cheers fixed it
On Tue, Aug 10, 2010 at 8:32 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Doh!!! I missed that. Yes, you need to link with mpif90 as well as compile
> with it. This should fix it.
>
> > -----Original Message-----
> > From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> > Sent: Tuesday, August 10, 2010 11:22 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] error when compiling pmemd
> >
> > Try changing the LOAD variable in your config.h to mpif90 as well.
> >
> > On Tue, Aug 10, 2010 at 2:14 PM, Jorgen Simonsen <jorgen589.gmail.com>
> > wrote:
> > > Hi,
> > >
> > > so I remove the -lmpi and -tpp7 and change the gcc to mpicc in the
> > config.h
> > > file.
> > >
> > > mpif90 -show
> > >
> > > gives
> > >
> > > ifort -I/opt/openmpi/1.3.3-1.el5.fys.ifort.11.0/include
> > > -I/opt/openmpi/1.3.3-1.el5.fys.ifort.11.0/lib64
> > > -L/opt/openmpi/1.3.3-1.el5.fys.ifort.11.0/lib64 -lmpi_f90 -lmpi_f77 -
> > lmpi
> > > -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil
> > >
> > > and which mpif90 gives
> > >
> > > /opt/openmpi/1.3.3-1.el5.fys.ifort.11.0/bin//mpif90
> > >
> > >
> > > make clean and recompile with make install but I still get the error
> > >
> > > ifort -o pmemd gbl_constants.o gbl_datatypes.o state_info.o
> > file_io_dat.o
> > > mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o
> > dynamics_dat.o
> > > img.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o
> > pme_recip_dat.o
> > > pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o
> > pme_fft_dat.o
> > > fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o nb_exclusions.o
> > cit.o
> > > dynamics.o bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o
> > loadbal.o
> > > shake.o prfs.o mol_list.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 pme_alltasks_setup.o pme_setup.o
> > > ene_frc_splines.o gb_alltasks_setup.o nextprmtop_section.o
> > /opt/intel/mkl/
> > > 10.1.3.027/lib/em64t/libmkl_em64t.a
> > > -L/opt/intel/mkl/10.1.3.027/lib/em64t/-lguide -lpthread
> > > -L/opt/openmpi/1.3.3-1.el5.fys.ifort.11.0/lib64 -limf
> > > -lsvml
> > > -Wl,-
> > 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
> > > 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_'
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > On Tue, Aug 10, 2010 at 7:35 PM, Ross Walker <ross.rosswalker.co.uk>
> > wrote:
> > >
> > >> Hi Jorgen,
> > >>
> > >> The config.h file looks okay. With mpif90 you do not need the -lmpi.
> > Change
> > >> gcc to mpicc. You can also take out the -tpp7. Check that all the
> > paths are
> > >> correct. That mpif90 -show points to the compiler you expect. Look
> > at what
> > >> 'which mpif90' gives you.
> > >>
> > >> Also make sure you do a full make clean before compiling again.
> > >>
> > >> All the best
> > >> Ross
> > >>
> > >> > -----Original Message-----
> > >> > From: Jorgen Simonsen [mailto:jorgen589.gmail.com]
> > >> > Sent: Tuesday, August 10, 2010 9:37 AM
> > >> > To: AMBER Mailing List
> > >> > Subject: Re: [AMBER] error when compiling pmemd
> > >> >
> > >> > here is the config.h file
> > >> >
> > >> > MATH_DEFINES =
> > >> > MATH_LIBS =
> > >> > IFORT_RPATH =
> > >> >
> > /opt/intel/Compiler/11.0/083/idb/lib/intel64:/opt/intel/Compiler/11.0/0
> > >> > 83/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.
> > >> > > > > > >
> > >> > > > > > >
> > >> > > > > > >
> > >> > > > > > >
> > >> > > > > > >
> > >> > > > > > > _______________________________________________
> > >> > > > > > > AMBER mailing list
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> > >> > > > > > >
> > >> > > > > > _______________________________________________
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> > >> > > > > >
> > >> > > > >
> > >> > > > >
> > >> > > > >
> > >> > > > > --
> > >> > > > > Jason M. Swails
> > >> > > > > Quantum Theory Project,
> > >> > > > > University of Florida
> > >> > > > > Ph.D. Graduate Student
> > >> > > > > 352-392-4032
> > >> > > > > _______________________________________________
> > >> > > > > AMBER mailing list
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> > >> > > > > 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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> > >>
> > >>
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> > >>
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Received on Tue Aug 10 2010 - 12:00:15 PDT
