AMBER Archive (2009)

Subject: Re: [AMBER] pmemd compile error

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Mar 23 2009 - 16:03:45 CDT

You need to read all the stuff on the amber website about compiling/linking
parallel sander or pmemd with mpi. It could be that the lam mpi you have
here was not built with the same fortran compiler specified as you used for
pmemd, and when that is the case, the "name mangling" of the mpi calls can
be wrong (so I would suspect that if you did not build lam with ifort
specified, that would be the problem; I think, though am not certain, that a
lam library that ships with your machine is unlikely to be usable with
ifort).
Regards - Bob Duke
----- Original Message -----
From: "Giorgos Lamprinidis" <lamprinidis_at_pharm.uoa.gr>
To: <amber_at_ambermd.org>
Sent: Monday, March 23, 2009 4:54 PM
Subject: [AMBER] pmemd compile error

> Dear all,
>
> I am trying to compile pmemd on a P4 computer runnig fedora 10.
> I have installed Intel Compiller ifort 11. The steps i followed were,
>
> 1) source /opt/intel/Compiler/11.0/081/bin/ia32/ifortvars_ia32.csh
> 2) ./configure linux_p4 ifort lam
> 3) make install
>
> and i get a lot of errors:
> cd src && make install
> make[1]: Entering directory `/opt/amber10/src/pmemd/src'
> ifort -o pmemd gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o
> mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o
> img.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o pme_recip_dat.o
> pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o
> pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o
> nb_exclusions.o cit.o dynamics.o bonds.o angles.o dihedrals.o
> extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o
> constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o
> pmemd_lib.o runfiles.o file_io.o bintraj.o pmemd_clib.o pmemd.o random.o
> degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o
> pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o
> nextprmtop_section.o -L/usr/local/lib -llamf77mpi -lmpi -llam -ldl
> -lpthread -limf -lsvml
> -Wl,-rpath=/opt/intel/Compiler/11.0/081/lib/ia32:/opt/intel/Compiler/11.0/081/lib/ia32
> mdin_ctrl_dat.o: In function `mdin_ctrl_dat_mod_mp_bcast_mdin_ctrl_dat_':
> mdin_ctrl_dat.f90:(.text+0x1c): undefined reference to `mpi_bcast_'
> mdin_ctrl_dat.f90:(.text+0x3c): undefined reference to `mpi_bcast_'
> mdin_ewald_dat.o: In function
> `mdin_ewald_dat_mod_mp_bcast_mdin_ewald_dat_':
> mdin_ewald_dat.f90:(.text+0x28c): undefined reference to `mpi_bcast_'
> mdin_ewald_dat.f90:(.text+0x2ac): undefined reference to `mpi_bcast_'
> prmtop_dat.o: In function `prmtop_dat_mod_mp_bcast_amber_prmtop_dat_':
> prmtop_dat.f90:(.text+0xa2f): undefined reference to `mpi_bcast_'
> prmtop_dat.o:prmtop_dat.f90:(.text+0xa73): more undefined references to
> `mpi_bcast_' follow
> dynamics_dat.o: In function `dynamics_dat_mod_mp_destroy_communicators_':
> dynamics_dat.f90:(.text+0x184): undefined reference to `mpi_comm_free_'
> dynamics_dat.f90:(.text+0x1bd): undefined reference to `mpi_group_free_'
> dynamics_dat.o: In function `dynamics_dat_mod_mp_create_communicators_':
> dynamics_dat.f90:(.text+0x33e): undefined reference to `mpi_group_incl_'
> dynamics_dat.f90:(.text+0x36b): undefined reference to `mpi_comm_create_'
> parallel.o: In function `parallel_mod_mp_pvt_mpi_gathervec_':
> parallel.f90:(.text+0x2fdf): undefined reference to `mpi_gatherv_'
> parallel.o: In function `parallel_mod_mp_mpi_gathervec_':
> parallel.f90:(.text+0x323d): undefined reference to `mpi_gatherv_'
> parallel.o: In function `parallel_mod_mp_pvt_mpi_allgathervec_':
> parallel.f90:(.text+0x348c): undefined reference to `mpi_allgatherv_'
> parallel.o: In function `parallel_mod_mp_mpi_allgathervec_':
> parallel.f90:(.text+0x36da): undefined reference to `mpi_allgatherv_'
> parallel.o: In function `parallel_mod_mp_pvt_distribute_crds_':
> parallel.f90:(.text+0x3976): undefined reference to `mpi_isend_'
> parallel.f90:(.text+0x39cd): undefined reference to `mpi_recv_'
> parallel.f90:(.text+0x3a4b): undefined reference to `mpi_wait_'
> parallel.o: In function `parallel_mod_mp_distribute_crds_':
> parallel.f90:(.text+0x3b9d): undefined reference to `mpi_isend_'
> parallel.f90:(.text+0x3bf7): undefined reference to `mpi_recv_'
> parallel.f90:(.text+0x3c82): undefined reference to `mpi_wait_'
> parallel.o: In function `parallel_mod_mp_pvt_distribute_img_frcs_':
> parallel.f90:(.text+0x3e10): undefined reference to `mpi_isend_'
> parallel.f90:(.text+0x3e59): undefined reference to `mpi_recv_'
> parallel.f90:(.text+0x3ed7): undefined reference to `mpi_wait_'
> parallel.o: In function `parallel_mod_mp_distribute_img_frcs_':
> parallel.f90:(.text+0x40c6): undefined reference to `mpi_isend_'
> parallel.f90:(.text+0x410d): undefined reference to `mpi_recv_'
> parallel.f90:(.text+0x418e): undefined reference to `mpi_wait_'
> parallel.o: In function `parallel_mod_mp_pvt_get_img_frc_distribution_':
> parallel.f90:(.text+0x4234): undefined reference to `mpi_isend_'
> parallel.f90:(.text+0x4273): undefined reference to `mpi_recv_'
> parallel.f90:(.text+0x428c): undefined reference to `mpi_get_count_'
> parallel.f90:(.text+0x42b1): undefined reference to `mpi_wait_'
> parallel.o: In function `parallel_mod_mp_get_img_frc_distribution_':
> parallel.f90:(.text+0x43b2): undefined reference to `mpi_isend_'
> parallel.f90:(.text+0x43f2): undefined reference to `mpi_recv_'
> parallel.f90:(.text+0x440e): undefined reference to `mpi_get_count_'
> parallel.f90:(.text+0x443d): undefined reference to `mpi_wait_'
> gb_parallel.o: In function `gb_parallel_mod_mp_gb_mpi_gathervec_':
> gb_parallel.f90:(.text+0x5e): undefined reference to `mpi_gatherv_'
> gb_parallel.o: In function `gb_parallel_mod_mp_gb_mpi_allgathervec_':
> gb_parallel.f90:(.text+0xcb): undefined reference to `mpi_allgatherv_'
> gb_parallel.o: In function `gb_parallel_mod_mp_gb_frcs_distrib_':
> gb_parallel.f90:(.text+0x134): undefined reference to
> `mpi_reduce_scatter_'
> pme_direct.o: In function `pme_direct_mod_mp_bcast_pme_direct_dat_':
> pme_direct.f90:(.text+0x6778): undefined reference to `mpi_bcast_'
> pme_slab_fft.o: In function `pme_slab_fft_mod_mp_zxy_xyz_trans_receive_':
> pme_slab_fft.f90:(.text+0x62): undefined reference to `mpi_recv_'
> pme_slab_fft.o: In function
> `pme_slab_fft_mod_mp_dist_zxy_xyz_transpose_.':
> pme_slab_fft.f90:(.text+0xb0d): undefined reference to `mpi_isend_'
> pme_slab_fft.f90:(.text+0xb8a): undefined reference to `mpi_recv_'
> pme_slab_fft.f90:(.text+0xd56): undefined reference to `mpi_wait_'
> pme_slab_fft.o: In function `pme_slab_fft_mod_mp_xyz_zxy_trans_receive_':
> pme_slab_fft.f90:(.text+0xf32): undefined reference to `mpi_recv_'
> pme_slab_fft.o: In function
> `pme_slab_fft_mod_mp_dist_xyz_zxy_transpose_.':
> pme_slab_fft.f90:(.text+0x1a69): undefined reference to `mpi_isend_'
> pme_slab_fft.f90:(.text+0x1ae2): undefined reference to `mpi_recv_'
> pme_slab_fft.f90:(.text+0x1ca5): undefined reference to `mpi_wait_'
> pme_blk_fft.o: In function `pme_blk_fft_mod_mp_do_zy_transpose_.':
> pme_blk_fft.f90:(.text+0x579): undefined reference to `mpi_irecv_'
> pme_blk_fft.f90:(.text+0x895): undefined reference to `mpi_isend_'
> pme_blk_fft.f90:(.text+0xb0c): undefined reference to `mpi_waitany_'
> pme_blk_fft.f90:(.text+0xcb2): undefined reference to `mpi_waitall_'
> pme_blk_fft.o: In function `pme_blk_fft_mod_mp_do_yx_transpose_.':
> pme_blk_fft.f90:(.text+0xef3): undefined reference to `mpi_irecv_'
> pme_blk_fft.f90:(.text+0x1209): undefined reference to `mpi_isend_'
> pme_blk_fft.f90:(.text+0x147b): undefined reference to `mpi_waitany_'
> pme_blk_fft.f90:(.text+0x1623): undefined reference to `mpi_waitall_'
> pme_blk_fft.o: In function `pme_blk_fft_mod_mp_do_xy_transpose_.':
> pme_blk_fft.f90:(.text+0x24c9): undefined reference to `mpi_irecv_'
> pme_blk_fft.f90:(.text+0x27e2): undefined reference to `mpi_isend_'
> pme_blk_fft.f90:(.text+0x2a58): undefined reference to `mpi_waitany_'
> pme_blk_fft.f90:(.text+0x2bfd): undefined reference to `mpi_waitall_'
> pme_blk_fft.o: In function `pme_blk_fft_mod_mp_do_yz_transpose_.':
> pme_blk_fft.f90:(.text+0x2e2b): undefined reference to `mpi_irecv_'
> pme_blk_fft.f90:(.text+0x3148): undefined reference to `mpi_isend_'
> pme_blk_fft.f90:(.text+0x33b8): undefined reference to `mpi_waitany_'
> pme_blk_fft.f90:(.text+0x3560): undefined reference to `mpi_waitall_'
> pme_force.o: In function `pme_force_mod_mp_dist_enes_virs_netfrcs_.':
> pme_force.f90:(.text+0x2545): undefined reference to `mpi_allreduce_'
> pme_force.f90:(.text+0x2614): undefined reference to `mpi_allreduce_'
> pme_force.f90:(.text+0x27ab): undefined reference to `mpi_allreduce_'
> pbc.o: In function `pbc_mod_mp_bcast_pbc_':
> pbc.f90:(.text+0x26ac): undefined reference to `mpi_bcast_'
> pbc.f90:(.text+0x26cc): undefined reference to `mpi_bcast_'
> dynamics.o: In function `dynamics_mod_mp_get_ekcom_':
> dynamics.f90:(.text+0xb45): undefined reference to `mpi_reduce_'
> dynamics.o: In function `dynamics_mod_mp_get_mol_com_':
> dynamics.f90:(.text+0x119e): undefined reference to `mpi_allreduce_'
> extra_pnts_nb14.o: In function
> `extra_pnts_nb14_mod_mp_bcast_extra_pnts_nb14_dat_':
> extra_pnts_nb14.f90:(.text+0x4ad8): undefined reference to `mpi_bcast_'
> extra_pnts_nb14.f90:(.text+0x4d3f): undefined reference to `mpi_bcast_'
> extra_pnts_nb14.f90:(.text+0x4da0): undefined reference to `mpi_bcast_'
> extra_pnts_nb14.f90:(.text+0x4dcf): undefined reference to `mpi_bcast_'
> runmd.o: In function `runmd_mod_mp_runmd_':
> runmd.f90:(.text+0xbd1): undefined reference to `mpi_allreduce_'
> runmd.f90:(.text+0xdfc): undefined reference to `mpi_allreduce_'
> runmd.f90:(.text+0x1ce0): undefined reference to `mpi_allreduce_'
> runmd.f90:(.text+0x2045): undefined reference to `mpi_allreduce_'
> loadbal.o: In function `loadbal_mod_mp_do_img_redistribution_':
> loadbal.f90:(.text+0x291): undefined reference to `mpi_gather_'
> loadbal.f90:(.text+0x7e7): undefined reference to `mpi_bcast_'
> loadbal.f90:(.text+0x9d5): undefined reference to `mpi_bcast_'
> loadbal.o: In function `loadbal_mod_mp_do_fft_redistribution_.':
> loadbal.f90:(.text+0x188b): undefined reference to `mpi_gather_'
> loadbal.f90:(.text+0x1a6f): undefined reference to `mpi_bcast_'
> loadbal.f90:(.text+0x1b3b): undefined reference to `mpi_bcast_'
> runmin.o: In function `runmin_mod_mp_runmin_slave_':
> runmin.f90:(.text+0xc1): undefined reference to `mpi_bcast_'
> runmin.f90:(.text+0x108): undefined reference to `mpi_bcast_'
> runmin.o: In function `runmin_mod_mp_runmin_master_':
> runmin.f90:(.text+0x608): undefined reference to `mpi_bcast_'
> runmin.o:runmin.f90:(.text+0x633): more undefined references to
> `mpi_bcast_' follow
> gb_ene.o: In function `gb_ene_mod_mp_gb_ene_':
> gb_ene.f90:(.text+0x192d): undefined reference to `mpi_allreduce_'
> gb_ene.o: In function `gb_ene_mod_mp_calc_born_radii_.':
> gb_ene.f90:(.text+0x430a): undefined reference to `mpi_allreduce_'
> gb_force.o: In function `gb_force_mod_mp_gb_distribute_enes_':
> gb_force.f90:(.text+0xaa): undefined reference to `mpi_allreduce_'
> gb_force.o: In function `gb_force_mod_mp_gb_force_':
> gb_force.f90:(.text+0x851): undefined reference to `mpi_allreduce_'
> timers.o: In function `timers_mod_mp_profile_parallel_cpu_.':
> timers.f90:(.text+0x927): undefined reference to `mpi_send_'
> timers.f90:(.text+0x23a4): undefined reference to `mpi_recv_'
> timers.f90:(.text+0x2af1): undefined reference to `mpi_send_'
> timers.f90:(.text+0x36b2): undefined reference to `mpi_recv_'
> timers.f90:(.text+0x3b05): undefined reference to `mpi_send_'
> timers.f90:(.text+0x4a8e): undefined reference to `mpi_recv_'
> timers.o: In function `timers_mod_mp_profile_owner_user_stats_':
> timers.f90:(.text+0x512b): undefined reference to `mpi_send_'
> timers.f90:(.text+0x777e): undefined reference to `mpi_recv_'
> pmemd_lib.o: In function `pmemd_lib_mod_mp_mstartup_':
> pmemd_lib.f90:(.text+0x6): undefined reference to `mpi_init_'
> pmemd_lib.f90:(.text+0x19): undefined reference to `mpi_comm_rank_'
> pmemd_lib.f90:(.text+0x2c): undefined reference to `mpi_comm_size_'
> pmemd_lib.f90:(.text+0x40): undefined reference to `mpi_comm_group_'
> pmemd_lib.o: In function `pmemd_lib_mod_mp_alloc_error_':
> pmemd_lib.f90:(.text+0x124): undefined reference to `mpi_group_free_'
> pmemd_lib.f90:(.text+0x13b): undefined reference to `mpi_abort_'
> pmemd_lib.o: In function `pmemd_lib_mod_mp_setup_alloc_error_':
> pmemd_lib.f90:(.text+0x1c9): undefined reference to `mpi_group_free_'
> pmemd_lib.f90:(.text+0x1dd): undefined reference to `mpi_abort_'
> pmemd_lib.o: In function `pmemd_lib_mod_mp_mexit_':
> pmemd_lib.f90:(.text+0x23b): undefined reference to `mpi_group_free_'
> pmemd_lib.f90:(.text+0x251): undefined reference to `mpi_finalize_'
> pmemd_lib.f90:(.text+0x2a1): undefined reference to `mpi_abort_'
> pmemd.o: In function `MAIN__':
> pmemd.f90:(.text+0x5ed): undefined reference to `mpi_bcast_'
> nmr_calls.o: In function `nmr_calls_mod_mp_bcast_nmr_dat_':
> nmr_calls.f90:(.text+0xbb48): undefined reference to `mpi_bcast_'
> nmr_calls.f90:(.text+0xbb68): undefined reference to `mpi_bcast_'
> nmr_calls.f90:(.text+0xbd8c): undefined reference to `mpi_bcast_'
> nmr_calls.f90:(.text+0xbdad): undefined reference to `mpi_bcast_'
> ene_frc_splines.o:ene_frc_splines.f90:(.text+0x1ae8): more undefined
> references to `mpi_bcast_' follow
> make[1]: *** [pmemd] Error 1
> make[1]: Leaving directory `/opt/amber10/src/pmemd/src'
> make: *** [install] Error 2
>
>
>
> any suggestions?
>
> Regards
> Dr. George Lamprinidis
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber