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AMBER Archive (2004)Subject: Re: AMBER: Question about compiling PMEMD
From: Robert Duke (rduke_at_email.unc.edu)
Tod -
Professor Duke,
SYSLIB=`../sysdir lib` ; ../Compile LOAD -o pmemd \
gbl_datatypes.o file_io_dat.o parallel_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o gbl_dat.o ew_dat.o ew_direct_cit_dat.o ew_direct_dat.o ew_dipole_dat.o ew_direct_cit.o ew_recip_cit.o ew_fft_cit.o ew_force_cit.o ew_fft.o ew_bspline.o ew_box.o force_cit.o runmd_cit.o runmd_cit7.o shake_cit.o runmin_cit.o axis_optimize_cit.o ew_lib.o pmemd_lib.o runfiles.o file_io.o parallel.o ew_direct.o ew_recip.o ew_force.o ew_dipole.o ew_recip_dipole.o ew_recip_reg.o shake.o pmemd_clib.o pmemd.o random.o runmin.o force.o runmd.o degcnt.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o alltasks_setup.o ew_setup.o nextprmtop_section.o help.o $SYSLIB;
ifc -i_dynamic -o pmemd gbl_datatypes.o file_io_dat.o parallel_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o
inpcrd_dat.o gbl_dat.o ew_dat.o ew_direct_cit_dat.o ew_direct_dat.o ew_dipole_dat.o ew_direct_cit.o ew_recip_cit.o
ew_fft_cit.o ew_force_cit.o ew_fft.o ew_bspline.o ew_box.o force_cit.o runmd_cit.o runmd_cit7.o shake_cit.o runmin_cit.o axis_optimize_cit.o ew_lib.o pmemd_lib.o runfiles.o file_io.o parallel.o ew_direct.o ew_recip.o ew_force.o ew_dipole.o ew_recip_dipole.o ew_recip_reg.o shake.o pmemd_clib.o pmemd.o random.o runmin.o force.o runmd.o degcnt.o
nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o alltasks_setup.o ew_setup.o nextprmtop_section.o help.o ../Machines/intel/sys.a -limf -lsvml -lPEPCF90 -L/opt/mpich-1.2.4/lib -lpthread -lmpich
parallel_dat.o: In function `parallel_dat_module..wrapped_cit_mpi_gathervec_.':
parallel_dat.o(.text+0x1e2): undefined reference to `mpi_gatherv_'
parallel_dat.o: In function `parallel_dat_module..wrapped_cit_mpi_allgathervec_.':
parallel_dat.o(.text+0x5f1): undefined reference to `mpi_allgatherv_'
mdin_ctrl_dat.o: In function `mdin_ctrl_dat_module..bcast_mdin_ctrl_dat_':
mdin_ctrl_dat.o(.text+0x41): undefined reference to `mpi_bcast_'
mdin_ctrl_dat.o(.text+0x84): undefined reference to `mpi_bcast_'
mdin_ewald_dat.o: In function `mdin_ewald_dat_module..bcast_mdin_ewald_dat_':
mdin_ewald_dat.o(.text+0x41): undefined reference to `mpi_bcast_'
mdin_ewald_dat.o(.text+0x84): undefined reference to `mpi_bcast_'
And so on. I think that I might be missing a library, but haven't been able to figure out what's wrong. Any ideas?
Regards,
Tod
The glass is neither half empty nor half full. It was simply designed too large to begin with.
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