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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Received on Thu Sep 09 2010 - 03:00:04 PDT
