AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem

From: Hall, Spencer <>
Date: Thu, 18 May 2006 15:44:14 -0700

Dear All,

I am able to compile the serial version of the Amber programs with no problem. I am running Red-Hat Enterprise-4 64, and i am using g95 for compilation. I compiled the mpich2 latest source with:

./configure --prefix=/projects/Biogroup/MPICH/mpich2.103 F90=g95 FC=g95 CC=gcc
make install

the env. variable MPI_HOME is set correctly as are the libraries and binaries in the correct paths. When I compile Amber 9 with:
./configure -mpich2 g95
make parallel

I get:
make[3]: Leaving directory `/projects/Biogroup/AMBER/amber9/src/lmod/xmin'
cd lmod; make
make[3]: Entering directory `/projects/Biogroup/AMBER/amber9/src/lmod/lmod'
Makefile:6: warning: overriding commands for target `.f.o'
../../config.h:82: warning: ignoring old commands for target `.f.o'
cpp -traditional -I/projects/Biogroup/MPICH/current/include -L/projects/Biogroup/MPICH/current/lib -P -DMPI -xassembler-with-cpp lmod.f > _lmod.f
g95 -c -O3 -fno-second-underscore -march=nocona -o lmod.o _lmod.f
make[3]: Leaving directory `/projects/Biogroup/AMBER/amber9/src/lmod/lmod'
ar rv lmod.a xmin/*.o lmod/*.o
ar: creating lmod.a
a - xmin/xmin.o
a - lmod/lmod.o
ranlib lmod.a
make[2]: Leaving directory `/projects/Biogroup/AMBER/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/projects/Biogroup/MPICH/mpich2.103/lib -lmpichf90 -lmpichf90 -lmpich -lpthread -lrt -lfmpich
evb_init.o(.data+0x458): undefined reference to `mpi_conversion_fn_null_'
evb_io.o(.data+0x458): undefined reference to `mpi_conversion_fn_null_'
qmmm_module.o(.data+0x578): undefined reference to `mpi_conversion_fn_null_'
egb.o(.data+0x20e8): undefined reference to `mpi_conversion_fn_null_'
egb.o(.data+0x2558): undefined reference to `mpi_conversion_fn_null_'
multisander.o(.data+0x458): more undefined references to `mpi_conversion_fn_null_' follow
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/projects/Biogroup/AMBER/amber9/src/sander'
make: *** [parallel] Error 2

The error seems to be a missing library header file for "mpi_conversion_fn_null_" which I can find matches in the libraries:
I find no matches in the include files. The above libraries are listed in the config.h file under the LOADLIB variable.

What am i missing to get this to compile? Do I need to compile the mpich2 libraries differently?

Thanks for any help or suggestions!

"EMF <COH.ORG>" made the following annotations.
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Received on Sun May 21 2006 - 06:07:09 PDT
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