Undefined symbols for architecture x86_64 error

eleonora_m_ · ‎12-20-2015

Hi

I'am trying to compile abinit 7.10 or other versions of the code on mac 10.10.2 macbook air with ifort 16.0.1

the command which ifort give me:

/opt/intel//compilers_and_libraries_2016.1.111/mac/bin/intel64/ifort

i try to compile with

./configure FC=ifort CC=icc CXX=icpc F77=ifort

but always i found with intel compiler this error

Undefined symbols for architecture x86_64:

"_m_profiling_abi_mp_abi_alloc_stat_abi_", referenced from:

_MAIN__ in abinit-abinit.o

_chkinp_ in lib57_iovars.a(chkinp.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_ab7_invars_mp_new_token_ in lib57_iovars.a(m_ab7_invars_f90.o)

_m_ab7_invars_mp_ab7_invars_load_ in lib57_iovars.a(m_ab7_invars_f90.o)

_m_ab7_invars_mp_free_token_ in lib57_iovars.a(m_ab7_invars_f90.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_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_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)

"_pseudo_pwscf_mp_ecutwfc_", referenced from:

_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)

"_pseudo_pwscf_mp_els_", referenced from:

_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)

"_pseudo_pwscf_mp_etotps_", referenced from:

_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_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)

_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)

"_pseudo_pwscf_mp_lchi_", referenced from:

_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_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)

_read_pseudo_nl_ 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_header_ 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)

...

"_pseudo_pwscf_mp_nbeta_", referenced from:

_upfheader2abi_ in lib57_iopsp_parser.a(upfheader2abi.o)

_read_pseudo_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)

_read_pseudo_nl_ 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_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)

_read_pseudo_pswfc_ in lib11_qespresso_ext.a(read_upf_pwscf.o)

"_pseudo_pwscf_mp_oc_", referenced from:

_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_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_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_header_ in lib11_qespresso_ext.a(read_upf_pwscf.o)

_upf2abinit_ in lib65_psp.a(upf2abinit.o)

ld: symbol(s) not found for architecture x86_64

make[3]: *** [abinit] Error 1

make[2]: *** [all-recursive] Error 1

make[1]: *** [all-recursive] Error 1

make: *** [all] Error 2

with gnu compiler i found no error

Please can you help me to solve this problem

thanks

eleonora

Steven_L_Intel1 · ‎12-20-2015

You did not show the actual build commands. The errors suggest you're not linking in the object file created by compiling module pseudo_pwscf.

eleonora_m_ · ‎12-20-2015

I configure abinit with ./configure FC=ifort CC=icc CXX=icpc F77=ifort

Sorry can you tell how to link the object file created during the compilation

Thans a lot for your patience

eleonora

Steven_L_Intel1 · ‎12-21-2015

That configure is something in your own environment, it is not using any part of the Intel product. You're apparently using a makefile - the makefile should include all of the .o files from compiling all the Fortran sources, including that of modules. You haven't shown the actual ifort commands run, so I don't know how to advise you.

mecej4 · ‎12-21-2015

I have never dealt with ABINIT and I do not know anything about whether it comes with pre-built libraries, etc., so the following is speculative.

The error messages given by the linker suggest that some of the libraries (files with the ".a" suffix) were built for 32-bit targets, whereas you are using the IFort and Icc compilers to build 64-bit targets. Typically, running the configure script for a package generates one or more makefiles, and at least some of these makefiles will contain a "clean" target. Running the command "make clean" on each of these should remove those incompatible library files and object files, following which you can attempt to build from scratch.