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
> >
>
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>
--
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 - 19:00:04 PDT
