Actually I don't think it much matters if you don't have icc for pmemd10 (it
will matter more-so for amber11 with the cuda build I think), I believe gcc
is sufficient for this (and it doesn't even need to be mpicc, as far as I
remember, gcc will suffice).
A couple things worth trying: does openMPI work? (or any other MPI, so we
can rule out something funny with mpich2) Or, can you roll back to an older
version of the intel compilers, and does that work? I use 11.1.069 with
mpich2-1.2.1p and it works just fine out of the box...
Good luck!
Jason
On Sun, Sep 12, 2010 at 9:56 PM, colvin <colvin4367.gmail.com> wrote:
> Hi Jason,
>
> Thanks for your reply.
>
> Yes, it is amber10, and NO. i do not have icc.
> Yes. I have sourced the intel environment setup scripts.
> Okay. i will try with icc this time.
>
> Thanks again.
>
> Regards,
> Colvin
>
>
>
>
> On Mon, Sep 13, 2010 at 9:50 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > Hello,
> >
> > On Sun, Sep 12, 2010 at 9:36 PM, colvin <colvin4367.gmail.com> wrote:
> >
> >> Hi Jason.
> >>
> >> mpif90 -show =
> >> /opt/intel/Compiler/11.1/073/bin/intel64/ifort -I/opt/mpich2/include
> >> -I/opt/mpich2/include -L/opt/mpich2/lib -L/opt/mpich2/lib -lmpichf90
> >> -lmpichf90 -lmpich -lopa -lpthread -lrt
> >>
> >> mpif77 -show =
> >> /opt/intel/Compiler/11.1/073/bin/intel64/ifort -I/opt/mpich2/include
> >> -L/opt/mpich2/lib -L/opt/mpich2/lib -lmpich -lopa -lpthread -lrt
> >>
> >> mpicc -show=
> >> gcc -I/opt/mpich2/include -L/opt/mpich2/lib -L/opt/mpich2/lib -lmpich
> >> -lopa -lpthread -lrt
> >>
> >
> > This right here may easily be your problem. Do you have icc? I believe
> > this is pmemd 10 that you're trying to install, right? Can you recompile
> > mpich2, but make sure that you specify CC=icc and CXX=icpc on the
> configure
> > line (along with F90=ifort and F77=ifort) so that the right compilers are
> > used. I'm not sure how much C code is actually used in pmemd, but it's
> > easier to link icc-created binaries to ifort-created binaries than
> gcc/ifort
> > linking, as far as I know... Also, have you sourced the intel
> environment
> > setup scripts? In your case,
> /opt/intel/Compiler/11.1/073/bin/ifortvars.sh
> > and the corresponding iccvars.sh? If not, you should probably do that as
> > well.
> >
> > Hopefully some of this helps (or others can provide more helpful advice,
> > since I haven't fiddled with amber10 in quite some time).
> >
> > Good luck!
> > Jason
> >
> >
> >>
> >> config.h (after the changes, including removing -tpp7 that you
> >> suggested, but also giving the same error as previous)
> >>
> >> MATH_DEFINES =
> >> MATH_LIBS =
> >> IFORT_RPATH = /opt/intel/Compiler/11.1/073/lib/intel64
> >> FFT_DEFINES = -DPUBFFT
> >> FFT_INCLUDE =
> >> FFT_LIBS =
> >> NETCDF_HOME =
> >> NETCDF_DEFINES =
> >> NETCDF_MOD =
> >> NETCDF_LIBS =
> >> MPI_HOME = /opt/mpich2
> >> MPI_DEFINES = -DMPI
> >> MPI_INCLUDE = -I$(MPI_HOME)/include
> >> MPI_LIBDIR =
> >> MPI_LIBS =
> >> 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 = -O0
> >> F90_OPT_MED = -O2
> >> F90_OPT_HI = -fast
> >> F90_OPT_DFLT = $(F90_OPT_HI)
> >>
> >> CC = mpicc
> >> CFLAGS =
> >>
> >> LOAD = mpif90
> >> LOADFLAGS =
> >> LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)
> >>
> >> Thank you very much!
> >>
> >> Regards,
> >> Colvin
> >>
> >> On Thu, Sep 9, 2010 at 9:10 PM, Jason Swails <jason.swails.gmail.com>
> >> wrote:
> >> > Hi Colvin,
> >> >
> >> > Google seems to suggest that this is a shared library problem, but
> I've
> >> > never seen it before. However, you do have a pretty new version of
> the
> >> > intel fortran compilers, so maybe something broke on their end. Here
> are
> >> a
> >> > couple things you could try, but first I'd like to know what the
> >> following
> >> > commands return:
> >> >
> >> > mpif90 -show
> >> > mpif77 -show
> >> > mpicc -show
> >> >
> >> > Try taking out -tpp7 from all of the foptflags variables (just leaving
> >> -O2
> >> > and -O0 for Low and Medium optimizations). Also, what does your
> config.h
> >> > file look like after you've made the changes that you mentioned?
> >> >
> >> > Good luck!
> >> > Jason
> >> >
> >> > On Thu, Sep 9, 2010 at 5:36 AM, colvin <colvin4367.gmail.com> wrote:
> >> >
> >> >> Hi.
> >> >>
> >> >> Thanks for the reply.
> >> >>
> >> >> I did change it (I have mentioned in my previous email), but still
> >> >> giving the same error.
> >> >>
> >> >>
> >> >> On Thu, Sep 9, 2010 at 5:19 PM, Per Jr. Greisen <pgreisen.gmail.com>
> >> >> wrote:
> >> >> > Hi,
> >> >> >
> >> >> > I think you should change your compiler to mpi - f.ex
> >> >> > F90 = mpif90
> >> >> > CC = mpicc
> >> >> > or whatever fortran compiler u have for mpi -
> >> >> >
> >> >> >
> >> >> > for the tp and intel there was a thread a couple of weeks ago where
> a
> >> >> > short discussion of the mpi-libraries and intel options were
> >> >> > discussed.
> >> >> >
> >> >> > hope it helps,
> >> >> >
> >> >> >
> >> >> > On Thu, Sep 9, 2010 at 11:04 AM, colvin <colvin4367.gmail.com>
> wrote:
> >> >> >> Hello,
> >> >> >>
> >> >> >> I am having problem in installing pmemd (in amber 10) in my intel
> >> xeon
> >> >> >> quad core machine, fedora 12.
> >> >> >>
> >> >> >> Prior to pmemd installation, i have installed ifort 11.1, and
> >> >> >> mpich2-1.2.1p1 (with F77=ifort, F90=ifort, CC=gcc, and CXX=g++).
> the
> >> >> >> MPI_HOME is set to the mpich2 installed directory.
> >> >> >>
> >> >> >> All bugfixes applied. In amber10/src/pmemd, i type ./configure
> >> >> >> linux_em64t ifort mpich2 and here is my config.h:
> >> >> >>
> >> >> >> MATH_DEFINES =
> >> >> >> MATH_LIBS =
> >> >> >> IFORT_RPATH = /opt/intel/Compiler/11.1/073/lib/intel64
> >> >> >> FFT_DEFINES = -DPUBFFT
> >> >> >> FFT_INCLUDE =
> >> >> >> FFT_LIBS =
> >> >> >> NETCDF_HOME =
> >> >> >> NETCDF_DEFINES =
> >> >> >> NETCDF_MOD =
> >> >> >> NETCDF_LIBS =
> >> >> >> MPI_HOME = /opt/mpich2
> >> >> >> MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
> >> >> >> MPI_INCLUDE = -I$(MPI_HOME)/include
> >> >> >> MPI_LIBDIR = $(MPI_HOME)/lib
> >> >> >> MPI_LIBS = -L$(MPI_LIBDIR) -lmpich -lrt -luuid -lpthread
> >> >> >> DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> >> >> >> CPP = /lib/cpp
> >> >> >> CPPFLAGS = -traditional -P
> >> >> >> F90_DEFINES = -DFFTLOADBAL_2PROC
> >> >> >>
> >> >> >> F90 = ifort
> >> >> >> 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)
> >> >> >>
> >> >> >> then, i type make install, here is the error:
> >> >> >> cd src && make install
> >> >> >> make[1]: Entering directory `/usr/local/amber10/src/pmemd/src'
> >> >> >> /lib/cpp -traditional -P -I/opt/mpich2/include -DPUBFFT -DMPI
> >> >> >> -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS -DDIRFRC_COMTRANS
> -DDIRFRC_NOVEC
> >> >> >> -DFFTLOADBAL_2PROC gbl_constants.fpp gbl_constants.f90
> >> >> >> ifort -c -auto -tpp7 -xP -ip -O3 gbl_constants.f90
> >> >> >> ifort: command line remark #10148: option '-tp' not supported
> >> >> >> /lib/cpp -traditional -P -I/opt/mpich2/include -DPUBFFT -DMPI
> >> >> >> -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS -DDIRFRC_COMTRANS
> -DDIRFRC_NOVEC
> >> >> >> -DFFTLOADBAL_2PROC gbl_datatypes.fpp gbl_datatypes.f90
> >> >> >> ifort -c -auto -tpp7 -xP -ip -O3 gbl_datatypes.f90
> >> >> >> ifort: command line remark #10148: option '-tp' not supported
> >> >> >>
> >> >> >> (discarded to make the email shorter)
> >> >> >>
> >> >> >> ifort -c -auto -tpp7 -xP -ip -O3 charmm_gold.f90
> >> >> >> ifort: command line remark #10148: option '-tp' not supported
> >> >> >> ifort -o pmemd gbl_constants.o gbl_datatypes.o state_info.o
> >> >> >> file_io_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o mdin_debugf_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 angles_ub.o dihedrals_imp.o cmap.o charmm.o
> >> >> >> charmm_gold.o -L/opt/mpich2/lib -lmpich -lrt -luuid -lpthread
> >> >> >> -limf -lsvml -Wl,-rpath=/opt/intel/Compiler/11.1/073/lib/intel64
> >> >> >> ld: pmemd: hidden symbol `__intel_cpu_indicator_init' in
> >> >> >> /opt/intel/Compiler/11.1/073/lib/intel64/libirc.a(cpu_disp.o) is
> >> >> >> referenced by DSO
> >> >> >> ld: final link failed: Nonrepresentable section on output
> >> >> >> make[1]: *** [pmemd] Error 1
> >> >> >> make[1]: Leaving directory `/usr/local/amber10/src/pmemd/src'
> >> >> >> make: *** [install] Error 2
> >> >> >>
> >> >> >>
> >> >> >> I search in the mailing list and do as per suggestion, to replace
> >> >> >> F90=ifort to mpif90, CC=gcc to mpicc, LOAD=ifort to mpif90, empty
> the
> >> >> >> MPI_LIBS and MPI_LIBDIR, remove -DSLOW_NONBLOCKING_MPI, change the
> >> >> >> content of F90_OPT_HI to "-fast"
> >> >> >>
> >> >> >>
> >> >> >> i try again after make clean, and this is what i get:
> >> >> >> cd src && make install
> >> >> >> make[1]: Entering directory `/usr/local/amber10/src/pmemd/src'
> >> >> >> /lib/cpp -traditional -P -I/opt/mpich2/include -DPUBFFT -DMPI
> >> >> >> -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC
> >> >> >> gbl_constants.fpp gbl_constants.f90
> >> >> >> mpif90 -c -auto -fast gbl_constants.f90
> >> >> >> /lib/cpp -traditional -P -I/opt/mpich2/include -DPUBFFT -DMPI
> >> >> >> -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> >> >> >>
> >> >> >> (discarded)
> >> >> >>
> >> >> >> ipo: remark #11000: performing multi-file optimizations
> >> >> >> ipo: remark #11005: generating object file /tmp/ipo_ifortb2fxSv.o
> >> >> >> ld: pmemd: hidden symbol `__intel_cpu_indicator_init' in
> >> >> >> /opt/intel/Compiler/11.1/073/lib/intel64/libirc.a(cpu_disp.o) is
> >> >> >> referenced by DSO
> >> >> >> ld: final link failed: Nonrepresentable section on output
> >> >> >> make[1]: *** [pmemd] Error 1
> >> >> >> make[1]: Leaving directory `/usr/local/amber10/src/pmemd/src'
> >> >> >> make: *** [install] Error 2
> >> >> >>
> >> >> >>
> >> >> >> I think this is something to do the the linking problem but i do
> not
> >> >> >> know how to solve it.
> >> >> >> mpif77 -link info output =
> >> >> >> /opt/intel/Compiler/11.1/073/bin/intel64/ifort
> -I/opt/mpich2/include
> >> >> >> -L/opt/mpich2/lib -L/opt/mpich2/lib -lmpich -lopa -lpthread -lrt
> >> >> >>
> >> >> >>
> >> >> >> Pls help. Thank you very much!
> >> >> >>
> >> >> >> Regards,
> >> >> >> Colvin
> >> >> >>
> >> >> >> _______________________________________________
> >> >> >> AMBER mailing list
> >> >> >> AMBER.ambermd.org
> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >>
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > Per
> >> >> >
> >> >> > _______________________________________________
> >> >> > 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
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > 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
> >> >
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> 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
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Sep 12 2010 - 19:30:03 PDT
