Hi Dan,
I assume you're using AT 1.5 - just to check, did you run
AT15_Amber11.py after configure?
-Dan
On Tue, Jul 12, 2011 at 7:35 AM, Daniel Sindhikara <sindhikara.gmail.com> wrote:
> Hello.
> I am trying to run AMBER11 on a mac. I have been using Ambertools
> successfully, but when I try to make serial in the $AMBERHOME/src/ directory
> I get some undefined symbols when trying to make sander (from command sudo
> make serial).
> My system is running Mac OSX10.6.8. I configured using ./configure
> -macAccelerate gnu
>
> Anyone run into this issue?
>
>
> Here is the start of the errors:
> gfortran-mp-4.5 -o sander constants.o state.o memory_module.o stack.o
> nose_hoover.o nose_hoover_vars.o nose_hoover_init.o qmmm_module.o trace.o
> lmod.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o egb.o remd.o findmask.o
> relax_mat.o nmr.o multitmd.o multisander.o sander.o trajene.o cshf.o
> nmrcal.o mtmdcall.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 csa.o rfree.o rgroup.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 constantph.o
> prn_dipoles.o ips.o sglds.o iwrap2.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 softcore.o mbar.o molecule.o
> xref.o dssp.o charmm.o qm_mm.o qm_ewald.o qm2_variable_solvent.o
> qmmm_qmtheorymodule.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 force.o /usr/local/amber11/lib/libsqm.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-cv-LCOD.o ncsu-cv-COS_OF_DIHEDRAL.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 \
> /usr/local/amber11/lib/libFpbsa.a /usr/local/amber11/lib/arpack.a
> -framework Accelerate ../../AmberTools/src/lib/nxtsec.o \
> ../../AmberTools/src/lib/sys.a /usr/local/amber11/lib/libnetcdf.a
> Undefined symbols:
> "_nf_put_varm_real_", referenced from:
> ___netcdf_MOD_nf90_put_var_7d_fourbytereal in libnetcdf.a(netcdf.o)
> ___netcdf_MOD_nf90_put_var_6d_fourbytereal in libnetcdf.a(netcdf.o)
> ___netcdf_MOD_nf90_put_var_5d_fourbytereal in libnetcdf.a(netcdf.o)
> ___netcdf_MOD_nf90_put_var_4d_fourbytereal in libnetcdf.a(netcdf.o)
> ___netcdf_MOD_nf90_put_var_3d_fourbytereal in libnetcdf.a(netcdf.o)
> ___netcdf_MOD_nf90_put_var_2d_fourbytereal in libnetcdf.a(netcdf.o)
> ___netcdf_MOD_nf90_put_var_1d_fourbytereal in libnetcdf.a(netcdf.o)
> "_nf_delete_", referenced from:
>
>
> --
> Dr. Daniel J. Sindhikara
> Institute for Molecular Science
> E-mail: sindhikara.gmail.com
> Website: http://sites.google.com/site/dansindhikara/
> --
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>
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Received on Tue Jul 12 2011 - 05:30:03 PDT
