AMBER Archive (2004)

Subject: AMBER: problem not with sander, but with mpich

From: spookie (rooksin_at_yahoo.co.uk)
Date: Mon Jun 28 2004 - 04:08:37 CDT

dear all,
      After a lot of trials and errors, i could
finally figure out that the problem of running
parallel jobs with sander is not with sander but with
the proper compilation of mpich by itself..
 
      as i could not get my sander running in parallel
on more than one node at a time, i tried re-compiling
amber8 from scratch..so, i got my fortran and icc
compilers for linux from intel and installed
them..then i tried loading my mpich1.2.5.2 on my RHL
9..when i tried doing this, it configures itself
properly with the flags i give...but then, it fails to
install properly...i finally found that it is nothing
but the famous double-underscore problem..it failed to
link itself with the f90 libraries and consequently it
throws the following error when i try compiling amber8
in parallel !!

        ../lmod/lmod.a -L/usr/local/mpich/lib -lmpich
\
        ../lapack/lapack.a ../blas/blas.a
../lib/nxtsec.o ../lib/sys.a
egb.o(.text+0x2004): In function `genborn_mp_egb_':
: undefined reference to `mpi_allreduce_'
egb.o(.text+0x308c): In function `genborn_mp_egb_':
: undefined reference to `mpi_allreduce_'
sander.o(.text+0x2b): In function `MAIN__':
: undefined reference to `mpi_init_'
sander.o(.text+0x57): In function `MAIN__':
: undefined reference to `mpi_comm_rank_'
sander.o(.text+0x7b): In function `MAIN__':
: undefined reference to `mpi_comm_size_'
sander.o(.text+0x97): In function `MAIN__':
: undefined reference to `mpi_barrier_'
sander.o(.text+0x10e): In function `MAIN__':
: undefined reference to `mpi_bcast_'
sander.o(.text+0x389): In function `MAIN__':
: undefined reference to `mpi_bcast_'
sander.o(.text+0x3c5): In function `MAIN__':
: undefined reference to `mpi_bcast_'
sander.o(.text+0x462): In function `MAIN__':
: undefined reference to `mpi_bcast_'
sander.o(.text+0x4cc): In function `MAIN__':
: undefined reference to `mpi_barrier_'
sander.o(.text+0x535): In function `MAIN__':
: undefined reference to `mpi_comm_split_'
sander.o(.text+0x683): In function `MAIN__':
: undefined reference to `mpi_comm_size_'
sander.o(.text+0x6a7): In function `MAIN__':
: undefined reference to `mpi_comm_rank_'
sander.o(.text+0x716): In function `MAIN__':
: undefined reference to `mpi_comm_split_'
sander.o(.text+0x842): In function `MAIN__':
: undefined reference to `mpi_comm_size_'
sander.o(.text+0x866): In function `MAIN__':
: undefined reference to `mpi_comm_rank_'
sander.o(.text+0x927): In function `MAIN__':
: undefined reference to `mpi_bcast_'
sander.o(.text+0x96b): In function `MAIN__':
: undefined reference to `mpi_bcast_'
sander.o(.text+0x9af): In function `MAIN__':
: undefined reference to `mpi_bcast_'
sander.o(.text+0x9f3): In function `MAIN__':
: undefined reference to `mpi_bcast_'
sander.o(.text+0xa37): In function `MAIN__':
: undefined reference to `mpi_bcast_'
sander.o(.text+0xa7b): more undefined references to
`mpi_bcast_' follow
sander.o(.text+0xdfb): In function `MAIN__':
: undefined reference to `mpi_barrier_'
sander.o(.text+0x1611): In function `MAIN__':
: undefined reference to `mpi_barrier_'
sander.o(.text+0x1c06): In function `MAIN__':
: undefined reference to `mpi_barrier_'
sander.o(.text+0x1c4b): In function `MAIN__':
: undefined reference to `mpi_comm_free_'
sander.o(.text+0x1c84): In function `MAIN__':
: undefined reference to `mpi_comm_free_'
sander.o(.text+0x3cea): In function `sander_':
: undefined reference to `mpi_bcast_'
sander.o(.text+0x3d06): In function `sander_':
: undefined reference to `mpi_barrier_'
sander.o(.text+0x56db): In function `sander_':
: undefined reference to `mpi_bcast_'
nmrcal.o(.text+0x1639): In function `nmrcal_':
: undefined reference to `mpi_bcast_'
nmrcal.o(.text+0x1675): In function `nmrcal_':
: undefined reference to `mpi_bcast_'
nmrcal.o(.text+0x16cc): In function `nmrcal_':
: undefined reference to `mpi_bcast_'
nmrcal.o(.text+0x171f): In function `nmrcal_':
: undefined reference to `mpi_bcast_'
nmrcal.o(.text+0x175c): more undefined references to
`mpi_bcast_' follow
runmd.o(.text+0x8d7): In function `runmd_':
: undefined reference to `mpi_allreduce_'
runmd.o(.text+0xfa6): In function `runmd_':
: undefined reference to `mpi_bcast_'
runmd.o(.text+0x1800): In function `runmd_':
: undefined reference to `mpi_allreduce_'
parallel.o(.text+0x52): In function `startup_':
: undefined reference to `mpi_bcast_'
parallel.o(.text+0x8b): In function `startup_':
: undefined reference to `mpi_bcast_'
parallel.o(.text+0xc4): In function `startup_':
: undefined reference to `mpi_bcast_'
parallel.o(.text+0xfd): In function `startup_':
: undefined reference to `mpi_bcast_'
parallel.o(.text+0x136): In function `startup_':
: undefined reference to `mpi_bcast_'
parallel.o(.text+0x16f): more undefined references to
`mpi_bcast_' follow
parallel.o(.text+0xc1c): In function `startup_':
: undefined reference to `mpi_barrier_'
parallel.o(.text+0xe36): In function `fdist_':
: undefined reference to `mpi_reduce_'
parallel.o(.text+0xf6d): In function `fdist_':
: undefined reference to `mpi_allreduce_'
parallel.o(.text+0x10ad): In function `fdist_':
: undefined reference to `mpi_allreduce_'
parallel.o(.text+0x136d): In function `fsum_':
: undefined reference to `mpi_sendrecv_'
parallel.o(.text+0x1644): In function `xdist_':
: undefined reference to `mpi_sendrecv_'
ew_force.o(.text+0x31): In function `ewald_force_':
: undefined reference to `mpi_comm_rank_'
ew_force.o(.text+0x48): In function `ewald_force_':
: undefined reference to `mpi_comm_size_'
ew_force.o(.text+0x434): In function `ewald_force_':
: undefined reference to `mpi_allreduce_'
ew_force.o(.text+0x471): In function `ewald_force_':
: undefined reference to `mpi_barrier_'
ew_force.o(.text+0x918): In function `ewald_force_':
: undefined reference to `mpi_allreduce_'
ew_force.o(.text+0xb9f): In function `ewald_force_':
: undefined reference to `mpi_comm_size_'
ew_force.o(.text+0xbb6): In function `ewald_force_':
: undefined reference to `mpi_comm_rank_'
ew_force.o(.text+0xcf6): In function `ewald_force_':
: undefined reference to `mpi_comm_rank_'
ew_force.o(.text+0xd0d): In function `ewald_force_':
: undefined reference to `mpi_comm_size_'
ew_force.o(.text+0x14e9): In function `ewald_force_':
: undefined reference to `mpi_comm_size_'
ew_force.o(.text+0x1500): In function `ewald_force_':
: undefined reference to `mpi_comm_rank_'
ew_force.o(.text+0x17b9): In function `ewald_force_':
: undefined reference to `mpi_comm_rank_'
ew_force.o(.text+0x17d0): In function `ewald_force_':
: undefined reference to `mpi_comm_size_'
ew_setup.o(.text+0x3069): In function `ew_startup_':
: undefined reference to `mpi_comm_size_'
ew_setup.o(.text+0x3080): In function `ew_startup_':
: undefined reference to `mpi_comm_rank_'
ew_setup.o(.text+0x3126): In function `ew_startup_':
: undefined reference to `mpi_comm_size_'
ew_setup.o(.text+0x313d): In function `ew_startup_':
: undefined reference to `mpi_comm_rank_'
ew_setup.o(.text+0x650a): In function
`startup_groups_':
: undefined reference to `mpi_bcast_'
ew_fft.o(.text+0x1243): In function
`xy_zx_transpose_.':
: undefined reference to `mpi_isend_'
ew_fft.o(.text+0x12e3): In function
`xy_zx_transpose_.':
: undefined reference to `mpi_recv_'
ew_fft.o(.text+0x14bd): In function
`xy_zx_transpose_.':
: undefined reference to `mpi_wait_'
ew_fft.o(.text+0x2e67): In function
`zx_xy_transpose_.':
: undefined reference to `mpi_isend_'
ew_fft.o(.text+0x2f07): In function
`zx_xy_transpose_.':
: undefined reference to `mpi_recv_'
ew_fft.o(.text+0x30c9): In function
`zx_xy_transpose_.':
: undefined reference to `mpi_wait_'
ew_fft.o(.text+0x3231): In function
`xy_zx_trans_recv_':
: undefined reference to `mpi_recv_'
ew_fft.o(.text+0x3495): In function `zx_trans_recv_':
: undefined reference to `mpi_recv_'
ew_direct.o(.text+0x8f0): In function `nonbond_list_':
: undefined reference to `mpi_barrier_'
ew_direct.o(.text+0xb07): In function `nonbond_list_':
: undefined reference to `mpi_comm_size_'
ew_direct.o(.text+0xb1e): In function `nonbond_list_':
: undefined reference to `mpi_comm_rank_'
ew_direct.o(.text+0x1d62): In function
`nonbond_list_':
: undefined reference to `mpi_allreduce_'
ew_direct.o(.text+0x2759): In function
`nonbond_list_':
: undefined reference to `mpi_allreduce_'
ew_direct.o(.text+0x2938): In function
`nonbond_list_':
: undefined reference to `mpi_allreduce_'
ew_direct.o(.text+0x2952): In function
`nonbond_list_':
: undefined reference to `mpi_comm_rank_'
ew_direct.o(.text+0x2969): In function
`nonbond_list_':
: undefined reference to `mpi_comm_size_'
ew_recip.o(.text+0xef3): In function
`do_pmesh_kspace_':
: undefined reference to `mpi_barrier_'
debug.o(.text+0x777): In function `debug_frc_':
: undefined reference to `mpi_barrier_'
debug.o(.text+0x96a): In function `debug_frc_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xa06): In function `debug_frc_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xa387): In function `get_analfrc_.':
: undefined reference to `mpi_barrier_'
debug.o(.text+0xa573): In function `get_analfrc_.':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xa63c): In function `get_analfrc_.':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xaba1): In function `merge_forces_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xb084): In function `force_dump_':
: undefined reference to `mpi_barrier_'
debug.o(.text+0xb25c): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xb2fa): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xb599): In function `force_dump_':
: undefined reference to `mpi_barrier_'
debug.o(.text+0xb76f): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xb80d): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xb977): In function `force_dump_':
: undefined reference to `mpi_barrier_'
debug.o(.text+0xbb4d): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xbbeb): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xbd55): In function `force_dump_':
: undefined reference to `mpi_barrier_'
debug.o(.text+0xbf2b): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xbfc9): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xc151): In function `force_dump_':
: undefined reference to `mpi_barrier_'
debug.o(.text+0xc327): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xc3c5): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xc58b): In function `force_dump_':
: undefined reference to `mpi_barrier_'
debug.o(.text+0xc760): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xc7fe): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xcafe): In function `force_dump_':
: undefined reference to `mpi_barrier_'
debug.o(.text+0xccd3): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xcd71): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xd04f): In function `force_dump_':
: undefined reference to `mpi_barrier_'
debug.o(.text+0xd226): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xd2bb): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xd673): In function `force_dump_':
: undefined reference to `mpi_barrier_'
debug.o(.text+0xd84a): In function `force_dump_':
: undefined reference to `mpi_reduce_'
debug.o(.text+0xd8dd): In function `force_dump_':
: undefined reference to `mpi_reduce_'
ew_dipole_recip.o(.text+0x6b0): In function
`do_pmesh_dipole_kspace_':
: undefined reference to `mpi_barrier_'
ew_dipole_recip.o(.text+0x836): In function
`do_pmesh_dipole_kspace_':
: undefined reference to `mpi_barrier_'
ew_dipole_recip.o(.text+0xb93): In function
`do_pmesh_dipole_kspace_':
: undefined reference to `mpi_barrier_'
mexit.o(.text+0x28): In function `mexit_':
: undefined reference to `mpi_abort_'
mexit.o(.text+0x4e): In function `mexit_':
: undefined reference to `mpi_finalize_'
new_time.o(.text+0x230): In function `timer_barrier_':
: undefined reference to `mpi_barrier_'
new_time.o(.text+0x7cb): In function `profile_time_':
: undefined reference to `mpi_send_'
new_time.o(.text+0xc4d): In function `profile_time_':
: undefined reference to `mpi_recv_'
make[1]: *** [sander] Error 1
make[1]: Leaving directory
`/usr/local/amber8/src/sander'
make: *** [parallel] Error 2

some how, i am sure that if i can get over with the
double underscore problem in mpich and compile it, i
can clear these errors in parallel compilation of
amber..for doing that, i added the
-Mnosecond_underscore while configuring mpich...but it
seems to work only with portland compilers and i have
intel ones..i even tried including
-fno-second-underscore in FFLAGS, but then it is being
ignored by my mpich make install step..

i'm sorry for such a long mail...i'm badly in need of
help ...

thanks in advance..
regards,

        
        
                
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