Hi,
I decided to get our AMBER12 installation (OSX 10.6.8, 64 bit, intel
compilers 12.1.6, openmpi 1.5.4) up-to-date with this sequence of commands:
cd $AMBERHOME
./patch_amber.py --update-tree
./configure -macAccelerate intel
make install
make clean
./configure -macAccelerate -mpi intel
make install
These patches were applied:
AmberTools: 30-35
Amber: 14,15
Serial compiliation went without trouble. But parallel conpilation ends
with:
(...)
> mpif90 -DBINTRAJ -DMPI -FR -I../../AmberTools/src/pbsa -I../../AmberTools/src/sqm -I../../AmberTools/src/rism -I../../include -I/a/progs/simu/amber12/include -I/a/progs/simu/amber12/include -o sander.MPI file_io_dat.o constants.o state.o memory_module.o stack.o nose_hoover.o nose_hoover_vars.o nose_hoover_init.o trace.o rmsgrd.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 sander_lib.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 pr
n_dipoles.o ips.o sglds.o iwrap2.o emap.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 binrestart.o spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o linear_response.o molecule.o xref.o dssp.o charmm.o crg_reloc.o amd.o qm_mm.o qm_ewald.o qmmm_vsolv.o qm2_extern_module.o qm2_extern_adf_module.o qm2_read_adf_results.o KFReader.o ArrayList.o qm2_extern_gms_module.o qm2_extern_tc_module.o qm2_extern_gau_module.o qm2_extern_orc_module.o qm2_extern_nw_module.o qmmm_adaptive_module.o prn_qmmm_dipole.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 evb_vars.o evb_mathf.o evb_init.o evb_bcast.o evb_dealloc.o check_input.o evb_io.o evb_keywrd.o exchange_gauss.o exchange_warshel.o react_flux_init.o react_path.o react_flux.o kappa_keck.o schlegel_dg.o schlegel_full.o schlegel_diis.o schlegel_gmres.o schlegel_gbasis.o schlegel_pgbasis.o bnd_strtch.o ang_bend.o dihed_tors.o torinternal.o evb_gfchk.o bmat_inv.o bmat_grad.o unitv.o crossv.o cart2internal.o wdc_bmat.o select_coord.o schlegel_uff.o schlegel_dihed.o schlegel_angle.o schlegel_poh_uff.o schlegel_poh_irc.o schlegel_hcn_cart.o schlegel_hcn_int_irc.o schlegel_hcn_cart_irc.o evb_outoptions.o evb_2stdebug.o egap_umb_2stdebug.o dg_debug.o evb_io_debug.o bmat_debug.o bmat_inv_debug.o evb_io_debug2.o morse_anal2num.o xwarshel_anal2num.o xgauss_anal2num.o vdw_anal2num.o rcdbonds_anal2num.o rcbond_anal2num.o dg_grad_anal2num.o evb_input.o evb_alloc.o evb_matrix.o morsify.o m
od_vdw.o evb_ntrfc.o evb_force.o out_evb.o dbonds_anal2num.o bond_anal2num.o evb_umb.o evb_umb_primitive.o force.o \
> -L/a/progs/simu/amber12/lib -lsqm -lFpbsa \
> ../lib/nxtsec.o ../lib/sys.a ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o ncsu-colvar.o ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-utils.o ncsu-constants.o ncsu-cv-ANGLE.o ncsu-cv-COM_ANGLE.o ncsu-cv-COM_DISTANCE.o ncsu-cv-COM_TORSION.o ncsu-cv-COS_OF_DIHEDRAL.o ncsu-cv-DISTANCE.o ncsu-cv-HANDEDNESS.o ncsu-cv-LCOD.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-cv-PCA.o ncsu-read-pca.o ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o mt19937.o -L/a/progs/simu/amber12/lib -lnetcdf \
> -larpack -lsvml -framework Accelerate \
> -shared-intel
> Undefined symbols:
> "_netcdf_mp_nf90_def_dim_", referenced from:
> _bintraj_mp_open_binary_files_ in bintraj.o
> _bintraj_mp_open_binary_files_ in bintraj.o
> _bintraj_mp_open_nc_file_ in bintraj.o
> _bintraj_mp_open_nc_file_ in bintraj.o
> _bintraj_mp_open_nc_file_ in bintraj.o
> _bintraj_mp_open_nc_file_ in bintraj.o
> _binrestart_mp_write_nc_restart_ in binrestart.o
> _binrestart_mp_write_nc_restart_ in binrestart.o
(...)
> _ncsu_umbrella_mp_umbrella_save_ in ncsu-umbrella.o
> _ncsu_umbrella_mp_umbrella_save_ in ncsu-umbrella.o
> _ncsu_umbrella_mp_umbrella_save_ in ncsu-umbrella.o
> _ncsu_umbrella_mp_umbrella_save_ in ncsu-umbrella.o
> _mt19937_mp_check_ncrc_ in mt19937.o
> "_netcdf_mp_nf90_def_var_scalar_", referenced from:
> _binrestart_mp_write_nc_restart_ in binrestart.o
> _binrestart_mp_write_nc_restart_ in binrestart.o
> "_netcdf_mp_nf90_put_att_one_fourbyteint_", referenced from:
> _ncsu_umbrella_mp_umbrella_save_ in ncsu-umbrella.o
> _mt19937_mp_mt19937_save_ in mt19937.o
> _mt19937_mp_mt19937_save_ in mt19937.o
> ld: symbol(s) not found
> make[2]: *** [sander.MPI] Error 1
> make[1]: *** [parallel] Error 2
> make: *** [install] Error 2
I have searched around, but found no clue about what may be going on.
Any ideas?
Cheers,
--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
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Received on Tue Feb 12 2013 - 07:00:02 PST
