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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Received on Thu Sep 09 2010 - 02:30:03 PDT
