AMBER Archive (2006)

Subject: Re: AMBER: G5 OSX serial compile error

From: Mathy Froeyen (matheus.froeyen_at_rega.kuleuven.ac.be)
Date: Thu Dec 28 2006 - 05:12:13 CST

dear kevin,

these undefined symbols seem to be routines in blas.a and lapack.a.

I had similar problems on Mac OS X 10.4.? using the NAG compiler,
but other missing symbols.

A solution at that time was to include the missing routines
(lapack/zheev.o etc) explicitly in the link phase.

I was told also that this problem is related to the use of
"ar' when creating libraries.
Instead use "libtool -c" to create the library.

best regards
mathy
-------------

On Tue, 26 Dec 2006, Kevin Kelliher wrote:

>
> Hi,
>
> I have an "underscore undefined symbols" error when I try to compile Amber 9
> on
> and Xserve G5 with OSX 10.3.9 and with the IBM XLF and XLC compilers:
>
> a - ../obj/delmolcl.o
> a - ../obj/rotatecl.o
> a - ../obj/reppcl.o
> a - ../obj/initmem.o
> a - ../obj/energyqmmm.o
> a - ../obj/doscfqmmm.o
> a - ../obj/fockqmmm.o
> a - ../obj/commandqmmm.o
> a - ../obj/initmem2.o
> a - ../obj/allocateMxAtomVarsqmmm.o
> ranlib libdivcon.a
> mv libdivcon.a ../src/qmmm/
> xlf90
> -qextname=ddot:fdate:flush:lsame:dscal:dnrm2:idamax:drot:dswap:dspmv:daxpy:dspr2:dgemm:dcopy:dgemv:dtrmv:dtrmm:dger:lsame:dspev:dgeev:dspevd:dsyev:dppsv:dspsv:dlamch:dsteqr:dgeqr2:dorm2r:dlacpy:dlarnv:dlascl:dlaset:dlartg:dlanst:dlaev2:dlapy2:dlasr
> -qfree=f90 -o sander evb_vars.o evb_input.o evb_init.o evb_alloc.o
> evb_dealloc.o check_input.o evb_io.o evb_keywrd.o exchange_CM.o evb_mcp.o
> evb_force.o diabatic.o evb_2stdebug.o egap_umb_2stdebug.o exchange_gauss.o
> exchange_warshel.o morsify.o morse_anal2num.o evb_matrix.o evb_ntrfc.o
> out_evb.o constants.o stack.o qmmm_module.o trace.o lmod.o decomp.o
> icosasurf.o egb.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 mdfil.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 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
> amoeba_runmd.o bintraj.o spatial_recip.o spatial_fft.o parms.o qm_mm.o
> qm_link_atoms.o qm_nb_list.o qm_extract_coords.o qm_ewald.o qm_gb.o
> qm_zero_charges.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_module.o
> qm2_dftb_broyden.o qm2_dftb_dispersion_egr.o qm2_dftb_dispersion_params.o
> qm2_dftb_dispersionread.o qm2_dftb_eglcao.o qm2_dftb_energy.o
> qm2_dftb_ewevge.o qm2_dftb_externalchgrad.o qm2_dftb_externalshift.o
> qm2_dftb_fermi.o qm2_dftb_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_long_range.o qm2_dftb_main.o qm2_dftb_my_gradient.o
> qm2_dftb_my_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
> \
> qm_div.o force.o \
> ../lmod/lmod.a ../dcqtp/src/qmmm/libdivcon.a \
> ../lapack/lapack.a ../blas/blas.a \
> ../lib/nxtsec.o ../lib/sys.a -Wl,-framework -Wl,Accelerate
> /usr/bin/ld: Undefined symbols:
> _dsygv
> _dsymm
> _dsyevx
> _zheev
> make[1]: *** [sander] Error 1
> make: *** [serial] Error 2
>
> Am I missing something in my LOADLIB in config.h?
> Does anyone happen to know of a way around this?
>
> Thanks,
> Kevin Kelliher
>
>
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