Hello,
I tried to compile AMBER 9 on IBM P7 computer but failed. The error message is:
=======================================================================================
/bin/true blas.a
make[1]: Leaving directory `/home/yf4/APPS/AMBER9/amber9/src/blas'
cd ../lmod; make
make[1]: Entering directory `/home/yf4/APPS/AMBER9/amber9/src/lmod'
cd xmin; make
make[2]: Entering directory `/home/yf4/APPS/AMBER9/amber9/src/lmod/xmin'
Makefile:6: warning: overriding commands for target `.f.o'
../../config.h:90: warning: ignoring old commands for target `.f.o'
make[2]: Nothing to be done for `install'.
make[2]: Leaving directory `/home/yf4/APPS/AMBER9/amber9/src/lmod/xmin'
cd lmod; make
make[2]: Entering directory `/home/yf4/APPS/AMBER9/amber9/src/lmod/lmod'
Makefile:6: warning: overriding commands for target `.f.o'
../../config.h:90: warning: ignoring old commands for target `.f.o'
make[2]: Nothing to be done for `install'.
make[2]: Leaving directory `/home/yf4/APPS/AMBER9/amber9/src/lmod/lmod'
ar rvs lmod.a xmin/*.o lmod/*.o
r - xmin/xmin.o
r - lmod/lmod.o
/bin/true lmod.a
make[1]: Leaving directory `/home/yf4/APPS/AMBER9/amber9/src/lmod'
cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
./checkparconf
/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.
Would you help me to figure out the problem?
Thanks,
Yubo Fan
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Received on Mon Mar 26 2012 - 12:00:03 PDT
