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
> >
> > _______________________________________________
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> > 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 Thu Sep 09 2010 - 06:30:03 PDT
