Hi,
I think this might be related to use of the '-static' flag during
configuration. Your openmpi distribution may have been built without
static libraries (which is not uncommon). Try configuring without
'-static' and see if that works for you.
-Dan
On Fri, Feb 3, 2012 at 11:03 AM, Yubo Fan <pengpengtadie.gmail.com> wrote:
> Hello,
>
> I tried to compile Amber 9 on a cluster. Intel 10.1 and openmpi 1.2.1
> were used. The config.h is:
> #==============================================================================
> # AMBER Makefile configuration for compiler/architecture: ifort_x86_64
> # Generated via command: ./configure -openmpi -bintraj -static ifort_x86_64
> #
> # Configuration script written mainly by Joe Krahn, Scott Brozell, and
> # Dave Case, with contributions from lots of people.
> #==============================================================================
>
> #------------------------------------------------------------------------------
> # Main AMBER source root directory
> #------------------------------------------------------------------------------
> AMBER_SRC=/share/home/01879/qxshao/amber9/src
>
> #------------------------------------------------------------------------------
> # AMBERBUILDFLAGS provides a hook into the build process for installers;
> # for example, to build debug versions of the amber programs
> # make -e AMBERBUILDFLAGS="-DDEBUG -g"
> #------------------------------------------------------------------------------
> AMBERBUILDFLAGS=
>
> #------------------------------------------------------------------------------
> # LOCALFLAGS is intended for program specific modifications to the
> # Fortran build process and may be modified by the program's local makefile
> #------------------------------------------------------------------------------
> LOCALFLAGS=
>
> #------------------------------------------------------------------------------
> # Availability and method of delivery of math and optional libraries
> #------------------------------------------------------------------------------
> USE_BLASLIB=$(VENDOR_SUPPLIED)
> USE_LAPACKLIB=$(VENDOR_SUPPLIED)
> USE_LMODLIB=$(LMOD_UNAVAILABLE)
>
> #------------------------------------------------------------------------------
> # C compiler
> #------------------------------------------------------------------------------
> CC= gcc
> CPLUSPLUS=g++
> CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2
> CPPFLAGS= -DBINTRAJ -I../netcdf/include $(AMBERBUILDFLAGS)
>
> #------------------------------------------------------------------------------
> # Fortran preprocessing and compiler.
> # FPPFLAGS holds the main Fortran options, such as whether MPI is used.
> #------------------------------------------------------------------------------
> FPPFLAGS= -I/opt/apps/intel10_1/openmpi/1.2.4/include -P -DMPI -DMKL
> -DBINTRAJ $(AMBERBUILDFLAGS)
> FPP= cpp -traditional $(FPPFLAGS)
> FC= mpif90
> FFLAGS= -w95 -mp1 -O0 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> FOPTFLAGS= -w95 -mp1 -ip -O3 -tpp7 -axWP $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> FREEFORMAT_FLAG= -FR
>
> #------------------------------------------------------------------------------
> # Loader:
> #------------------------------------------------------------------------------
> LOAD= mpif90 -static $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> LOADCC= gcc -static $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> LOADLIB= -L/opt/apps/intel10_1/openmpi/1.2.4/lib -lmpi_f90 -lmpi_f77
> -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil
> /opt/apps/intel/mkl/10.0.1.014/lib/em64t/libmkl_lapack.a
> /opt/apps/intel/mkl/10.0.1.014/lib/em64t/lib
> mkl_em64t.a -L/opt/apps/intel/mkl/10.0.1.014/lib/em64t -lguide -lpthread
> LM= -lm
> LOADPTRAJ= mpif90 -static -nofor_main $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> XHOME= /usr/X11R6
> XLIBS= -L/usr/X11R6/lib64 -L/usr/X11R6/lib
>
> #------------------------------------------------------------------------------
> # Other stuff:
> #------------------------------------------------------------------------------
> .SUFFIXES: .f90
> EMPTY=
> AR=ar rv $(EMPTY)
> M4=m4
> RANLIB=ranlib
> SFX=
> NETCDF=netcdf.mod
> NETCDFLIB=../netcdf/lib/libnetcdf.a
> MODULEDIR=-I
> MAKEDEPEND=$(AMBER_SRC)/../bin/amber_makedepend
> SLKO=skipDFTB
>
> # default rules for Fortran and C compilation:
>
> .f.o: $<
> $(FPP) $< > _$<
> $(FC) -c $(FFLAGS) -o $. _$<
>
> .c.o:
> $(CC) -c $(CFLAGS) $(CPPFLAGS) -o $. $<
>
> ==================================================================================
>
> The compiling (make parallel) failed with error message:
>
>
> cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
> mpif90 -static -FR -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 ../netcdf/lib/libnetcdf.a
> -L/opt/apps/intel10_1/openmpi/1.2.4/lib -lmpi_f90 -lmpi_f77 -lmpi
> -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil
> /opt/apps/intel/mkl/10.0.1.014/lib/em64t/libmkl_lapack.a
> /opt/apps/intel/mkl/10.0.1.014/lib/em64t/libmkl_em64t.a
> -L/opt/apps/intel/mkl/10.0.1.014/lib/em64t -lguide -lpthread
> ld: cannot find -lmpi_f90
> make[1]: *** [sander.MPI] Error 1
> make[1]: Leaving directory `/share/home/01879/qxshao/amber9/src/sander'
> make: *** [parallel] Error 2
>
> ===============================================================
>
> Help needed.
>
> Thanks,
> Yubo
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Fri Feb 03 2012 - 10:30:02 PST
