AMBER Archive (2006)

Subject: Re: AMBER: amber9 parralel compiling

From: Nikola Trbovic (nt2146_at_columbia.edu)
Date: Thu Nov 30 2006 - 11:06:12 CST

Here's the output for the failing step and some warnings before it.
Before that everything seems to be running fine:

cd ../lmod; make
make[2]: Entering directory `/usr/local/amber9/src/lmod'
cd xmin; make
make[3]: Entering directory `/usr/local/amber9/src/lmod/xmin'
Makefile:6: warning: overriding commands for target `.f.o'
../../config.h:82: warning: ignoring old commands for target `.f.o'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/local/amber9/src/lmod/xmin'
cd lmod; make
make[3]: Entering directory `/usr/local/amber9/src/lmod/lmod'
Makefile:6: warning: overriding commands for target `.f.o'
../../config.h:82: warning: ignoring old commands for target `.f.o'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/local/amber9/src/lmod/lmod'
ar rv lmod.a xmin/*.o lmod/*.o
r - xmin/xmin.o
r - lmod/lmod.o
ranlib lmod.a
make[2]: Leaving directory `/usr/local/amber9/src/lmod'
cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
g95 -ffree-form -o sander.MPI evb_vars.o evb_input.o evb_init.o
evb_alloc.o evb_dealloc.o check_input.o evb_io.o evb_keywrd.o
exchange_CM.o evb_mcp.o evb_force.o diabatic.o evb_2stdebug.o
egap_umb_2stdebug.o exchange_gauss.o exchange_warshel.o morsify.o
morse_anal2num.o evb_matrix.o evb_ntrfc.o out_evb.o constants.o stack.o
qmmm_module.o trace.o lmod.o decomp.o icosasurf.o egb.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 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 qm_mm.o qm_link_atoms.o qm_nb_list.o qm_extract_coords.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_module.o qm2_dftb_broyden.o
qm2_dftb_dispersion_egr.o qm2_dftb_dispersion_params.o
qm2_dftb_dispersionread.o qm2_dftb_eglcao.o qm2_dftb_energy.o
qm2_dftb_ewevge.o qm2_dftb_externalchgrad.o qm2_dftb_externalshift.o
qm2_dftb_fermi.o qm2_dftb_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_long_range.o qm2_dftb_main.o qm2_dftb_my_gradient.o
qm2_dftb_my_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 \
                   qm_div.o force.o \
        ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
        ../lib/nxtsec.o ../lib/sys.a -L/usr/local/lam_amber/lib -
L/usr/local/lam_amber/lib -llamf77mpi -lmpi -llam -lutil -ldl -lpthread
evb_init.o(.text+0x4f7): In function `evb_init_':
: undefined reference to `mpi_bcast_'
evb_init.o(.text+0x549): In function `evb_init_':
: undefined reference to `mpi_bcast_'
evb_init.o(.text+0xb31): In function `evb_init_':
: undefined reference to `mpi_bcast_'
evb_init.o(.text+0xbca): In function `evb_init_':
: undefined reference to `mpi_bcast_'
evb_init.o(.text+0xc81): In function `evb_init_':
: undefined reference to `mpi_bcast_'
evb_init.o(.text+0xcfe): more undefined references to `mpi_bcast_'
follow
evb_init.o(.data+0x840): undefined reference to `mpi_comm_dup_fn_'
evb_init.o(.data+0x848): undefined reference to
`mpi_comm_null_delete_fn_'
evb_init.o(.data+0x850): undefined reference to `mpi_comm_null_copy_fn_'
evb_init.o(.data+0x858): undefined reference to `mpi_dup_fn_'
evb_init.o(.data+0x860): undefined reference to `mpi_null_delete_fn_'
evb_init.o(.data+0x868): undefined reference to `mpi_null_copy_fn_'
evb_init.o(.data+0x870): undefined reference to `mpi_type_null_copy_fn_'
evb_init.o(.data+0x878): undefined reference to
`mpi_type_null_delete_fn_'
evb_init.o(.data+0x880): undefined reference to `mpi_win_dup_fn_'
evb_init.o(.data+0x888): undefined reference to
`mpi_win_null_delete_fn_'
... many more undefined references. It concludes with:
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/usr/local/amber9/src/sander'
make: *** [parallel] Error 2

Thanks a lot!

On Thu, 2006-11-30 at 08:50 -0800, David A. Case wrote:
> On Thu, Nov 30, 2006, Nikola Trbovic wrote:
> >
> > qm2_scf.o(.text+0x4e0): In function `qm2_scf_':
> > : undefined reference to `mpi_allreduce_'
>
> You generally *do* need to compile your mpi version with the same compiler
> you are using for Amber, but my understanding is that you did that.
>
> Can you post the complete output for the final step that failed? This is
> essentially the link step. (Easy way is to do "make sander.MPI" twice,
> and save the output from the second run. The first run will have done all
> the compiles, and the second should just try to link).
>
> ...thanks...dac
>
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