Hi,
On Mon, Mar 26, 2012 at 01:44:03PM -0500, Yubo Fan wrote:
>
> I tried to compile AMBER 9 on IBM P7 computer but failed. The error message is:
>
> =======================================================================================
> /users/yf4/UTILS/OPENMPI/1.4.3/bin/mpif90 -qfree=f90 -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/users/yf4/UTILS/OPENMPI/1.4.3/lib -lmpi_f90 -lmpi_f77 -lmpi
> -lopen-rte -lopen-pal -libverbs -ltorque -lnuma -ldl
> -Wl,--export-dynamic -lnsl -lutil -lpthread
> /usr/bin/ld: cannot find -lrdmacm
> make: *** [sander.MPI] Error 1
> =======================================================================================
>
> The config.h is:
> =======================================================================================
> #==============================================================================
> # AMBER Makefile configuration for compiler/architecture: xlf90_suse
> # Generated via command: ./configure -openmpi -bintraj xlf90_suse
> #
> # 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=/users/yf4/APPS/AMBER9/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=$(SOURCE_COMPILED)
> USE_LAPACKLIB=$(SOURCE_COMPILED)
> USE_LMODLIB=$(LMOD_UNAVAILABLE)
>
> #------------------------------------------------------------------------------
> # C compiler
> #------------------------------------------------------------------------------
> CC= xlc
> CPLUSPLUS=xlC
> #CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2
> CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 $(AMBERBUILDFLAGS)
> #CPPFLAGS=-DCLINK_PLAIN -DBINTRAJ
> -I/users/yf4/APPS/AMBER10/NETCDF/include $(AMBERBUILDFLAGS)
> CPPFLAGS=-DCLINK_PLAIN -DBINTRAJ -I../netcdf/include $(AMBERBUILDFLAGS)
>
> #------------------------------------------------------------------------------
> # Fortran preprocessing and compiler.
> # FPPFLAGS holds the main Fortran options, such as whether MPI is used.
> #------------------------------------------------------------------------------
> FPPFLAGS= -I/users/yf4/UTILS/OPENMPI/1.4.3/include -P -DMPI
> -DCLINK_PLAIN -DXLF90 -DBINTRAJ $(AMBERBUILDFLAGS)
> #FPP= /opt/ibmcmp/xlf/8.1/exe/cpp $(FPPFLAGS)
> FPP= /opt/apps/ibm/xlf/13.1/exe/cpp $(FPPFLAGS)
> #FC= xlf90
> FC= /users/yf4/UTILS/OPENMPI/1.4.3/bin/mpif90
> FFLAGS= -qfixed -c $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> FOPTFLAGS= -qfixed -O3 -qmaxmem=-1 -qarch=auto -qtune=auto -c
> $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> FREEFORMAT_FLAG= -qfree=f90
>
> #------------------------------------------------------------------------------
> # Loader:
> #------------------------------------------------------------------------------
> #LOAD= xlf90 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> LOAD= /users/yf4/UTILS/OPENMPI/1.4.3/bin/mpif90 $(LOCALFLAGS)
> $(AMBERBUILDFLAGS)
> LOADCC= xlc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> LOADLIB= -L/users/yf4/UTILS/OPENMPI/1.4.3/lib -lmpi_f90 -lmpi_f77
> -lmpi -lopen-rte -lopen-pal -lrdmacm -libverbs -ltorque -lnuma -ldl
> -Wl,--export-dynamic -lnsl -lutil -lpthread
> LM= -lm
> LOADPTRaJ= xlf90 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> XHOME= /usr/X11R6
> XLIBS= -L/usr/X11R6/lib
>
> #------------------------------------------------------------------------------
> # Other stuff:
> #------------------------------------------------------------------------------
> .SUFFIXES: .f90
> EMPTY=
> AR=ar rvs $(EMPTY)
> M4=m4
> RANLIB=/bin/true
> SFX=
> NETCDF=netcdf.mod
> NETCDFLIB=../netcdf/lib/libnetcdf.a
> #NETCDF=/users/yf4/APPS/AMBER10/NETCDF/include/netcdf.mod
> #NETCDFLIB=/users/yf4/APPS/AMBER10/NETCDF/lib/libnetcdf.a
> MODULEDIR=-I
> MAKEDEPEND=$(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 $. $<
>
>
> =======================================================================================
>
> xlf and xlc has been loaded and OpenMPI/NetCDF have been precompiled correctly.
Are you sure about that ?
Have you tested openmpi by compiling and running something with mpif90 ?
In amber9 LOADLIB is assigned based on the output of mpif90;
so your mpif90 is the source of librdmacm:
LOADLIB= -L/users/yf4/UTILS/OPENMPI/1.4.3/lib -lmpi_f90 -lmpi_f77
-lmpi -lopen-rte -lopen-pal -lrdmacm -libverbs -ltorque -lnuma -ldl
-Wl,--export-dynamic -lnsl -lutil -lpthread
You should contact the installer of your openmpi.
See also
http://www.open-mpi.org/community/lists/users/2011/05/16454.php
scott
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Received on Mon Mar 26 2012 - 12:30:07 PDT
