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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Received on Tue Jul 12 2011 - 05:00:04 PDT
