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
>> >
>>
>> _______________________________________________
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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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Received on Sun Sep 12 2010 - 19:00:05 PDT
