Make error [lslib_tester.x] Error 1, [CMakeFiles/lslib_teste

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keyares

Make error [lslib_tester.x] Error 1, [CMakeFiles/lslib_teste

Post by keyares » 16 Mar 2015, 11:52

Actually I install this program successfully without mpi flag.
This time I compiled it with MKL and error happened after I installed Intel MKL. It seems a problem with the Xcode. I have switched between Xcode and command line tool. But it doesn't work. My platform is OS X 10.10. It is really troublesome to compile program on this OS version.
I ran the setup command ./setup --fc=mpif90 --cc=mpicc --cxx=mpicxx --mkl=sequential. And everything looked fine.
Then errors happened during the linking stage.
I will be very grateful if some pro can help me figure it out.
BTW my dalton version is Dalton 2015
Thank you for your kind attention.

Linking C static library lib/liblsdalton.a
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../liblsutillib_precision.a.objlist
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../libmatrixmlib.a.objlist
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../liblsutillib_common.a.objlist
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../libmatrixolib.a.objlist
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../libmatrixulib.a.objlist
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../libpdpacklib.a.objlist
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../liblsutiltypelib_common.a.objlist
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../liblsutillib.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../libfmmlib.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../libdftfunclib.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../liblsint.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../libpbclib.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-data.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffdata.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-krsp-op.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-matop.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-msc.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-nfinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-scf.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_compare.F90.o) has no symbols
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../libddynamlib.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-data.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffdata.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-krsp-op.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-matop.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-msc.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-nfinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-scf.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_compare.F90.o) has no symbols
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../libdeclib.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-data.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffdata.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-krsp-op.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-matop.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-msc.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-nfinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-scf.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_compare.F90.o) has no symbols
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../libsolverutillib.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-data.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffdata.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-krsp-op.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-matop.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-msc.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-nfinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-scf.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_compare.F90.o) has no symbols
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../librspsolverlib.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-data.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffdata.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-krsp-op.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-matop.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-msc.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-nfinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-scf.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_compare.F90.o) has no symbols
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../liblinearslib.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-data.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffdata.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-krsp-op.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-matop.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-msc.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-nfinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-scf.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_compare.F90.o) has no symbols
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../libgeooptlib.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-data.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffdata.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-krsp-op.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-matop.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-msc.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-nfinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-scf.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_compare.F90.o) has no symbols
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../libxcfun_interface.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-data.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffdata.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-krsp-op.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-matop.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-msc.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-nfinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-scf.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_compare.F90.o) has no symbols
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../liblsdaltonmain.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-data.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffdata.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-krsp-op.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-matop.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-msc.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-nfinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-scf.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_compare.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(numerical_derivatives.F90.o) has no symbols
Running: /usr/bin/ar ru /Applications/DALTON/build/lib/liblsdalton.a @../librsp_prop.a.objlist
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-data.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffdata.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-krsp-op.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-matop.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-msc.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-nfinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-scf.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_compare.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(numerical_derivatives.F90.o) has no symbols
Running: /usr/bin/ranlib /Applications/DALTON/build/lib/liblsdalton.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_lattice_vectors.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-data.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffdata.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-ffinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-krsp-op.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-matop.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-msc.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-nfinteractions.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc-scf.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(pbc_compare.F90.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Applications/DALTON/build/lib/liblsdalton.a(numerical_derivatives.F90.o) has no symbols
[ 99%] Built target lsdalton
Linking Fortran executable lslib_tester.x
ld: warning: directory not found for option '-L/Applications/DALTON/build/external/pelib-build/external/lib'
ld: warning: directory not found for option '-L/Applications/DALTON/build/external/qfitlib-build/external/lib'
ld: warning: directory not found for option '-L/Applications/DALTON/build/external/ls-matrix-defop-build/external/lib'
ld: warning: directory not found for option '-L/Applications/DALTON/build/external/ls-openrsp-build/external/lib'
Undefined symbols for architecture x86_64:
"_cbifmm_module_mp_maxbufi_", referenced from:
_getmmbufinfo_ in liblsdalton.a(mm_input.F90.o)
_setmmbufinfo_ in liblsdalton.a(mm_input.F90.o)
"_cbifmm_module_mp_maxbufn_", referenced from:
_getmmbufinfo_ in liblsdalton.a(mm_input.F90.o)
_setmmbufinfo_ in liblsdalton.a(mm_input.F90.o)
"_cbifmm_module_mp_maxbufr_", referenced from:
_getmmbufinfo_ in liblsdalton.a(mm_input.F90.o)
_setmmbufinfo_ in liblsdalton.a(mm_input.F90.o)
"_cbifmm_module_mp_mmbuflen_", referenced from:
_getmmbufinfo_ in liblsdalton.a(mm_input.F90.o)
_setmmbufinfo_ in liblsdalton.a(mm_input.F90.o)
"_cbifmm_module_mp_usebufmm_", referenced from:
_getmmbufinfo_ in liblsdalton.a(mm_input.F90.o)
_setmmbufinfo_ in liblsdalton.a(mm_input.F90.o)
"_dec_typedef_module_mp_decinfo_", referenced from:
_configuration_mp_dec_meaningful_input_ in liblsdalton.a(configuration.F90.o)
_configuration_mp_set_final_config_and_print_ in liblsdalton.a(configuration.F90.o)
_lsdalton_driver_ in liblsdalton.a(LSDALTON.F90.o)
_dec_main_mod_mp_dec_main_prog_input_ in liblsdalton.a(dec_main.F90.o)
_dec_main_mod_mp_dec_main_prog_ in liblsdalton.a(dec_main.F90.o)
_dec_main_mod_mp_dec_main_prog_file_ in liblsdalton.a(dec_main.F90.o)
_dec_main_mod_mp_get_mp2gradient_and_energy_from_inputs_ in liblsdalton.a(dec_main.F90.o)
...
"_density_fitting_mp_fit_", referenced from:
_mm_get_grad_ in liblsdalton.a(mm_driver.F90.o)
_mm_interface_mod_mp_mm_connect_interface_ in liblsdalton.a(mm_interface.F90.o)
_mm_interface_mod_mp_mm_read_in_raw_data_ in liblsdalton.a(mm_interface.F90.o)
_mm_interface_mod_mp_mm_get_raw_data_ in liblsdalton.a(mm_interface.F90.o)
_mm_aux_qlm_builder_mp_mm_get_aux_qlm_ in liblsdalton.a(mm_interface.F90.o)
_mm_aux_qlm_builder_mp_get_normalised_qlm_ in liblsdalton.a(mm_interface.F90.o)
_mm_interface_mod_mp_mm_get_n_mms_from_file_ in liblsdalton.a(mm_interface.F90.o)
...
"_lsdalton_fock_module_mp_lsint_fock_data_", referenced from:
_dal_interface_mp_di_get_gbdssingle_ in liblsdalton.a(dalton_interface.F90.o)
_dal_interface_mp_di_get_gbds_and_xc_linrsp_array_ in liblsdalton.a(dalton_interface.F90.o)
_dal_interface_mp_di_get_gbds_and_xc_linrsp_single_ in liblsdalton.a(dalton_interface.F90.o)
_dal_interface_mp_di_get_gbdsarray_ in liblsdalton.a(dalton_interface.F90.o)
_dal_interface_mp_di_get_gbdsarray_admm_ in liblsdalton.a(dalton_interface.F90.o)
_dal_interface_mp_di_get_dipole_ in liblsdalton.a(dalton_interface.F90.o)
_dal_interface_mp_di_get_gaol_lsdalton_ in liblsdalton.a(dalton_interface.F90.o)
...
ld: symbol(s) not found for architecture x86_64
make[2]: *** [lslib_tester.x] Error 1
make[1]: *** [CMakeFiles/lslib_tester.x.dir/all] Error 2
make: *** [all] Error 2

keyares

Re: Make error [lslib_tester.x] Error 1, [CMakeFiles/lslib_t

Post by keyares » 17 Mar 2015, 09:54

99% and fail... really embarrassing...
no body can help......

lyzhao
Posts: 74
Joined: 11 Nov 2013, 00:36
First name(s): Youzhao
Last name(s): Lan
Affiliation: Institute of Physical Chemistry
Country: China

Re: Make error [lslib_tester.x] Error 1, [CMakeFiles/lslib_t

Post by lyzhao » 17 Mar 2015, 11:29

I am not a expert and use the linux OS,
I share with you my setup:
./setup build4DFTLAPACK --fc=mpif90 --cc=mpicc --cxx=mpicxx --mpi --mkl=parallel --blas=/public/home/lyzhao/soft/lapack-3.5.0/intel/librefblas.a --lapack=/public/home/lyzhao/soft/lapack-3.5.0/intel/liblapack.a --cmake=/public/home/lyzhao/soft/cmake-2.8.12.1-Linux-i386/bin/cmake

system env:
intel64_2011.4.191_InclMKL_10.3.4.191, non-commercial free version
openmpi 1.4.3
lapack 3.5.0

if successful, then run /public/home/lyzhao/soft/cmake-2.8.12.1-Linux-i386/bin/ctest for run test.
It is strange for me that you use mpi* but not use -mpi flag.

Good luck
Youzhao Lan

taylor
Posts: 600
Joined: 15 Oct 2013, 05:37
First name(s): Peter
Middle name(s): Robert
Last name(s): Taylor
Affiliation: Tianjin University
Country: China

Re: Make error [lslib_tester.x] Error 1, [CMakeFiles/lslib_t

Post by taylor » 17 Mar 2015, 12:27

I admit to some confusion here. You say "Actually I install this program successfully without mpi flag". Are you implying, then, that when you install without MPI, that is, in a strictly non-MPI parallel version (the Intel libraries may provide some thread-level parallelism even in this case), the code compiles, links, and runs all the tests? If so, it is hard to avoid the conclusion that there is a problem with your MPI installation. Clearly you are running on a Mac, from what you describe. First, in that case why do you want an MPI build anyway? The Mac is a single-socket machine with a multicore chip; unless you are running some quite unusual calculations you are likely much better off with exploiting thread-level parallelism in the Intel libraries (or specifying OpenMP parallelism if you are running LSDalton). Much of the more elaborate components of Dalton (CC, response, parts of CI/MCSCF) are heavily dependent on matrix multiplication, and you can't do much better than let the Intel libraries look after that on a single-socket multicore system.

If you are intending to run on some sort of multi-node Mac-based system, I think you need to verify the MPI (presumably OpenMPI, rather than Intel's MPI from Intel Cluster Studio?) setup first. Does the OpenMPI "hello world" test case run? I have some difficulties seeing how Xcode can be the problem: surely this relates only to Xwindows-based applications? How would this be causing a problem in Dalton linking --- as far as I know we do not link against any of the X Window system libraries on any operating system?

In short, what is it you want to do that you cannot accomplish, on your Mac, with the non-MPI installation?

Best regards
Pete

keyares

Re: Make error [lslib_tester.x] Error 1, [CMakeFiles/lslib_t

Post by keyares » 17 Mar 2015, 22:34

taylor wrote:I admit to some confusion here. You say "Actually I install this program successfully without mpi flag". Are you implying, then, that when you install without MPI, that is, in a strictly non-MPI parallel version (the Intel libraries may provide some thread-level parallelism even in this case), the code compiles, links, and runs all the tests? If so, it is hard to avoid the conclusion that there is a problem with your MPI installation. Clearly you are running on a Mac, from what you describe. First, in that case why do you want an MPI build anyway? The Mac is a single-socket machine with a multicore chip; unless you are running some quite unusual calculations you are likely much better off with exploiting thread-level parallelism in the Intel libraries (or specifying OpenMP parallelism if you are running LSDalton). Much of the more elaborate components of Dalton (CC, response, parts of CI/MCSCF) are heavily dependent on matrix multiplication, and you can't do much better than let the Intel libraries look after that on a single-socket multicore system.

If you are intending to run on some sort of multi-node Mac-based system, I think you need to verify the MPI (presumably OpenMPI, rather than Intel's MPI from Intel Cluster Studio?) setup first. Does the OpenMPI "hello world" test case run? I have some difficulties seeing how Xcode can be the problem: surely this relates only to Xwindows-based applications? How would this be causing a problem in Dalton linking --- as far as I know we do not link against any of the X Window system libraries on any operating system?

In short, what is it you want to do that you cannot accomplish, on your Mac, with the non-MPI installation?

Best regards
Pete
Dear Pete
Thank you very much for your reply!
It is very kind of you.
And I have to mention that the Intel MKL studio does not include Inter MPI for OS X (I thought it did).
I have tried to compile it with GCC or omp, and I actually made it. The problem is that Dalton is not omp paralleled and it is really time consuming if I run some NMR or spin-spin coupling properties. I have tried calcultions on ADF and gamess with multi threads and they were much faster (I7 can support 8 threads). If I use dalton without parallelism, the usage of CPU is only 1/8. I have installed the latest mpich by homebrew, and the build processing and most of compiling were successful with flags (./setup --fc=mpif90 --cc=mpicc --cxx=mpicxx --mkl=sequential). The error only happened on the link stage for file liblsdalton.a.
Such kind of errors are very common according to google search results. I think this problem is caused by some small tricks I don't realize.
Best regards
Sincerely yours
Wen-Xuan Wang

bast
Posts: 1210
Joined: 26 Aug 2013, 13:22
First name(s): Radovan
Last name(s): Bast
Affiliation: none
Country: Germany

Re: Make error [lslib_tester.x] Error 1, [CMakeFiles/lslib_t

Post by bast » 18 Mar 2015, 00:11

hi,

can you please clearly summarize what worked and what failed?
under which conditions are you able to compile and under which
conditions does compilation/linking fail?

the warnings about "has no symbols" i can understand because these
files really have no symbols - they are empty
(to other developers: all code got removed with "make release" and in this case
it would be good to leave a dummy routine in the source file).

best wishes,
radovan

taylor
Posts: 600
Joined: 15 Oct 2013, 05:37
First name(s): Peter
Middle name(s): Robert
Last name(s): Taylor
Affiliation: Tianjin University
Country: China

Re: Make error [lslib_tester.x] Error 1, [CMakeFiles/lslib_t

Post by taylor » 18 Mar 2015, 11:26

A couple of points. First, yeah, it's easy to get caught with this Intel software business --- I was a bit shocked to discover that VLSCI (my operation: petascale and still the most powerful facility in the world dedicated to life sciences computing) had only the Intel "Composer Suite" and therefore, among other issues, did not have Intel's MPI. To get that you have to have Intel Cluster Studio, which is a different product and, more importantly, commands a different price...

I have a number of dissatisfactions with OpenMPI, and I won't go on about most of them here, although I'm tempted. From my perspective the biggest is dealing with 64-bit builds. In my view the only way to make this work is to download the source and configure (time to go to the pub and have a couple of rounds, or maybe dinner...) and then build it (a post-dinner round...) yourself. Unless you have a systems support team that really pays attention to these things, and to be fair my guys at VLSCI are ace at this, there will be some crappy little thing that has not been properly 64-bit-ized and at link time everything will fail.

All that said, let me make some comments about parallelism at various levels. At the most fine-grained, as long as you are not somehow (in your environment, or in the Dalton runscript) setting the number of threads (both OMP and MKL) to less than your core count, the library routines should take care of threading and you should, for computational steps that exercise e.g. matrix operations, see the appropriate speed-up. Note that the Intel libraries assume hyper-threading unless you've turned this off: it means that a quad-core platform will happily tell you it's running eight threads and show 800% CPU activity, but this is just fantasy. Something that is as CPU intensive as the sort of arithmetic done in the bowels of any quantum chemistry code will keep a CPU so busy that hyper-threading is irrelevant: a simple matrix multiply test program will show there's no speed-up beyond the number of cores. Nor should there be if the library matrix multiply has been coded right --- the vendors learned a lot from Goto's BLAS routines a long while ago in this context.

Given that you are concerned about performance you should be asking/answering a number of questions of yourself here. If you want to run very large calculations (we have run NMR chemical shifts on systems with 15,000 basis functions here at VLSCI) you should definitely be looking at LSDalton, and then as I have said in another posting it will be a matter of load-balancing as to how many MPI tasks, or Scalapack tasks, etc., you initiate, compared to the level of threading. LSDalton, unlike Dalton, handles both coarse-grained and fine-grained parallelism simultaneously, whereas Dalton uses coarse-grained (MPI) parallelism for some calculations, and fine-grained (thread-level, either library or OpenMP) for others. If you are running much smaller calculations (perhaps 500 basis functions or less), and/or you want to be able to control the symmetry of electronic states (LSDalton does not use symmetry), and/or what you want to calculate is not available in LSDalton but only in Dalton, then you will want to run the latter. And then you will need to put some effort into establishing what makes the most sense performance-wise. Do your calculations benefit most from using a (relatively) few, say, four or eight threads, on a single CPU? Or is the MPI parallelism available for, e.g., wave function and response calculation at some levels adequate/best for your needs?

There is no simple answer! But if you are telling the forum that Dalton does not see the speed-up that other codes do, then your installation is faulty or you are monitoring parts of the calculation that cannot be threaded/parallelized, like reading the input file. If you have installed the code so that it uses the Intel MKL libraries, and you are not doing anything (either implicitly through your environment or explicitly, say within the Dalton runscript) to limit the number of threads created at runtime, you should see Dalton, when it goes into segments that do (say) matrix multiplication, use as many threads as cores or, with hyper-threading, as many pseudo-cores as the machine thinks it has.

A final note. At the end of the day, the issue is not how many threads, or how many teraflops. It is "how long does it take me to get the answer to my question?", and "is the answer right?". We're pretty confident with both Dalton and LSDalton that the answer to the latter question is "yes", and to me this is the far more important question!

Best regards
Pete

keyares

Re: Make error [lslib_tester.x] Error 1, [CMakeFiles/lslib_t

Post by keyares » 18 Mar 2015, 12:15

Dear Pete and radovan
Thank you very much for your replies.
I think I can use lsdalton compiled with OpenMP, because I have no requirement on symmetry for now.

All best
Wen-Xuan Wang

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