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
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
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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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Sep 12 2010 - 19:00:03 PDT
