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
>> > > > > > > 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
>> > > > > _______________________________________________
>> > > > > 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
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
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>>
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Received on Tue Aug 10 2010 - 11:30:06 PDT
