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OpenMX3.9 installation error
Date: 2020/10/28 19:57
Name: Gilad Gani   <giladg@campus.technion.ac.il>

Dear All,

I am trying to install OpenMX 3.9 using MKL and GNU compilers, and having the following errors while trying to execute the make command :

elpa_solve_evp_complex_2stage_double_impl.o: In function `elpa_solve_evp_complex_2stage_double_impl_':
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0xe9): undefined reference to `mpi_comm_rank_'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0xfc): undefined reference to `mpi_comm_size_'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x117): undefined reference to `mpi_comm_rank_'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x135): undefined reference to `mpi_comm_size_'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x150): undefined reference to `mpi_comm_rank_'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x16b): undefined reference to `mpi_comm_size_'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x54e): undefined reference to `mpi_bcast_'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x56d): undefined reference to `mpi_bcast_'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x897): undefined reference to `mpi_comm_rank_'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x8aa): undefined reference to `mpi_comm_size_'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x8c5): undefined reference to `mpi_comm_rank_'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x8e3): undefined reference to `mpi_comm_size_'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x903): undefined reference to `mpi_comm_rank_'
elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x91e): undefined reference to `mpi_comm_size_'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_critical'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float8_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_4'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_master'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_fini'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_reduce'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_flush'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8u'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_4'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_fork_call'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_push_num_threads'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_ordered'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_barrier'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_cmplx8_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_global_thread_num'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_4'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_critical'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_serialized_parallel'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_fixed4_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_reduce_nowait'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float4_max'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_master'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_single'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_fixed8_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_cmplx4_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_ok_to_fork'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_single'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_ordered'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_reduce_nowait'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_serialized_parallel'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float4_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float8_max'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_reduce'


The ouptput of the make command is as follows :

mpicc -O3 -fopenmp -I/usr/local/fftw3/include -I/opt/intel/mkl/include -I./elpa-2018.05.001 openmx.o openmx_common.o Input_std.o Inputtools.o init.o LU_inverse.o ReLU_inverse.o truncation.o readfile.o FT_PAO.o FT_NLP.o FT_ProExpn_VNA.o FT_VNA.o FT_ProductPAO.o Hamiltonian_Cluster.o Hamiltonian_Cluster_Hs.o Hamiltonian_Cluster_NC_Hs2.o Hamiltonian_Band_NC_Hs2.o Overlap_Cluster_NC_Ss2.o Overlap_Band_NC_Ss2.o Overlap_Cluster.o Overlap_Cluster_Ss.o Set_ContMat_Cluster_LNO.o Hamiltonian_Band.o Matrix_Band_LNO.o Overlap_Band.o Hamiltonian_Cluster_NC.o Hamiltonian_Band_NC.o Hamiltonian_Cluster_SO.o Get_OneD_HS_Col.o SetPara_DFT.o XC_Ceperly_Alder.o XC_CA_LSDA.o XC_PW92C.o XC_PBE.o XC_EX.o DFT.o Mixing_DM.o Mixing_H.o Mixing_V.o Force.o Stress.o Poisson.o Poisson_ESM.o Cluster_DFT_Col.o Cluster_DFT_NonCol.o Cluster_DFT_Dosout.o Cluster_DFT_ON2.o Cluster_DFT_LNO.o Band_DFT_Col.o Band_DFT_NonCol.o Band_DFT_NonCol_GB.o Band_DFT_kpath.o Band_DFT_kpath_LNO.o Band_DFT_MO.o Unfolding_Bands.o Band_DFT_Dosout.o Set_Density_Grid.o Set_Orbitals_Grid.o Set_Aden_Grid.o Gauss_Legendre.o zero_cfrac.o xyz2spherical.o AngularF.o RadialF.o Dr_RadialF.o PhiF.o VNAF.o Dr_VNAF.o VH_AtomF.o Dr_VH_AtomF.o RF_BesselF.o QuickSort.o Nonlocal_RadialF.o KumoF.o Dr_KumoF.o Mulliken_Charge.o Occupation_Number_LDA_U.o Eff_Hub_Pot.o Coulomb_Interaction.o EulerAngle_Spin.o Smoothing_Func.o Orbital_Moment.o Pot_NeutralAtom.o Simple_Mixing_DM.o DIIS_Mixing_DM.o ADIIS_Mixing_DM.o GR_Pulay_DM.o Kerker_Mixing_Rhok.o DIIS_Mixing_Rhok.o Total_Energy.o Contract_Hamiltonian.o Contract_iHNL.o Cont_Matrix0.o Cont_Matrix1.o Cont_Matrix2.o Cont_Matrix3.o Cont_Matrix4.o Opt_Contraction.o Initial_CntCoes.o Initial_CntCoes2.o Set_XC_Grid.o Get_Orbitals.o Get_dOrbitals.o Get_Cnt_Orbitals.o Get_Cnt_dOrbitals.o Gaunt.o Find_CGrids.o MD_pac.o RestartFileDFT.o Output_CompTime.o Merge_LogFile.o Make_FracCoord.o Make_InputFile_with_FinalCoord.o Output_Energy_Decomposition.o Divide_Conquer.o Divide_Conquer_LNO.o Krylov.o Divide_Conquer_Dosout.o EGAC_DFT.o LNO.o Eigen_lapack.o Eigen_lapack2.o Eigen_lapack3.o EigenBand_lapack.o Eigen_PReHH.o BroadCast_ReMatrix.o Eigen_PHH.o BroadCast_ComplexMatrix.o lapack_dstedc1.o lapack_dstedc2.o lapack_dstedc3.o lapack_dstegr1.o lapack_dstegr2.o lapack_dstegr3.o lapack_dstevx1.o lapack_dstevx2.o lapack_dstevx3.o lapack_dstevx4.o lapack_dstevx5.o lapack_dsteqr1.o Nonlocal_Basis.o Set_OLP_Kin.o Set_Nonlocal.o Set_ProExpn_VNA.o Set_CoreHoleMatrix.o Set_OLP_p.o Set_Hamiltonian.o Set_Vpot.o Voronoi_Charge.o Voronoi_Orbital_Moment.o Fuzzy_Weight.o dampingF.o deri_dampingF.o Spherical_Bessel.o iterout.o iterout_md.o Allocate_Arrays.o Free_Arrays.o Init_List_YOUSO.o outputfile1.o malloc_multidimarray.o PrintMemory.o PrintMemory_Fix.o dtime.o OutData.o OutData_Binary.o init_alloc_first.o File_CntCoes.o SCF2File.o mimic_sse.o Make_Comm_Worlds.o Set_Allocate_Atom2CPU.o Cutoff.o Generating_MP_Special_Kpt.o Maketest.o Runtest.o Memory_Leak_test.o Force_test.o Stress_test.o Show_DFT_DATA.o Generate_Wannier.o TRAN_Allocate.o TRAN_DFT.o TRAN_DFT_Dosout.o TRAN_Apply_Bias2e.o TRAN_Deallocate_Electrode_Grid.o TRAN_Deallocate_RestartFile.o TRAN_RestartFile.o TRAN_Calc_CentGreen.o TRAN_Input_std.o TRAN_Set_CentOverlap.o TRAN_Calc_CentGreenLesser.o TRAN_Input_std_Atoms.o TRAN_Set_Electrode_Grid.o TRAN_Calc_GridBound.o TRAN_Set_IntegPath.o TRAN_Output_HKS.o TRAN_Set_MP.o TRAN_Calc_SelfEnergy.o TRAN_Output_Trans_HS.o TRAN_Calc_Hopping_G.o TRAN_Calc_SurfGreen.o TRAN_Set_SurfOverlap.o TRAN_Add_Density_Lead.o TRAN_Add_ADensity_Lead.o TRAN_Set_Value.o TRAN_Poisson.o TRAN_adjust_Ngrid.o TRAN_Print.o TRAN_Print_Grid.o Lapack_LU_inverse.o TRAN_Distribute_Node.o TRAN_Output_HKS_Write_Grid.o TRAN_Credit.o TRAN_Check_Region_Lead.o TRAN_Check_Region.o TRAN_Check_Input.o DFTDvdW_init.o DFTD3vdW_init.o neb.o neb_run.o neb_check.o TRAN_Allocate_NC.o TRAN_DFT_NC.o TRAN_Set_CentOverlap_NC.o TRAN_Set_SurfOverlap_NC.o TRAN_Calc_OneTransmission.o TRAN_Main_Analysis.o TRAN_Main_Analysis_NC.o MTRAN_EigenChannel.o TRAN_Channel_Functions.o TRAN_Channel_Output.o TRAN_Calc_CurrentDensity.o TRAN_CDen_Main.o elpa1.o solve_evp_real.o solve_evp_complex.o NBO_Cluster.o NBO_Krylov.o Population_Analysis_Wannier.o Population_Analysis_Wannier2.o NabraMatrixElements.o Set_dOrbitals_Grid.o Calc_optical.o Band_DFT_NonCol_Optical.o Cluster_DFT_Optical.o Band_DFT_Col_Optical_ScaLAPACK.o Cluster_DFT_Optical_ScaLAPACK.o mod_precision.o elpa_utilities.o elpa1_compute_real.o elpa1_compute_complex.o aligned_mem.o elpa2_determine_workload.o mod_redist_band_real.o mod_redist_band_complex.o mod_pack_unpack_cpu_real.o mod_pack_unpack_cpu_complex.o real.o complex.o mod_single_hh_trafo_real.o mod_compute_hh_trafo_real.o mod_compute_hh_trafo_complex.o elpa2_compute_real.o elpa2_compute_complex.o elpa_solve_evp_real_2stage_double_impl.o elpa_solve_evp_complex_2stage_double_impl.o -L/usr/local/fftw3/lib -lfftw3 -L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64 -L/opt/intel/mkl/lib/intel64/ -lmkl_intel_thread -lmkl_core -lpthread -L/usr/bin/gfortran -lgfortran -lm -o openmx
makefile:199: recipe for target 'openmx' failed




Thank you all in advance,
Gilad
メンテ
Page: [1]

Re: OpenMX3.9 installation error ( No.1 )
Date: 2020/10/29 01:08
Name: Naoya Yamaguchi

Hi,

Please add MPI libraries you use to "LIB".
You may refer to the following.
p. 11 in http://www.openmx-square.org/tech_notes/OpenMX-Compile.pdf
http://www.openmx-square.org/forum/patio.cgi?mode=view&no=2354

Regards,
Naoya Yamaguchi
メンテ
Re: OpenMX3.9 installation error ( No.2 )
Date: 2020/10/29 18:28
Name: Gilad Gani  <giladg@campus.technion.ac.il>

Hi,

Thank you for the quick reply.
I've tried to add the MPI libraries I use, including the ones in the references you have attached, but I still get the same error.
I'm adding the LIB line that I used in makefile

LIB= -L/usr/local/fftw3/lib -lfftw3 -L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64 -L/opt/intel/mkl/lib/intel64/ -lmkl_intel_thread -lmkl_core -lpthread -L/usr/bin/gfortran -lgfortran

Thank you,
Gilad
メンテ
Re: OpenMX3.9 installation error ( No.3 )
Date: 2020/10/29 19:44
Name: Gilad Gani  <giladg@campus.technion.ac.il>

Just an update, now I have a different error(it seems that the errors regarding the fortran copmpiler are fixed)

DFT.o: In function `Allocate_Free_Band_Col':
DFT.c:(.text+0x3ce): undefined reference to `Cfree_blacs_system_handle'
DFT.c:(.text+0x3db): undefined reference to `Cblacs_gridexit'
DFT.c:(.text+0xf37): undefined reference to `numroc_'
DFT.c:(.text+0xf63): undefined reference to `numroc_'
DFT.c:(.text+0xf81): undefined reference to `Csys2blacs_handle'
DFT.c:(.text+0xfae): undefined reference to `Cblacs_gridinit'
DFT.c:(.text+0x10a2): undefined reference to `descinit_'
DFT.c:(.text+0x10d3): undefined reference to `descinit_'
DFT.c:(.text+0x1104): undefined reference to `descinit_'
DFT.o: In function `Allocate_Free_Band_NonCol':
DFT.c:(.text+0x19bf): undefined reference to `Cfree_blacs_system_handle'
DFT.c:(.text+0x19cc): undefined reference to `Cblacs_gridexit'
DFT.c:(.text+0x19fd): undefined reference to `Cfree_blacs_system_handle'
DFT.c:(.text+0x1a0a): undefined reference to `Cblacs_gridexit'
DFT.c:(.text+0x25c7): undefined reference to `numroc_'
DFT.c:(.text+0x25f3): undefined reference to `numroc_'
DFT.c:(.text+0x2611): undefined reference to `Csys2blacs_handle'
DFT.c:(.text+0x263e): undefined reference to `Cblacs_gridinit'
DFT.c:(.text+0x279f): undefined reference to `descinit_'
DFT.c:(.text+0x27cf): undefined reference to `descinit_'
DFT.c:(.text+0x27ff): undefined reference to `descinit_'
DFT.c:(.text+0x2992): undefined reference to `numroc_'
DFT.c:(.text+0x29be): undefined reference to `numroc_'
DFT.c:(.text+0x29dc): undefined reference to `Csys2blacs_handle'
DFT.c:(.text+0x2a09): undefined reference to `Cblacs_gridinit'
DFT.c:(.text+0x2afc): undefined reference to `descinit_'
DFT.c:(.text+0x2b2c): undefined reference to `descinit_'
DFT.c:(.text+0x2b5c): undefined reference to `descinit_'
DFT.o: In function `Allocate_Free_Cluster_Col':
DFT.c:(.text+0x3670): undefined reference to `Cfree_blacs_system_handle'
DFT.c:(.text+0x367d): undefined reference to `Cblacs_gridexit'
DFT.c:(.text+0x3b67): undefined reference to `numroc_'
DFT.c:(.text+0x3b93): undefined reference to `numroc_'
DFT.c:(.text+0x3bb1): undefined reference to `Csys2blacs_handle'
DFT.c:(.text+0x3bde): undefined reference to `Cblacs_gridinit'
DFT.c:(.text+0x3cd0): undefined reference to `descinit_'
DFT.c:(.text+0x3cff): undefined reference to `descinit_'
DFT.c:(.text+0x3d2e): undefined reference to `descinit_'
DFT.o: In function `Allocate_Free_Cluster_NonCol':
DFT.c:(.text+0x4225): undefined reference to `Cfree_blacs_system_handle'
DFT.c:(.text+0x4232): undefined reference to `Cblacs_gridexit'
DFT.c:(.text+0x4263): undefined reference to `Cfree_blacs_system_handle'
DFT.c:(.text+0x4270): undefined reference to `Cblacs_gridexit'
DFT.c:(.text+0x45e9): undefined reference to `numroc_'
DFT.c:(.text+0x4615): undefined reference to `numroc_'
DFT.c:(.text+0x4628): undefined reference to `Csys2blacs_handle'
DFT.c:(.text+0x4655): undefined reference to `Cblacs_gridinit'
DFT.c:(.text+0x477b): undefined reference to `descinit_'
DFT.c:(.text+0x47ab): undefined reference to `descinit_'
DFT.c:(.text+0x47db): undefined reference to `descinit_'
DFT.c:(.text+0x4972): undefined reference to `numroc_'
DFT.c:(.text+0x499e): undefined reference to `numroc_'
DFT.c:(.text+0x49b1): undefined reference to `Csys2blacs_handle'
DFT.c:(.text+0x49de): undefined reference to `Cblacs_gridinit'
DFT.c:(.text+0x4abb): undefined reference to `descinit_'
DFT.c:(.text+0x4aeb): undefined reference to `descinit_'
DFT.c:(.text+0x4b1b): undefined reference to `descinit_'
DFT.o: In function `DFT':
DFT.c:(.text+0xa4bb): undefined reference to `Cfree_blacs_system_handle'
DFT.c:(.text+0xa4c8): undefined reference to `Cblacs_gridexit'
DFT.c:(.text+0xa4f9): undefined reference to `Cfree_blacs_system_handle'
DFT.c:(.text+0xa506): undefined reference to `Cblacs_gridexit'
DFT.c:(.text+0xc035): undefined reference to `Cfree_blacs_system_handle'
DFT.c:(.text+0xc042): undefined reference to `Cblacs_gridexit'
Cluster_DFT_Col.o: In function `Cluster_DFT_Col':
Cluster_DFT_Col.c:(.text+0x1253): undefined reference to `Cblacs_barrier'
Cluster_DFT_Col.c:(.text+0x12ac): undefined reference to `pdgemm_'
Cluster_DFT_Col.c:(.text+0x12ea): undefined reference to `Cblacs_barrier'
Cluster_DFT_Col.c:(.text+0x1348): undefined reference to `pdgemm_'
Cluster_DFT_Col.c:(.text+0x147a): undefined reference to `Cblacs_barrier'
Cluster_DFT_Col.c:(.text+0x14d1): undefined reference to `pdgemm_'
Cluster_DFT_NonCol.o: In function `Cluster_DFT_NonCol':
Cluster_DFT_NonCol.c:(.text+0x22a9): undefined reference to `Cblacs_barrier'
Cluster_DFT_NonCol.c:(.text+0x2311): undefined reference to `pdgemm_'
Cluster_DFT_NonCol.c:(.text+0x2351): undefined reference to `Cblacs_barrier'
Cluster_DFT_NonCol.c:(.text+0x23a2): undefined reference to `pdgemm_'
Cluster_DFT_NonCol.c:(.text+0x23e0): undefined reference to `Cblacs_barrier'
Cluster_DFT_NonCol.c:(.text+0x2430): undefined reference to `pdgemm_'
Cluster_DFT_NonCol.c:(.text+0x2470): undefined reference to `Cblacs_barrier'
Cluster_DFT_NonCol.c:(.text+0x24c1): undefined reference to `pdgemm_'
Cluster_DFT_NonCol.c:(.text+0x24ff): undefined reference to `Cblacs_barrier'
Cluster_DFT_NonCol.c:(.text+0x254f): undefined reference to `pdgemm_'
Cluster_DFT_NonCol.c:(.text+0x258f): undefined reference to `Cblacs_barrier'
Cluster_DFT_NonCol.c:(.text+0x25e0): undefined reference to `pdgemm_'
Cluster_DFT_NonCol.c:(.text+0x261e): undefined reference to `Cblacs_barrier'
Cluster_DFT_NonCol.c:(.text+0x266e): undefined reference to `pdgemm_'
Cluster_DFT_NonCol.c:(.text+0x26ae): undefined reference to `Cblacs_barrier'
Cluster_DFT_NonCol.c:(.text+0x26ff): undefined reference to `pdgemm_'
Cluster_DFT_NonCol.c:(.text+0x273d): undefined reference to `Cblacs_barrier'
Cluster_DFT_NonCol.c:(.text+0x278d): undefined reference to `pdgemm_'
Cluster_DFT_NonCol.c:(.text+0x27cd): undefined reference to `Cblacs_barrier'
Cluster_DFT_NonCol.c:(.text+0x281e): undefined reference to `pdgemm_'
Cluster_DFT_NonCol.c:(.text+0x285c): undefined reference to `Cblacs_barrier'
Cluster_DFT_NonCol.c:(.text+0x28ac): undefined reference to `pdgemm_'
Cluster_DFT_NonCol.c:(.text+0x28ec): undefined reference to `Cblacs_barrier'
Cluster_DFT_NonCol.c:(.text+0x293d): undefined reference to `pdgemm_'
Cluster_DFT_NonCol.c:(.text+0x2ab2): undefined reference to `Cblacs_barrier'
Cluster_DFT_NonCol.c:(.text+0x2b07): undefined reference to `pzgemm_'
Band_DFT_Col.o: In function `Band_DFT_Col':
Band_DFT_Col.c:(.text+0x1233): undefined reference to `Cblacs_barrier'
Band_DFT_Col.c:(.text+0x129b): undefined reference to `pzgemm_'
Band_DFT_Col.c:(.text+0x1301): undefined reference to `Cblacs_barrier'
Band_DFT_Col.c:(.text+0x1366): undefined reference to `pzgemm_'
Band_DFT_Col.c:(.text+0x3284): undefined reference to `Cblacs_barrier'
Band_DFT_Col.c:(.text+0x32ee): undefined reference to `pzgemm_'
Band_DFT_Col.c:(.text+0x334f): undefined reference to `Cblacs_barrier'
Band_DFT_Col.c:(.text+0x33b4): undefined reference to `pzgemm_'
Band_DFT_Col.c:(.text+0x3517): undefined reference to `pzgemm_'
Band_DFT_Col.c:(.text+0x352f): undefined reference to `Cblacs_barrier'
Band_DFT_Col.c:(.text+0x461c): undefined reference to `pzgemm_'
Band_DFT_Col.c:(.text+0x4634): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.o: In function `Band_DFT_NonCol':
Band_DFT_NonCol.c:(.text+0x5cc6): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x5d27): undefined reference to `pzgemm_'
Band_DFT_NonCol.c:(.text+0x5db2): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x5dfc): undefined reference to `pzgemm_'
Band_DFT_NonCol.c:(.text+0x5e87): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x5ecd): undefined reference to `pzgemm_'
Band_DFT_NonCol.c:(.text+0x5f58): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x5fa2): undefined reference to `pzgemm_'
Band_DFT_NonCol.c:(.text+0x602d): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x6073): undefined reference to `pzgemm_'
Band_DFT_NonCol.c:(.text+0x60fe): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x614b): undefined reference to `pzgemm_'
Band_DFT_NonCol.c:(.text+0x66dc): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x6746): undefined reference to `pzgemm_'
Band_DFT_NonCol.c:(.text+0x7551): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x75b2): undefined reference to `pzgemm_'
Band_DFT_NonCol.c:(.text+0x763d): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x7687): undefined reference to `pzgemm_'
Band_DFT_NonCol.c:(.text+0x7712): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x7758): undefined reference to `pzgemm_'
Band_DFT_NonCol.c:(.text+0x77e3): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x782d): undefined reference to `pzgemm_'
Band_DFT_NonCol.c:(.text+0x78b8): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x78fe): undefined reference to `pzgemm_'
Band_DFT_NonCol.c:(.text+0x7989): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x79d6): undefined reference to `pzgemm_'
Band_DFT_NonCol.c:(.text+0x7c86): undefined reference to `Cblacs_barrier'
Band_DFT_NonCol.c:(.text+0x7cde): undefined reference to `pzgemm_'
TRAN_DFT.o: In function `TRAN_DFT':
TRAN_DFT.c:(.text+0x51d5): undefined reference to `numroc_'
TRAN_DFT.c:(.text+0x51fd): undefined reference to `numroc_'
TRAN_DFT.c:(.text+0x521b): undefined reference to `Csys2blacs_handle'
TRAN_DFT.c:(.text+0x5248): undefined reference to `Cblacs_gridinit'
TRAN_DFT.c:(.text+0x534b): undefined reference to `descinit_'
TRAN_DFT.c:(.text+0x5387): undefined reference to `descinit_'
TRAN_DFT.c:(.text+0x53bb): undefined reference to `descinit_'
TRAN_DFT.c:(.text+0x580b): undefined reference to `Cfree_blacs_system_handle'
TRAN_DFT.c:(.text+0x5818): undefined reference to `Cblacs_gridexit'
TRAN_DFT_NC.o: In function `TRAN_DFT_NC':
TRAN_DFT_NC.c:(.text+0x5ea0): undefined reference to `numroc_'
TRAN_DFT_NC.c:(.text+0x5ed0): undefined reference to `numroc_'
TRAN_DFT_NC.c:(.text+0x5eed): undefined reference to `Csys2blacs_handle'
TRAN_DFT_NC.c:(.text+0x5f1a): undefined reference to `Cblacs_gridinit'
TRAN_DFT_NC.c:(.text+0x608f): undefined reference to `descinit_'
TRAN_DFT_NC.c:(.text+0x60d5): undefined reference to `descinit_'
TRAN_DFT_NC.c:(.text+0x6113): undefined reference to `descinit_'
TRAN_DFT_NC.c:(.text+0x62b8): undefined reference to `numroc_'
TRAN_DFT_NC.c:(.text+0x62e8): undefined reference to `numroc_'
TRAN_DFT_NC.c:(.text+0x6305): undefined reference to `Csys2blacs_handle'
TRAN_DFT_NC.c:(.text+0x6332): undefined reference to `Cblacs_gridinit'
TRAN_DFT_NC.c:(.text+0x643b): undefined reference to `descinit_'
TRAN_DFT_NC.c:(.text+0x6481): undefined reference to `descinit_'
TRAN_DFT_NC.c:(.text+0x64bf): undefined reference to `descinit_'
TRAN_DFT_NC.c:(.text+0x6844): undefined reference to `Cfree_blacs_system_handle'
TRAN_DFT_NC.c:(.text+0x6851): undefined reference to `Cblacs_gridexit'
TRAN_DFT_NC.c:(.text+0x6885): undefined reference to `Cfree_blacs_system_handle'
TRAN_DFT_NC.c:(.text+0x6892): undefined reference to `Cblacs_gridexit'
Band_DFT_Col_Optical_ScaLAPACK.o: In function `Band_DFT_Col_Optical_ScaLAPACK':
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0xd86): undefined reference to `numroc_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0xdae): undefined reference to `numroc_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0xdcf): undefined reference to `Csys2blacs_handle'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0xdfc): undefined reference to `Cblacs_gridinit'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0xef5): undefined reference to `descinit_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0xf26): undefined reference to `descinit_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0xf57): undefined reference to `descinit_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x121f): undefined reference to `numroc_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x124f): undefined reference to `numroc_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x1270): undefined reference to `Csys2blacs_handle'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x129d): undefined reference to `Cblacs_gridinit'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x139e): undefined reference to `descinit_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x13d7): undefined reference to `descinit_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x140d): undefined reference to `descinit_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x282e): undefined reference to `Cblacs_barrier'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x289a): undefined reference to `pzgemm_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x28ea): undefined reference to `Cblacs_barrier'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x2958): undefined reference to `pzgemm_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x442a): undefined reference to `Cblacs_barrier'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x4496): undefined reference to `pzgemm_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x44e6): undefined reference to `Cblacs_barrier'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x4554): undefined reference to `pzgemm_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x4b77): undefined reference to `pzgemm_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x4b8f): undefined reference to `Cblacs_barrier'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x57d0): undefined reference to `pzgemm_'
Band_DFT_Col_Optical_ScaLAPACK.c:(.text+0x57e8): undefined reference to `Cblacs_barrier'
Cluster_DFT_Optical_ScaLAPACK.o: In function `Cluster_collinear_Optical':
/home/giladg/openmx3.9/source/Cluster_DFT_Optical_ScaLAPACK.c:542: undefined reference to `Cblacs_barrier'
/home/giladg/openmx3.9/source/Cluster_DFT_Optical_ScaLAPACK.c:543: undefined reference to `pdgemm_'
/home/giladg/openmx3.9/source/Cluster_DFT_Optical_ScaLAPACK.c:551: undefined reference to `Cblacs_barrier'
/home/giladg/openmx3.9/source/Cluster_DFT_Optical_ScaLAPACK.c:552: undefined reference to `pdgemm_'
/home/giladg/openmx3.9/source/Cluster_DFT_Optical_ScaLAPACK.c:590: undefined reference to `pdgemm_'
/home/giladg/openmx3.9/source/Cluster_DFT_Optical_ScaLAPACK.c:591: undefined reference to `Cblacs_barrier'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_critical'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float8_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_4'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_master'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_fini'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_reduce'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_flush'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8u'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_4'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_fork_call'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_push_num_threads'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_ordered'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_barrier'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_cmplx8_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_global_thread_num'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_4'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_critical'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_serialized_parallel'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_fixed4_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_reduce_nowait'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float4_max'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_master'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_single'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_fixed8_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_cmplx4_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_ok_to_fork'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_single'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_ordered'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_reduce_nowait'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_serialized_parallel'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float4_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float8_max'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_reduce'

Thank you in advance,
Gilad
メンテ
Re: OpenMX3.9 installation error ( No.4 )
Date: 2020/10/30 00:24
Name: Naoya Yamaguchi

Dear Gilad,

Please try to add "-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" to the beginning of values for "LIB".

Regards,
Naoya Yamaguchi
メンテ
Re: OpenMX3.9 installation error ( No.5 )
Date: 2020/10/29 22:43
Name: Gilad Gani  <giladg@campus.technion.ac.il>

Hi,

Many thanks, the number of error lines has reduced and it seems that I'm one step closer to install OpenMX.

Now the only errors are:

/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_critical'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float8_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_4'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_master'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_fini'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_reduce'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_flush'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8u'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_4'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_fork_call'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_push_num_threads'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_ordered'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_barrier'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_cmplx8_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_global_thread_num'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_4'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_critical'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_serialized_parallel'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_fixed4_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_reduce_nowait'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float4_max'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_master'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_single'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_8'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_fixed8_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_cmplx4_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_ok_to_fork'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_single'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_ordered'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_reduce_nowait'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_serialized_parallel'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float4_add'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float8_max'
/opt/intel/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_reduce'


Thank you,
Gilad
メンテ
Re: OpenMX3.9 installation error ( No.6 )
Date: 2020/10/30 00:35
Name: Naoya Yamaguchi

Dear Gilad,

If you use GCC, not Intel compilers, you should use "-lmkl_gf_lp64" and "-lmkl_gnu_thread" instead of "-lmkl_intel_lp64" and "-lmkl_intel_thread".

Regards,
Naoya Yamaguchi
メンテ
Re: OpenMX3.9 installation error ( No.7 )
Date: 2020/11/01 17:27
Name: Gilad Gani  <giladg@campus.technion.ac.il>

Dear Naoya,

Thank you so much!!

I managed to install OpenMX.

I do have one more problem, with the test file.

I used the command : % mpirun -np 1 openmx Methane.dat > met.std & (from the manual), and i got the following error:

"openmx: error while loading shared libraries: libmkl_scalapack_lp64.so: cannot open shared object file: No such file or directory"

"[1]+ Exit 127 mpirun -np 1 openmx Methane.dat > met.std"

and the ouptput file (met.std) is as follows:

"
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[12842,1],0]
Exit code: 127
--------------------------------------------------------------------------
"


Thank you again for all of the help,
Gilad
メンテ
Re: OpenMX3.9 installation error ( No.8 )
Date: 2020/11/01 17:39
Name: Naoya Yamaguchi

Dear Gilad,

Please try the following.
LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64 mpirun -np 1 openmx Methane.dat > met.std &

Regards,
Naoya Yamaguchi
メンテ
Re: OpenMX3.9 installation error ( No.9 )
Date: 2020/11/01 18:56
Name: Gilad Gani  <giladg@campus.technion.ac.il>

It works!! Thank you very much!
I'm closing this thread, if I will have any other issues, I will open a new thread.

best regards
Gilad
メンテ

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