AMBER Archive (2004)

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

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Mon Jun 28 2004 - 07:48:51 CDT

I didn't follow this thread from the beginning but it looks like
installing and setting up fortran compilers, mpich and amber8 from
scratch is a good idea. Somewhat detailed description of doing this
(which should work for your setup, i.e. linux cluster with RH9) is at
the following amber webpage:
http://amber.scripps.edu/cluster_info/#compile_a8

The double underscore problem should not be a problem if you compiled
both your mpich libraries and amber8 with intel compilers. It's always a
good idea to give as much detail as possible when you describe your
installation procedure, e.g. how exactly you ./configure-d your mpich,
how you ./configure-d amber8, etc.

Cheers,
-Viktor

spookie wrote:

>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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