here is the config.h file
MATH_DEFINES =
MATH_LIBS =
IFORT_RPATH =
/opt/intel/Compiler/11.0/083/idb/lib/intel64:/opt/intel/Compiler/11.0/083/lib/intel64:/opt/openmpi/1.3.3-1.el5.fys.ifort.11.0/lib64:/usr/local/lib
MATH_DEFINES = -DMKL
MATH_LIBS = /opt/intel/mkl/10.1.3.027/lib/em64t/libmkl_em64t.a-L/opt/intel/mkl/
10.1.3.027/lib/em64t/ -lguide -lpthread
FFT_DEFINES = -DPUBFFT
FFT_INCLUDE =
FFT_LIBS =
NETCDF_HOME =
NETCDF_DEFINES =
NETCDF_MOD =
NETCDF_LIBS =
MPI_HOME = /opt/openmpi/1.3.3-1.el5.fys.ifort.11.0
MPI_DEFINES = -DMPI
MPI_INCLUDE = -I$(MPI_HOME)/include
MPI_LIBDIR = $(MPI_HOME)/lib64
MPI_LIBS = -L$(MPI_LIBDIR)
DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
CPP = /lib/cpp
CPPFLAGS = -traditional -P
F90_DEFINES = -DFFTLOADBAL_2PROC
F90 = mpif90
MODULE_SUFFIX = mod
F90FLAGS = -c -auto
F90_OPT_DBG = -g -traceback
F90_OPT_LO = -tpp7 -O0
F90_OPT_MED = -tpp7 -O2
F90_OPT_HI = -tpp7 -xP -ip -O3
F90_OPT_DFLT = $(F90_OPT_HI)
CC = gcc
CFLAGS =
LOAD = ifort
LOADFLAGS =
LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)
I have tried with and without -lmpi in the mpilib parameter but gave same
error.
On Tue, Aug 10, 2010 at 3:05 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Can you post your config.h file here?
>
> On Tue, Aug 10, 2010 at 2:55 AM, Jorgen Simonsen <jorgen589.gmail.com
> >wrote:
>
> > Hi
> >
> > I remove this from the -lpiif from the MPI_LIBS in the config.h file but
> > get an error on undefined mpi links
> >
> > mdin_ctrl_dat.o: In function `mdin_ctrl_dat_mod_mp_bcast_mdin_ctrl_dat_':
> > mdin_ctrl_dat.f90:(.text+0x21): undefined reference to `mpi_bcast_'
> > mdin_ctrl_dat.f90:(.text+0x45): 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+0x281): undefined reference to `mpi_bcast_'
> > mdin_ewald_dat.f90:(.text+0x2a5): undefined reference to `mpi_bcast_'
> > prmtop_dat.o: In function `prmtop_dat_mod_mp_bcast_amber_prmtop_dat_':
> > prmtop_dat.f90:(.text+0xa64): undefined reference to `mpi_bcast_'
> > prmtop_dat.o:prmtop_dat.f90:(.text+0xaad): more undefined references to
> > `mpi_bcast_' follow
> > dynamics_dat.o: In function `dynamics_dat_mod_mp_destroy_communicators_':
> > dynamics_dat.f90:(.text+0x1b0): undefined reference to `mpi_comm_free_'
> > dynamics_dat.f90:(.text+0x1fe): undefined reference to `mpi_group_free_'
> > dynamics_dat.o: In function `dynamics_dat_mod_mp_create_communicators_':
> > dynamics_dat.f90:(.text+0x3c7): undefined reference to `mpi_group_incl_'
> > dynamics_dat.f90:(.text+0x3f1): undefined reference to `mpi_comm_create_'
> > parallel.o: In function `parallel_mod_mp_pvt_mpi_gathervec_':
> > parallel.f90:(.text+0x5ce4): undefined reference to `mpi_gatherv_'
> > parallel.o: In function `parallel_mod_mp_mpi_gathervec_':
> > parallel.f90:(.text+0x5f5d): undefined reference to `mpi_gatherv_'
> > parallel.o: In function `parallel_mod_mp_pvt_mpi_allgathervec_':
> > etc etc
> >
> > On Mon, Aug 9, 2010 at 9:57 PM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> > > On Mon, Aug 9, 2010 at 12:20 PM, Jorgen Simonsen <jorgen589.gmail.com
> > > >wrote:
> > >
> > > > Hi
> > > >
> > > > I fix it it was something with the path to mpi libraries but I get
> > > another
> > > > error later on in the compilation
> > > >
> > > > ld: cannot find -lmpiif
> > > >
> > >
> > > If you are using mpif90 as the compiler and linker, remove all mpi
> > > libraries
> > > from MPI_LIBRARY (or something like that) in the config.h file, since
> > > mpif90
> > > implicitly takes care of those.
> > >
> > > Good luck!
> > > Jason
> > >
> > >
> > > >
> > > > during this I get the warning
> > > >
> > > > ifort: command line remark #10148: option '-tp' not supported
> > > >
> > > >
> > > > can I ignore this one?
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, Aug 9, 2010 at 3:06 PM, Ross Walker <ross.rosswalker.co.uk>
> > > wrote:
> > > >
> > > > > Hi Jorgen,
> > > > >
> > > > > > the error message is
> > > > > >
> > > > > > module gbl_constants_mod
> > > > > >
> > > > > > implicit none
> > > > > >
> > > > > > ! Global constants:
> > > > > ...
> > > > > > end module gbl_constants_mod
> > > > > > make[1]: *** [gbl_constants.o] Error 1
> > > > > > make[1]: Leaving directory `/home/Programs/amber10/src/pmemd/src'
> > > > > > make: *** [install] Error 2
> > > > >
> > > > > This is an extremely weird error message since it is not actually
> an
> > > > error
> > > > > message it is simply echoing the file to the screen. I suspect
> there
> > > are
> > > > > issues with your precompiler. Can you please post your config.h
> file
> > > > along
> > > > > with details of your system, gcc, cpp versions etc. Also please
> > confirm
> > > > > that
> > > > > you can compile the rest of AMBER fine using your current login and
> > > > > environment setup - try it again just to be sure.
> > > > >
> > > > > Also did you apply all of the bugfixes?
> > > > >
> > > > > All the best
> > > > > Ross
> > > > >
> > > > > /\
> > > > > \/
> > > > > |\oss Walker
> > > > >
> > > > > ---------------------------------------------------------
> > > > > | Assistant Research Professor |
> > > > > | San Diego Supercomputer Center |
> > > > > | Adjunct Assistant Professor |
> > > > > | Dept. of Chemistry and Biochemistry |
> > > > > | University of California San Diego |
> > > > > | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> > > > > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > > > > ---------------------------------------------------------
> > > > >
> > > > > Note: Electronic Mail is not secure, has no guarantee of delivery,
> > may
> > > > not
> > > > > be read every day, and should not be used for urgent or sensitive
> > > issues.
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
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> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
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> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Aug 10 2010 - 10:00:06 PDT
