AMBER Archive (2008)

Subject: AMBER: Amber installation

From: jacopo.sgrignani_at_unifi.it
Date: Fri Apr 11 2008 - 08:23:24 CDT

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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