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
>
> _______________________________________________
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>
--
Per
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Received on Thu Sep 09 2010 - 02:30:04 PDT
