AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error

From: Yu Chen <>
Date: Wed, 23 Apr 2008 14:03:13 -0400 (EDT)


I made some progress on Intel compilers with version 10(seems can't use
64bit compiler with AmberTools). But got stuck with some "Undefined
symbols, "_ts_module_mp_boptts_", referenced from:
       _ts_module_mp_boptts_$non_lazy_ptr in libdivcon.a" ... problems

Here is the details, thanks in advance for any helps:

#1. versions of the compilers:
icc -V:
Intel(R) C Compiler for applications running on IA-32, Version 10.1
Build 20080312 Package ID: m_cc_p_10.1.014
g77 -V: (I made g77 a link to ifort)
Intel(R) Fortran Compiler for applications running on IA-32, Version 10.1
Build 20080312 Package ID: m_fc_p_10.1.014

# configure/test AmberTools
./configure_at icc
   (the generated config.h file is attached as text file)
"make -f Makefile_at" finished compiling.
"make -f Makefile_at test" in test/ directory which passed all except c60

# configure/compile Amber10
./configure_amber ifort_macosx
   Despite the following outputs, it succeeded.
   Configuring netcdf; (may be time-consuming)
  rm: conftest.dSYM: is a directory
  ./configure: line 22335: type: -m32: not found
   NETCDF configure succeeded.
then I edit the config_amber.h file replace the gcc with icc and g++ with
icpc (config_amber.h is attached too)

./make serial
  lots of outputs, here is the relevent outputs:
  ar: creating archive libdivcon.a
  a - ../obj/chgRdKeys.o
  a - ../obj/ioRdKeys.o
  a - ../obj/pbsolver_qmmm.o
  a - ../obj/allocateScrfVars_qmmm.o
  ranlib libdivcon.a
  mv libdivcon.a ../src/qmmm/
  ifort -FR -o sander constants.o nose_hoover.o nose_hoover_vars.o
  nose_hoover_init.o stack.o qmmm_module.o qm2_dftb_module.o trace.o lmod.o
  decomp.o icosasurf.o egb.o remd.o findmask.o pb_force.o pb_exmol.o
  pb_mpfrc.o pb_direct.o pb_list.o np_force.o sa_driver.o relax_mat.o nmr.o
  multisander.o sander.o trajene.o cshf.o nmrcal.o pearsn.o printe.o
  runmin.o rdparm.o mdread.o locmem.o runmd.o getcor.o degcnt.o decnvh.o
  fastwt.o parallel.o shake.o ene.o mdwrit.o minrit.o set.o dynlib.o
  nmlsrc.o ew_force.o ew_setup.o ew_box.o ew_bspline.o ew_fft.o
  nonbond_list.o short_ene.o ew_recip.o pcshift.o align.o csa.o rfree.o
  rgroup.o random.o amopen.o debug.o ew_recip_reg.o ew_handle_dips.o
  ew_dipole_recip.o mexit.o new_time.o extra_pts.o thermo_int.o matinv.o
  assert.o mmtsb.o mmtsb_client.o erfcfun.o veclib.o is_init.o constantph.o
  prn_dipoles.o ips.o sglds.o amoeba_valence.o amoeba_multipoles.o
  amoeba_recip.o amoeba_interface.o amoeba_direct.o amoeba_mdin.o
  amoeba_adjust.o amoeba_self.o amoeba_vdw.o amoeba_induced.o
  bintraj.o spatial_recip.o spatial_fft.o parms.o softcore.o molecule.o
  xref.o dssp.o qm_mm.o qm_link_atoms.o qm_ewald.o qm_gb.o
  qm_print_info.o qm_assign_atom_types.o qm2_allocate_e_repul.o
  qm2_calc_charges.o qm2_calc_rij_and_eqns.o qm2_dihed.o qm2_energy.o
  qm2_fock.o qm2_get_qm_forces.o qm2_get_qmmm_forces.o qm2_h1elec.o
  qm2_hcore_qmqm.o qm2_hcore_qmmm.o qm2_identify_peptide_links.o
  qm2_load_params_and_allocate.o qm2_repp.o qm2_rotate_qmqm.o qm2_scf.o
  qm2_setup_orb_exp.o qm2_smallest_number.o qm2_dftb_broyden.o
  qm2_dftb_dispersion_egr.o qm2_dftb_dispersion_params.o
  qm2_dftb_dispersionread.o qm2_dftb_scf.o qm2_dftb_energy.o
  qm2_dftb_ewevge.o qm2_dftb_externalshift.o qm2_dftb_fermi.o
  qm2_dftb_get_qm_forces.o qm2_dftb_gamma.o qm2_dftb_gammamat.o
  qm2_dftb_get_qmmm_forces.o qm2_dftb_gettab.o qm2_dftb_load_params.o
  qm2_dftb_mulliken.o qm2_dftb_repulsiv.o qm2_dftb_self.o qm2_dftb_shift.o
  qm2_dftb_short_range.o qm2_dftb_skpar.o qm2_dftb_slkode.o
  qm2_dftb_slktrafo.o qm2_dftb_read_cm3.o qm2_dftb_cm3.o qm2_dftb_ewald.o
  qm2_dftb_gb.o pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o
  cmd_matrix.o \
                 lscivr_vars.o lsc_init.o lsc_xp.o qm_div.o force.o \
                 ../lmod/lmod.a ../dcqtp/src/qmmm/libdivcon.a mt19937.o
  ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o
  ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-utils.o ncsu-colvar.o
  ncsu-constants.o ncsu-cv-ANGLE.o ncsu-cv-DISTANCE.o ncsu-cv-HANDEDNESS.o
  ncsu-cv-MULTI_RMSD.o ncsu-cv-N_OF_BONDS.o ncsu-cv-N_OF_STRUCTURES.o
  ncsu-cv-R_OF_GYRATION.o ncsu-cv-TORSION.o ncsu-lexer.o ncsu-parser.o
  ncsu-pmd-hooks.o ncsu-rmsd.o ncsu-sander-hooks.o ncsu-sander-proxy.o
  ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o \
                 ../lapack/lapack.a ../blas/blas.a \
                 ../lib/nxtsec.o ../lib/sys.a ../netcdf/lib/libnetcdf.a
-framework Accelerate
Undefined symbols:
   "_ts_module_mp_boptts_", referenced from:
       _ts_module_mp_boptts_$non_lazy_ptr in
       _ts_module_mp_boptts_$non_lazy_ptr in
       _ts_module_mp_boptts_$non_lazy_ptr in libdivcon.a(allocateMinVars.o)
       _ts_module_mp_boptts_$non_lazy_ptr in libdivcon.a(tsRdKeys.o)
   "_ts_module_mp_bopttsbaker_", referenced from:
       _ts_module_mp_bopttsbaker_$non_lazy_ptr in libdivcon.a(tsRdKeys.o)
   "_ts_module_mp_bopttsnr_", referenced from:
       _ts_module_mp_bopttsnr_$non_lazy_ptr in libdivcon.a(tsRdKeys.o)
   "_ts_module_mp_bopttsprfo_", referenced from:
       _ts_module_mp_bopttsprfo_$non_lazy_ptr in libdivcon.a(tsRdKeys.o)
   "_ts_module_mp_bopttsqna_", referenced from:
       _ts_module_mp_bopttsqna_$non_lazy_ptr in libdivcon.a(tsRdKeys.o)
ld: symbol(s) not found
make[1]: *** [sander] Error 1
make: *** [serial] Error 2



Yu Chen
Howard Hughes Medical Institute
Chemistry Building, Rm 182
University of Maryland at Baltimore County
1000 Hilltop Circle
Baltimore, MD 21250

phone: (410)455-1728 (primary)
         (410)455-6347 (secondary)
fax: (410)455-1174

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Received on Sun Apr 27 2008 - 06:07:17 PDT
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