AMBER Archive (2009)

Subject: [AMBER] pmemd ifort problem

From: Sel Ercan (slmrcn_at_ymail.com)
Date: Fri Oct 23 2009 - 09:57:59 CDT

Hi all.
I have installed parallel installation of amber9 with success.But I have problem with PMEMD installation. Here is configuration options and error.
>./configure linux_em64t ifort mpich2 pubfft bintraj
and here is config.h:
MATH_DEFINES =
MATH_LIBS =
IFORT_RPATH = /opt/intel/fce/9.0/lib:/opt/intel/fce/9.0/lib:/opt/intel/mkl/8.1.1/lib/em64t:/usr/local/mpich2/lib:/usr/local/vmd/lib:/usr/local/Accelrys/DSVisualizer20/lib
MATH_DEFINES = -DMKL
MATH_LIBS = -L/opt/intel/mkl/8.1.1/lib/em64t -lmkl_em64t -lpthread
FFT_DEFINES = -DPUBFFT
FFT_INCLUDE =
FFT_LIBS =
NETCDF_HOME = /usr/local/amber9/src/netcdf
NETCDF_DEFINES = -DBINTRAJ
NETCDF_MOD = netcdf.mod
NETCDF_LIBS = $(NETCDF_HOME)/lib/libnetcdf.a
MPI_HOME = /usr/local/mpich2
MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
MPI_INCLUDE = -I$(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 -xW -ip -O3
F90_OPT_DFLT = $(F90_OPT_HI)

CC = gcc
CFLAGS =

LOAD = ifort
LOADFLAGS =
LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)

and this is error:
ifort -c -auto -tpp7 -xW -ip -O3 erfcfun.f90
ifort -o pmemd gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o parallel_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o parallel.o pme_direct.o pme_recip.o pme_fft.o fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o cit.o dynamics.o bonds.o angles.o dihedrals.o runmd.o loadbal.o shake.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 alltasks_setup.o pme_setup.o ene_frc_splines.o nextprmtop_section.o /usr/local/amber9/src/netcdf/lib/libnetcdf.a -L/opt/intel/mkl/8.1.1/lib/em64t -lmkl_em64t -lpthread -L/usr/local/mpich2/lib -lmpich -lrt -luuid -lpthread -limf -lsvml -Wl,-rpath=/opt/intel/fce/9.0/lib:/opt/intel/fce/9.0/lib:/opt/intel/mkl/8.1.1/lib/em64t:/usr/local/mpich2/lib:/usr/local/vmd/lib:/usr/local/Accelrys/DSVisualizer20/lib
IPO link: can not find -luuid
ifort: error: problem during multi-file optimization compilation (code 1)
make[1]: *** [pmemd] Error 1
make[1]: Leaving directory `/usr/local/amber9/src/pmemd/src'
make: *** [install] Error 2

best regards

      
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