I’m running about the coarse-grained MD using LAMMPS.
My compile option is
openmpi = Fedora Core 6, mpic++, OpenMPI-1.1, FFTW2
SHELL = /bin/sh
---------------------------------------------------------------------
compiler/linker settings
specify flags and libraries needed for your compiler
CC = /appl/mpi/intel/openmpi/bin/mpic++
CCFLAGS = -g -O3 -fast\
-funroll-loops -fstrict-aliasing -Wall -Wno-uninitializedi -W
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = /appl/mpi/intel/openmpi/bin/mpic++
LINKFLAGS = -O
LIB = -lstdc++
SIZE = size
ARCHIVE = ar
ARFLAGS = -rcsv
SHLIBFLAGS = -shared
---------------------------------------------------------------------
LAMMPS-specific settings
specify settings for LAMMPS features you will use
if you change any -D setting, do full re-compile after “make clean”
LAMMPS ifdef settings, OPTIONAL
see possible settings in doc/Section_start.html#2_2 (step 4)
LMP_INC = -DLAMMPS_GZIP
MPI library, REQUIRED
see discussion in doc/Section_start.html#2_2 (step 5)
can point to dummy MPI library in src/STUBS as in Makefile.serial
INC = path for mpi.h, MPI compiler settings
PATH = path for MPI library
LIB = name of MPI library
MPI_INC = /appl/mpi/intel/openmpi/include -DMPICH_IGNORE_CXX_SEEK
MPI_PATH = -L /appl/mpi/intel/openmpi/lib
MPI_LIB = -lpthread -lmpi
FFT library, OPTIONAL
see discussion in doc/Section_start.html#2_2 (step 6)
can be left blank to use provided KISS FFT library
INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
PATH = path for FFT library
LIB = name of FFT library
FFT_INC = -DFFT_FFTW -I/appl/lammps/fftw2/include
FFT_PATH = -L/appl/lammps/fftw2/lib
FFT_LIB = -lfftw
JPEG library, OPTIONAL
see discussion in doc/Section_start.html#2_2 (step 7)
only needed if -DLAMMPS_JPEG listed with LMP_INC
INC = path for jpeglib.h
PATH = path for JPEG library
LIB = name of JPEG library
JPG_INC =
JPG_PATH =
JPG_LIB =
---------------------------------------------------------------------
build rules and dependencies
no need to edit this section
include Makefile.package.settings
include Makefile.package
EXTRA_INC = (LMP_INC) (PKG_INC) (MPI_INC) (FFT_INC) (JPG_INC) (PKG_SYSINC)
EXTRA_PATH = (PKG_PATH) (MPI_PATH) (FFT_PATH) (JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = (PKG_LIB) (MPI_LIB) (FFT_LIB) (JPG_LIB) $(PKG_SYSLIB)
Path to src files
vpath %.cpp …
vpath %.h …
Link target
(EXE): (OBJ)
(LINK) (LINKFLAGS) (EXTRA_PATH) (OBJ) (EXTRA_LIB) (LIB) -o $(EXE)
(SIZE) (EXE)
Library targets
lib: $(OBJ)
(ARCHIVE) (ARFLAGS) (EXE) (OBJ)
shlib: $(OBJ)
(CC) (CCFLAGS) (SHFLAGS) (SHLIBFLAGS) (EXTRA_PATH) -o (EXE) \
(OBJ) (EXTRA_LIB) $(LIB)
Compilation rules
.o:.cpp
(CC) (CCFLAGS) (SHFLAGS) (EXTRA_INC) -c $<
.d:.cpp
(CC) (CCFLAGS) (EXTRA_INC) (DEPFLAGS) < > @
Individual dependencies
DEPENDS = $(OBJ:.o=.d)
sinclude $(DEPENDS)
I attach my running file and result file. I tried to omp package and my optional change, but it is not efficient. I don’t know solution of this problem.
Please help me.
Sincerely
Sei-hwan Ahn
min1.dna (3.47 KB)
