[lammps] Other time is not parrallel.

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)

data.PNG

  I'm running about the coarse-grained MD using LAMMPS.

My compile option is

[...]

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.

what happens if you run with regular fix langevin?

axel.