Re: AMBER: problem compiling Amber9 on 64-machine

From: S.Sundar Raman <>
Date: Wed, 1 Aug 2007 21:16:10 +0530

dear amber experts

I am also trying to install amber9 in amd opteron processor with pgf90
compiler. Serial version of amber9 compiled and worked fine. When I am
trying to compile the parallel version i am getting the following troubles.
First i try to install open mpi latest version. When i compiled with pgf90,
I found the following error.

make[2]: Entering directory `/usr/local/openmpi-1.2.3/ompi/mpi/f90'

/bin/sh ../../../libtool --mode=link pgf90 -I../../../ompi/include
-I../../../ompi/include -I. -I. -I../../../ompi/mpi/f90 -export-dynamic -o -rpath /usr/local/mpi/lib mpi.lo mpi_sizeof.lo
mpi_comm_spawn_multiple_f90.lo mpi_testall_f90.lo mpi_testsome_f90.lo
mpi_waitall_f90.lo mpi_waitsome_f90.lo mpi_wtick_f90.lo mpi_wtime_f90.lo
-lnsl -lutil -lm

libtool: link: pgf90 -shared -fPIC -Mnomain .libs/mpi.o .libs/mpi_sizeof.o

f90.o .libs/mpi_testall_f90.o .libs/mpi_testsome_f90.o
.libs/mpi_waitall_f90.o .libs/mpi_waitsome_f90.o .libs/mpi_wtick_f90.o
.libs/mpi_wtime_f90.o -lnsl -lutil -lm -Wl,-soname -Wl, -o

/usr/bin/ld: .libs/mpi.o: relocation R_X86_64_PC32 against `__pgio_ini' can
not be used when making a shared object; recompile with -fPIC

/usr/bin/ld: final link failed: Bad value

make[2]: *** [] Error 2

make[2]: Leaving directory `/usr/local/openmpi-1.2.3/ompi/mpi/f90'

make[1]: *** [all-recursive] Error 1

make[1]: Leaving directory `/usr/local/openmpi-1.2.3/ompi/mpi/f90'

make: *** [all] Error 2

therefore i tried to use lam,

i compiled lam with pgf90 compiler and it was compiled successfully. but
when i m trying to compile amber using lam with pgf90 i ended up with the
following error

make[3]: Leaving directory `/amber/amber9/src/lmod/lmod'
ar rv lmod.a xmin/*.o lmod/*.o
r - xmin/xmin.o
r - lmod/lmod.o
ranlib lmod.a
make[2]: Leaving directory `/amber/amber9/src/lmod'
cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
pgf90 -tp p7 -Mfree -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.oew_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
erfcfun.o veclib.o is_init.o constantph.o prn_dipoles.o ips.o
sglds.oamoeba_valence.o amoeba_multipoles.o amoeba_recip.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 -L/opt/lam/gnu/lib -L/root/test/lam-
7.1.4/build1/lib -llammpio -llamf77mpi -lmpi -llam -lutil -ldl -lpthread
/usr/bin/ld: skipping incompatible /opt/lam/gnu/lib/liblammpio.a when
searching for -llammpio
/usr/bin/ld: skipping incompatible /root/test/lam-7.1.4/build1/lib/liblammpio.a
when searching for -llammpio
/usr/bin/ld: cannot find -llammpio
make[1]: *** [sander.MPI] Error 2
make[1]: Leaving directory `/amber/amber9/src/sander'
make: *** [parallel] Error 2

I don't know how to solve this problem. Therefore I am looking for a help
from amber experts.

Thank you

Eagerly waiting for you reply
S.Sundar Raman
Chemical Lab,
ph: 044-24411830
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Aug 05 2007 - 06:07:10 PDT
Custom Search