Hi Jason,
Yo are right. It is nothing to do with icc. I tried icc, and it is
still giving the same error. So i move to ifort 11.1.069 as suggested
and finally, pmemd installation was completed without errors.
Thank you very much!
Regards,
Colvin
On Mon, Sep 13, 2010 at 10:18 AM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> _______________________________________________
> 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
Received on Mon Sep 13 2010 - 05:30:03 PDT
