Dear Dr. Ross Walker,
Thanks a lot for your support.
Now I have recompiled mpich with explicitly indicating
by setting "setenv FC <path>ifort" and "setenv F77
<path>ifort" and made sure that mpich uses ifort
during compilation. I also set mpirun to my new mpich
installation.
I then said: "./configure -mpich -p4 ifort_ia32" and
things go smoothly until I get a new error :(
Here are the last few-lines after "make parallel"
-------------------------------------------------------
cd ../lmod; cp lmodprmtop ../../exe; chmod 0755
../../exe/lmodprmtop
ifort -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
-L/usr/people/camm/kopposa1/mpich2-1.0.6/lib
-lmpichf90 -lmpichf90 -lmpich -lpthread -lrt -lsvml
ld: skipping incompatible
/usr/people/camm/kopposa1/mpich2-1.0.6/lib/libmpich.a
when searching for -lmpich
ld: cannot find -lmpich
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory
`/netfs/people/camm/kopposa1/amber9/src/sander'
make: *** [parallel] Error 2
---------------------------------------------------------
I dont understand why its saying :
"-L/usr/people/camm/kopposa1/mpich2-1.0.6/lib
-lmpichf90 -lmpichf90 -lmpich -lpthread -lrt -lsvml
ld: skipping incompatible"
Thanks a lot for your time.
With best regards,
Sampath.
--- Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Sampath,
>
> I suspect that when you installed mpich in your home
> directory you did not
> explicitly tell it to use the Intel ifort compiler.
> You should clean the
> mpich installation and then rebuild it telling it to
> use ifort - something
> like export FCC=ifort, F90=ifort - although you will
> need to chekc the mpich
> documentation for the correct way of doing this.
>
> Also check that you MPI_HOME and path variables are
> set to point to the
> correct mpi installation. Do:
>
> which mpirun
>
> if you get /usr/bin/mpirun or something else which
> is not your new mpich
> installation then you need to edit your path, likely
> in .bashrc/.cshrc to
> make sure the mpich bin directory precedes /usr/bin
> etc.
>
> Good luck,
>
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:-
> ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on
> request |
>
> Note: Electronic Mail is not secure, has no
> guarantee of delivery, may not
> be read every day, and should not be used for urgent
> or sensitive issues.
>
> > -----Original Message-----
> > From: owner-amber.scripps.edu
> > [mailto:owner-amber.scripps.edu] On Behalf Of
> Sampath Koppole
> > Sent: Tuesday, November 13, 2007 06:05
> > To: amber.scripps.edu
> > Subject: AMBER: Parallel Amber compilation
> problems !!
> >
> > Hello,
> > I am trying to compile Amber in parallel (after
> > successfully compiling the serial version !!). I
> have
> > tried to follow the instructions in the INSTALL
> file
> > as closely as I can.
> >
> > To give you a little background:
> >
> > I installed (successfully) MPICH-1.2.7 (in my home
> > directory) and set MPI_HOME to this directory by :
> > setenv MPI_HOME $HOME/mpich-1.2.7p1/
> >
> > I then configured with "./configure -mpich -p4
> > ifort_ia32"
> >
> > and did a "make clean" after which I ran "make
> > parallel" but this crashes very early with the
> > following:
> >
> >
>
---------------------------------------------------------
> > evb_init.o(.text+0x741): In function `evb_init_':
> > : undefined reference to `mpi_bcast_'
> > evb_init.o(.text+0x77a): In function `evb_init_':
> > : undefined reference to `mpi_bcast_'
> > evb_init.o(.text+0x107e): In function `evb_init_':
> > : undefined reference to `mpi_bcast_'
> > evb_init.o(.text+0x141f): In function `evb_init_':
> > : undefined reference to `mpi_bcast_'
> > evb_init.o(.text+0x1970): In function `evb_init_':
> > : undefined reference to `mpi_bcast_'
> > .
> > .
> > .
> > .
> > goes on ...
> > .
> > .
> > .
> > .
> > .
> > .
> > force.o(.text+0x80e3): In function `force_.A':
> > : undefined reference to `mpi_bcast_'
> > force.o(.text+0x810b): In function `force_.A':
> > : undefined reference to `mpi_bcast_'
> > force.o(.text+0x8132): In function `force_.A':
> > : undefined reference to `mpi_bcast_'
> > force.o(.text+0x8170): In function `force_.A':
> > : undefined reference to `mpi_bcast_'
> > force.o(.text+0x8198): more undefined references
> to
> > `mpi_bcast_' follow
> > make[1]: *** [sander.MPI] Error 1
> > make[1]: Leaving directory
> > `/netfs/people/camm/kopposa1/amber9/src/sander'
> > make: *** [parallel] Error 2
> >
>
------------------------------------------------------
> >
> > Is there something I have missed doing ??
> >
> > Thanks a lot for your help.
> >
> > With best regards,
> > Sampath.
> >
> >
> >
> >
> >
>
______________________________________________________________
> > ______________________
> > Be a better pen pal.
> > Text or chat with friends inside Yahoo! Mail. See
> how.
> > http://overview.mail.yahoo.com/
> >
>
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> > ---------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to
> majordomo.scripps.edu
> >
>
>
>
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Received on Sun Nov 18 2007 - 06:07:05 PST
