AMBER Archive (2007)

Subject: AMBER: Problem compiling AMBER 9 on ppc64

From: Eric Shamay (eric.shamay_at_gmail.com)
Date: Tue Sep 04 2007 - 11:14:07 CDT

I'm attempting a 2nd installation of amber9 on an IBM POWER4+ system using
the xlf/xlc compiler suite (v9.1).

After running the ./configure xlf90_aix I manage to compile a great deal,
but inevitably come to the error messages (posted below).

It looks to me like a linking issue with the compiler - I'm missing the link
to some library and this should go away with the proper -L/path/to/lib or
-llibname type parameter to the compiler. Does anyone know what the issue is
with this? I've attached my config.h for the curious, as well as version
output for my compilers.

Thanks!
~Eric Shamay

17:05:34 eshamay_at_p690 (~/amber9/src) xlf90 -qversion
 IBM(R) XL Fortran Advanced Edition V9.1 for Linux(R)

17:06:02 eshamay_at_p690 (~/amber9/src) xlC -qversion
 IBM(R) XL C/C++ Advanced Edition V7.0 for Linux(R)
 Version: 07.00.0001.0001

17:06:05 eshamay_at_p690 (~/amber9/src) xlc -qversion
 IBM(R) XL C/C++ Advanced Edition V7.0 for Linux(R)
 Version: 07.00.0001.0001

---> eshamay_at_p690 (~/amber9/src) make serial
<snip>
make[2]: Leaving directory `/mnt/netapp/home/users/eshamay/amber9/src/dcqtp'

xlf90 -qfree=f90 -o sander 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
mmtsb.ommtsb_client.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_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 ../dcqtp/src/qmmm/libdivcon.a \
        ../lapack/lapack.a ../blas/blas.a \
        ../lib/nxtsec.o ../lib/sys.a -L/usr/lib -lblas
runmin.o(.text+0xa0c): In function `runmin':
: undefined reference to `ddot'
runmin.o(.text+0x12c0): In function `runmin':
: undefined reference to `ddot'
runmin.o(.text+0x166c): In function `runmin':
: undefined reference to `ddot'
runmin.o(.text+0x2104): In function `runmin':
: undefined reference to `ddot'
runmin.o(.text+0x2224): In function `runmin':
: undefined reference to `ddot'
runmin.o(.text+0x2254): more undefined references to `ddot' follow
qm2_dftb_my_mulliken.o(.text+0xab0): In function `mulliken':
: undefined reference to `dsymm'
../dcqtp/src/qmmm/libdivcon.a(lbfgs.o)(.text+0x81c): In function `lbfgs':
: undefined reference to `ddot'
../dcqtp/src/qmmm/libdivcon.a(lbfgs.o)(.text+0x860): In function `lbfgs':
: undefined reference to `ddot'
../dcqtp/src/qmmm/libdivcon.a(lbfgs.o)(.text+0xf5c): In function `lbfgs':
: undefined reference to `ddot'
../dcqtp/src/qmmm/libdivcon.a(lbfgs.o)(.text+0xfa0): In function `lbfgs':
: undefined reference to `ddot'
../dcqtp/src/qmmm/libdivcon.a(lbfgs.o)(.text+0x1194): In function `lbfgs':
: undefined reference to `ddot'
../dcqtp/src/qmmm/libdivcon.a(lbfgs.o)(.text+0x120c): In function `lbfgs':
: undefined reference to `daxpy'
../dcqtp/src/qmmm/libdivcon.a(lbfgs.o)(.text+0x13f0): In function `lbfgs':
: undefined reference to `ddot'
../dcqtp/src/qmmm/libdivcon.a(lbfgs.o)(.text+0x1460): In function `lbfgs':
: undefined reference to `daxpy'
../dcqtp/src/qmmm/libdivcon.a(lbfgs.o)(.text+0x16bc): In function `lbfgs':
: undefined reference to `ddot'
../dcqtp/src/qmmm/libdivcon.a(tsqna.o)(.text+0x2a2c): In function `tsqna':
: undefined reference to `ddot'
../dcqtp/src/qmmm/libdivcon.a(tsrfo.o)(.text+0x242c): In function `tsrfo':

<snip>

../lapack/lapack.a(zlarfb.o)(.text+0x3250): In function `zlarfb':
: undefined reference to `zgemm'
../lapack/lapack.a(zlarfb.o)(.text+0x32e0): In function `zlarfb':
: undefined reference to `ztrmm'
../lapack/lapack.a(zung2r.o)(.text+0x42c): In function `zung2r':
: undefined reference to `zscal'
../lapack/lapack.a(zlarf.o)(.text+0x10c): In function `zlarf':
: undefined reference to `zgemv'
../lapack/lapack.a(zlarf.o)(.text+0x148): In function `zlarf':
: undefined reference to `zgerc'
../lapack/lapack.a(zlarf.o)(.text+0x1f4): In function `zlarf':
: undefined reference to `zgemv'
../lapack/lapack.a(zlarf.o)(.text+0x230): In function `zlarf':
: undefined reference to `zgerc'
make[1]: *** [sander] Error 1
make[1]: Leaving directory
`/mnt/netapp/home/users/eshamay/amber9/src/sander'
make: *** [serial] Error 2 

-- 
~Eric Shamay
----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu