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Dear developers and users I try to install abinit a software for electronic structure properties but when i try to install it with
./configure FC=ifort CC=icc CXX=icpc i found this error
Undefined symbols for architecture x86_64:
"_m_profiling_mp_abi_alloc_stat_", referenced from:
_drvaim_ in lib63_bader.a(drvaim.o)
_m_xmpi_mp_xmpi_distab_4d_ in lib12_hide_mpi.a(m_xmpi.o)
_m_xmpi_mp_xallgatherv_mpi_int1_dp1_ in lib12_hide_mpi.a(m_xmpi.o)
_m_xmpi_mp_xallgatherv_mpi_coeff2d_ in lib12_hide_mpi.a(m_xmpi.o)
_m_xmpi_mp_xallgatherv_mpi_coeff2d_indx_ in lib12_hide_mpi.a(m_xmpi.o)
_m_xmpi_mp_xgatherv_mpi_int1_dp1_ in lib12_hide_mpi.a(m_xmpi.o)
_addout_ in lib63_bader.a(addout.o)
...
"_m_profiling_mp_sz1_", referenced from:
_m_pawrhoij_mp_symrhoij_ in lib42_libpaw.a(m_pawrhoij.o)
"_m_profiling_mp_sz2_", referenced from:
_m_pawrhoij_mp_symrhoij_ in lib42_libpaw.a(m_pawrhoij.o)
ld: symbol(s) not found for architecture x86_64
make[5]: *** [aim] Error 1
make[5]: *** Waiting for unfinished jobs....
Undefined symbols for architecture x86_64:
"_m_profiling_mp_abi_alloc_stat_", referenced from:
_MAIN__ in anaddb-anaddb.o
_anaddb_dtset_clean_ in lib77_ddb.a(anaddb_dtset_clean.o)
_asria_calc_ in lib72_response.a(asria_calc.o)
_asrprs_ in lib72_response.a(asrprs.o)
_chneu9_ in lib72_response.a(chneu9.o)
_destroy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
...
"_m_profiling_mp_sz1_", referenced from:
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_m_pawtab_mp_pawtab_bcast_ in lib42_libpaw.a(m_pawtab.o)
_complete_gkk_ in lib77_ddb.a(complete_gkk.o)
_m_pawrhoij_mp_symrhoij_ in lib42_libpaw.a(m_pawrhoij.o)
"_m_profiling_mp_sz2_", referenced from:
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_get_all_gkq_ in lib77_ddb.a(get_all_gkq.o)
_m_pawtab_mp_pawtab_bcast_ in lib42_libpaw.a(m_pawtab.o)
_complete_gkk_ in lib77_ddb.a(complete_gkk.o)
_m_pawrhoij_mp_symrhoij_ in lib42_libpaw.a(m_pawrhoij.o)
"_m_profiling_mp_sz3_", referenced from:
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_get_all_gkq_ in lib77_ddb.a(get_all_gkq.o)
"_m_profiling_mp_sz4_", referenced from:
_get_all_gkq_ in lib77_ddb.a(get_all_gkq.o)
"_m_profiling_mp_sz5_", referenced from:
_get_all_gkq_ in lib77_ddb.a(get_all_gkq.o)
"_m_profiling_mp_sz6_", referenced from:
_get_all_gkq_ in lib77_ddb.a(get_all_gkq.o)
ld: symbol(s) not found for architecture x86_64
make[5]: *** [anaddb] Error 1
Undefined symbols for architecture x86_64:
"_m_profiling_mp_abi_alloc_stat_", referenced from:
_MAIN__ in abinit-abinit.o
_chkinp_ in lib57_iovars.a(chkinp.o)
_destroy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_set_mpi_enreg_fft_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_driver_ in lib95_drive.a(driver.o)
_m_ab7_invars_mp_ab7_invars_set_flags_ in lib57_iovars.a(m_ab7_invars_f90.o)
...
"_m_profiling_mp_sz1_", referenced from:
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_m_pawang_mp_pawang_init_ in lib42_libpaw.a(m_pawang.o)
_m_pawtab_mp_pawtab_bcast_ in lib42_libpaw.a(m_pawtab.o)
_respfn_ in lib95_drive.a(respfn.o)
_m_paw_an_mp_paw_an_gather_ in lib42_libpaw.a(m_paw_an.o)
_m_paw_an_mp_paw_an_copy_ in lib42_libpaw.a(m_paw_an.o)
_m_paw_an_mp_paw_an_gather_..0 in lib42_libpaw.a(m_paw_an.o)
...
"_m_profiling_mp_sz2_", referenced from:
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_m_pawang_mp_pawang_init_ in lib42_libpaw.a(m_pawang.o)
_m_pawtab_mp_pawtab_bcast_ in lib42_libpaw.a(m_pawtab.o)
_respfn_ in lib95_drive.a(respfn.o)
_d2frnl_ in lib72_response.a(d2frnl.o)
_m_paw_an_mp_paw_an_gather_ in lib42_libpaw.a(m_paw_an.o)
_m_paw_an_mp_paw_an_gather_..0 in lib42_libpaw.a(m_paw_an.o)
...
"_m_profiling_mp_sz3_", referenced from:
_copy_mpi_enreg_ in lib51_manage_mpi.a(mpi_enreg_tools.o)
_m_pawang_mp_pawang_init_ in lib42_libpaw.a(m_pawang.o)
_d2frnl_ in lib72_response.a(d2frnl.o)
_m_paw_an_mp_paw_an_gather_ in lib42_libpaw.a(m_paw_an.o)
_m_paw_an_mp_paw_an_gather_..0 in lib42_libpaw.a(m_paw_an.o)
_m_paw_ij_mp_paw_ij_gather_ in lib42_libpaw.a(m_paw_ij.o)
_m_paw_ij_mp_paw_ij_copy_ in lib42_libpaw.a(m_paw_ij.o)
...
"_m_profiling_mp_sz4_", referenced from:
_m_paw_ij_mp_paw_ij_gather_ in lib42_libpaw.a(m_paw_ij.o)
_m_paw_ij_mp_paw_ij_copy_ in lib42_libpaw.a(m_paw_ij.o)
_m_paw_ij_mp_paw_ij_gather_..0 in lib42_libpaw.a(m_paw_ij.o)
_m_bandfft_kpt_mp_copy_bandfft_kpt_ in lib66_wfs.a(m_bandfft_kpt.o)
"_pseudo_pwscf_mp_betar_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_chi_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_pswfc_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_dft_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_dion_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_ecutrho_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_ecutwfc_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_els_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_etotps_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_ikk2_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_isus_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_lchi_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_lll_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_lmax_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_mesh_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_mesh_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_rhoatom_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_pswfc_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_local_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_nlcc_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
...
"_pseudo_pwscf_mp_nbeta_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_nlcc_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_nqf_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_nqlc_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_ntwfc_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_pswfc_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_oc_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_psd_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_pseudotype_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_qfcoef_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_qfunc_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_qqq_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_r_", referenced from:
_read_pseudo_mesh_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_rab_", referenced from:
_read_pseudo_mesh_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_rho_at_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_rhoatom_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_rho_atc_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_nlcc_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_rinner_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_vloc0_", referenced from:
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_local_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_pseudo_pwscf_mp_zp_", referenced from:
_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)
_read_pseudo_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
_upf2abinit_ in lib65_psp.a(upf2abinit.o)
"_unlink_", referenced from:
_mlwfovlp_ in lib67_common.a(mlwfovlp.o)
ld: symbol(s) not found for architecture x86_64
make[5]: *** [abinit] Error 1
make[4]: *** [all-recursive] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all] Error 2
make[1]: *** [multi] Error 2
make: *** [mj4] Error 2
Please can you help me to solve it?
thanks a lot
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It looks as if you haven't rebuilt .mod files (or otherwise don't have the right ones on include path). Those must be rebuilt when moving from 32- to 64-bit compilation, or from a non-Intel compiler to ifort.
If you are using MPI, your MPI must be compatible with ifort (Intel64 as opposed to 32-bit MPI installation). For .mod files supplied by MPI, using the 64-bit mpi wrapper for ifort ought to set the include path correctly.
Also, with MPI, your application may expect the MPI wrappers to be given in the configure command, or found by using the specific setup scripts supplied with the application. Depending on the MPI version, the ifort wrapper might be named mpif90, mpiifort, or mpifort;
ifort doesn't supply MPI unless you have installed the Intel Cluster Studio (or separate Intel MPI) package, where the wrappers for Intel compilers are named mpiifort, mpiicc, mpiicpc. If you are using an open source MPI (OpenMPI or MPICH2 suggested for this application), you must build and install according to the recipe supplied on the corresponding web site.
If you didn't want to build with MPI, you must study the installation instructions about how to select the non-parallel version.
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It looks like you're missing the object files that contain the source for (at least) two modules: m_profiling and pseudo_pwscf, so you should look again at your makefile.
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Dear Tim Thanks to help me.
how can i rebuild .mod files
Or how can i put it in the correct path
Thanks
Dearly Lorenzo
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The MPI wrapper file would set up the include for its own .mod files, and I would expect that when you build according to instructions, any .mod files created by abinit would be included.
One would hope there would be a make clean command so that you could wipe out any incorrectly built files, once you got configuration issues corrected.
If the instructions aren't clear enough, or take too much study, this forum is hardly the place to deal with it.
If you chose the OpenMPI, their site gives excellent instructions.
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