Hi, Ambers,
I am trying to compile parallel Amber 11 on snow leopard (10.6.4) with gcc/gfortran, and got duplicate symbol error as in the subject (full error message at the end of the email), wondering if some one can give some advices. Thanks in advance!
Here is the information first:
I am using gcc/gfortran 4.5.0, mpich2-mx (Myrinet modified version of MPICH2), the AmberTool and Amber serial version all compiled and tested just fine. No errors. I did "make clean" before "make parallel".
$which mpif90
/common2/SL_upgrade/mpich2-mx/bin/mpif90
$mpif90 -show
gfortran -fno-underscoring -O -L/opt/mx/lib64 -L/opt/mx/lib -I/common2/SL_upgrade/mpich2-mx/include -I/common2/SL_upgrade/mpich2-mx/include -L/common2/SL_upgrade/mpich2-mx/lib -L/common2/SL_upgrade/mpich2-mx/lib -lmpichf90 -lmpichf90 -lpmpich -lmpich -lopa -lmyriexpress
...
....
ranlib arpack.a
mv arpack.a /common2/SL_upgrade/SRC-4-SL_UPGRADE/AMBER/v11/amber11/lib
mpif90 -o sander.MPI 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 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 mod_vdw.o evb_ntrfc.o evb_f
orce.o out_evb.o dbonds_anal2num.o bond_anal2num.o evb_umb.o evb_umb_primitive.o force.o \
/common2/SL_upgrade/SRC-4-SL_UPGRADE/AMBER/v11/amber11/lib/libsqm.a /common2/SL_upgrade/SRC-4-SL_UPGRADE/AMBER/v11/amber11/lib/libFpbsa.a /common2/SL_upgrade/SRC-4-SL_UPGRADE/AMBER/v11/amber11/lib/arpack.a /common2/SL_upgrade/SRC-4-SL_UPGRADE/AMBER/v11/amber11/lib/lapack.a /common2/SL_upgrade/SRC-4-SL_UPGRADE/AMBER/v11/amber11/lib/blas.a \
../lib/nxtsec.o ../lib/sys.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 ../netcdf/lib/libnetcdf.a
ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
collect2: ld returned 1 exit status
make[1]: *** [sander.MPI] Error 1
make: *** [parallel] Error 2
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Received on Wed Jun 30 2010 - 20:30:05 PDT
