AMBER Archive (2006)

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

From: Michael Crowley (
Date: Mon May 22 2006 - 13:28:58 CDT

Be careful with the fortran compiler designation in the configure of mpich2.
As far as I can tell, you do not use the FC=g95 as a configure argument, it
will ignore it. Read the install manual, I think it is in a part that tells
the differences between MPICH and MPICH2. It specifies that you need to set
environment variables instead, before running configure

setenv FC g95

I send this just in case it has not been noted already and in case it does
make a difference to the trouble you are having.

On Thursday 18 May 2006 15:44, Hall, Spencer wrote:
> 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: cd
> ./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:
> libfmpich.a
> libmpich.a
> libmpichf90.a
> 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!
> -Spencer
> "EMF <COH.ORG>" made the following annotations.
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Physical mail:   Dr. Michael F. Crowley
                 Department of Molecular Biology, TPC6
                 The Scripps Research Institute
                 10550 North Torrey Pines Road
                 La Jolla, California 92037

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