AMBER Archive (2006)

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

From: Hall, Spencer (SHall_at_coh.org)
Date: Tue May 23 2006 - 16:15:08 CDT

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.

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

        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
        Ross
         

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________________________________

                From: owner-amber_at_scripps.edu
[mailto:owner-amber_at_scripps.edu] On Behalf Of Hall, Spencer
                Sent: Thursday, May 18, 2006 15:44
                To: amber_at_scripps.edu
                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
with:
                cd $AMBERHOME/src
                ./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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