Hello there,
I am trying to install PMEMD but the installation
fails with the follwing message:
-------------------------------------------------------------------------------------------------
camm25> make install
cd src && make install
make[1]: Entering directory
`/netfs/people/camm/kopposa1/amber9/src/pmemd/src'
cpp -traditional -P
-I/usr/people/camm/kopposa1/mpich2-1.0.6/include
-DPUBFFT -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS
-DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
-DFFTLOADBAL_2PROC gbl_constants.fpp gbl_constants.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
-L/usr/prog/intel/mkl/100011/lib/em64t -lmkl_em64t
-lpthread -L/usr/people/camm/kopposa1/mpich2-1.0.6/lib
-lmpich -lrt -luuid -lpthread -limf -lsvml
-Wl,-rpath=:/usr/people/camm/kopposa1/gcc/lib64:/usr/prog/msi/LicensePack/linux/lib:/usr/prog/msi/FELIX2004/Linux_2_Intel_32/lib:/usr/prog/msi/2000.3L/Linux_2_Intel_32/biosymso:/usr/prog/msi/CAT470/irix6m3/biosymso:/usr/prog/mdl/isis213/lib:/usr/prog/mdl/ih33/bin:/usr/prog/oracle/Linux/9.2.0/lib:/usr/prog/sge/60u3/lib/lx24-amd64:/usr/scnpr/intel/mkl/90/lib/32:/usr/scnpr/intel/mpi/30/lib:/usr/scnpr/intel/fc/91045/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
`/netfs/people/camm/kopposa1/amber9/src/pmemd/src'
make: *** [install] Error 2
-----------------------------------------------------------
For your information, I have also attached the
config.h file that was created with "./configure
linux_em64t ifort mpich2"
---------------------------------------------------------------------
MATH_DEFINES =
MATH_LIBS =
IFORT_RPATH =
:/usr/people/camm/kopposa1/gcc/lib64:/usr/prog/msi/LicensePack/linux/lib:/usr/prog/msi/FELIX2004/Linux_2_Intel_32/lib:/usr/prog/msi/2000.3L/Linux_2_Intel_32/biosymso:/usr/prog/msi/CAT470/irix6m3/biosymso:/usr/prog/mdl/isis213/lib:/usr/prog/mdl/ih33/bin:/usr/prog/oracle/Linux/9.2.0/lib:/usr/prog/sge/60u3/lib/lx24-amd64:/usr/prog/intel/fce/101008/lib/:/usr/prog/intel/mkl/100011/lib/64:/usr/prog/intel/mkl/100011/lib/em64t
MATH_DEFINES = -DMKL
MATH_LIBS = -L/usr/prog/intel/mkl/100011/lib/em64t
-lmkl_em64t -lpthread
FFT_DEFINES = -DPUBFFT
FFT_INCLUDE =
FFT_LIBS =
NETCDF_HOME =
NETCDF_DEFINES =
NETCDF_MOD =
NETCDF_LIBS =
MPI_HOME = /usr/people/camm/kopposa1/mpich2-1.0.6
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 = 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)
------------------------------------------------------------------
FYI:
1) I have MPICH2 installation compiled with the same
ifort compiler that I m using to compile pmemd
2) Same Ifort compiler was used to compile parallel
Sander (Sander.MPI) which went quite smoothly without
any problems.
Thanks a lot for your help,
Cheers,
Sampath
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Received on Sun Dec 09 2007 - 06:07:26 PST
