AMBER Archive (2006)

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

From: Ross Walker (
Date: Thu May 18 2006 - 18:37:30 CDT

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 problem.
Let me know if this helps.
All the best

|\oss Walker

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From: [] 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
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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