AMBER Archive (2006)

Subject: Re: AMBER: problems about compiling a parallel version of AMBER 9

From: Kateryna Miroshnychenko (kateryna_mirosh_at_ire.kharkov.ua)
Date: Tue Jun 27 2006 - 03:41:21 CDT

Dear Chengwen,

  It looks like your message parallel interface library (mpich or
  mpich2 or lam whatever you have) was compiled with other compiler
  than ifort. So the solution will be to recompile it with ifort. If
  on any reason you can't do it, try to add flag -assume 2underscores
  to ifort in config.h

regards,
Katya
  
> Sorry, I make some mistake.
> the error messages after "make parallel" is : (I attatch those lines at the bottom which seems to be error messages)
> ........................
> ........................
> ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
> ../lib/nxtsec.o ../lib/sys.a -L/opt/intel/mkl721/lib/32 -lvml -lmkl_lapack -lmkl -lguide -
> lpthread
> 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_'
> evb_init.o(.text+0x1bee): more undefined references to `mpi_bcast_' follow
> qmmm_module.o(.text+0x16d5): In function `qmmm_module_mp_qmmm_mpi_setup_':
> : undefined reference to `mpi_recv_'
> qmmm_module.o(.text+0x18ac): In function `qmmm_module_mp_qmmm_mpi_setup_':
> : undefined reference to `mpi_send_'
> qmmm_module.o(.text+0x1b2c): In function `qmmm_module_mp_qmmm_mpi_setup_':
> : undefined reference to `mpi_recv_'
> qmmm_module.o(.text+0x1cfa): In function `qmmm_module_mp_qmmm_mpi_setup_':
> : undefined reference to `mpi_send_'
> egb.o(.text+0x2fd3): In function `genborn_mp_egb_':
> : undefined reference to `mpi_allreduce_'
> egb.o(.text+0x65d9): In function `genborn_mp_egb_calc_radii_':
> : undefined reference to `mpi_allreduce_'
> multisander.o (.text+0x3e): In function `MAIN__':
> : undefined reference to `mpi_init_'
> multisander.o(.text+0x67): In function `MAIN__':
> : undefined reference to `mpi_comm_rank_'
> multisander.o(.text+0x88): In function `MAIN__':
> : undefined reference to `mpi_comm_size_'
> multisander.o(.text+0xa1): In function `MAIN__':
> : undefined reference to `mpi_barrier_'
> multisander.o(.text+0x115): In function `MAIN__':
> : undefined reference to `mpi_bcast_'
> multisander.o(.text+0x2f6): In function `MAIN__':
> : undefined reference to `mpi_bcast_'
> multisander.o(.text+0x560): In function `MAIN__':
> : undefined reference to `mpi_bcast_'
> multisander.o(.text+0x599): In function `MAIN__':
> : undefined reference to `mpi_bcast_'
> multisander.o(.text+0x633): In function `MAIN__':
> : undefined reference to `mpi_bcast_'
> multisander.o(.text+0x69d): In function `MAIN__':
> : undefined reference to `mpi_barrier_'
> multisander.o(.text+0x704): In function `MAIN__':
> : undefined reference to `mpi_comm_split_'
> multisander.o(.text+0x852): In function `MAIN__':
> : undefined reference to `mpi_comm_size_'
> multisander.o(.text+0x873): In function `MAIN__':
> : undefined reference to `mpi_comm_rank_'
> multisander.o(.text+0x8df): In function `MAIN__':
> : undefined reference to `mpi_comm_split_'
> multisander.o(.text+0x9f7): In function `MAIN__':
> : undefined reference to `mpi_comm_size_'
> multisander.o(.text+0xa18): In function `MAIN__':
> : undefined reference to `mpi_comm_rank_'
> multisander.o(.text+0xc53): In function `MAIN__':
> : undefined reference to `mpi_bcast_'
> multisander.o(.text+0xc6c): In function `MAIN__':
> : undefined reference to `mpi_barrier_'
> multisander.o(.text+0x1244): In function `MAIN__':
> : undefined reference to `mpi_barrier_'
> multisander.o(.text+0x1880): In function `MAIN__':
> : undefined reference to `mpi_barrier_'
> multisander.o(.text+0x19c7): In function `MAIN__':
> : undefined reference to `mpi_allgather_'
> multisander.o(.text+0x3014): In function `MAIN__':
> : undefined reference to `mpi_barrier_'
> multisander.o(.text+0x31ba): In function `MAIN__':
> : undefined reference to `mpi_barrier_'
> multisander.o(.text+0x323e): In function `MAIN__':
> : undefined reference to `mpi_comm_free_'
> multisander.o(.text+0x3275): In function `MAIN__':
> : undefined reference to `mpi_comm_free_'
> multisander.o(.text+0x33bc): In function `subrem_':
> : undefined reference to `mpi_allgather_'
> multisander.o(.text+0x3405): In function `subrem_':
> : undefined reference to `mpi_allgather_'
> multisander.o(.text+0x344e): In function `subrem_':
> : undefined reference to `mpi_allgather_'
> multisander.o(.text+0x460d): In function `subrem_':
> : undefined reference to `mpi_barrier_'
> multisander.o(.text+0x465c): In function `subrem_':
> : undefined reference to `mpi_send_'
> multisander.o(.text+0x46e8): In function `subrem_':
> : undefined reference to `mpi_barrier_'
> multisander.o(.text+0x4740): In function `subrem_':
> : undefined reference to `mpi_recv_'
> multisander.o(.text+0x4801): In function `subrem_':
> : undefined reference to `mpi_barrier_'
> multisander.o(.text+0x4852): In function `subrem_':
> : undefined reference to `mpi_gather_'
> multisander.o(.text+0x48a3): In function `subrem_':
> : undefined reference to `mpi_gather_'
> multisander.o(.text+0x48e4): In function `subrem_':
> : undefined reference to `mpi_allreduce_'
> sander.o(.text+0x262a): In function `sander_':
> : undefined reference to `mpi_bcast_'
> sander.o(.text+0x2663): In function `sander_':
> : undefined reference to `mpi_bcast_'
> sander.o(.text+0x269c): In function `sander_':
> : undefined reference to `mpi_bcast_'
> sander.o(.text+0x26ba): In function `sander_':
> : undefined reference to `mpi_barrier_'
> sander.o(.text+0x2ce6): In function `sander_':
> : undefined reference to `mpi_bcast_'
> sander.o(.text+0x59bc): In function `sander_':
> : undefined reference to `mpi_bcast_'
> nmrcal.o(.text+0x1264): In function `nmrcal_':
> : undefined reference to `mpi_bcast_'
> nmrcal.o(.text+0x12a0): In function `nmrcal_':
> : undefined reference to `mpi_bcast_'
> nmrcal.o(.text+0x12f1): In function `nmrcal_':
> : undefined reference to `mpi_bcast_'
> nmrcal.o(.text+0x1342): more undefined references to `mpi_bcast_' follow
> runmin.o(.text+0x600): In function `runmin_':
> : undefined reference to `mpi_sendrecv_'
> runmin.o(.text+0x64b): In function `runmin_':
> : undefined reference to `mpi_sendrecv_'
> runmin.o(.text+0x6e7): In function `runmin_':
> : undefined reference to `mpi_bcast_'
> runmin.o(.text+0x711): In function `runmin_':
> : undefined reference to `mpi_bcast_'
> mdread.o(.text+0xfc64): In function `mdread2_':
> : undefined reference to `mpi_bcast_'
> mdread.o(.text+0xfca8): In function `mdread2_':
> : undefined reference to `mpi_bcast_'
> mdread.o(.text+0xfdf9): In function `mdread2_':
> : undefined reference to `mpi_sendrecv_'
> mdread.o(.text+0xfe6d): In function `mdread2_':
> : undefined reference to `mpi_sendrecv_'
> runmd.o(.text+0xbb2): In function `runmd_':
> : undefined reference to `mpi_allreduce_'
> runmd.o(.text+0xea5): In function `runmd_':
> : undefined reference to `mpi_sendrecv_'
> runmd.o(.text+0xeed): In function `runmd_':
> : undefined reference to `mpi_sendrecv_'
> runmd.o(.text+0x10a5): In function `runmd_':
> : undefined reference to `mpi_bcast_'
> runmd.o(.text+0x10cb): In function `runmd_':
> : undefined reference to `mpi_bcast_'
> runmd.o(.text+0x1d5c): In function `runmd_':
> : undefined reference to `mpi_allreduce_'
> runmd.o(.text+0x490c): In function `runmd_':
> : undefined reference to `mpi_bcast_'
> runmd.o(.text+0x55f2): In function `runmd_':
> : undefined reference to `mpi_sendrecv_'
> runmd.o(.text+0x5672): In function `runmd_':
> : undefined reference to `mpi_sendrecv_'
> runmd.o(.text+0x57d2): In function `runmd_':
> : undefined reference to `mpi_bcast_'
> runmd.o(.text+0x5830): In function `runmd_':
> : undefined reference to `mpi_bcast_'
> 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): more undefined references to `mpi_bcast_' follow
> parallel.o(.text+0xb3d): In function `startup_':
> : undefined reference to `mpi_barrier_'
> parallel.o (.text+0xd24): In function `fdist_':
> : undefined reference to `mpi_reduce_'
> parallel.o(.text+0xe44): In function `fdist_':
> : undefined reference to `mpi_allreduce_'
> parallel.o(.text+0xf7a): In function `fdist_':
> : undefined reference to `mpi_allreduce_'
> parallel.o(.text+0x122e): In function `fsum_':
> : undefined reference to `mpi_sendrecv_'
> parallel.o(.text+0x1329): In function `fsum_':
> : undefined reference to `mpi_reduce_scatter_'
> parallel.o(.text+0x158b): In function `xdist_':
> : undefined reference to `mpi_sendrecv_'
> parallel.o(.text+0x1651): In function `xdist_':
> : undefined reference to `mpi_allgatherv_'
> ew_force.o(.text+0x3e): In function `ewald_force_':
> : undefined reference to `mpi_comm_rank_'
> ew_force.o(.text+0x54): In function `ewald_force_':
> : undefined reference to `mpi_comm_size_'
> ew_force.o(.text+0x37c): In function `ewald_force_':
> : undefined reference to `mpi_comm_size_'
> ew_force.o(.text+0x392): In function `ewald_force_':
> : undefined reference to `mpi_comm_rank_'
> ew_force.o(.text+0xe82): In function `ewald_force_':
> : undefined reference to `mpi_comm_rank_'
> ew_force.o(.text+0xe98): In function `ewald_force_':
> : undefined reference to `mpi_comm_size_'
> ew_force.o(.text+0xf8d): In function `ewald_force_':
> : undefined reference to `mpi_allreduce_'
> ew_force.o(.text+0x12f7): In function `ewald_force_':
> : undefined reference to `mpi_allreduce_'
> ew_force.o(.text+0x1502): In function `ewald_force_':
> : undefined reference to `mpi_comm_size_'
> ew_force.o(.text+0x1518): In function `ewald_force_':
> : undefined reference to `mpi_comm_rank_'
> ew_force.o(.text+0x1646): In function `ewald_force_':
> : undefined reference to `mpi_comm_rank_'
> ew_force.o(.text+0x165c): In function `ewald_force_':
> : undefined reference to `mpi_comm_size_'
> ew_force.o(.text+0x1b3f): In function `ewald_force_':
> : undefined reference to `mpi_comm_size_'
> ew_force.o(.text+0x1b55): In function `ewald_force_':
> : undefined reference to `mpi_comm_rank_'
> ew_force.o(.text+0x1ce2): In function `ewald_force_':
> : undefined reference to `mpi_comm_rank_'
> ew_force.o(.text+0x1cf8): In function `ewald_force_':
> : undefined reference to `mpi_comm_size_'
> ew_setup.o(.text+0x18b1): In function `ew_startup_':
> : undefined reference to `mpi_comm_size_'
> ew_setup.o(.text+0x18c8): In function `ew_startup_':
> : undefined reference to `mpi_comm_rank_'
> ew_setup.o(.text+0x195f): In function `ew_startup_':
> : undefined reference to `mpi_comm_size_'
> ew_setup.o(.text+0x1976): In function `ew_startup_':
> : undefined reference to `mpi_comm_rank_'
> ew_setup.o(.text+0x4bc0): In function `startup_groups_':
> : undefined reference to `mpi_bcast_'
> ew_fft.o(.text+0xa63): In function `xy_zx_transpose_.':
> : undefined reference to `mpi_wait_'
> ew_fft.o(.text+0xbdc): In function `xy_zx_transpose_.':
> : undefined reference to `mpi_isend_'
> ew_fft.o(.text+0xc7f): In function `xy_zx_transpose_.':
> : undefined reference to `mpi_recv_'
> ew_fft.o(.text+0x1f50): In function `zx_xy_transpose_.':
> : undefined reference to `mpi_wait_'
> ew_fft.o(.text+0x20ef): In function `zx_xy_transpose_.':
> : undefined reference to `mpi_isend_'
> ew_fft.o(.text+0x2192): In function `zx_xy_transpose_.':
> : undefined reference to `mpi_recv_'
> ew_fft.o(.text+0x242d): In function `xy_zx_trans_recv_':
> : undefined reference to `mpi_recv_'
> ew_fft.o(.text+0x25ec): In function `zx_trans_recv_':
> : undefined reference to `mpi_recv_'
> nonbond_list.o(.text+0x2ab2): In function `nblist_mp_nonbond_list_':
> : undefined reference to `mpi_barrier_'
> nonbond_list.o(.text+0x2e88): In function `nblist_mp_nonbond_list_':
> : undefined reference to `mpi_comm_size_'
> nonbond_list.o(.text+0x2ea1): In function `nblist_mp_nonbond_list_':
> : undefined reference to `mpi_comm_rank_'
> nonbond_list.o(.text+0x4080): In function `nblist_mp_nonbond_list_':
> : undefined reference to `mpi_allreduce_'
> nonbond_list.o(.text+0x4229): In function `nblist_mp_nonbond_list_':
> : undefined reference to `mpi_allreduce_'
> nonbond_list.o(.text+0x4242): In function `nblist_mp_nonbond_list_':
> : undefined reference to `mpi_comm_rank_'
> nonbond_list.o(.text+0x425b): In function `nblist_mp_nonbond_list_':
> : undefined reference to `mpi_comm_size_'
> nonbond_list.o(.text+0x454e): In function `nblist_mp_nonbond_list_':
> : undefined reference to `mpi_allreduce_'
> ew_recip.o(.text+0x10a4): In function `ew_recip_mp_do_pmesh_kspace_':
> : undefined reference to `mpi_barrier_'
> debug.o(.text+0x9f8c): In function `get_analfrc_.':
> : undefined reference to `mpi_barrier_'
> debug.o(.text+0xa16d): In function `get_analfrc_.':
> : undefined reference to `mpi_reduce_'
> debug.o(.text+0xa1ec): In function `get_analfrc_.':
> : undefined reference to `mpi_reduce_'
> debug.o(.text+0xa784): In function `merge_forces_':
> : undefined reference to `mpi_reduce_'
> ew_dipole_recip.o(.text+0x734): In function `ew_dipole_recip_mp_do_pmesh_dipole_kspace_':
> : undefined reference to `mpi_barrier_'
> ew_dipole_recip.o(.text+0x8f1): In function `ew_dipole_recip_mp_do_pmesh_dipole_kspace_':
> : undefined reference to `mpi_barrier_'
> ew_dipole_recip.o(.text+0xc96): In function `ew_dipole_recip_mp_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+0x200): In function `timer_barrier_':
> : undefined reference to `mpi_barrier_'
> new_time.o(.text+0x68e): In function `profile_time_':
> : undefined reference to `mpi_send_'
> new_time.o(.text+0xa83): In function `profile_time_':
> : undefined reference to `mpi_recv_'
> ips.o(.text+0x134d): In function `ipsupdate_.':
> : undefined reference to `mpi_allreduce_'
> sglds.o(.text+0x566): In function `sgldw_':
> : undefined reference to `mpi_allreduce_'
> sglds.o(.text+0x9a1): In function `sgmdw_':
> : undefined reference to `mpi_allreduce_'
> spatial_recip.o(.text+0xe4e): In function `ew_recip_spatial_mp_spatial_do_pmesh_kspace_':
> : undefined reference to `mpi_barrier_'
> spatial_fft.o(.text+0x99b): In function `fft_mp_transpose_.':
> : undefined reference to `mpi_type_contiguous_'
> spatial_fft.o(.text+0x9af): In function `fft_mp_transpose_.':
> : undefined reference to `mpi_type_commit_'
> spatial_fft.o(.text+0xd07): In function `fft_mp_transpose_.':
> : undefined reference to `mpi_waitany_'
> spatial_fft.o(.text+0xe6e): In function `fft_mp_transpose_.':
> : undefined reference to `mpi_waitall_'
> spatial_fft.o(.text+0xe82): In function `fft_mp_transpose_.':
> : undefined reference to `mpi_type_free_'
> spatial_fft.o(.text+0x10ff): In function `fft_mp_transpose_.':
> : undefined reference to `mpi_isend_'
> spatial_fft.o(.text+0x1233): In function `fft_mp_transpose_.':
> : undefined reference to `mpi_irecv_'
> spatial_fft.o(.text+0x17b2): In function `fft_mp_ftranspose_.':
> : undefined reference to `mpi_type_contiguous_'
> spatial_fft.o(.text+0x17c6): In function `fft_mp_ftranspose_.':
> : undefined reference to `mpi_type_commit_'
> spatial_fft.o(.text+0x1b39): In function `fft_mp_ftranspose_.':
> : undefined reference to `mpi_waitany_'
> spatial_fft.o(.text+0x1ca2): In function `fft_mp_ftranspose_.':
> : undefined reference to `mpi_waitall_'
> spatial_fft.o(.text+0x1cd0): In function `fft_mp_ftranspose_.':
> : undefined reference to `mpi_type_free_'
> spatial_fft.o(.text+0x1f8d): In function `fft_mp_ftranspose_.':
> : undefined reference to `mpi_isend_'
> spatial_fft.o(.text+0x20b1): In function `fft_mp_ftranspose_.':
> : undefined reference to `mpi_irecv_'
> qm_ewald.o(.text+0x70e): In function `qm_ewald_setup_':
> : undefined reference to `mpi_recv_'
> qm_ewald.o(.text+0x8fd): In function `qm_ewald_setup_':
> : undefined reference to `mpi_send_'
> qm2_load_params_and_allocate.o(.text+0x165de): In function `qm2_load_params_and_allocate_':
> : undefined reference to `mpi_allgather_'
> qm2_scf.o(.text+0x495): In function `qm2_scf_':
> : undefined reference to `mpi_reduce_'
> qm2_scf.o(.text+0x6fe): In function `qm2_scf_':
> : undefined reference to `mpi_bcast_'
> qm2_scf.o(.text+0xe86): In function `qm2_scf_':
> : undefined reference to `mpi_allreduce_'
> force.o(.text+0x194b): In function `force_':
> : undefined reference to `mpi_bcast_'
> force.o(.text+0x19ce): In function `force_':
> : undefined reference to `mpi_allgather_'
> force.o(.text+0x1a00): In function `force_':
> : undefined reference to `mpi_allgather_'
> force.o(.text+0x2329): In function `force_':
> : undefined reference to `mpi_bcast_'
> force.o(.text+0x236d): In function `force_':
> : undefined reference to `mpi_bcast_'
> force.o(.text+0x2395): In function `force_':
> : undefined reference to `mpi_bcast_'
> force.o(.text+0x23bc): In function `force_':
> : undefined reference to `mpi_bcast_'
> force.o(.text+0x23fa): In function `force_':
> : undefined reference to `mpi_bcast_'
> force.o(.text+0x2422): more undefined references to `mpi_bcast_' follow
> make[1]: *** [ sander.MPI] Error 1
> make[1]: Leaving directory `/usr/local/amber9/src/sander'
> make: *** [parallel] Error 2

********************************************
 Kateryna Miroshnychenko
post-graduate student
Department of Biological Physics,
Institute of Radiophysics and Electronics,
National Academy of Sciences of Ukraine,
12, Proskura st., Kharkiv, 61085, Ukraine
E-mail:kateryna_mirosh_at_ire.kharkov.ua
********************************************

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