Re: AMBER: Question about compiling PMEMD

From: Robert Duke <rduke.email.unc.edu>
Date: Thu, 22 Apr 2004 08:10:47 -0400

Tod -
One other point. I would recommend upgrading to mpich 1.2.5.2, because it will probably have better support for ifc; I can't recollect the version number, but for older versions of mpich I actually had to hack the configure process to get mpich built with ifc as the fortran compiler. This version is available at http://www-unix.mcs.anl.gov/mpi/mpich/
Regards - Bob Duke
  ----- Original Message -----
  From: Tod Pascal
  To: amber.scripps.edu
  Sent: Thursday, April 22, 2004 2:29 AM
  Subject: RE: AMBER: Question about compiling PMEMD


  Professor Duke,
  Thanks for the information. I was able to download version 7.1 and got it installed. The code seems to compile all the way, however crashes at the linking stage with the following error:

   

  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.
  -- Some Engineer

   




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Received on Thu Apr 22 2004 - 13:53:00 PDT
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