AMBER Archive (2009)

Subject: [AMBER] pmemd compile error

From: Giorgos Lamprinidis (lamprinidis_at_pharm.uoa.gr)
Date: Mon Mar 23 2009 - 15:54:37 CDT

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

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