Hi,
I guess there is a problem with the configure script. After installing the
serial version, I am doing the following:
('setenv AMBERHOME /home/yildirim/amber9' was set in the serial version)
cd $AMBERHOME/src
make clean
configure -mpich ifort_ia32
make parallel
and the error I am getting is the same; namely,
make[2]: Leaving directory `/home/yildirim/amber9/src/lmod'
cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
ifort -FR -o sander evb_vars.o evb_ntrfc.o evb_input.o check_input.o
evb_io.o evb_drvr.o evb_keywrd.o exchange_CM.o evb_mcp.o evb_matrix.o
evb_force.o diabatic.o evb_2stdebug.o constants.o stack.o qmmm_module.o
trace.o lmod.o decomp.o icosasurf.o egb.o findmask.o pb_force.o
relax_mat.o nmr.o multisander.o sander.o trajene.o cshf.o nmrcal.o
pearsn.o printe.o runmin.o force.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
pb_init.o constantph.o prn_dipoles.o neb.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 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_dhc.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_helect.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 \
../lmod/lmod.a -L/home/yildirim/mpich-1.2.7_icc/lib -lfmpich2g
-lmpi ../lapack/lapack.a ../blas/blas.a \
../lib/nxtsec.o ../lib/sys.a
ld: cannot find -lfmpich2g
make[1]: *** [sander] Error 1
make[1]: Leaving directory `/home/yildirim/amber9/src/sander'
make: *** [parallel] Error 2
PS: I have installed mpich-1.2.7_icc, and tested using this ver. of MPICH.
On Tue, 29 Nov 2005, Xuebin Qiao wrote:
> Hi,
>
> It seems you try to link with MPICH2 library. Check whether you have
> installed MPICH2 not MPICH. If not, upgrade to newer version or choose
other
> configure option. Although I do not have amber9 source, I guess they
still
> support old -mpich option.
>
> best regards
>
> qxb
>
> On 11/29/05, Ilyas Yildirim < yildirim.pas.rochester.edu> wrote:
> >
> > Dear All,
> >
> > I have updated the latest code from chagall and succesfully compiled
the
> > serial version of AMBER 8. When I try to compiled the parallel
version,
> > following the 'parallel installation protocol' I am ending with an
error
> > message as follows:
> >
> > -------------------------------------------
> > cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
> > ifort -FR -o sander evb_vars.o evb_ntrfc.o evb_input.o
check_input.o
> > evb_io.o evb_drvr.o evb_keywrd.o exchange_CM.o evb_mcp.o evb_matrix.o
> > evb_force.o diabatic.o evb_2stdebug.o constants.o stack.o
qmmm_module.o
> > trace.o lmod.o decomp.o icosasurf.o egb.o findmask.o pb_force.o
> > relax_mat.o
> > nmr.o multisander.o sander.o trajene.o cshf.o nmrcal.o pearsn.o
printe.o
> > runmin.o force.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 pb_init.o constantph.o prn_dipoles.o
> > neb.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
> > 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_dhc.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_helect.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 \
> > ../lmod/lmod.a -L/usr/local/mpich/lib -lfmpich2g -lmpi
> > ../lapack/lapack.a ../blas/blas.a \
> > ../lib/nxtsec.o ../lib/sys.a
> > ld: cannot find -lfmpich2g
> > make[1]: *** [sander] Error 1
> > make[1]: Leaving directory /home/yildirim/amber9/src/sander'
> > make: *** [parallel] Error 2
> > arde00:/home/yildirim/amber9/src>
> >
> > ------------------------------------------------------
> >
> > I could install the parallel ver. before, but not anymore after I have
> > updated AMBER 9. Can someone tell me what might be the problem? I am
> > guessing that something in MPICH protocol is changed, or? Thanks.
> >
> > Best,
> >
> > --
> > Ilyas Yildirim
> > ---------------------------------------------------------------
> > - Department of Chemisty - -
> > - University of Rochester - -
> > - Hutchison Hall, # B10 - -
> > - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> > -
http://www.pas.rochester.edu/~yildirim/<
http://www.pas.rochester.edu/%7Eyi
ldirim/>
> > -
> > ---------------------------------------------------------------
> >
> >
>
>
> --
> ... there have been two really clean,
> consistent models of programming so far:
> the C model and the Lisp model.
> These two seem points of high ground,
> with swampy lowlands between them.
>
> --Paul Graham
>
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
---------------------------------------------------------------
Received on Wed Apr 05 2006 - 23:49:47 PDT
