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

From: Hall, Spencer <>
Date: Tue, 23 May 2006 14:15:08 -0700

Hi Ross,
I tried the "-static" option and still it gives the "undefined reference
to `mpi_conversion_fn_null_''. I also tried a freash install with that
option and still it did not work.
I did finally get it to work, but I had to switch to Openmpi using the
--with-devel-headers option when it was configured since without it
fails in several places in compiling Amber parallel.

 -----Original Message-----
From: [] On Behalf
Of Ross Walker
Sent: Thursday, May 18, 2006 4:38 PM
Subject: RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64

        Hi Spencer.
        Can you try ./configure -mpich2 -static g95
        I.e. get the linker to link statically. It seems that there are
no .so files built when you compile MPICH2 and so this may be the
        Let me know if this helps.
        All the best

        |\oss Walker
        | HPC Consultant and Staff Scientist |
        | San Diego Supercomputer Center |
        | Tel: +1 858 822 0854 | EMail:- |
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[] On Behalf Of Hall, Spencer
                Sent: Thursday, May 18, 2006 15:44
                Subject: AMBER: Compiling parallel Amber 9 on Red-Hat
Enterprise 64 problem

                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
                cd $AMBERHOME/src
                ./configure -mpich2 g95
                make parallel
                I get:
                make[3]: Leaving directory
                cd lmod; make
                make[3]: Entering directory
                Makefile:6: warning: overriding commands for target
                ../../config.h:82: warning: ignoring old commands for
target `.f.o'
                cpp -traditional
-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
                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
                cd ../lmod; cp lmodprmtop ../../exe; chmod 0755
                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
                evb_io.o(.data+0x458): undefined reference to
                qmmm_module.o(.data+0x578): undefined reference to
                egb.o(.data+0x20e8): undefined reference to
                egb.o(.data+0x2558): undefined reference to
                multisander.o(.data+0x458): more undefined references to
`mpi_conversion_fn_null_' follow
                make[1]: *** [sander.MPI] Error 1
                make[1]: Leaving directory
                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 Wed May 24 2006 - 06:07:16 PDT
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