AMBER Archive (2009)

Subject: [AMBER] Compiling amber 9 with openMPI

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Tue Jun 23 2009 - 08:31:58 CDT

Dear Amber users,

I am not able to compile Amber9 with intel openmpi (with and without intel
MKL)on linux cluster.
Please take a look, and give me a hand.

The followings are the configuration options I used.

./configure -openmpi -static -bintraj ifort_x86_64

I modified the config.h like the following.

# C compiler
#------------------------------------------------------------------------------
CC= mpicc
CPLUSPLUS=mpic++
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/usr/mpi/intel/openmpi//include -P -DMPI -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= mpicc -static $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB= -L/usr/ofed/lib -L/opt/torque/lib64 -Wl,--rpath
-Wl,/opt/torque/lib64 -L/usr/mpi/intel/openmpi-1.2.6/lib64 -lmpi_f90
-lmpi_f77 -lmpi -lopen-rte -lopen-pal -libverbs -lrt -ltorque -ldl
-Wl,--export-dynamic -lnsl -lutil
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 following is the last part of the error.

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/usr/ofed/lib -L/opt/torque/lib64 -Wl,--rpath -Wl,/opt/torque/lib64
-L/usr/mpi/intel/openmpi-1.2.6/lib64 -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte
-lopen-pal -libverbs -lrt -ltorque -ldl -Wl,--export-dynamic -lnsl -lutil
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(dlopen.o): In function
`vm_open':
(.text+0x79): warning: Using 'dlopen' in statically linked applications
requires at runtime the shared libraries from the glibc version used for
linking
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-rte.a(sys_info.o): In function
`orte_sys_info':
(.text+0x21c): warning: Using 'getpwuid' in statically linked applications
requires at runtime the shared libraries from the glibc version used for
linking
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(if.o): In function
`opal_ifislocal':
(.text+0xd): warning: Using 'gethostbyname' in statically linked
applications requires at runtime the shared libraries from the glibc version
used for linking
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `__malloc_check_init':
(.text+0x1060): multiple definition of `__malloc_check_init'
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o):(.text+0x5d38):
first defined here
ld: Warning: size of symbol `__malloc_check_init' changed from 144 in
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o) to 105 in
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `_int_free':
(.text+0x2230): multiple definition of `_int_free'
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o):(.text+0x2398):
first defined here
ld: Warning: size of symbol `_int_free' changed from 1192 in
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o) to 2080 in
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `_int_malloc':
(.text+0x2a50): multiple definition of `_int_malloc'
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o):(.text+0xdc8):
first defined here
ld: Warning: size of symbol `_int_malloc' changed from 4806 in
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o) to 3754 in
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `_int_memalign':
(.text+0x3900): multiple definition of `_int_memalign'
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o):(.text+0x724):
first defined here
ld: Warning: size of symbol `_int_memalign' changed from 494 in
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o) to 550 in
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `_int_valloc':
(.text+0x3c30): multiple definition of `_int_valloc'
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o):(.text+0x3e68):
first defined here
ld: Warning: size of symbol `_int_valloc' changed from 416 in
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o) to 62 in
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `_int_realloc':
(.text+0x3d80): multiple definition of `_int_realloc'
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o):(.text+0x208e):
first defined here
ld: Warning: size of symbol `_int_realloc' changed from 778 in
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o) to 1411 in
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `free':
(.text+0x5f20): multiple definition of `free'
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o):(.text+0xb58):
first defined here
ld: Warning: size of symbol `free' changed from 270 in
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o) to 454 in
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `malloc':
(.text+0x4690): multiple definition of `malloc'
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o):(.text+0xc66):
first defined here
ld: Warning: size of symbol `malloc' changed from 354 in
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o) to 466 in
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `realloc':
(.text+0x60f0): multiple definition of `realloc'
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o):(.text+0x96e):
first defined here
ld: Warning: size of symbol `realloc' changed from 490 in
/usr/mpi/intel/openmpi-1.2.6/lib64/libopen-pal.a(lt1-malloc.o) to 1184 in
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libc.a(malloc.o)
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory
`/panfs/storage.local/other/scratch-myunggi/amber-openmpi-old/src/sander'
make: *** [parallel] Error 2 

-- 
Best wishes,

Myunggi Yi
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334

http://sites.google.com/site/myunggi/
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