Hi Martin,
It looks like a lot of the old object files from a serial compilation are
being used. qm_mm_div is only present in serial sander.
Try:
cd $AMBERHOME/src/
make clean
make parallel
All the best
Ross
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Martin Stennett
Sent: Friday, February 02, 2007 00:22
To: amber.scripps.edu
Subject: AMBER: Problem with paralell installation
I've managed to get a serial installation running, but having installed
OpenMPI onto my machine I get an error on compiling "make parallel"
What needs to be changed to get rid of this error?
Starting installation of Amber9 (parallel) at Thu Feb 1 15:41:30 GMT 2007.
cd sander; make parallel
make[1]: Entering directory
`/fs/socrates/disk1/stennett/ambersrc/src/sander'
./checkparconf
cd ../lib; make sys.a
make[2]: Entering directory `/fs/socrates/disk1/stennett/ambersrc/src/lib'
make[2]: `sys.a' is up to date.
make[2]: Leaving directory `/fs/socrates/disk1/stennett/ambersrc/src/lib'
cd ../lib; make nxtsec.o
make[2]: Entering directory `/fs/socrates/disk1/stennett/ambersrc/src/lib'
make[2]: `nxtsec.o' is up to date.
make[2]: Leaving directory `/fs/socrates/disk1/stennett/ambersrc/src/lib'
cd ../lapack; make
make[2]: Entering directory
`/fs/socrates/disk1/stennett/ambersrc/src/lapack'
Makefile:7: warning: overriding commands for target `.f.o'
../config.h:82: warning: ignoring old commands for target `.f.o'
ar rv lapack.a dsyev.o dsygv.o dlansy.o dsytrd.o dorgtr.o dsteqr.o dsterf.o
dlascl.o dlamch.o xerbla.o ilaenv.o dlassq.o dsytd2.o dlatrd.o dorgql.o
dorgqr.o dlasrt.o dlaset.o dlanst.o dlaev2.o dlasr.o dlapy2.o dlartg.o
dlae2.o dorg2r.o dlarft.o dlarfb.o dorg2l.o dlarfg.o dlarf.o dspev.o
dlansp.o dsptrd.o dopgtr.o dppsv.o dspsv.o dgeev.o dsptrs.o dsptrf.o
dpptrs.o dpptrf.o dgebak.o dtrevc.o dlacpy.o dhseqr.o dorghr.o dgehrd.o
dgebal.o dlange.o dlabad.o dlahqr.o dlarfx.o dlanhs.o dlaln2.o dgehd2.o
dlahrd.o dlanv2.o dladiv.o dgerq2.o dorm2r.o dlarnv.o dgeqr2.o dlaruv.o
dspevd.o dstedc.o dopmtr.o dlaed0.o dlaed1.o dlaed7.o dlaeda.o dlaed8.o
dlaed9.o dlamrg.o dlaed2.o dlaed3.o dpotrf.o dsygst.o dpotf2.o dsygs2.o
dlaebz.o dlagtf.o dlagts.o dormqr.o dormql.o dorm2l.o dlaed4.o dlaed5.o
dlaed6.o ieeeck.o dsyevx.o dsyevd.o dstebz.o dstein.o dormtr.o zheev.o
lsame.o zlanhe.o zlascl.o zhetrd.o zungtr.o zsteqr.o zlassq.o zlatrd.o
zhetd2.o zungql.o zungqr.o zlasr.o zlaset.o zlacgv.o zlarfg.o zung2l.o
zlarft.o zlarfb.o zung2r.o dlapy3.o zladiv.o zlarf.o
r - dsyev.o
r - dsygv.o
r - dlansy.o
r - dsytrd.o
r - dorgtr.o
r - dsteqr.o
r - dsterf.o
r - dlascl.o
r - dlamch.o
r - xerbla.o
r - ilaenv.o
r - dlassq.o
r - dsytd2.o
r - dlatrd.o
r - dorgql.o
r - dorgqr.o
r - dlasrt.o
r - dlaset.o
r - dlanst.o
r - dlaev2.o
r - dlasr.o
r - dlapy2.o
r - dlartg.o
r - dlae2.o
r - dorg2r.o
r - dlarft.o
r - dlarfb.o
r - dorg2l.o
r - dlarfg.o
r - dlarf.o
r - dspev.o
r - dlansp.o
r - dsptrd.o
r - dopgtr.o
r - dppsv.o
r - dspsv.o
r - dgeev.o
r - dsptrs.o
r - dsptrf.o
r - dpptrs.o
r - dpptrf.o
r - dgebak.o
r - dtrevc.o
r - dlacpy.o
r - dhseqr.o
r - dorghr.o
r - dgehrd.o
r - dgebal.o
r - dlange.o
r - dlabad.o
r - dlahqr.o
r - dlarfx.o
r - dlanhs.o
r - dlaln2.o
r - dgehd2.o
r - dlahrd.o
r - dlanv2.o
r - dladiv.o
r - dgerq2.o
r - dorm2r.o
r - dlarnv.o
r - dgeqr2.o
r - dlaruv.o
r - dspevd.o
r - dstedc.o
r - dopmtr.o
r - dlaed0.o
r - dlaed1.o
r - dlaed7.o
r - dlaeda.o
r - dlaed8.o
r - dlaed9.o
r - dlamrg.o
r - dlaed2.o
r - dlaed3.o
r - dpotrf.o
r - dsygst.o
r - dpotf2.o
r - dsygs2.o
r - dlaebz.o
r - dlagtf.o
r - dlagts.o
r - dormqr.o
r - dormql.o
r - dorm2l.o
r - dlaed4.o
r - dlaed5.o
r - dlaed6.o
r - ieeeck.o
r - dsyevx.o
r - dsyevd.o
r - dstebz.o
r - dstein.o
r - dormtr.o
r - zheev.o
r - lsame.o
r - zlanhe.o
r - zlascl.o
r - zhetrd.o
r - zungtr.o
r - zsteqr.o
r - zlassq.o
r - zlatrd.o
r - zhetd2.o
r - zungql.o
r - zungqr.o
r - zlasr.o
r - zlaset.o
r - zlacgv.o
r - zlarfg.o
r - zung2l.o
r - zlarft.o
r - zlarfb.o
r - zung2r.o
r - dlapy3.o
r - zladiv.o
r - zlarf.o
ranlib lapack.a
make[2]: Leaving directory `/fs/socrates/disk1/stennett/ambersrc/src/lapack'
cd ../blas; make
make[2]: Entering directory `/fs/socrates/disk1/stennett/ambersrc/src/blas'
Makefile:7: warning: overriding commands for target `.f.o'
../config.h:82: warning: ignoring old commands for target `.f.o'
ar rv blas.a dasum.o daxpy.o dcabs1.o dcopy.o ddot.o dgbmv.o dgemm.o dgemv.o
dger.o dnrm2.o drot.o drotg.o dsbmv.o dscal.o dspmv.o dspr.o dspr2.o dswap.o
dsymm.o dsymv.o dsyr.o dsyr2.o dsyr2k.o dsyrk.o dtbmv.o dtbsv.o dtpmv.o
dtpsv.o dtrmm.o dtrmv.o dtrsm.o dtrsv.o dummy.o dzasum.o dznrm2.o idamax.o
isamax.o lsame.o scopy.o sswap.o sscal.o sasum.o snrm2.o sdot.o ssyr2k.o
saxpy.o sgemv.o ssyr2.o ssymv.o sgemm.o strmm.o strmv.o sger.o zher2k.o
zswap.o zgemv.o zhemv.o zscal.o zdotc.o zaxpy.o zher2.o zdscal.o ztrmv.o
zcopy.o ztrmm.o zgemm.o zgerc.o
r - dasum.o
r - daxpy.o
r - dcabs1.o
r - dcopy.o
r - ddot.o
r - dgbmv.o
r - dgemm.o
r - dgemv.o
r - dger.o
r - dnrm2.o
r - drot.o
r - drotg.o
r - dsbmv.o
r - dscal.o
r - dspmv.o
r - dspr.o
r - dspr2.o
r - dswap.o
r - dsymm.o
r - dsymv.o
r - dsyr.o
r - dsyr2.o
r - dsyr2k.o
r - dsyrk.o
r - dtbmv.o
r - dtbsv.o
r - dtpmv.o
r - dtpsv.o
r - dtrmm.o
r - dtrmv.o
r - dtrsm.o
r - dtrsv.o
r - dummy.o
r - dzasum.o
r - dznrm2.o
r - idamax.o
r - isamax.o
r - lsame.o
r - scopy.o
r - sswap.o
r - sscal.o
r - sasum.o
r - snrm2.o
r - sdot.o
r - ssyr2k.o
r - saxpy.o
r - sgemv.o
r - ssyr2.o
r - ssymv.o
r - sgemm.o
r - strmm.o
r - strmv.o
r - sger.o
r - zher2k.o
r - zswap.o
r - zgemv.o
r - zhemv.o
r - zscal.o
r - zdotc.o
r - zaxpy.o
r - zher2.o
r - zdscal.o
r - ztrmv.o
r - zcopy.o
r - ztrmm.o
r - zgemm.o
r - zgerc.o
ranlib blas.a
make[2]: Leaving directory `/fs/socrates/disk1/stennett/ambersrc/src/blas'
cd ../lmod; make
make[2]: Entering directory `/fs/socrates/disk1/stennett/ambersrc/src/lmod'
cd xmin; make
make[3]: Entering directory
`/fs/socrates/disk1/stennett/ambersrc/src/lmod/xmin'
Makefile:6: warning: overriding commands for target `.f.o'
../../config.h:82: warning: ignoring old commands for target `.f.o'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory
`/fs/socrates/disk1/stennett/ambersrc/src/lmod/xmin'
cd lmod; make
make[3]: Entering directory
`/fs/socrates/disk1/stennett/ambersrc/src/lmod/lmod'
Makefile:6: warning: overriding commands for target `.f.o'
../../config.h:82: warning: ignoring old commands for target `.f.o'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory
`/fs/socrates/disk1/stennett/ambersrc/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 `/fs/socrates/disk1/stennett/ambersrc/src/lmod'
cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
g95 -ffree-form -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 -L/usr/local/lib -lmpi_f90 -lmpi -lorte
-lopal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
qm_div.o: In function `qm_div_':
_qm_div.f:(.text+0x4f0): undefined reference to `qm_mm_div_'
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/fs/socrates/disk1/stennett/ambersrc/src/sander'
make: *** [parallel] Error 2
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Received on Sun Feb 04 2007 - 06:07:55 PST
