AMBER Archive (2006)

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

From: Chengwen Chen (chenchengwen_at_gmail.com)
Date: Mon Jun 26 2006 - 23:41:05 CDT

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

On 6/23/06, Wei Zhang <zweig_at_scripps.edu> wrote:
>
> it says "can't find ifort", you may need run some command like "source
> /opt/intel_fc_80/bin/ifortvars.csh" first to put ifort in you path.
>
> Chengwen Chen wrote:
>
> > Dear all,
> >
> > I have succesfully compiled serial version of AMBER 9 on Redhat Linux.
> > But when I tried to compile the parallel version, some problems
> > aroused, which I think come from Open MPI. Open MPI 1.0.2 was used.
> > When I compliled Open MPI, no error message occurred. The messages of
> > compiling is attatched below.
> > Would you kindly give me some advices? Thank you very much in advance.
> >
> > Best Wishes,
> > Chengwen Chen
> >
> >
> >
> >
> >
> > [root_at_wolf46 tmp]# cd openmpi-1.0.2
> > [[root_at_wolf46 openmpi-1.0.2]# mkdir build
> > [root_at_wolf46 openmpi-1.0.2]# cd build
> > [root_at_wolf46 build]# ../configure --prefix=/usr/local/openmpi
> > --enable-mpi-f90
> > .............................
> > [root_at_wolf46 build]# make all install
> > ...............................
> >
> > [root_at_wolf46 build]# cd /usr/local/amber9/src/
> > [root_at_wolf46 src]# export PATH=/opt/intel/fc/9.0/bin:$PATH
> > [root_at_wolf46 src]# export MKL_HOME=/opt/intel/mkl721
> > [root_at_wolf46 src]# export AMBERHOME=/usr/local/amber9
> > [root_at_wolf46 src]# export MPI_HOME=/usr/local/openmpi
> > [root_at_wolf46 src]# export PATH=$MPI_HOME/bin:$PATH
> > [root_at_wolf46 src]# ./configure -openmpi ifort_ia32
> > AMBERHOME is set to /usr/local/amber9
> > Setting up Amber configuration file for architecture: ifort_ia32
> > Using parallel communications library: openmpi
> > MPI_HOME is set to /usr/local/openmpi
> >
> --------------------------------------------------------------------------
> > Unfortunately, this installation of Open MPI was not compiled with
> > Fortran 90 support. As such, the mpif90 compiler is non-functional.
> >
> --------------------------------------------------------------------------
> > MKL_HOME is set to /opt/intel/mkl721/
> > Using MKL libraries from /opt/intel/mkl721//lib/32
> >
> > The configuration file, config.h, was successfully created.
> >
> > [root_at_wolf46 src]# make parallel
> > Starting installation of Amber9 (parallel) at Thu Jun 22 14:56:50 HKT
> > 2006.
> > cd sander; make parallel
> > make[1]: Entering directory `/usr/local/amber9/src/sander'
> > ./checkparconf
> > cpp -traditional -I/usr/local/openmpi/include -P -DMPI -DMKL
> > evb_vars.f > _evb_vars.f
> > ifort -c -w95 -mp1 -O0 -FR -o evb_vars.o _evb_vars.f
> > make[1]: ifort: Command not found
> > make[1]: *** [evb_vars.o] Error 127
> > make[1]: Leaving directory `/usr/local/amber9/src/sander'
> > make: *** [parallel] Error 2
> >
> >
>
>
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