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
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Received on Fri Feb 03 2012 - 08:30:02 PST
