/libmpifort.so (found version "3.1") -- Found MPI: TRUE (found version "3.1")
-- Found BLACS: /opt/ohpc/pub/compiler/intel/2018_4/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so -- Found SCALAPACK: /opt/ohpc/pub/compiler/intel/2018_4/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64/libmkl_scalapack_lp64.so -- Looking for Fortran sgemm -- Looking for Fortran sgemm - not found -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Found BLAS: /opt/ohpc/pub/compiler/intel/2018_4/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/ohpc/pub/compiler/intel/2018_4/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/ohpc/pub/compiler/intel/2018_4/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64_lin/libmkl_core.so;/home/apps/gcc/gcc-13.1.0/build/lib64/libgomp.so;-lpthread;-lm;-ldl
-- Looking for Fortran cheev -- Looking for Fortran cheev - found -- Found LAPACK: /opt/ohpc/pub/compiler/intel/2018_4/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/ohpc/pub/compiler/intel/2018_4/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/ohpc/pub/compiler/intel/2018_4/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64_lin/libmkl_core.so;/home/apps/gcc/gcc-13.1.0/build/lib64/libgomp.so;-lpthread;-lm;-ldl;-lpthread;-lm;-ldl
-- Found OpenMP_C: -fopenmp (found version "3.1") -- Found OpenMP_CXX: -fopenmp (found version "3.1") -- Found OpenMP_Fortran: -fopenmp (found version "3.1") -- Found OpenMP: TRUE (found version "3.1")
-- Found HDF5: /home/apps/hdf5-1.12.3/build/lib/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.12.3")
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") found components: doxygen missing components: dot -- Found Sphinx: /home/DDD/anaconda3/bin/sphinx-build
Doxygen configured -- Configuring incomplete, errors occurred! See also "/home/DDD/wd/program/zip/phoebe-develop/build/CMakeFiles/CMakeOutput.log". See also "/home/DDD/wd/program/zip/phoebe-develop/build/CMakeFiles/CMakeError.log".

jcoulter12 commented 4 months ago

Hi @DI20028,

Fortunately the answer is super simple -- I have a PR which fixes this, but I haven't quite merged it yet. It seems the most recent version of CMake deprecated a policy I had set in our CMakeLists.

All you need to do to make things work is go into CMakeLists.txt and delete the line which says: cmake_policy(SET CMP0144 NEW)

Then delete your build directory and repeat the build steps.

Let me know if this doesn't fix things, Jenny

jcoulter12 commented 4 months ago

Ah, I actually see you also might have missed a part of the installation instructions. In order to have the kokkos package, you need to run as on the installation page, this line to clone the code:

git clone --recurse-submodules https://github.com/mir-group/phoebe.git

If you forgot to do this, you can fix this by running:

git submodule update --init

and then running CMake again.

DI20028 commented 4 months ago

Thank you for reply. I have configured correctly. But during make I have still found the error. I have also attached the error file for your reference. error.txt

wd@wd:~/program/code/phoebe/build$ cmake .. -- The C compiler identification is GNU 9.4.0 -- The CXX compiler identification is GNU 9.4.0 -- The Fortran compiler identification is GNU 9.4.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working Fortran compiler: /usr/bin/gfortran -- Check for working Fortran compiler: /usr/bin/gfortran -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /usr/bin/gfortran supports Fortran 90 -- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes /home/wd/program/code/phoebe /home/wd/program/code/phoebe/src/algebra/Matrix.cpp/home/wd/program/code/phoebe/src/algebra/PMatrix.cpp/home/wd/program/code/phoebe/src/algebra/SMatrix.cpp/home/wd/program/code/phoebe/src/apps/app.cpp/home/wd/program/code/phoebe/src/apps/bands_app.cpp/home/wd/program/code/phoebe/src/apps/dos_app.cpp/home/wd/program/code/phoebe/src/apps/electron_wannier_transport_app.cpp/home/wd/program/code/phoebe/src/apps/elph_plot_app.cpp/home/wd/program/code/phoebe/src/apps/elph_qe_to_phoebe_app.cpp/home/wd/program/code/phoebe/src/apps/lifetimes_app.cpp/home/wd/program/code/phoebe/src/apps/ph_el_lifetimes.cpp/home/wd/program/code/phoebe/src/apps/phonon_transport_app.cpp/home/wd/program/code/phoebe/src/apps/qe_to_phoebe_epa.cpp/home/wd/program/code/phoebe/src/apps/qe_to_phoebe_utils.cpp/home/wd/program/code/phoebe/src/apps/qe_to_phoebe_wannier.cpp/home/wd/program/code/phoebe/src/apps/transport_epa_app.cpp/home/wd/program/code/phoebe/src/bands/active_bandstructure.cpp/home/wd/program/code/phoebe/src/bands/bandstructure.cpp/home/wd/program/code/phoebe/src/bands/window.cpp/home/wd/program/code/phoebe/src/bte/drift.cpp/home/wd/program/code/phoebe/src/bte/el_scattering.cpp/home/wd/program/code/phoebe/src/bte/helper_3rd_state.cpp/home/wd/program/code/phoebe/src/bte/helper_el_scattering.cpp/home/wd/program/code/phoebe/src/bte/ph_scattering.cpp/home/wd/program/code/phoebe/src/bte/phel_scattering.cpp/home/wd/program/code/phoebe/src/bte/scattering.cpp/home/wd/program/code/phoebe/src/bte/vector_bte.cpp/home/wd/program/code/phoebe/src/bte/vector_epa.cpp/home/wd/program/code/phoebe/src/common_kokkos.cpp/home/wd/program/code/phoebe/src/constants/periodic_table.cpp/home/wd/program/code/phoebe/src/context.cpp/home/wd/program/code/phoebe/src/crystal.cpp/home/wd/program/code/phoebe/src/delta_function.cpp/home/wd/program/code/phoebe/src/exceptions.cpp/home/wd/program/code/phoebe/src/harmonic/electron_h0_fourier.cpp/home/wd/program/code/phoebe/src/harmonic/electron_h0_wannier.cpp/home/wd/program/code/phoebe/src/harmonic/harmonic.cpp/home/wd/program/code/phoebe/src/harmonic/phonon_h0.cpp/home/wd/program/code/phoebe/src/harmonic/phonon_h0_kokkos.cpp/home/wd/program/code/phoebe/src/harmonic/phonon_h0_sum_rule.cpp/home/wd/program/code/phoebe/src/interaction/interaction_3ph.cpp/home/wd/program/code/phoebe/src/interaction/interaction_elph.cpp/home/wd/program/code/phoebe/src/interaction/interaction_elph_parsing.cpp/home/wd/program/code/phoebe/src/interaction/interaction_epa.cpp/home/wd/program/code/phoebe/src/io.cpp/home/wd/program/code/phoebe/src/mpi/mpiController.cpp/home/wd/program/code/phoebe/src/mpi/mpiHelper.cpp/home/wd/program/code/phoebe/src/observable/electron_viscosity.cpp/home/wd/program/code/phoebe/src/observable/observable.cpp/home/wd/program/code/phoebe/src/observable/onsager.cpp/home/wd/program/code/phoebe/src/observable/phonon_thermal_cond.cpp/home/wd/program/code/phoebe/src/observable/phonon_viscosity.cpp/home/wd/program/code/phoebe/src/observable/specific_heat.cpp/home/wd/program/code/phoebe/src/observable/viscosity_io.cpp/home/wd/program/code/phoebe/src/observable/wigner_electron.cpp/home/wd/program/code/phoebe/src/observable/wigner_phonon_thermal_cond.cpp/home/wd/program/code/phoebe/src/parser/ifc3_parser.cpp/home/wd/program/code/phoebe/src/parser/parser.cpp/home/wd/program/code/phoebe/src/parser/phonopy_input_parser.cpp/home/wd/program/code/phoebe/src/parser/qe_input_parser.cpp/home/wd/program/code/phoebe/src/particle.cpp/home/wd/program/code/phoebe/src/points.cpp/home/wd/program/code/phoebe/src/statistics_sweep.cpp/home/wd/program/code/phoebe/src/utilities.cpp -- Setting default Kokkos CXX standard to 17 -- The project name is: Kokkos -- Using internal gtest for testing -- Configured git information in /home/wd/program/code/phoebe/build/generated/Kokkos_Version_Info.cpp -- Using -std=c++17 for C++17 standard as feature -- Built-in Execution Spaces: -- Device Parallel: NoTypeDefined -- Host Parallel: Kokkos::OpenMP -- Host Serial: NONE -- -- Architectures: -- Found TPLLIBDL: /usr/include
-- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP_Fortran: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5")
-- Using internal desul_atomics copy -- Kokkos Devices: OPENMP, Kokkos Backends: OPENMP -- The project name is: KokkosKernels CMake Warning at lib/kokkos-kernels/cmake/kokkoskernels_features.cmake:18 (MESSAGE): Disabling SUPERNODAL_SPTRSV - this capability is only supported with LayoutLeft Call Stack (most recent call first): lib/kokkos-kernels/CMakeLists.txt:215 (INCLUDE)

================================ Kokkos Kernels version: 4.1.0

Kokkos Kernels ETI Types Devices:
Scalars:
Ordinals: Offsets:
Layouts:

Kokkos Kernels components COMMON: ON BATCHED: ON BLAS: ON GRAPH: ON SPARSE: ON ODE: ON

Kokkos Kernels TPLs (None)

-- Skipping ETI files for Batched_Gemm_nt_nt_bll because not all components are enabled -- Skipping ETI files for Batched_Gemm_nt_t_bll because not all components are enabled -- Skipping ETI files for Batched_Gemm_t_nt_bll because not all components are enabled -- Skipping ETI files for Batched_Gemm_t_t_bll because not all components are enabled -- Skipping ETI files for Batched_Gemm_nt_nt_blr because not all components are enabled -- Skipping ETI files for Batched_Gemm_nt_t_blr because not all components are enabled -- Skipping ETI files for Batched_Gemm_t_nt_blr because not all components are enabled -- Skipping ETI files for Batched_Gemm_t_t_blr because not all components are enabled -- Creating ETI files for Blas1_abs -- Creating ETI files for Blas1_abs_mv -- Creating ETI files for Blas1_scal -- Creating ETI files for Blas1_scal_mv -- Creating ETI files for Blas1_dot -- Creating ETI files for Blas1_dot_mv -- Creating ETI files for Blas_gesv -- Creating ETI files for Blas1_axpby -- Creating ETI files for Blas1_axpby_mv -- Creating ETI files for Blas1_update -- Creating ETI files for Blas1_update_mv -- Creating ETI files for Blas1_sum -- Creating ETI files for Blas1_sum_mv -- Creating ETI files for Blas1_nrm1 -- Creating ETI files for Blas1_nrm1_mv -- Creating ETI files for Blas1_nrm2w -- Creating ETI files for Blas1_nrm2w_mv -- Creating ETI files for Blas1_nrminf -- Creating ETI files for Blas1_nrminf_mv -- Creating ETI files for Blas1_iamax -- Creating ETI files for Blas1_iamax_mv -- Creating ETI files for Blas1_nrm2 -- Creating ETI files for Blas1_nrm2_mv -- Creating ETI files for Blas1_mult -- Creating ETI files for Blas1_mult_mv -- Creating ETI files for Blas1_reciprocal -- Creating ETI files for Blas1_reciprocal_mv -- Creating ETI files for Blas1_rot -- Creating ETI files for Blas1_rotg -- Creating ETI files for Blas1_rotm -- Creating ETI files for Blas1_rotmg -- Creating ETI files for Blas1_swap -- Creating ETI files for Blas2_gemv -- Creating ETI files for Blas2_ger -- Creating ETI files for Blas3_gemm -- Creating ETI files for Blas3_trsm -- Creating ETI files for Blas3_trmm -- Creating ETI files for Blas_trtri -- Skipping ETI files for Graph_color_d1 because not all components are enabled -- Skipping ETI files for Sparse_sptrsv_solve because not all components are enabled -- Skipping ETI files for Sparse_spmv_struct because not all components are enabled -- Skipping ETI files for Sparse_spmv_mv_struct because not all components are enabled -- Skipping ETI files for Sparse_spmv_bsrmatrix because not all components are enabled -- Skipping ETI files for Sparse_spmv_mv_bsrmatrix because not all components are enabled -- Skipping ETI files for Sparse_spmv because not all components are enabled -- Skipping ETI files for Sparse_spmv_mv because not all components are enabled -- Skipping ETI files for Sparse_spgemm_symbolic because not all components are enabled -- Skipping ETI files for Sparse_spgemm_numeric because not all components are enabled -- Skipping ETI files for Sparse_spgemm_noreuse because not all components are enabled -- Skipping ETI files for Sparse_bspgemm_numeric because not all components are enabled -- Skipping ETI files for Sparse_spgemm_jacobi because not all components are enabled -- Skipping ETI files for Sparse_spadd_symbolic because not all components are enabled -- Skipping ETI files for Sparse_spadd_numeric because not all components are enabled -- Skipping ETI files for Sparse_spiluk_symbolic because not all components are enabled -- Skipping ETI files for Sparse_spiluk_numeric because not all components are enabled -- Skipping ETI files for Sparse_par_ilut_symbolic because not all components are enabled -- Skipping ETI files for Sparse_par_ilut_numeric because not all components are enabled -- Skipping ETI files for Sparse_gmres because not all components are enabled -- Skipping ETI files for Sparse_sptrsv_symbolic because not all components are enabled -- Skipping ETI files for Sparse_trsv because not all components are enabled -- Skipping ETI files for Sparse_gauss_seidel_symbolic because not all components are enabled -- Skipping ETI files for Sparse_gauss_seidel_numeric because not all components are enabled -- Skipping ETI files for Sparse_gauss_seidel_apply because not all components are enabled -- Found Python: /usr/bin/python3.8 (found version "3.8.10") found components: Interpreter -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE
-- Using the multi-header code from /home/wd/program/code/phoebe/build/json_src/include/ -- Found MPI_C: /home/wd/program/intel/oneapi/mpi/2021.4.0/lib/release/libmpi.so (found version "3.1") -- Found MPI_CXX: /home/wd/program/intel/oneapi/mpi/2021.4.0/lib/libmpicxx.so (found version "3.1") -- Found MPI_Fortran: /home/wd/program/intel/oneapi/mpi/2021.4.0/lib/libmpifort.so (found version "3.1") -- Found MPI: TRUE (found version "3.1")
-- Found BLACS: /home/wd/program/intel/oneapi/mkl/2021.4.0/lib/intel64/libmkl_blacs_intelmpi_lp64.so -- Found SCALAPACK: /home/wd/program/intel/oneapi/mkl/2021.4.0/lib/intel64/libmkl_scalapack_lp64.so -- Looking for Fortran sgemm -- Looking for Fortran sgemm - not found -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Found BLAS: /home/wd/program/intel/oneapi/mkl/2021.4.0/lib/intel64/libmkl_gf_lp64.so;/home/wd/program/intel/oneapi/mkl/2021.4.0/lib/intel64/libmkl_gnu_thread.so;/home/wd/program/intel/oneapi/mkl/2021.4.0/lib/intel64/libmkl_core.so;/usr/lib/gcc/x86_64-linux-gnu/9/libgomp.so;-lpthread;-lm;-ldl
-- Looking for Fortran cheev -- Looking for Fortran cheev - found -- A library with LAPACK API found. -- Found OpenMP_C: -fopenmp
-- Found OpenMP_CXX: -fopenmp
-- Found OpenMP_Fortran: -fopenmp
-- Found OpenMP: TRUE
-- HDF5: Using hdf5 compiler wrapper to determine C configuration -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.4")
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.17") found components: doxygen missing components: dot -- Found Sphinx: /usr/bin/sphinx-build
Doxygen configured -- Configuring done -- Generating done -- Build files have been written to: /home/wd/program/code/phoebe/build

wd@wd:~/program/code/phoebe/build$ make -j4

Scanning dependencies of target eigen_dep Scanning dependencies of target pugixml_dep Scanning dependencies of target spglib_dep Scanning dependencies of target highfive_dep [ 1%] Creating directories for 'spglib_dep' [ 1%] Creating directories for 'eigen_dep' [ 1%] Creating directories for 'highfive_dep' [ 1%] Creating directories for 'pugixml_dep' [ 4%] Performing download step (git clone) for 'pugixml_dep' [ 4%] Performing download step (git clone) for 'highfive_dep' [ 6%] Performing download step (git clone) for 'spglib_dep' [ 6%] Performing download step (git clone) for 'eigen_dep' Cloning into 'highfive_src'... Cloning into 'pugixml_src'... Cloning into 'eigen_src'... Cloning into 'spglib_src'... Already on 'master' Your branch is up to date with 'origin/master'. [ 7%] No patch step for 'pugixml_dep' [ 7%] No update step for 'pugixml_dep' [ 7%] Performing configure step for 'pugixml_dep' -- The CXX compiler identification is GNU 9.4.0 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project:

CMAKE_C_COMPILER

-- Build files have been written to: /home/wd/program/code/phoebe/build/pugixml_build [ 9%] Performing build step for 'pugixml_dep' Scanning dependencies of target pugixml-static [ 50%] Building CXX object CMakeFiles/pugixml-static.dir/src/pugixml.cpp.o Switched to a new branch 'master' Branch 'master' set up to track remote branch 'master' from 'origin'. [ 11%] No patch step for 'spglib_dep' [ 11%] No update step for 'spglib_dep' [ 11%] Performing configure step for 'spglib_dep' -- The C compiler identification is GNU 9.4.0 -- Check for working C compiler: /usr/bin/cc Already on 'master' Your branch is up to date with 'origin/master'. -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info Submodule 'deps/hpc-coding-conventions' (https://github.com/BlueBrain/hpc-coding-conventions.git) registered for path 'deps/hpc-coding-conventions' Cloning into '/home/wd/program/code/phoebe/build/highfive_src/deps/hpc-coding-conventions'... -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Build type: Release -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5")
-- Configuring done -- Generating done -- Build files have been written to: /home/wd/program/code/phoebe/build/spglib_build [ 12%] Performing build step for 'spglib_dep' Scanning dependencies of target symspg_static [ 2%] Building C object CMakeFiles/symspg_static.dir/src/arithmetic.c.o [ 4%] Building C object CMakeFiles/symspg_static.dir/src/cell.c.o [ 6%] Building C object CMakeFiles/symspg_static.dir/src/debug.c.o [ 8%] Building C object CMakeFiles/symspg_static.dir/src/delaunay.c.o [ 10%] Building C object CMakeFiles/symspg_static.dir/src/determination.c.o [ 12%] Building C object CMakeFiles/symspg_static.dir/src/hall_symbol.c.o [ 14%] Building C object CMakeFiles/symspg_static.dir/src/kgrid.c.o Submodule path 'deps/hpc-coding-conventions': checked out '609237f2774309ed08c92c92248e2f39de5b11d2' [ 16%] Building C object CMakeFiles/symspg_static.dir/src/kpoint.c.o [ 12%] No patch step for 'highfive_dep' [ 12%] No update step for 'highfive_dep' [ 14%] Performing configure step for 'highfive_dep' -- The C compiler identification is GNU 9.4.0 -- The CXX compiler identification is GNU 9.4.0 -- Check for working C compiler: /usr/bin/cc [ 18%] Building C object CMakeFiles/symspg_static.dir/src/magnetic_spacegroup.c.o -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info [ 20%] Building C object CMakeFiles/symspg_static.dir/src/mathfunc.c.o -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test COMPILER_SUPPORTS_CXX11 [ 22%] Building C object CMakeFiles/symspg_static.dir/src/msg_database.c.o -- Performing Test COMPILER_SUPPORTS_CXX11 - Success -- Performing Test COMPILER_SUPPORTS_CXX14 -- Performing Test COMPILER_SUPPORTS_CXX14 - Success -- HDF5: Using hdf5 compiler wrapper to determine C configuration -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.4")
CMake Warning at CMake/HighFiveTargetDeps.cmake:17 (message): Parallel HDF5 requested but libhdf5 doesnt support it Call Stack (most recent call first): CMakeLists.txt:67 (include)

[ 25%] Building C object CMakeFiles/symspg_static.dir/src/niggli.c.o [ 27%] Building C object CMakeFiles/symspg_static.dir/src/overlap.c.o -- Found MPI_C: /home/wd/program/intel/oneapi/mpi/2021.4.0/lib/release/libmpi.so (found version "3.1") [ 29%] Building C object CMakeFiles/symspg_static.dir/src/pointgroup.c.o [ 31%] Building C object CMakeFiles/symspg_static.dir/src/primitive.c.o -- Found MPI_CXX: /home/wd/program/intel/oneapi/mpi/2021.4.0/lib/libmpicxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1")
-- Configuring done -- Generating done -- Build files have been written to: /home/wd/program/code/phoebe/build/highfive_dep-prefix/src/highfive_dep-build [ 14%] Performing build step for 'highfive_dep' [ 15%] Performing install step for 'highfive_dep' [ 33%] Building C object CMakeFiles/symspg_static.dir/src/refinement.c.o Install the project... -- Install configuration: "Release" -- Installing: /home/wd/program/code/phoebe/build/highfive_src/share/HighFive/CMake/HighFiveTargetDeps.cmake -- Installing: /home/wd/program/code/phoebe/build/highfive_src/share/HighFive/CMake/HighFiveConfig.cmake -- Installing: /home/wd/program/code/phoebe/build/highfive_src/share/HighFive/CMake/HighFiveConfigVersion.cmake -- Installing: /home/wd/program/code/phoebe/build/highfive_src/share/HighFive/CMake/HighFiveTargets.cmake -- Up-to-date: /home/wd/program/code/phoebe/build/highfive_src/include -- Up-to-date: /home/wd/program/code/phoebe/build/highfive_src/include/highfive -- Installing: /home/wd/program/code/phoebe/build/highfive_src/include/highfive/H5Version.hpp [ 15%] Completed 'highfive_dep' [ 15%] Built target highfive_dep Scanning dependencies of target kokkossimd [ 17%] Building CXX object lib/kokkos/simd/src/CMakeFiles/kokkossimd.dir/Kokkos_SIMD_dummy.cpp.o [ 17%] Linking CXX static library libkokkossimd.a [ 17%] Built target kokkossimd Scanning dependencies of target kokkoscore [ 19%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_CPUDiscovery.cpp.o [ 35%] Building C object CMakeFiles/symspg_static.dir/src/site_symmetry.c.o [ 19%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_Command_Line_Parsing.cpp.o [ 37%] Building C object CMakeFiles/symspg_static.dir/src/sitesym_database.c.o [ 39%] Building C object CMakeFiles/symspg_static.dir/src/spacegroup.c.o [ 41%] Building C object CMakeFiles/symspg_static.dir/src/spg_database.c.o [ 43%] Building C object CMakeFiles/symspg_static.dir/src/spglib.c.o [ 45%] Building C object CMakeFiles/symspg_static.dir/src/spin.c.o [ 47%] Building C object CMakeFiles/symspg_static.dir/src/symmetry.c.o [100%] Linking CXX static library libpugixml.a [100%] Built target pugixml-static [ 20%] No install step for 'pugixml_dep' [ 20%] Completed 'pugixml_dep' [ 20%] Built target pugixml_dep Scanning dependencies of target AlwaysCheckGit [ 50%] Linking C static library libsymspg.a -- Configured git information in /home/wd/program/code/phoebe/build/lib/kokkos/generated/Kokkos_Version_Info.cpp [ 20%] Built target AlwaysCheckGit [ 22%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_Core.cpp.o [ 50%] Built target symspg_static Scanning dependencies of target symspg [ 52%] Building C object CMakeFiles/symspg.dir/src/arithmetic.c.o [ 54%] Building C object CMakeFiles/symspg.dir/src/cell.c.o [ 56%] Building C object CMakeFiles/symspg.dir/src/debug.c.o [ 58%] Building C object CMakeFiles/symspg.dir/src/delaunay.c.o [ 60%] Building C object CMakeFiles/symspg.dir/src/determination.c.o [ 62%] Building C object CMakeFiles/symspg.dir/src/hall_symbol.c.o [ 64%] Building C object CMakeFiles/symspg.dir/src/kgrid.c.o [ 66%] Building C object CMakeFiles/symspg.dir/src/kpoint.c.o [ 68%] Building C object CMakeFiles/symspg.dir/src/magnetic_spacegroup.c.o [ 70%] Building C object CMakeFiles/symspg.dir/src/mathfunc.c.o [ 72%] Building C object CMakeFiles/symspg.dir/src/msg_database.c.o [ 75%] Building C object CMakeFiles/symspg.dir/src/niggli.c.o [ 77%] Building C object CMakeFiles/symspg.dir/src/overlap.c.o [ 79%] Building C object CMakeFiles/symspg.dir/src/pointgroup.c.o [ 81%] Building C object CMakeFiles/symspg.dir/src/primitive.c.o [ 83%] Building C object CMakeFiles/symspg.dir/src/refinement.c.o [ 85%] Building C object CMakeFiles/symspg.dir/src/site_symmetry.c.o [ 87%] Building C object CMakeFiles/symspg.dir/src/sitesym_database.c.o [ 89%] Building C object CMakeFiles/symspg.dir/src/spacegroup.c.o [ 91%] Building C object CMakeFiles/symspg.dir/src/spg_database.c.o [ 93%] Building C object CMakeFiles/symspg.dir/src/spglib.c.o [ 95%] Building C object CMakeFiles/symspg.dir/src/spin.c.o [ 97%] Building C object CMakeFiles/symspg.dir/src/symmetry.c.o Note: switching to '3.4.0'.

You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example:

git switch -c

Or undo this operation with:

git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 3147391d9 Change version to 3.4.0. [100%] Linking C shared library libsymspg.so [ 22%] No patch step for 'eigen_dep' [100%] Built target symspg [ 23%] No update step for 'eigen_dep' [ 25%] No install step for 'spglib_dep' [ 26%] No configure step for 'eigen_dep' [ 26%] Completed 'spglib_dep' [ 26%] No build step for 'eigen_dep' [ 26%] Built target spglib_dep [ 26%] No install step for 'eigen_dep' Scanning dependencies of target gtest [ 26%] Building CXX object _deps/googletest-build/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o [ 28%] Completed 'eigen_dep' [ 28%] Built target eigen_dep [ 28%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_Error.cpp.o [ 28%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_ExecPolicy.cpp.o [ 30%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_HostBarrier.cpp.o [ 30%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_HostSpace.cpp.o [ 31%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_HostSpace_deepcopy.cpp.o [ 31%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_HostThreadTeam.cpp.o [ 33%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_MemoryPool.cpp.o [ 33%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_MemorySpace.cpp.o [ 34%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_Profiling.cpp.o [ 34%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_SharedAlloc.cpp.o [ 36%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_Spinwait.cpp.o [ 36%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_Stacktrace.cpp.o /home/wd/program/code/phoebe/lib/kokkos/core/src/impl/Kokkos_Profiling.cpp: In function ‘Kokkos::Tools::Impl::InitializationStatus Kokkos::Tools::Impl::parse_environment_variables(Kokkos::Tools::InitArguments&)’: /home/wd/program/code/phoebe/lib/kokkos/core/src/impl/Kokkos_Profiling.cpp:180:79: warning: missing initializer for member ‘Kokkos::Tools::Impl::InitializationStatus::error_message’ [-Wmissing-field-initializers] 180 | Kokkos::Tools::Impl::InitializationStatus::InitializationResult::success}; | ^ /home/wd/program/code/phoebe/lib/kokkos/core/src/impl/Kokkos_Profiling.cpp: In function ‘Kokkos::Tools::Impl::InitializationStatus Kokkos::Tools::Impl::initialize_tools_subsystem(const Kokkos::Tools::InitArguments&)’: /home/wd/program/code/phoebe/lib/kokkos/core/src/impl/Kokkos_Profiling.cpp:195:69: warning: missing initializer for member ‘Kokkos::Tools::Impl::InitializationStatus::error_message’ [-Wmissing-field-initializers] 195 | return {InitializationStatus::InitializationResult::help_request}; | ^ /home/wd/program/code/phoebe/lib/kokkos/core/src/impl/Kokkos_Profiling.cpp:201:62: warning: missing initializer for member ‘Kokkos::Tools::Impl::InitializationStatus::error_message’ [-Wmissing-field-initializers] 201 | return {InitializationStatus::InitializationResult::success}; | ^ Scanning dependencies of target impl_git_version [ 38%] Building CXX object lib/kokkos/CMakeFiles/impl_git_version.dir///generated/Kokkos_Version_Info.cpp.o [ 38%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_hwloc.cpp.o [ 38%] Linking CXX static library libimpl_git_version.a [ 38%] Built target impl_git_version [ 39%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/OpenMP/Kokkos_OpenMP_Instance.cpp.o [ 39%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir/OpenMP/Kokkos_OpenMP_Task.cpp.o [ 41%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir///tpls/desul/src/Lock_Array_CUDA.cpp.o [ 41%] Building CXX object lib/kokkos/core/src/CMakeFiles/kokkoscore.dir///tpls/desul/src/Lock_Array_HIP.cpp.o [ 42%] Linking CXX static library libkokkoscore.a [ 42%] Built target kokkoscore Scanning dependencies of target kokkoscontainers [ 44%] Building CXX object lib/kokkos/containers/src/CMakeFiles/kokkoscontainers.dir/impl/Kokkos_UnorderedMap_impl.cpp.o [ 44%] Linking CXX static library libkokkoscontainers.a [ 44%] Built target kokkoscontainers Scanning dependencies of target kokkoskernels [ 44%] Building CXX object lib/kokkos-kernels/CMakeFiles/kokkoskernels.dir/common/src/dummy.cpp.o [ 46%] Building CXX object lib/kokkos-kernels/CMakeFiles/kokkoskernels.dir/sparse/tpls/KokkosKernels_tpl_handles.cpp.o [ 46%] Linking CXX static library libkokkoskernels.a [ 46%] Built target kokkoskernels Scanning dependencies of target phoebe [ 47%] Building CXX object CMakeFiles/phoebe.dir/src/algebra/Matrix.cpp.o [ 47%] Building CXX object CMakeFiles/phoebe.dir/src/main.cpp.o [ 47%] Building CXX object CMakeFiles/phoebe.dir/src/algebra/PMatrix.cpp.o [ 49%] Linking CXX static library ../../../lib/libgtest.a [ 49%] Built target gtest [ 50%] Building CXX object CMakeFiles/phoebe.dir/src/algebra/SMatrix.cpp.o [ 50%] Building CXX object CMakeFiles/phoebe.dir/src/apps/app.cpp.o /home/wd/program/code/phoebe/src/algebra/Matrix.cpp: In member function ‘std::tuple<std::vector<double, std::allocator >, Matrix > Matrix::diagonalize(int, bool) [with T = double]’: /home/wd/program/code/phoebe/src/algebra/Matrix.cpp:69:46: warning: unused parameter ‘checkNegativeEigenvalues’ [-Wunused-parameter] 69 | bool checkNegativeEigenvalues) { | ~^~~~~~~~ [ 52%] Building CXX object CMakeFiles/phoebe.dir/src/apps/bands_app.cpp.o [ 52%] Building CXX object CMakeFiles/phoebe.dir/src/apps/dos_app.cpp.o [ 53%] Building CXX object CMakeFiles/phoebe.dir/src/apps/electron_wannier_transport_app.cpp.o Scanning dependencies of target gmock [ 55%] Building CXX object _deps/googletest-build/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o [ 55%] Linking CXX static library ../../../lib/libgmock.a [ 55%] Built target gmock [ 55%] Building CXX object CMakeFiles/phoebe.dir/src/apps/elph_plot_app.cpp.o [ 57%] Building CXX object CMakeFiles/phoebe.dir/src/apps/elph_qe_to_phoebe_app.cpp.o Scanning dependencies of target gtest_main [ 57%] Building CXX object _deps/googletest-build/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o [ 58%] Linking CXX static library ../../../lib/libgtest_main.a [ 58%] Built target gtest_main [ 58%] Building CXX object CMakeFiles/phoebe.dir/src/apps/lifetimes_app.cpp.o In file included from /home/wd/program/code/phoebe/build/highfive_src/include/highfive/H5FileDriver.hpp:34, from /home/wd/program/code/phoebe/build/highfive_src/include/highfive/H5File.hpp:14, from /home/wd/program/code/phoebe/build/highfive_src/include/highfive/H5Easy.hpp:58, from /home/wd/program/code/phoebe/src/apps/elph_plot_app.cpp:11: /home/wd/program/code/phoebe/build/highfive_src/include/highfive/bits/H5FileDriver_misc.hpp: In instantiation of ‘void HighFive::{anonymous}::MPIOFileAccess<Comm, Info>::apply(hid_t) const [with Comm = int; Info = int; hid_t = long int]’: /home/wd/program/code/phoebe/build/highfive_src/include/highfive/bits/H5PropertyList_misc.hpp:79:5: required from ‘void HighFive::PropertyList::add(const P&) [with P = HighFive::{anonymous}::MPIOFileAccess<int, int>; HighFive::PropertyType T = HighFive::PropertyType::FILE_ACCESS]’ /home/wd/program/code/phoebe/build/highfive_src/include/highfive/bits/H5FileDriver_misc.hpp:47:5: required from ‘HighFive::MPIOFileDriver::MPIOFileDriver(Comm, Info) [with Comm = int; Info = int]’ /home/wd/program/code/phoebe/src/apps/elph_plot_app.cpp:250:65: required from here /home/wd/program/code/phoebe/build/highfive_src/include/highfive/bits/H5FileDriver_misc.hpp:33:25: error: ‘H5Pset_fapl_mpio’ was not declared in this scope 33 | if (H5Pset_fapl_mpio(list, _comm, _info) < 0) { | ~~~~^~~~~~~~ [ 58%] Building CXX object CMakeFiles/phoebe.dir/src/apps/ph_el_lifetimes.cpp.o make[2]: [CMakeFiles/phoebe.dir/build.make:167: CMakeFiles/phoebe.dir/src/apps/elph_plot_app.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... Scanning dependencies of target gmock_main [ 58%] Building CXX object _deps/googletest-build/googlemock/CMakeFiles/gmock_main.dir/src/gmock_main.cc.o [ 60%] Linking CXX static library ../../../lib/libgmock_main.a [ 60%] Built target gmock_main make[1]: [CMakeFiles/Makefile2:560: CMakeFiles/phoebe.dir/all] Error 2 make: [Makefile:141: all] Error 2

jcoulter12 commented 4 months ago

Hi,

If you look closely, it's pretty easy to tell what happened: 

-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.4")
...
CMake Warning at CMake/HighFiveTargetDeps.cmake:17 (message):
Parallel HDF5 requested but libhdf5 doesnt support it

You tried to build Phoebe with the default parallel HDF5 (recommended) but you only have serial HDF5 on your machine.

Is this perhaps an Ubuntu build? If you read the section of the installation page for Ubuntu, https://phoebe.readthedocs.io/en/develop/installation.html#ubuntu you will see a few comments about HDF5 -- you may need to specify the path to the desired copy of HDF5 (see the CMake flags provided in the section linked and change them to match your machine's paths), and you need to be sure you have installed something along the lines of: sudo apt install -y libopenblas-dev liblapack-dev libhdf5-openmpi-dev libscalapack-openmpi-dev python3-pip gfortran cmake

where for this error the most important line one is libhdf5-openmpi-dev.

Thanks, and otherwise let me know more about the machine you're trying to build for, Jenny

DI20028 commented 4 months ago

Thank you for replying. Now I have successfully installed the package. I have one other query related to phononLifetimes app. Suppose I use Quantum Espresso (QE) code, and the phonon lifetime is obtained in meV units. So can Phoebe code automatically detect the interface calculator when I take the input file (fc2.hdf5, fc3.hdf5, and phono3py_disp.yaml) for output obtained from Phono3py? Or we will have to mention anywhere in the input file which code (VASP or QE) is using. 

jcoulter12 commented 4 months ago

Yes, it will take care of the units for you. If you use QE the units will be in one of those files, and we will read them in. If you use VASP, I think the units aren't written, but then we know to use VASP's units if none are written. I think you should be able to confirm this yourself by running the phononLifetimesApps, then plotting the bandstructure as shown in that tutorial -- if the units were bad, you would see the phonon bands come out with very wrong energy units.

Also -- if you're going to use the phononLifetimes app specifically, I would also ask that you run: git checkout minorFixes and just run make again. There's a slight bugfix on this branch (a change in an internal cutoff, also in the same unmerged pull request). I have seen it only affect one case, but better to be safe.

Happy to answer any other questions about the calculation itself as well.

DI20028 commented 4 months ago

Dear Coulter, thank you for your reply and advice.

jcoulter12 commented 4 months ago

No problem, happy to help -- if you have more questions, feel free to open a git discussion.