HI All;
I have read through the archives and followed the instructions posted for
compiling Amber10 on Mac running Snow Leopard (10.6) using gcc/gfortran,
but am running into an undefined symbols error when compiling just the
serial version of Amber10 (ambertools 1.4 and 1.3 compiled just fine).
The results of gcc -v are:
gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin10/4.5.0/lto-w
rapper
Target: x86_64-apple-darwin10
Configured with: ../gcc-4.5-20100107/configure --enable-languages=fortran
--host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10 : (reconfigured)
../gcc-4.5-20100107/configure --enable-languages=fortran,c++
--host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10
Thread model: posix
gcc version 4.5.0 20100107 (experimental) (GCC)
The results of gfortran v are:
gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin10/4.5.0/lto-w
rapper
Target: x86_64-apple-darwin10
Configured with: ../gcc-4.5-20100107/configure --enable-languages=fortran
--host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10 : (reconfigured)
../gcc-4.5-20100107/configure --enable-languages=fortran,c++
--host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10
Thread model: posix
gcc version 4.5.0 20100107 (experimental) (GCC)
When compiling amber 10, it dies during the make of sander, and I get the
following:
.
.
.
mv libdivcon.a ../src/qmmm/
gfortran -ffree-form -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 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 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 softcore.o
molecule.o xref.o dssp.o qm_mm.o qm_link_atoms.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_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 \
/usr/local/lib/amber11/lib/lapack.a
/usr/local/lib/amber11/lib/blas.a \
../lib/nxtsec.o ../lib/sys.a ../netcdf/lib/libnetcdf.a
Undefined symbols:
"_ambsecond_", referenced from:
_dsaupd_ in lmod.a(dsaupd.o)
_dsaupd_ in lmod.a(dsaupd.o)
_dsaup2_ in lmod.a(dsaup2.o)
_dsaup2_ in lmod.a(dsaup2.o)
_dsaup2_ in lmod.a(dsaup2.o)
.
.
.
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [sander] Error 1
make: *** [serial] Error 2
Note that I had to modify the Makefile in /sander because it was pointing to
the wrong path for lapack.a and blas.a, as when the lapack and blas
subdirectories get compiled the .a files get moves to the amber11/lib
directory.
While I have seen many posts about undefined symbols, none of them seem
quite applicable to this problem and I canšt seem to track down what the
problem is.
Thank you;
Aurora
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Received on Mon May 24 2010 - 10:30:03 PDT
