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[交流]
集群安装lammps心得体会,与大家共同学习已有2人参与
由于集群系统崩溃,重装2018版的lammps,一开始装的fftw是3.3.7版本,编译出现以下报错:
错误提示:
fft3d.o:在函数‘fft_3d’中:
/home/tree/Software/lammps/src/Obj_mpi/../fft3d.cpp:151:对‘fftwf_execute_dft’未定义的引用
/home/tree/Software/lammps/src/Obj_mpi/../fft3d.cpp:214:对‘fftwf_execute_dft’未定义的引用
/home/tree/Software/lammps/src/Obj_mpi/../fft3d.cpp:277:对‘fftwf_execute_dft’未定义的引用
/home/tree/Software/lammps/src/Obj_mpi/../fft3d.cpp:151:对‘fftwf_execute_dft’未定义的引用
/home/tree/Software/lammps/src/Obj_mpi/../fft3d.cpp:214:对‘fftwf_execute_dft’未定义的引用
fft3d.o:/home/tree/Software/lammps/src/Obj_mpi/../fft3d.cpp:277: 跟着更多未定义的参考到 fftwf_execute_dft..............
解决办法:
发现是fftw问题,我重装了老版本3.2.2的fftw,发现一次编译通过。
fftw下载地址: ftp://ftp.fftw.org/pub/fftw/
有相同问题的,可以借鉴一下
下面是make mpi文件
# mpi = MPI with its default compiler
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = /public/software/mpi/openmpi/intel/2.1.2/bin/mpicxx #修改的地方
CCFLAGS = -g -O3
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = /public/software/mpi/openmpi/intel/2.1.2/bin/mpicxx #修改的地方
LINKFLAGS = -g -O
LIB =
SIZE = size
ARCHIVE = ar
ARFLAGS = -rc
SHLIBFLAGS = -shared
# ---------------------------------------------------------------------
# LAMMPS-specific settings, all OPTIONAL
# specify settings for LAMMPS features you will use
# if you change any -D setting, do full re-compile after "make clean"
# LAMMPS ifdef settings
# see possible settings in Section 2.2 (step 4) of manual
LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64
# MPI library
# see discussion in Section 2.2 (step 5) of manual
# MPI wrapper compiler/linker can provide this info
# can point to dummy MPI library in src/STUBS as in Makefile.serial
# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
# INC = path for mpi.h, MPI compiler settings
# PATH = path for MPI library
# LIB = name of MPI library
MPI_INC = -I/public/software/mpi/openmpi/intel/2.1.2/include -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 #修改的地方
MPI_PATH = -L/public/software/mpi/openmpi/intel/2.1.2/lib #修改的地方
MPI_LIB = -lmpi #修改的地方
# FFT library
# see discussion in Section 2.2 (step 6) of manual
# 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/public/software/fftw2/fftw/include #修改的地方
FFT_PATH = -L/public/software/fftw2/fftw/lib #修改的地方
FFT_LIB = -lfftw3 #修改的地方
# JPEG and/or PNG library
# see discussion in Section 2.2 (step 7) of manual
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
# INC = path(s) for jpeglib.h and/or png.h
# PATH = path(s) for JPEG library and/or PNG library
# LIB = name(s) of JPEG library and/or PNG library
JPG_INC =
JPG_PATH =
JPG_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not 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)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)
# Path to src files
vpath %.cpp ..
vpath %.h ..
# Link target
$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library targets
lib: $(OBJ) $(EXTRA_LINK_DEPENDS)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
shlib: $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
$(OBJ) $(EXTRA_LIB) $(LIB)
# Compilation rules
%.o:%.cpp
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
# Individual dependencies
depend : fastdep.exe $(SRC)
@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
fastdep.exe: ../DEPEND/fastdep.c
cc -O -o $@ $<
sinclude .depend |
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