ABINIT Discussion Forums

I have compiled the abinit sources on my (Mac OS 10.7) eight-core mac and find that I can get every file to compile, only to find some unresolved references in the final linking state in 98_main. I have the intel compilers (ifort and icc 12.1.3) and I have compiled openmpi-1.4.5 (the latest stable release of openmpi) using these compilers. I naturally, have the mkl libraries as well (they come with the fortran compiler). I used the following line to configure abinit.

../configure --enable-mpi --with-mpi-prefix=/opt/openmpi --with-linalg-flavor=mkl --enable-gui --with-PACKAGE=fox --enable-64bit CC=mpicc FC=mpif90 CXX=mpicxx

The linking details are below, but are generally references to libraries of the form "pseudo_pwscf_mp_nlcc" where "mp" seems to be the key word. I am attempting to carry out mpi parallelization and cannot find these files.

I also noticed on the macintosh that the /usr/bin/cpp has trouble with the libxc library (I ended up using the fpp that comes with the intel compilers without incident. There also seems to be a parsing error (perhaps due to the use of accented characters in the atompaw source in libxc_ini. Where can I find these libraries (or if they are for mp parallelization, switch them off? Perhaps my configuration could be improved? Any suggestions?


Linking error follows:

/Users/paulfons/Ports/abinit/build/config/wrappers/wrap-mpiLFC -free -module /Users/paulfons/Ports/abinit/build/src/mods -O2 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp -g -extend-source -vec-report0 -noaltparam -nofpscomp -static-intel -static-libgcc -static-intel -static-libgcc -o abinit abinit-abinit.o -static-intel -static-libgcc ../../src/95_drive/lib95_drive.a ../../src/93_rdm/lib93_rdm.a ../../src/79_seqpar_mpi/lib79_seqpar_mpi.a ../../src/77_ddb/lib77_ddb.a ../../src/77_suscep/lib77_suscep.a ../../src/72_response/lib72_response.a ../../src/71_bse/lib71_bse.a ../../src/70_gw/lib70_gw.a ../../src/69_wfdesc/lib69_wfdesc.a ../../src/68_dmft/lib68_dmft.a ../../src/68_recursion/lib68_recursion.a ../../src/68_rsprc/lib68_rsprc.a ../../src/67_common/lib67_common.a ../../src/66_paw/lib66_paw.a ../../src/66_wfs/lib66_wfs.a ../../src/65_psp/lib65_psp.a ../../src/65_nonlocal/lib65_nonlocal.a ../../src/64_atompaw/lib64_atompaw.a ../../src/62_occeig/lib62_occeig.a ../../src/62_iowfdenpot/lib62_iowfdenpot.a ../../src/62_wvl_wfs/lib62_wvl_wfs.a ../../src/62_poisson/lib62_poisson.a ../../src/62_cg_noabirule/lib62_cg_noabirule.a ../../src/61_ionetcdf/lib61_ionetcdf.a ../../src/59_io_mpi/lib59_io_mpi.a ../../src/57_iovars/lib57_iovars.a ../../src/56_recipspace/lib56_recipspace.a ../../src/56_xc/lib56_xc.a ../../src/56_mixing/lib56_mixing.a ../../src/53_abiutil/lib53_abiutil.a ../../src/53_spacepar/lib53_spacepar.a ../../src/53_ffts/lib53_ffts.a ../../src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a ../../src/51_manage_mpi/lib51_manage_mpi.a ../../src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a ../../src/47_xml/lib47_xml.a ../../src/45_psp_parser/lib45_psp_parser.a ../../src/44_geomoptim/lib44_geomoptim.a ../../src/43_ptgroups/lib43_ptgroups.a ../../src/43_abitypes_defs/lib43_abitypes_defs.a ../../src/42_nlstrain/lib42_nlstrain.a ../../src/42_geometry/lib42_geometry.a ../../src/42_parser/lib42_parser.a ../../src/42_wvl_wrappers/lib42_wvl_wrappers.a ../../src/32_util/lib32_util.a ../../src/28_numeric_noabirule/lib28_numeric_noabirule.a ../../src/27_toolbox_oop/lib27_toolbox_oop.a ../../src/18_timing/lib18_timing.a ../../src/16_hideleave/lib16_hideleave.a ../../src/14_hidewrite/lib14_hidewrite.a ../../src/12_hide_mpi/lib12_hide_mpi.a ../../src/11_qespresso_ext/lib11_qespresso_ext.a ../../src/13_memory_mpi/lib13_memory_mpi.a ../../src/10_defs/lib10_defs.a ../../src/01_linalg_ext/lib01_linalg_ext.a ../../src/01_interfaces_ext/lib01_interfaces_ext.a -L/Users/paulfons/Ports/abinit/build/fallbacks/exports/lib -lwannier90 -L/Users/paulfons/Ports/abinit/build/fallbacks/exports/lib -lbigdft -lpoissonsolver -labinit -L/Users/paulfons/Ports/abinit/build/fallbacks/exports/lib -lxc -L/Users/paulfons/Ports/abinit/build/fallbacks/exports/lib -letsf_io_low_level -letsf_io_utils -letsf_io -L/Users/paulfons/Ports/abinit/build/fallbacks/exports/lib -lnetcdf -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
Undefined symbols for architecture x86_64:
"_unlink_", referenced from:
_mlwfovlp_ in lib67_common.a(mlwfovlp.o)
"_pseudo_pwscf_mp_nlcc_", referenced from:
_upfheader2abi_ in lib45_psp_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_lll_", referenced from:
_upfheader2abi_ in lib45_psp_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_nbeta_", referenced from:
_upfheader2abi_ in lib45_psp_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_zp_", referenced from:
_upfheader2abi_ in lib45_psp_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_psd_", referenced from:
_upfheader2abi_ in lib45_psp_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_lmax_", referenced from:
_upfheader2abi_ in lib45_psp_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_dft_", referenced from:
_upfheader2abi_ in lib45_psp_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_qfcoef_", referenced from:
_read_pseudo_nl_ in lib11_qespresso_ext.a(read_upf_pwscf.o)
"_pseudo_pwscf_mp_rinner_", 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_nqf_", 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_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_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_ikk2_", referenced from:
_read_pseudo_nl_ 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