You gave no indication of what you tried, so we won't actually be able to
provide useful advice.
We need to know *exactly* which commands you used, what changes (if any) you
made to resulting files (i.e. the config.h), and the order in which you
executed those commands in order to help. Also keep in mind that you *must*
run "make clean" in $AMBERHOME/src/pmemd before any fresh attempt in order
to clean up the directory of temporary files from previous, failed attempts.
As Dan pointed out before, your MPI links to GNU compilers while the errors
you're getting here are related to missing symbols in intel compiler
libraries; an indication that you're somehow illegally mixing the 2 (but we
can't tell how).
HTH,
Jason
On Mon, Aug 8, 2011 at 9:47 AM, hari krishna <haricoolguy111.gmail.com>wrote:
> Hi
>
> I tried with the following config, but i got the same error.
>
> *./configure linux_em64t ifort intelmpi pubfft nobintraj*
>
>
> /home/p_kumar/intel/composerxe-2011.5.220/compiler/lib/intel64/libsvml.so:
> undefined reference to `__intel_cpu_indicator_init'
> /home/p_kumar/intel/composerxe-2011.5.220/compiler/lib/intel64/libsvml.so:
> undefined reference to `__intel_cpu_indicator'
> collect2: ld returned 1 exit status
> make[1]: *** [pmemd] Error 1
> make[1]: Leaving directory `/home/p_kumar/amber10/src/pmemd/src'
> make: *** [all] Error 2
>
>
>
> On Mon, Aug 8, 2011 at 6:57 PM, hari krishna <haricoolguy111.gmail.com
> >wrote:
>
> > currently i dont have intel MPI library can i use gfortran as a compiler
> >
> > On Mon, Aug 8, 2011 at 6:45 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >> Your MPI_HOME is pointing to a gnu compilation, but you are attempting
> to
> >> compile with intel compilers. For ./configure ifort you should use an
> MPI
> >> installation compiled with intel compilers as well.
> >>
> >> -Dan
> >>
> >> On Aug 8, 2011, at 8:42 AM, hari krishna <haricoolguy111.gmail.com>
> >> wrote:
> >>
> >> > I am using AMBER10 below is the config.h file
> >> > platform: X86_64
> >> > compiler: ifort
> >> > mpi: mpich2
> >> > not using netcdf as default
> >> >
> >> > *./configure linux64_opteron ifort mpich2 pubfft nobintraj* (this is
> the
> >> one
> >> > i tried now)
> >> >
> >> > MATH_DEFINES =
> >> > MATH_LIBS =
> >> > IFORT_RPATH =
> >> >
> >>
> /home/p_kumar/intel/composerxe-2011.5.220/compiler/lib/intel64:/home/p_kumar/intel/composerxe-2011.5.220/compiler/lib/intel64:/home/p_kumar/intel/composerxe-2011.5.220/mkl/lib/intel64:/home/p_kumar/intel/composerxe-2011.5.220/compiler/lib/ia32:/home/p_kumar/intel/composerxe-2011.5.220/compiler/lib/ia32:/home/p_kumar/intel/composerxe-2011.5.220/mkl/lib/ia32:/home/p_kumar/intel/composerxe-2011.5.220/compiler/lib/intel64:/home/p_kumar/intel/composerxe-2011.5.220/compiler/lib/intel64:/home/p_kumar/intel/composerxe-2011.5.220/mkl/lib/intel64:/home/p_kumar/intel/composerxe-2011.5.220/compiler/lib/ia32:/home/p_kumar/intel/composerxe-2011.5.220/compiler/lib/ia32:/home/p_kumar/intel/composerxe-2011.5.220/mkl/lib/ia32:/home/p_kumar/intel/composerxe-2011.5.220/mpirt/lib/ia32:/home/p_kumar/intel/composerxe-2011.5.220/mpirt/lib/intel64:/home/p_kumar/intel/composerxe-2011.5.220/mpirt/lib/ia32:/home/p_kumar/intel/composerxe-2011.5.220/mpirt/lib/intel64
> >> > FFT_DEFINES = -DPUBFFT
> >> > FFT_INCLUDE =
> >> > FFT_LIBS =
> >> > NETCDF_HOME =
> >> > NETCDF_DEFINES =
> >> > NETCDF_MOD =
> >> > NETCDF_LIBS =
> >> > MPI_HOME = /opt/mpich2/gnu
> >> > MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
> >> > MPI_INCLUDE = -I$(MPI_HOME)/include
> >> > MPI_LIBDIR = $(MPI_HOME)/lib
> >> > MPI_LIBS =
> >> > DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_NOVEC
> >> > CPP = /lib/cpp
> >> > CPPFLAGS = -traditional -P
> >> > F90_DEFINES = -DFFTLOADBAL_2PROC
> >> >
> >> > F90 = mpif90
> >> > MODULE_SUFFIX = mod
> >> > F90FLAGS = -c -auto
> >> > F90_OPT_DBG = -g -traceback
> >> > F90_OPT_LO = -O0
> >> > F90_OPT_MED = -O2
> >> > F90_OPT_HI = -xW -ip -O3
> >> > CC = gcc
> >> > CFLAGS =
> >> >
> >> > LOAD = mpif90
> >> > LOADFLAGS =
> >> > LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)
> >> >
> >> > Error Message
> >> >
> >> >
> >>
> /home/p_kumar/intel/composerxe-2011.5.220/compiler/lib/intel64/libsvml.so:
> >> > undefined reference to `__intel_cpu_indicator_init'
> >> >
> >>
> /home/p_kumar/intel/composerxe-2011.5.220/compiler/lib/intel64/libsvml.so:
> >> > undefined reference to `__intel_cpu_indicator'
> >> > collect2: ld returned 1 exit status
> >> > make[1]: *** [pmemd] Error 1
> >> > make[1]: Leaving directory `/home/p_kumar/amber10/src/pmemd/src'
> >> > make: *** [all] Error 2
> >> >
> >> >
> >> > On Mon, Aug 8, 2011 at 5:45 PM, David A Case <
> case.biomaps.rutgers.edu
> >> >wrote:
> >> >
> >> >> On Mon, Aug 08, 2011, hari krishna wrote:
> >> >>>
> >> >>> *./configure linux64_opteron gfortran mpi pubfft bintraj *
> >> >>
> >> >> This looks like a very old version of Amber; what version is it?
> >> >>
> >> >>> ---
> >> >>> *make *
> >> >>>
> >> >>> *end module gbl_constants_mod
> >> >>> gbl_constants.f90
> >> >>> make[1]: gbl_constants.f90: Command not found
> >> >>
> >> >> We need more details of the error message. Also, does sander compile
> >> >> correctly? It's probably also good to post the config.h file that is
> >> >> created
> >> >> by configure.
> >> >>
> >> >> ...dac
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Aug 08 2011 - 08:00:04 PDT
