AMBER Archive (2006)

Subject: Re: AMBER: compiler error for Amber9

From: Robert Duke (
Date: Wed Jun 07 2006 - 10:03:15 CDT

Okay, I am only responding about pmemd here, and will leave the rest to folks who have actually used open-mpi. If, in the amber/src/pmemd dir, you enter ./configure -help, you will note that open-mpi is not a supported option for pmemd, so I am not sure how you built your config.h for pmemd. However, a sane approach, given the lack of open-mpi support would be to configure for linux64_opteron, pgf90, and mpich2, and THEN go back and hack the config.h to get the mpi libraries right. You can probably make a good guess on the mpi libraries looking at sander; you should not need the f90 interface libraries, and I would probably just try changing -lmpich to -lmpi first. What I don't know about is if libmpi in open-mpi has a bunch of other dependencies. Support for open-mpi is not included with pmemd because it was not very thoroughly documented at time of release - if I recollect there was just a README and no manual. This seemed a little too close to the bleeding edge for me to support in pmemd. I tend to try to support stuff that is known to be fast and stable, and try to let other folks do the alpha/beta testing of other people's code :-) Hope this helps.
Regards - Bob Duke
  ----- Original Message -----
  From: Weihua Li
  Sent: Wednesday, June 07, 2006 10:34 AM
  Subject: AMBER: compiler error for Amber9

  Dear all,
          CPU: AMD opeteron Linux86-64
           I used the following command to configure the open-mpi-1.0.2.
          ./configure --prefix=/home/ytang/gdata/whli/openmpi CC=pgcc CXX=pgCC F90=pgf90 --with-openib
         and set environment variables in .bashrc as follows:
             export MPI_HOME=/home/ytang/gdata/whli/openmpi
            export PATH=$MPI_HOME/bin:$PATH

  In the ~openmpi/lib directory: libmpi_f90.a mpi_kinds.mod mpi.mod openmpi
  For PMEMD module:

  pgf90 -o pmemd gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o parallel_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd
  _dat.o dynamics_dat.o img.o parallel.o pme_direct.o pme_recip.o pme_fft.o fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o cit.o dynamics.o b
  onds.o angles.o dihedrals.o runmd.o loadbal.o shake.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 alltasks_s
  etup.o pme_setup.o ene_frc_splines.o nextprmtop_section.o -L/home/ytang/gdata/whli/openmpi/lib -lmpich
  /usr/bin/ld: cannot find -lmpich
  make[1]: *** [pmemd] Error 2
  make[1]: Leaving directory `/gdata/lun8/ytang/whli/amber9/src/pmemd/src'
  make: *** [install] Error 2

  For sander module:

   ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
  ../lib/nxtsec.o ../lib/sys.a -L/home/ytang/gdata/whli/openmpi/lib -lmpi_f90 -lmpi -lorte -lopal -lutil -lnsl -lpthread -ldl -Wl,--export-dynamic -lm -lutil -lnsl -lpthread -ldl
  /usr/bin/ld: skipping incompatible /home/ytang/gdata/whli/openmpi/lib/libmpi_f90.a when searching for -lmpi_f90
  /usr/bin/ld: cannot find -lmpi_f90
  make[1]: *** [sander.MPI] Error 2
  make[1]: Leaving directory `/gdata/lun8/ytang/whli/amber9/src/sander'
  make: *** [parallel] Error 2

  I know it must be something wrong with the installation of open-mpi, but I don't know where it is.

  Could you please give me some advice?

  Best regards,

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