AMBER Archive (2008)

Subject: RE: AMBER: Amber installation

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Apr 11 2008 - 13:09:14 CDT

Hi Jacopo

This usually occurs because the version of lam you are using (probably the
default installed one) was built against a different compiler than you are
using for amber.

Check with

which mpirun

if it returns /usr/bin/mpirun

then it is the default copy you are using.

I would suggest downloading a copy of lam (or mpich2 etc) and build this
using ifort (set the environment variables FC=ifort F90=ifort) before
configuring it. Then once this is done make sure it is in your path variable
BEFORE /usr/bin etc such that 'which mpirun' returns the new installation.
Also set MPI_HOME to point to this location. Then you should be able to
build and link amber successfully.

Good luck,

Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of
> jacopo.sgrignani_at_unifi.it
> Sent: Friday, April 11, 2008 06:23
> To: amber_at_scripps.edu
> Subject: AMBER: Amber installation
>
> Hi,
> I have already tried to send this mail before, but I'm not
> sure I did it
> in the right way.
> I have tried to compile a sander parallel version using lam
> and gfortran
> (but also intel compiler), but at the end of the process I can get
> always the same error.
> Could anybody help me?
>
> Thanks
>
> Jacopo
>
> This is the last part og my log file.
>
> qm_div.o force.o \
> ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
> ../lib/nxtsec.o ../lib/sys.a -lmpi
> evb_init.o: In function `evb_init_':
> _evb_init.f:(.text+0x508): undefined reference to `mpi_bcast_'
> _evb_init.f:(.text+0x52e): undefined reference to `mpi_bcast_'
> _evb_init.f:(.text+0xb84): undefined reference to `mpi_bcast_'
> _evb_init.f:(.text+0xca9): undefined reference to `mpi_bcast_'
> _evb_init.f:(.text+0xdef): undefined reference to `mpi_bcast_'
> evb_init.o:_evb_init.f:(.text+0xf11): more undefined references to
> `mpi_bcast_' follow
> qmmm_module.o: In function `__qmmm_module__qmmm_mpi_setup':
> _qmmm_module.f:(.text+0x1322): undefined reference to `mpi_send_'
> _qmmm_module.f:(.text+0x1575): undefined reference to `mpi_recv_'
> _qmmm_module.f:(.text+0x18f9): undefined reference to `mpi_recv_'
> _qmmm_module.f:(.text+0x1a58): undefined reference to `mpi_send_'
> egb.o: In function `__genborn__egb':
> _egb.f:(.text+0x2c71): undefined reference to `mpi_allreduce_'
> egb.o: In function `__genborn__egb_calc_radii':
> _egb.f:(.text+0x6732): undefined reference to `mpi_allreduce_'
> multisander.o: In function `MAIN__':
> _multisander.f:(.text+0x42): undefined reference to `mpi_init_'
> _multisander.f:(.text+0x5f): undefined reference to `mpi_comm_rank_'
> _multisander.f:(.text+0x72): undefined reference to `mpi_comm_size_'
> _multisander.f:(.text+0x80): undefined reference to `mpi_barrier_'
> _multisander.f:(.text+0xeb): undefined reference to `mpi_bcast_'
> _multisander.f:(.text+0x27c): undefined reference to `mpi_bcast_'
> _multisander.f:(.text+0x434): undefined reference to `mpi_bcast_'
> _multisander.f:(.text+0x45a): undefined reference to `mpi_bcast_'
> _multisander.f:(.text+0x520): undefined reference to `mpi_bcast_'
> _multisander.f:(.text+0x5ab): undefined reference to `mpi_barrier_'
> _multisander.f:(.text+0x606): undefined reference to `mpi_comm_split_'
> _multisander.f:(.text+0x6f3): undefined reference to `mpi_comm_size_'
> _multisander.f:(.text+0x706): undefined reference to `mpi_comm_rank_'
> _multisander.f:(.text+0x76a): undefined reference to `mpi_comm_split_'
> _multisander.f:(.text+0x82b): undefined reference to `mpi_comm_size_'
> _multisander.f:(.text+0x83e): undefined reference to `mpi_comm_rank_'
> _multisander.f:(.text+0xa0b): undefined reference to `mpi_bcast_'
> _multisander.f:(.text+0xa19): undefined reference to `mpi_barrier_'
> _multisander.f:(.text+0xfbd): undefined reference to `mpi_barrier_'
> _multisander.f:(.text+0x1636): undefined reference to `mpi_barrier_'
> _multisander.f:(.text+0x1753): undefined reference to `mpi_allgather_'
> _multisander.f:(.text+0x2ad6): undefined reference to `mpi_barrier_'
> _multisander.f:(.text+0x2c66): undefined reference to `mpi_barrier_'
> _multisander.f:(.text+0x2cf3): undefined reference to `mpi_comm_free_'
> _multisander.f:(.text+0x2d21): undefined reference to `mpi_comm_free_'
> multisander.o: In function `subrem_':
> _multisander.f:(.text+0x2e8f): undefined reference to `mpi_allgather_'
> _multisander.f:(.text+0x2ec7): undefined reference to `mpi_allgather_'
> _multisander.f:(.text+0x2eff): undefined reference to `mpi_allgather_'
> _multisander.f:(.text+0x3ed4): undefined reference to `mpi_barrier_'
> _multisander.f:(.text+0x3f0e): undefined reference to `mpi_send_'
> _multisander.f:(.text+0x3f93): undefined reference to `mpi_barrier_'
> _multisander.f:(.text+0x3fd7): undefined reference to `mpi_recv_'
> _multisander.f:(.text+0x409c): undefined reference to `mpi_barrier_'
> _multisander.f:(.text+0x40dd): undefined reference to `mpi_gather_'
> _multisander.f:(.text+0x411e): undefined reference to `mpi_gather_'
> _multisander.f:(.text+0x414f): undefined reference to `mpi_allreduce_'
> sander.o: In function `sander_':
> _sander.f:(.text+0x260f): undefined reference to `mpi_bcast_'
> _sander.f:(.text+0x2638): undefined reference to `mpi_bcast_'
> _sander.f:(.text+0x2661): undefined reference to `mpi_bcast_'
> _sander.f:(.text+0x2677): undefined reference to `mpi_barrier_'
> _sander.f:(.text+0x2a8b): undefined reference to `mpi_bcast_'
> _sander.f:(.text+0x4e63): undefined reference to `mpi_bcast_'
> nmrcal.o: In function `master.0.nmrcal_':
> _nmrcal.f:(.text+0x2ed3): undefined reference to `mpi_bcast_'
> _nmrcal.f:(.text+0x2ef9): undefined reference to `mpi_bcast_'
> _nmrcal.f:(.text+0x2f39): undefined reference to `mpi_bcast_'
> nmrcal.o:_nmrcal.f:(.text+0x2f75): more undefined references to
> `mpi_bcast_' follow
> runmin.o: In function `runmin_':
> _runmin.f:(.text+0x1593): undefined reference to `mpi_sendrecv_'
> _runmin.f:(.text+0x15fa): undefined reference to `mpi_sendrecv_'
> mdread.o: In function `mdread2_':
> _mdread.f:(.text+0xf2fe): undefined reference to `mpi_bcast_'
> _mdread.f:(.text+0xf339): undefined reference to `mpi_bcast_'
> _mdread.f:(.text+0xf45f): undefined reference to `mpi_sendrecv_'
> _mdread.f:(.text+0xf4ce): undefined reference to `mpi_sendrecv_'
> runmd.o: In function `runmd_':
> _runmd.f:(.text+0xd28): undefined reference to `mpi_allreduce_'
> _runmd.f:(.text+0xf20): undefined reference to `mpi_bcast_'
> _runmd.f:(.text+0xf45): undefined reference to `mpi_bcast_'
> _runmd.f:(.text+0x19aa): undefined reference to `mpi_allreduce_'
> _runmd.f:(.text+0x33cc): undefined reference to `mpi_sendrecv_'
> _runmd.f:(.text+0x3429): undefined reference to `mpi_sendrecv_'
> _runmd.f:(.text+0x37f2): undefined reference to `mpi_bcast_'
> _runmd.f:(.text+0x5484): undefined reference to `mpi_bcast_'
> _runmd.f:(.text+0x54a9): undefined reference to `mpi_bcast_'
> _runmd.f:(.text+0x5f90): undefined reference to `mpi_sendrecv_'
> _runmd.f:(.text+0x5fed): undefined reference to `mpi_sendrecv_'
> parallel.o: In function `startup_':
> _parallel.f:(.text+0x48): undefined reference to `mpi_bcast_'
> _parallel.f:(.text+0x6e): undefined reference to `mpi_bcast_'
> _parallel.f:(.text+0x94): undefined reference to `mpi_bcast_'
> _parallel.f:(.text+0xba): undefined reference to `mpi_bcast_'
> _parallel.f:(.text+0xe0): undefined reference to `mpi_bcast_'
> parallel.o:_parallel.f:(.text+0x106): more undefined references to
> `mpi_bcast_' follow
> parallel.o: In function `startup_':
> _parallel.f:(.text+0x7b6): undefined reference to `mpi_barrier_'
> parallel.o: In function `fdist_':
> _parallel.f:(.text+0x9dd): undefined reference to `mpi_reduce_'
> _parallel.f:(.text+0xb44): undefined reference to `mpi_allreduce_'
> _parallel.f:(.text+0xc9b): undefined reference to `mpi_allreduce_'
> parallel.o: In function `fsum_':
> _parallel.f:(.text+0xffe): undefined reference to `mpi_sendrecv_'
> _parallel.f:(.text+0x1122): undefined reference to
> `mpi_reduce_scatter_'
> parallel.o: In function `xdist_':
> _parallel.f:(.text+0x13d5): undefined reference to `mpi_sendrecv_'
> _parallel.f:(.text+0x149e): undefined reference to `mpi_allgatherv_'
> ew_force.o: In function `ewald_force_':
> _ew_force.f:(.text+0x29ff): undefined reference to `mpi_comm_rank_'
> _ew_force.f:(.text+0x2a16): undefined reference to `mpi_comm_size_'
> _ew_force.f:(.text+0x2d85): undefined reference to `mpi_allreduce_'
> _ew_force.f:(.text+0x2f89): undefined reference to `mpi_allreduce_'
> _ew_force.f:(.text+0x335a): undefined reference to `mpi_comm_size_'
> _ew_force.f:(.text+0x3371): undefined reference to `mpi_comm_rank_'
> _ew_force.f:(.text+0x3555): undefined reference to `mpi_comm_rank_'
> _ew_force.f:(.text+0x356c): undefined reference to `mpi_comm_size_'
> _ew_force.f:(.text+0x3b5a): undefined reference to `mpi_comm_size_'
> _ew_force.f:(.text+0x3b71): undefined reference to `mpi_comm_rank_'
> _ew_force.f:(.text+0x447a): undefined reference to `mpi_comm_rank_'
> _ew_force.f:(.text+0x4491): undefined reference to `mpi_comm_size_'
> _ew_force.f:(.text+0x4622): undefined reference to `mpi_comm_size_'
> _ew_force.f:(.text+0x4639): undefined reference to `mpi_comm_rank_'
> ew_setup.o: In function `startup_groups_':
> _ew_setup.f:(.text+0x6ae): undefined reference to `mpi_bcast_'
> ew_setup.o: In function `ew_startup_':
> _ew_setup.f:(.text+0x3738): undefined reference to `mpi_comm_size_'
> _ew_setup.f:(.text+0x374a): undefined reference to `mpi_comm_rank_'
> _ew_setup.f:(.text+0x376a): undefined reference to `mpi_comm_size_'
> _ew_setup.f:(.text+0x377c): undefined reference to `mpi_comm_rank_'
> ew_fft.o: In function `zx_trans_recv_':
> _ew_fft.f:(.text+0x5e9d): undefined reference to `mpi_recv_'
> ew_fft.o: In function `zx_xy_transpose_':
> _ew_fft.f:(.text+0x61a3): undefined reference to `mpi_isend_'
> _ew_fft.f:(.text+0x61e7): undefined reference to `mpi_wait_'
> ew_fft.o: In function `xy_zx_trans_recv_':
> _ew_fft.f:(.text+0x62e2): undefined reference to `mpi_recv_'
> ew_fft.o: In function `xy_zx_transpose_':
> _ew_fft.f:(.text+0x6660): undefined reference to `mpi_isend_'
> _ew_fft.f:(.text+0x66b3): undefined reference to `mpi_wait_'
> nonbond_list.o: In function `__nblist__nonbond_list':
> _nonbond_list.f:(.text+0x75b5): undefined reference to `mpi_barrier_'
> _nonbond_list.f:(.text+0x76f9): undefined reference to
> `mpi_comm_size_'
> _nonbond_list.f:(.text+0x7710): undefined reference to
> `mpi_comm_rank_'
> _nonbond_list.f:(.text+0x7fe9): undefined reference to
> `mpi_allreduce_'
> _nonbond_list.f:(.text+0x840b): undefined reference to
> `mpi_allreduce_'
> _nonbond_list.f:(.text+0x84b4): undefined reference to
> `mpi_allreduce_'
> _nonbond_list.f:(.text+0x84cb): undefined reference to
> `mpi_comm_rank_'
> _nonbond_list.f:(.text+0x84e2): undefined reference to
> `mpi_comm_size_'
> ew_recip.o: In function `__ew_recip__do_pmesh_kspace':
> _ew_recip.f:(.text+0x3817): undefined reference to `mpi_barrier_'
> debug.o: In function `merge_forces_':
> _debug.f:(.text+0x1def): undefined reference to `mpi_reduce_'
> debug.o: In function `get_analfrc_':
> _debug.f:(.text+0x98eb): undefined reference to `mpi_barrier_'
> ew_dipole_recip.o: In function
> `__ew_dipole_recip__do_pmesh_dipole_kspace':
> _ew_dipole_recip.f:(.text+0x25ba): undefined reference to
> `mpi_barrier_'
> _ew_dipole_recip.f:(.text+0x27cc): undefined reference to
> `mpi_barrier_'
> _ew_dipole_recip.f:(.text+0x2c77): undefined reference to
> `mpi_barrier_'
> mexit.o: In function `mexit_':
> _mexit.f:(.text+0x28): undefined reference to `mpi_abort_'
> _mexit.f:(.text+0x3a): undefined reference to `mpi_finalize_'
> new_time.o: In function `profile_time_':
> _new_time.f:(.text+0x3e9): undefined reference to `mpi_send_'
> _new_time.f:(.text+0x762): undefined reference to `mpi_recv_'
> new_time.o: In function `timer_barrier_':
> _new_time.f:(.text+0x1b94): undefined reference to `mpi_barrier_'
> ips.o: In function `ipsupdate_':
> _ips.f:(.text+0xbeb): undefined reference to `mpi_allreduce_'
> sglds.o: In function `sgmdw_':
> _sglds.f:(.text+0x363): undefined reference to `mpi_allreduce_'
> sglds.o: In function `sgldw_':
> _sglds.f:(.text+0xadb): undefined reference to `mpi_allreduce_'
> spatial_recip.o: In function
> `__ew_recip_spatial__spatial_do_pmesh_kspace':
> _spatial_recip.f:(.text+0x402a): undefined reference to `mpi_barrier_'
> spatial_fft.o: In function `__fft__transpose':
> _spatial_fft.f:(.text+0x1837): undefined reference to
> `mpi_type_contiguous_'
> _spatial_fft.f:(.text+0x1849): undefined reference to
> `mpi_type_commit_'
> _spatial_fft.f:(.text+0x1b10): undefined reference to `mpi_irecv_'
> _spatial_fft.f:(.text+0x1d87): undefined reference to `mpi_isend_'
> _spatial_fft.f:(.text+0x1fe7): undefined reference to `mpi_waitany_'
> _spatial_fft.f:(.text+0x2187): undefined reference to `mpi_waitall_'
> _spatial_fft.f:(.text+0x2199): undefined reference to `mpi_type_free_'
> spatial_fft.o: In function `__fft__ftranspose':
> _spatial_fft.f:(.text+0x23e2): undefined reference to
> `mpi_type_contiguous_'
> _spatial_fft.f:(.text+0x23f4): undefined reference to
> `mpi_type_commit_'
> _spatial_fft.f:(.text+0x26dc): undefined reference to `mpi_irecv_'
> _spatial_fft.f:(.text+0x2977): undefined reference to `mpi_isend_'
> _spatial_fft.f:(.text+0x2bde): undefined reference to `mpi_waitany_'
> _spatial_fft.f:(.text+0x2d7b): undefined reference to `mpi_waitall_'
> _spatial_fft.f:(.text+0x2da7): undefined reference to `mpi_type_free_'
> qm_ewald.o: In function `qm_ewald_setup_':
> _qm_ewald.f:(.text+0x4b68): undefined reference to `mpi_gather_'
> qm2_load_params_and_allocate.o: In function
> `qm2_load_params_and_allocate_':
> _qm2_load_params_and_allocate.f:(.text+0x1ac8a): undefined
> reference to
> `mpi_allgather_'
> qm2_scf.o: In function `qm2_scf_':
> _qm2_scf.f:(.text+0x2590): undefined reference to `mpi_allreduce_'
> _qm2_scf.f:(.text+0x286c): undefined reference to `mpi_reduce_'
> _qm2_scf.f:(.text+0x2989): undefined reference to `mpi_bcast_'
> force.o: In function `force_':
> _force.f:(.text+0x1463): undefined reference to `mpi_bcast_'
> _force.f:(.text+0x1b58): undefined reference to `mpi_bcast_'
> _force.f:(.text+0x1b94): undefined reference to `mpi_bcast_'
> _force.f:(.text+0x1bb6): undefined reference to `mpi_bcast_'
> force.o:_force.f:(.text+0x1bdb): more undefined references to
> `mpi_bcast_' follow
> force.o: In function `force_':
> _force.f:(.text+0x23c7): undefined reference to `mpi_allgather_'
> _force.f:(.text+0x23f5): undefined reference to `mpi_allgather_'
> collect2: ld returned 1 exit status
> make[1]: *** [sander.MPI] Error 1
> make[1]: Leaving directory `/usr/local/amber9/src/sander'
> make: *** [parallel] Error 2
> --------------------------------------------------------------
> ---------
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