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Merge branch 'master' into collected-small-changes

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Axel Kohlmeyer 2020-10-14 13:11:30 -04:00
parent 7f804512b7 d27c7cd2fc
commit 18091f15e0
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62 changed files with 340 additions and 26423 deletions
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108
bench/KEPLER/Makefile.cpu
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@ -1,108 +0,0 @@
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = icc
CCFLAGS = -O
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = icc
LINKFLAGS = -O
LIB = -lstdc++
SIZE = size
ARCHIVE = ar
ARFLAGS = -rc
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 =
# 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 = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
MPI_LIB = -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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 7)
# 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 = -ljpeg
# ---------------------------------------------------------------------
# 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)

108
bench/KEPLER/Makefile.cuda
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@ -1,108 +0,0 @@
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = icc
CCFLAGS = -O
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = icc
LINKFLAGS = -O
LIB = -lstdc++
SIZE = size
ARCHIVE = ar
ARFLAGS = -rc
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 =
# 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 = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
MPI_LIB = -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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 7)
# 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 = -ljpeg
# ---------------------------------------------------------------------
# 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)

108
bench/KEPLER/Makefile.gpu
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@ -1,108 +0,0 @@
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = icc
CCFLAGS = -O
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = icc
LINKFLAGS = -O
LIB = -lstdc++
SIZE = size
ARCHIVE = ar
ARFLAGS = -rc
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 =
# 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 = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
MPI_LIB = -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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 7)
# 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 = -ljpeg
# ---------------------------------------------------------------------
# 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)

50
bench/KEPLER/Makefile.gpu.double
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# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.standard
CUDA_HOME = /home/projects/cuda/6.0.37
NVCC = nvcc
# Kepler CUDA
CUDA_ARCH = -arch=sm_35
# Tesla CUDA
#CUDA_ARCH = -arch=sm_21
# newer CUDA
#CUDA_ARCH = -arch=sm_13
# older CUDA
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
# this setting should match LAMMPS Makefile
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
LMP_INC = -DLAMMPS_SMALLBIG
# precision for GPU calculations
# -D_SINGLE_SINGLE # Single precision for all calculations
# -D_DOUBLE_DOUBLE # Double precision for all calculations
# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
CUDA_PRECISION = -D_DOUBLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
BIN_DIR = ./
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
include Nvidia.makefile

50
bench/KEPLER/Makefile.gpu.mixed
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@ -1,50 +0,0 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.standard
CUDA_HOME = /home/projects/cuda/6.0.37
NVCC = nvcc
# Kepler CUDA
CUDA_ARCH = -arch=sm_35
# Tesla CUDA
#CUDA_ARCH = -arch=sm_21
# newer CUDA
#CUDA_ARCH = -arch=sm_13
# older CUDA
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
# this setting should match LAMMPS Makefile
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
LMP_INC = -DLAMMPS_SMALLBIG
# precision for GPU calculations
# -D_SINGLE_SINGLE # Single precision for all calculations
# -D_DOUBLE_DOUBLE # Double precision for all calculations
# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
CUDA_PRECISION = -D_SINGLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
BIN_DIR = ./
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
include Nvidia.makefile

50
bench/KEPLER/Makefile.gpu.single
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# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.standard
CUDA_HOME = /home/projects/cuda/6.0.37
NVCC = nvcc
# Kepler CUDA
CUDA_ARCH = -arch=sm_35
# Tesla CUDA
#CUDA_ARCH = -arch=sm_21
# newer CUDA
#CUDA_ARCH = -arch=sm_13
# older CUDA
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
# this setting should match LAMMPS Makefile
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
LMP_INC = -DLAMMPS_SMALLBIG
# precision for GPU calculations
# -D_SINGLE_SINGLE # Single precision for all calculations
# -D_DOUBLE_DOUBLE # Double precision for all calculations
# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
CUDA_PRECISION = -D_SINGLE_SINGLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
BIN_DIR = ./
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
include Nvidia.makefile

109
bench/KEPLER/Makefile.intel.cpu
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# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = icc
CCFLAGS = -O3 -openmp -DLAMMPS_MEMALIGN=64 -no-offload \
-xHost -fno-alias -ansi-alias -restrict -override-limits
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = icc
LINKFLAGS = -O -openmp
LIB = -lstdc++
SIZE = size
ARCHIVE = ar
ARFLAGS = -rc
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 -DLAMMPS_JPEG
# 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 = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
MPI_LIB = -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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 7)
# 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 = -ljpeg
# ---------------------------------------------------------------------
# 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)

113
bench/KEPLER/Makefile.kokkos.cuda
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@ -1,113 +0,0 @@
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = nvcc
CCFLAGS = -O3 -arch=sm_35
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpicxx
LINKFLAGS = -O
LIB = -lstdc++
SIZE = size
ARCHIVE = ar
ARFLAGS = -rc
SHLIBFLAGS = -shared
OMP = yes
CUDA = yes
# ---------------------------------------------------------------------
# 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 =
# 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 = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
MPI_LIB = -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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 7)
# 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 = -ljpeg
# ---------------------------------------------------------------------
# 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:%.cu
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
%.o:%.cpp
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
DEPENDS = $(OBJ:.o=.d)
sinclude $(DEPENDS)

110
bench/KEPLER/Makefile.kokkos.omp
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@ -1,110 +0,0 @@
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = icc
CCFLAGS = -O
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = icc
LINKFLAGS = -O
LIB = -lstdc++
SIZE = size
ARCHIVE = ar
ARFLAGS = -rc
SHLIBFLAGS = -shared
OMP = yes
# ---------------------------------------------------------------------
# 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 =
# 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 = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
MPI_LIB = -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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 7)
# 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 = -ljpeg
# ---------------------------------------------------------------------
# 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)

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@ -1,108 +0,0 @@
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = icc
CCFLAGS = -O3 -openmp -restrict -ansi-alias
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = icc
LINKFLAGS = -O -openmp
LIB = -lstdc++
SIZE = size
ARCHIVE = ar
ARFLAGS = -rc
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 =
# 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 = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
MPI_LIB = -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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 7)
# 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 = -ljpeg
# ---------------------------------------------------------------------
# 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)

108
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@ -1,108 +0,0 @@
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = icc
CCFLAGS = -O -restrict
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = icc
LINKFLAGS = -O
LIB = -lstdc++
SIZE = size
ARCHIVE = ar
ARFLAGS = -rc
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 =
# 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 = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
MPI_LIB = -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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 7)
# 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 = -ljpeg
# ---------------------------------------------------------------------
# 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)

68
bench/KEPLER/README
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@ -1,68 +0,0 @@
These are build and input and run scripts used to run the LJ benchmark
in the top-level bench directory using all the various accelerator
packages currently available in LAMMPS. The results of running these
benchmarks on a GPU cluster with Kepler GPUs are shown on the "GPU
(Kepler)" section of the Benchmark page of the LAMMPS WWW site:
lammps.sandia.gov/bench.
The specifics of the benchmark machine are as follows:
It is a small GPU cluster at Sandia National Labs called "shannon". It
has 32 nodes, each with two 8-core Sandy Bridge Xeon CPUs (E5-2670,
2.6GHz, HT deactivated), for a total of 512 cores. Twenty-four of the
nodes have two NVIDIA Kepler GPUs (K20x, 2688 732 MHz cores). LAMMPS
was compiled with the Intel icc compiler, using module
openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37.
------------------------------------------------------------------------
You can, of course, build LAMMPS yourself with any of the accelerator
packages installed for your platform.
The build.py script will build LAMMPS for the various accelerlator
packages using the Makefile.* files in this dir, which you can edit if
necessary for your platform. You must set the "lmpdir" variable at
the top of build.py to the home directory of LAMMPS as installed on
your system. Note that the build.py script hardcodes the arch setting
for the USER-CUDA package, which should be matched to the GPUs on your
system, e.g. sm_35 for Kepler GPUs. For the GPU package, this setting
is in the Makefile.gpu.* files, as is the CUDA_HOME variable which
should point to where NVIDIA Cuda software is installed on your
system.
Once the Makefiles are in place, then typing, for example,
python build.py cpu gpu
will build executables for the CPU (no accelerators), and 3 variants
(double, mixed, single precision) of the GPU package. See the list of
possible targets at the top of the build.py script.
Note that the build.py script will un-install all packages in your
LAMMPS directory, then only install the ones needed for the benchmark.
The Makefile.* files in this dir are copied into lammps/src/MAKE, as a
dummy Makefile.foo, so they will not conflict with makefiles that may
already be there. The build.py script also builds the auxiliary GPU
and USER-CUDA library as needed.
LAMMPS executables that are generated by build.py are copied into this
directory when the script finishes each build.
------------------------------------------------------------------------
The in.* files can be run with any of the accelerator packages,
if you specify the appropriate command-line switches. These
include switches to set the problem size and number of timesteps
to run.
The run*.sh scripts have sample mpirun commands for running the input
scripts on a single node or on multiple nodes for the strong and weak
scaling results shown on the benchmark web page. These scripts are
provided for illustration purposes, to show what command-line
arguments are used with each accelerator package.
Note that we generate these run scripts, either for interactive or
batch submission, via Python scripts which often produces a long list
of runs to exercise a combination of options. To perform a quick
benchmark calculation on your platform, you will typically only want
to run a few commands out of any of the run*.sh scripts.

187
bench/KEPLER/build.py
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@ -1,187 +0,0 @@
#!/usr/local/bin/python
# Syntax: build.py target1 target2 ...
# targets:
# cpu, opt, omp,
# gpu/double, gpu/mixed, gpu/single,
# cuda/double, cuda/mixed, cuda/single,
# intel/cpu, intel/phi,
# kokkos/omp, kokkos/phi, kokkos/cuda
# gpu = gpu/double + gpu/mixed + gpu/single
# cuda = cuda/double + cuda/mixed + cuda/single
# intel = intel/cpu + intel/phi
# kokkos = kokkos/omp + kokkos/phi + kokkos/cuda
# all = cpu + opt + omp + gpu + cuda + intel + kokkos
# create exectuables for different packages
# MUST set lmpdir to path of LAMMPS home directory
import sys,commands,os
lmpdir = "~/lammps"
# build LAMMPS
# copy makefile into src/MAKE as Makefile.foo, then remove it
def build_lammps(makefile,pkg):
print "Building LAMMPS with %s and %s packages ..." % (makefile,pkg)
commands.getoutput("cp %s %s/src/MAKE/Makefile.foo" % (makefile,lmpdir))
cwd = os.getcwd()
os.chdir(os.path.expanduser(lmpdir + "/src"))
str = "make clean-foo"
txt = commands.getoutput(str)
str = "make no-all"
txt = commands.getoutput(str)
for package in pkg:
str = "make yes-%s" % package
txt = commands.getoutput(str)
print txt
str = "make -j 16 foo"
txt = commands.getoutput(str)
os.remove("MAKE/Makefile.foo")
os.chdir(cwd)
# build GPU library in LAMMPS
# copy makefile into lib/gpu as Makefile.foo, then remove it
def build_gpu(makefile):
print "Building GPU lib with %s ..." % makefile
commands.getoutput("cp %s %s/lib/gpu/Makefile.foo" % (makefile,lmpdir))
cwd = os.getcwd()
os.chdir(os.path.expanduser(lmpdir + "/lib/gpu"))
str = "make -f Makefile.foo clean"
txt = commands.getoutput(str)
str = "make -j 16 -f Makefile.foo"
txt = commands.getoutput(str)
os.remove("Makefile.foo")
os.chdir(cwd)
# build CUDA library in LAMMPS
# set precision and arch explicitly as options to make in lib/cuda
def build_cuda(precision,arch):
print "Building USER-CUDA lib with %s and arch sm_%d ..." % (precision,arch)
cwd = os.getcwd()
os.chdir(os.path.expanduser(lmpdir + "/lib/cuda"))
str = "make clean"
txt = commands.getoutput(str)
if precision == "double": pflag = 2
elif precision == "mixed": pflag = 4
elif precision == "single": pflag = 1
str = "make -j 16 precision=%d arch=%s" % (pflag,arch)
txt = commands.getoutput(str)
os.chdir(cwd)
# main program
# convert target keywords into target flags
cpu = opt = omp = 0
gpu = gpu_double = gpu_mixed = gpu_single = 0
cuda = cuda_double = cuda_mixed = cuda_single = 0
intel = intel_cpu = intel_phi = 0
kokkos = kokkos_omp = kokkos_phi = kokkos_cuda = 0
targets = sys.argv[1:]
for target in targets:
if target == "cpu": cpu = 1
elif target == "opt": opt = 1
elif target == "omp": omp = 1
elif target == "gpu/double": gpu_double = 1
elif target == "gpu/mixed": gpu_mixed = 1
elif target == "gpu/single": gpu_single = 1
elif target == "gpu": gpu = 1
elif target == "cuda/double": cuda_double = 1
elif target == "cuda/mixed": cuda_mixed = 1
elif target == "cuda/single": cuda_single = 1
elif target == "cuda": cuda = 1
elif target == "intel/cpu": intel_cpu = 1
elif target == "intel/phi": intel_phi = 1
elif target == "intel": intel = 1
elif target == "kokkos/omp": kokkos_omp = 1
elif target == "kokkos/phi": kokkos_phi = 1
elif target == "kokkos/cuda": kokkos_cuda = 1
elif target == "kokkos": kokkos = 1
elif target == "all": cpu = omp = gpu = cuda = intel = kokkos = 1
else: print "Target",target,"is unknown"
if gpu: gpu_double = gpu_mixed = gpu_single = 1
if cuda: cuda_double = cuda_mixed = cuda_single = 1
if intel: intel_cpu = intel_phi = 1
if kokkos: kokkos_omp = kokkos_phi = kokkos_cuda = 1
# CPU
if cpu:
build_lammps(makefile = "Makefile.cpu", pkg = [])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_cpu" % lmpdir)
# OPT
if opt:
build_lammps(makefile = "Makefile.opt", pkg = ["opt"])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_opt" % lmpdir)
# OMP
if omp:
build_lammps(makefile = "Makefile.omp", pkg = ["user-omp"])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_omp" % lmpdir)
# GPU, 3 precisions
if gpu_double:
build_gpu(makefile = "Makefile.gpu.double")
build_lammps(makefile = "Makefile.gpu", pkg = ["gpu"])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_gpu_double" % lmpdir)
if gpu_mixed:
build_gpu(makefile = "Makefile.gpu.mixed")
build_lammps(makefile = "Makefile.gpu", pkg = ["gpu"])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_gpu_mixed" % lmpdir)
if gpu_single:
build_gpu(makefile = "Makefile.gpu.single")
build_lammps(makefile = "Makefile.gpu", pkg = ["gpu"])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_gpu_single" % lmpdir)
# CUDA, 3 precisions
if cuda_double:
build_cuda(precision = "double", arch = 35)
build_lammps(makefile = "Makefile.cuda", pkg = ["kspace","user-cuda"])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_cuda_double" % lmpdir)
if cuda_mixed:
build_cuda(precision = "mixed", arch = 35)
build_lammps(makefile = "Makefile.cuda", pkg = ["kspace","user-cuda"])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_cuda_mixed" % lmpdir)
if cuda_single:
build_cuda(precision = "single", arch = 35)
build_lammps(makefile = "Makefile.cuda", pkg = ["kspace","user-cuda"])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_cuda_single" % lmpdir)
# INTEL, CPU and Phi
if intel_cpu:
build_lammps(makefile = "Makefile.intel.cpu", pkg = ["user-intel"])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_intel_cpu" % lmpdir)
if intel_phi:
build_lammps(makefile = "Makefile.intel.phi", pkg = ["user-intel","user-omp"])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_intel_phi" % lmpdir)
# KOKKOS, all variants
if kokkos_omp:
build_lammps(makefile = "Makefile.kokkos.omp", pkg = ["kokkos"])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_kokkos_omp" % lmpdir)
if kokkos_phi:
build_lammps(makefile = "Makefile.kokkos.phi", pkg = ["kokkos"])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_kokkos_phi" % lmpdir)
if kokkos_cuda:
build_lammps(makefile = "Makefile.kokkos.cuda", pkg = ["kokkos"])
print commands.getoutput("mv %s/src/lmp_foo ./lmp_kokkos_cuda" % lmpdir)

22
bench/KEPLER/in.lj
View File

@ -1,22 +0,0 @@
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
run $t

29
bench/KEPLER/run_cpu.sh
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@ -1,29 +0,0 @@
#!/bin/bash
#SBATCH -N 1 --time=12:00:00
mpirun -np 1 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cpu.128K.1
mpirun -np 2 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cpu.128K.2
mpirun -np 4 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cpu.128K.4
mpirun -np 6 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cpu.128K.6
mpirun -np 8 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cpu.128K.8
mpirun -np 10 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cpu.128K.10
mpirun -np 12 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cpu.128K.12
mpirun -np 14 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cpu.128K.14
mpirun -np 16 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cpu.128K.16

20
bench/KEPLER/run_cuda.sh
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@ -1,20 +0,0 @@
#!/bin/bash
#SBATCH -N 1 --time=12:00:00
mpirun -N 1 lmp_cuda_double -c on -sf cuda -pk cuda 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cuda.double.128K.1
mpirun -N 2 lmp_cuda_double -c on -sf cuda -pk cuda 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cuda.double.128K.2
mpirun -N 1 lmp_cuda_mixed -c on -sf cuda -pk cuda 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cuda.mixed.128K.1
mpirun -N 2 lmp_cuda_mixed -c on -sf cuda -pk cuda 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cuda.mixed.128K.2
mpirun -N 1 lmp_cuda_single -c on -sf cuda -pk cuda 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cuda.single.128K.1
mpirun -N 2 lmp_cuda_single -c on -sf cuda -pk cuda 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.cuda.single.128K.2

155
bench/KEPLER/run_gpu.sh
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@ -1,155 +0,0 @@
#!/bin/bash
#SBATCH -N 1 --time=12:00:00
mpirun -np 1 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.1.1
mpirun -np 2 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.2.1
mpirun -np 2 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.2.2
mpirun -np 4 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.4.1
mpirun -np 4 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.4.2
mpirun -np 6 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.6.1
mpirun -np 6 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.6.2
mpirun -np 8 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.8.1
mpirun -np 8 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.8.2
mpirun -np 10 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.10.1
mpirun -np 10 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.10.2
mpirun -np 12 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.12.1
mpirun -np 12 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.12.2
mpirun -np 14 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.14.1
mpirun -np 14 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.14.2
mpirun -np 16 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.16.1
mpirun -np 16 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.single.128K.16.2
mpirun -np 1 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.1.1
mpirun -np 2 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.2.1
mpirun -np 2 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.2.2
mpirun -np 4 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.4.1
mpirun -np 4 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.4.2
mpirun -np 6 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.6.1
mpirun -np 6 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.6.2
mpirun -np 8 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.8.1
mpirun -np 8 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.8.2
mpirun -np 10 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.10.1
mpirun -np 10 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.10.2
mpirun -np 12 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.12.1
mpirun -np 12 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.12.2
mpirun -np 14 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.14.1
mpirun -np 14 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.14.2
mpirun -np 16 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.16.1
mpirun -np 16 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.16.2
mpirun -np 1 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.1.1
mpirun -np 2 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.2.1
mpirun -np 2 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.2.2
mpirun -np 4 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.4.1
mpirun -np 4 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.4.2
mpirun -np 6 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.6.1
mpirun -np 6 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.6.2
mpirun -np 8 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.8.1
mpirun -np 8 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.8.2
mpirun -np 10 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.10.1
mpirun -np 10 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.10.2
mpirun -np 12 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.12.1
mpirun -np 12 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.12.2
mpirun -np 14 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.14.1
mpirun -np 14 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.14.2
mpirun -np 16 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.16.1
mpirun -np 16 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.gpu.double.128K.16.2

83
bench/KEPLER/run_intel_cpu.sh
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@ -1,83 +0,0 @@
#!/bin/bash
#SBATCH -N 1 --time=12:00:00
mpirun -np 1 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.1
mpirun -np 2 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.2
mpirun -np 4 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.4
mpirun -np 6 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.6
mpirun -np 8 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.8
mpirun -np 10 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.10
mpirun -np 12 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.12
mpirun -np 14 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.14
mpirun -np 16 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.16
mpirun -np 1 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.1
mpirun -np 2 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.2
mpirun -np 4 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.4
mpirun -np 6 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.6
mpirun -np 8 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.8
mpirun -np 10 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.10
mpirun -np 12 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.12
mpirun -np 14 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.14
mpirun -np 16 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.16
mpirun -np 1 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.1
mpirun -np 2 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.2
mpirun -np 4 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.4
mpirun -np 6 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.6
mpirun -np 8 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.8
mpirun -np 10 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.10
mpirun -np 12 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.12
mpirun -np 14 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.14
mpirun -np 16 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.16

74
bench/KEPLER/run_kokkos_cuda.sh
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@ -1,74 +0,0 @@
#!/bin/bash
#SBATCH -N 1 --time=12:00:00
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 1 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.1
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 2 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.2
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 3 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.3
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 4 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.4
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 5 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.5
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 6 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.6
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 7 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.7
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 8 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.8
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 9 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.9
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 10 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.10
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 11 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.11
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 12 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.12
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 13 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.13
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 14 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.14
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 15 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.15
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 16 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.16
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 1 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.1
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 2 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.2
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 3 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.3
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 4 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.4
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 5 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.5
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 6 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.6
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 7 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.7
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 8 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.8

17
bench/KEPLER/run_kokkos_omp.sh
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@ -1,17 +0,0 @@
#!/bin/bash
#SBATCH -N 1 --time=12:00:00
mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 16 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.omp.128K.1.16
mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 8 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.omp.128K.2.8
mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 4 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.omp.128K.4.4
mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 2 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.omp.128K.8.2
mpirun -np half -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos neigh half newton on comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.kokkos.omp.128K.16.1

17
bench/KEPLER/run_omp.sh
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@ -1,17 +0,0 @@
#!/bin/bash
#SBATCH -N 1 --time=12:00:00
mpirun -np 1 lmp_omp -sf omp -pk omp 16 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.omp.128K.1.16
mpirun -np 2 lmp_omp -sf omp -pk omp 8 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.omp.128K.2.8
mpirun -np 4 lmp_omp -sf omp -pk omp 4 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.omp.128K.4.4
mpirun -np 8 lmp_omp -sf omp -pk omp 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.omp.128K.8.2
mpirun -np 16 lmp_omp -sf omp -pk omp 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.omp.128K.16.1

29
bench/KEPLER/run_opt.sh
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@ -1,29 +0,0 @@
#!/bin/bash
#SBATCH -N 1 --time=12:00:00
mpirun -np 1 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.opt.128K.1
mpirun -np 2 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.opt.128K.2
mpirun -np 4 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.opt.128K.4
mpirun -np 6 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.opt.128K.6
mpirun -np 8 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.opt.128K.8
mpirun -np 10 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.opt.128K.10
mpirun -np 12 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.opt.128K.12
mpirun -np 14 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.opt.128K.14
mpirun -np 16 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
mv log.lammps log.10Sep14.lj.opt.128K.16

20
bench/KEPLER/run_strong.sh
View File

@ -1,20 +0,0 @@
#!/bin/bash
#SBATCH -N 16 --time=12:00:00
mpirun -npernode 16 lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
mv log.lammps log.28Jun14.lj.cpu.2048K.16.16
mpirun -npernode 16 lmp_omp -sf omp -pk omp 1 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
mv log.lammps log.28Jun14.lj.omp.2048K.16.1.16
mpirun -npernode 2 lmp_cuda -c on -sf cuda -pk cuda 2 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
mv log.lammps log.28Jun14.lj.cuda.2048K.2.16
mpirun -npernode 14 lmp_gpu -sf gpu -pk gpu 2 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
mv log.lammps log.28Jun14.lj.gpu.2048K.2.14.16
mpirun -npernode 2 lmp_kokkos_cuda -k on g 2 t 1 -sf kk -pk kokkos comm device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
mv log.lammps log.28Jun14.lj.kokkos.cuda.2048K.2.1.16
mpirun -np 256 -bind-to core -map-by core -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos comm device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
mv log.lammps log.28Jun14.lj.kokkos.omp.2048K.16.1.16

20
bench/KEPLER/run_weak.sh
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@ -1,20 +0,0 @@
#!/bin/bash
#SBATCH -N 16 --time=12:00:00
mpirun -npernode 16 lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
mv log.lammps log.28Jun14.lj.cpu.512K.16.16
mpirun -npernode 16 lmp_omp -sf omp -pk omp 1 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
mv log.lammps log.28Jun14.lj.omp.512K.16.1.16
mpirun -npernode 2 lmp_cuda -c on -sf cuda -pk cuda 2 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
mv log.lammps log.28Jun14.lj.cuda.512K.2.16
mpirun -npernode 14 lmp_gpu -sf gpu -pk gpu 2 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
mv log.lammps log.28Jun14.lj.gpu.512K.2.14.16
mpirun -npernode 2 lmp_kokkos_cuda -k on g 2 t 1 -sf kk -pk kokkos comm device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
mv log.lammps log.28Jun14.lj.kokkos.cuda.512K.2.1.16
mpirun -np 256 -bind-to core -map-by core -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos comm device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
mv log.lammps log.28Jun14.lj.kokkos.omp.512K.16.1.16

87
doc/src/Tools.rst
View File

@ -406,7 +406,7 @@ LAMMPS shell
.. versionadded:: 9Oct2020
Overview
========
^^^^^^^^
The LAMMPS Shell, ``lammps-shell`` is a program that functions very
similar to the regular LAMMPS executable but has several modifications
@ -433,7 +433,7 @@ These enhancements makes the LAMMPS shell an attractive choice for
interactive LAMMPS sessions in graphical user interfaces.
TAB-expansion
=============
^^^^^^^^^^^^^
When writing commands interactively at the shell prompt, you can hit
the TAB key at any time to try and complete the text. This completion
@ -461,7 +461,7 @@ available in that executable.
and directories.
Command line editing and history
================================
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
When typing commands, command line editing similar to what BASH
provides is available. Thus it is possible to move around the
@ -490,7 +490,7 @@ readline, please see the available documentation at:
<http://www.gnu.org/s/readline/#Documentation>`_
Additional commands
===================
^^^^^^^^^^^^^^^^^^^
The following commands are added to the LAMMPS shell on top of the
regular LAMMPS commands:
@ -500,6 +500,11 @@ regular LAMMPS commands:
help (or ?) print a brief help message
history display the current command history list
clear_history wipe out the current command history list
save_history <range> <file>
write commands from the history to file.
The range is given as <from>-<to>, where <from> and <to>
may be empty. Example: save_history 100- in.recent
source <file> read commands from file (same as "include")
pwd print current working directory
cd <directory> change current working directory (same as pwd if no directory)
mem print current and maximum memory usage
@ -512,7 +517,7 @@ while using the '\|' character will always pass the following text
to the operating system's shell command.
Compilation
===========
^^^^^^^^^^^
Compilation of the LAMMPS shell can be enabled by setting the CMake
variable ``BUILD_LAMMPS_SHELL`` to "on" or using the makefile in the
@ -522,11 +527,81 @@ customization depending on the features and settings used for
compiling LAMMPS.
Limitations
===========
^^^^^^^^^^^
The LAMMPS shell was not designed for use with MPI parallelization
via ``mpirun`` or ``mpiexec`` or ``srun``.
Readline customization
^^^^^^^^^^^^^^^^^^^^^^
The behavior of the readline functionality can be customized in the
``${HOME}/.inputrc`` file. This can be used to alter the default
settings or change the key-bindings. The LAMMPS Shell sets the
application name ``lammps-shell``, so settings can be either applied
globally or only for the LAMMPS shell by bracketing them between
``$if lammps-shell`` and ``$endif`` like in the following example:
.. code-block:: bash
$if lammps-shell
# disable "beep" or "screen flash"
set bell-style none
# bind the "Insert" key to toggle overwrite mode
"\e[2~": overwrite-mode
$endif
More details about this are in the `readline documentation <https://tiswww.cwru.edu/php/chet/readline/rluserman.html#SEC9>`_.
LAMMPS Shell tips and tricks
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Enable tilde expansion
""""""""""""""""""""""
Adding ``set expand-tilde on`` to ``${HOME}/.inputrc`` is recommended as
this will change the filename expansion behavior to replace any text
starting with "~" by the full path to the corresponding user's home
directory. While the expansion of filenames **will** happen on all
arguments where the context is not known (e.g. ``~/compile/lamm<TAB>``
will expand to ``~/compile/lammps/``), it will not replace the tilde by
default. But since LAMMPS does not do tilde expansion itself (unlike a
shell), this will result in errors. Instead the tilde-expression should
be expanded into a valid path, where the plain "~/" stands for the
current user's home directory and "~someuser/" stands for
"/home/someuser" or whatever the full path to that user's home directory
is.
File extension association
""""""""""""""""""""""""""
Since the LAMMPS shell (unlike the regular LAMMPS executable) does not
exit when an input file is passed on the command line with the "-in" or
"-i" flag (the behavior is like for ``python -i <filename>``), it makes
the LAMMPS shell suitable for associating it with input files based on
their filename extension (e.g. ".lmp"). Since ``lammps-shell`` is a
console application, you have to run it inside a terminal program with a
command line like this:
.. code-block:: bash
xterm -title "LAMMPS Shell" -e /path/to/lammps-shell -i in.file.lmp
Use history create input file
"""""""""""""""""""""""""""""
When experimenting with commands to interactively to figure out a
suitable choice of settings or simply the correct syntax, you may want
to record part of your commands to a file for later use. This can be
done with the ``save_history`` commands, which allows to selectively
write a section of the command history to a file (Example:
``save_history 25-30 in.run``). This file can be further edited
(Example: ``|vim in.run``) and then the file read back in and tried out
(Example: ``source in.run``). If the input also creates a system box,
you first need to use the :doc:`clear` command.
----------
.. _arc:

2
doc/utils/sphinx-config/false_positives.txt
View File

@ -2598,6 +2598,7 @@ rdf
RDideal
rdx
reacter
Readline
realTypeMap
real_t
README
@ -2891,6 +2892,7 @@ Sodani
Soderlind
solvated
solvation
someuser
Sorensen
soundspeed
sourceforge

41
examples/accelerate/Make.list
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@ -1,41 +0,0 @@
# desktop builds for dual hex-core Xeons and Fermi GPUs
# use mpicxx or nvcc with its default compiler
# use default FFT support = KISS library
# build with one accelerator package
cpu: -d ../.. -j 16 -p none asphere molecule kspace rigid orig -o cpu file clean mpi
omp: -d ../.. -j 16 -p none asphere molecule kspace rigid omp orig -o omp file clean mpi
opt: -d ../.. -j 16 -p none asphere molecule kspace rigid opt orig -o opt file clean mpi
cuda_double: -d ../.. -j 16 -p none asphere molecule kspace rigid cuda orig -cuda mode=double arch=21 -o cuda_double lib-cuda file clean mpi
cuda_mixed: -d ../.. -j 16 -p none asphere molecule kspace rigid cuda orig -cuda mode=mixed arch=21 -o cuda_mixed lib-cuda file clean mpi
cuda_single: -d ../.. -j 16 -p none asphere molecule kspace rigid cuda orig -cuda mode=single arch=21 -o cuda_single lib-cuda file clean mpi
gpu_double: -d ../.. -j 16 -p none asphere molecule kspace rigid gpu orig -gpu mode=double arch=21 -o gpu_double lib-gpu file clean mpi
gpu_mixed: -d ../.. -j 16 -p none asphere molecule kspace rigid gpu orig -gpu mode=mixed arch=21 -o gpu_mixed lib-gpu file clean mpi
gpu_single: -d ../.. -j 16 -p none asphere molecule kspace rigid gpu orig -gpu mode=single arch=21 -o gpu_single lib-gpu file clean mpi
intel_cpu: -d ../.. -j 16 -p none asphere molecule kspace rigid intel omp orig -cc mpi wrap=icc -intel cpu -o intel_cpu file clean mpi
#intel_phi: -d ../.. -j 16 -p none asphere molecule kspace rigid intel omp orig -intel phi -o intel_phi file clean mpi
kokkos_omp: -d ../.. -j 16 -p none asphere molecule kspace rigid kokkos orig -kokkos omp -o kokkos_omp file clean mpi
kokkos_cuda: -d ../.. -j 16 -p none asphere molecule kspace rigid kokkos orig -cc nvcc wrap=mpi -kokkos cuda arch=21 -o kokkos_cuda file clean mpi
#kokkos_phi: -d ../.. -j 16 -p none asphere molecule kspace rigid kokkos orig -kokkos phi -o kokkos_phi file clean mpi
# build with all accelerator packages for CPU
all_cpu: -d ../.. -j 16 -p asphere molecule kspace rigid none opt omp intel kokkos orig -cc mpi wrap=icc -intel cpu -kokkos omp -o all_cpu file clean mpi
# build with all accelerator packages for GPU
all_gpu: -d ../.. -j 16 -p none asphere molecule kspace rigid omp gpu cuda kokkos orig -cc nvcc wrap=mpi -cuda mode=double arch=21 -gpu mode=double arch=21 -kokkos cuda arch=21 -o all_gpu lib-all file clean mpi

106
examples/accelerate/README
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@ -1,106 +0,0 @@
These are example scripts that can be run with any of
the acclerator packages in LAMMPS:
GPU, USER-INTEL, KOKKOS, USER-OMP, OPT
The easiest way to build LAMMPS with these packages
is via the flags described in Section 4 of the manual.
The easiest way to run these scripts is by using the appropriate
Details on the individual accelerator packages
can be found in doc/Section_accelerate.html.
---------------------
Build LAMMPS with one or more of the accelerator packages
Note that in addition to any accelerator packages, these packages also
need to be installed to run all of the example scripts: ASPHERE,
MOLECULE, KSPACE, RIGID.
These two targets will build a single LAMMPS executable with all the
CPU accelerator packages installed (USER-INTEL for CPU, KOKKOS for
OMP, USER-OMP, OPT) or all the GPU accelerator packages installed
(GPU, KOKKOS for CUDA):
For any build with GPU, or KOKKOS for CUDA, be sure to set
the arch=XX setting to the appropriate value for the GPUs and Cuda
environment on your system.
---------------------
Running with each of the accelerator packages
All of the input scripts have a default problem size and number of
timesteps:
in.lj = LJ melt with cutoff of 2.5 = 32K atoms for 100 steps
in.lj.5.0 = same with cutoff of 5.0 = 32K atoms for 100 steps
in.phosphate = 11K atoms for 100 steps
in.rhodo = 32K atoms for 100 steps
in.lc = 33K atoms for 100 steps (after 200 steps equilibration)
These can be reset using the x,y,z and t variables in the command
line. E.g. adding "-v x 2 -v y 2 -v z 4 -t 1000" to any of the run
command below would run a 16x larger problem (2x2x4) for 1000 steps.
Here are example run commands using each of the accelerator packages:
** CPU only
lmp_cpu < in.lj
mpirun -np 4 lmp_cpu -in in.lj
** OPT package
lmp_opt -sf opt < in.lj
mpirun -np 4 lmp_opt -sf opt -in in.lj
** USER-OMP package
lmp_omp -sf omp -pk omp 1 < in.lj
mpirun -np 4 lmp_omp -sf opt -pk omp 1 -in in.lj # 4 MPI, 1 thread/MPI
mpirun -np 2 lmp_omp -sf opt -pk omp 4 -in in.lj # 2 MPI, 4 thread/MPI
** GPU package
lmp_gpu_double -sf gpu < in.lj
mpirun -np 8 lmp_gpu_double -sf gpu < in.lj # 8 MPI, 8 MPI/GPU
mpirun -np 12 lmp_gpu_double -sf gpu -pk gpu 2 < in.lj # 12 MPI, 6 MPI/GPU
mpirun -np 4 lmp_gpu_double -sf gpu -pk gpu 2 tpa 8 < in.lj.5.0 # 4 MPI, 2 MPI/GPU
Note that when running in.lj.5.0 (which has a long cutoff) with the
GPU package, the "-pk tpa" setting should be > 1 (e.g. 8) for best
performance.
** KOKKOS package for OMP
lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos neigh half < in.lj
mpirun -np 2 lmp_kokkos_omp -k on t 4 -sf kk < in.lj # 2 MPI, 4 thread/MPI
Note that when running with just 1 thread/MPI, "-pk kokkos neigh half"
was specified to use half neighbor lists which are faster when running
on just 1 thread.
** KOKKOS package for CUDA
lmp_kokkos_cuda -k on t 1 -sf kk < in.lj # 1 thread, 1 GPU
mpirun -np 2 lmp_kokkos_cuda -k on t 6 g 2 -sf kk < in.lj # 2 MPI, 6 thread/MPI, 1 MPI/GPU
** KOKKOS package for PHI
mpirun -np 1 lmp_kokkos_phi -k on t 240 -sf kk -in in.lj # 1 MPI, 240 threads/MPI
mpirun -np 30 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj # 30 MPI, 8 threads/MPI
** USER-INTEL package for CPU
lmp_intel_cpu -sf intel < in.lj
mpirun -np 4 lmp_intl_cpu -sf intel < in.lj # 4 MPI
mpirun -np 4 lmp_intl_cpu -sf intel -pk omp 2 < in.lj # 4 MPI, 2 thread/MPI
** USER-INTEL package for PHI
lmp_intel_phi -sf intel -pk intel 1 omp 16 < in.lc # 1 MPI, 16 CPU thread/MPI, 1 Phi, 240 Phi thread/MPI
mpirun -np 4 lmp_intel_phi -sf intel -pk intel 1 omp 2 < in.lc # 4 MPI, 2 CPU threads/MPI, 1 Phi, 60 Phi thread/MPI
Note that there is currently no Phi support for pair_style lj/cut in
the USER-INTEL package.

21922
examples/accelerate/data.phosphate
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File diff suppressed because it is too large Load Diff

57
examples/accelerate/in.lc
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@ -1,57 +0,0 @@
# Gay-Berne benchmark
# biaxial ellipsoid mesogens in isotropic phase
# shape: 2 1.5 1
# cutoff 4.0 with skin 0.8
# NPT, T=2.4, P=8.0
variable x index 1
variable y index 1
variable z index 1
variable t index 100
variable i equal $x*32
variable j equal $y*32
variable k equal $z*32
units lj
atom_style ellipsoid
# create lattice of ellipsoids
lattice sc 0.22
region box block 0 $i 0 $j 0 $k
create_box 1 box
create_atoms 1 box
set type 1 mass 1.5
set type 1 shape 1 1.5 2
set group all quat/random 982381
compute rot all temp/asphere
group spheroid type 1
variable dof equal count(spheroid)+3
compute_modify rot extra/dof ${dof}
velocity all create 2.4 41787 loop geom
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2
neighbor 0.8 bin
timestep 0.002
thermo 100
# equilibration run
fix 1 all npt/asphere temp 2.4 2.4 0.1 iso 5.0 8.0 0.1
compute_modify 1_temp extra/dof ${dof}
run 200
# dynamics run
reset_timestep 0
unfix 1
fix 1 all nve/asphere
run $t

33
examples/accelerate/in.lj
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@ -1,33 +0,0 @@
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable t index 100
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run $t

33
examples/accelerate/in.lj.5.0
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@ -1,33 +0,0 @@
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable t index 100
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 5.0
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run $t

33
examples/accelerate/in.phosphate
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@ -1,33 +0,0 @@
# GI-System
variable x index 1
variable y index 1
variable z index 1
variable t index 100
units metal
atom_style charge
read_data data.phosphate
replicate $x $y $z
pair_style lj/cut/coul/long 15.0
pair_coeff 1 1 0.0 0.29
pair_coeff 1 2 0.0 0.29
pair_coeff 1 3 0.000668 2.5738064
pair_coeff 2 2 0.0 0.29
pair_coeff 2 3 0.004251 1.91988674
pair_coeff 3 3 0.012185 2.91706967
kspace_style pppm 1e-5
neighbor 2.0 bin
thermo 100
timestep 0.001
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
run $t

34
examples/accelerate/in.rhodo
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@ -1,34 +0,0 @@
# Rhodopsin model
variable x index 1
variable y index 1
variable z index 1
variable t index 100
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data ../../bench/data.rhodo
replicate $x $y $z
fix 1 all shake 0.0001 5 0 m 1.0 a 232
fix 2 all npt temp 300.0 300.0 100.0 &
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 100
thermo_style multi
timestep 2.0
run $t

80
examples/accelerate/log.lj.1Feb14.gpu.1
View File

@ -1,80 +0,0 @@
LAMMPS (1 Feb 2014)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut/gpu 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 46.8462 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733683 0 -4.6133768 -5.0196737
100 0.75865617 -5.760326 0 -4.6223462 0.19586079
200 0.75643086 -5.7572859 0 -4.6226441 0.22641241
300 0.74927423 -5.7463997 0 -4.6224927 0.29737707
400 0.74049393 -5.7329259 0 -4.6221893 0.3776681
500 0.73092107 -5.7182622 0 -4.6218849 0.46900655
600 0.72320925 -5.7064076 0 -4.6215979 0.53444495
700 0.71560947 -5.6946702 0 -4.6212602 0.59905402
800 0.71306623 -5.6906095 0 -4.6210143 0.62859381
900 0.70675364 -5.6807352 0 -4.6206089 0.68471945
1000 0.7044073 -5.6771664 0 -4.6205596 0.70033364
Loop time of 21.016 on 1 procs for 1000 steps with 256000 atoms
Pair time (%) = 13.4638 (64.0646)
Neigh time (%) = 6.74725e-05 (0.000321052)
Comm time (%) = 1.09447 (5.20779)
Outpt time (%) = 0.0103211 (0.0491108)
Other time (%) = 6.44732 (30.6781)
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 69917 ave 69917 max 69917 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

80
examples/accelerate/log.lj.1Feb14.gpu.4
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@ -1,80 +0,0 @@
LAMMPS (1 Feb 2014)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut/gpu 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 14.5208 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733683 0 -4.6133768 -5.0196737
100 0.75865617 -5.760326 0 -4.6223462 0.19586079
200 0.75643087 -5.7572859 0 -4.6226441 0.2264124
300 0.74927423 -5.7463997 0 -4.6224927 0.29737713
400 0.7404939 -5.7329258 0 -4.6221893 0.37766836
500 0.73092104 -5.7182626 0 -4.6218853 0.46900587
600 0.72320865 -5.7064076 0 -4.6215989 0.53444677
700 0.71560468 -5.6946635 0 -4.6212607 0.59907258
800 0.7130474 -5.6905859 0 -4.621019 0.62875333
900 0.70683795 -5.680864 0 -4.6206112 0.6839564
1000 0.70454326 -5.6773491 0 -4.6205384 0.69975744
Loop time of 8.72938 on 4 procs for 1000 steps with 256000 atoms
Pair time (%) = 5.30046 (60.7198)
Neigh time (%) = 5.78761e-05 (0.000663004)
Comm time (%) = 1.62433 (18.6076)
Outpt time (%) = 0.0129588 (0.14845)
Other time (%) = 1.79157 (20.5235)
Nlocal: 64000 ave 64066 max 63924 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 30535 ave 30559 max 30518 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

68
examples/accelerate/log.lj.1Feb14.kokkos.cuda.1
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LAMMPS (27 May 2014)
KOKKOS mode is enabled (../lammps.cpp:468)
using 6 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100
Memory usage per processor = 16.9509 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 0.57192 on 6 procs (1 MPI x 6 OpenMP) for 100 steps with 32000 atoms
Pair time (%) = 0.205416 (35.917)
Neigh time (%) = 0.112468 (19.665)
Comm time (%) = 0.174223 (30.4629)
Outpt time (%) = 0.000159025 (0.0278055)
Other time (%) = 0.0796535 (13.9274)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19657 ave 19657 max 19657 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.40567e+06 ave 2.40567e+06 max 2.40567e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2405666
Ave neighs/atom = 75.1771
Neighbor list builds = 5
Dangerous builds = 0

68
examples/accelerate/log.lj.1Feb14.kokkos.cuda.2
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LAMMPS (27 May 2014)
KOKKOS mode is enabled (../lammps.cpp:468)
using 6 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100
Memory usage per processor = 8.95027 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 0.689608 on 12 procs (2 MPI x 6 OpenMP) for 100 steps with 32000 atoms
Pair time (%) = 0.210953 (30.5903)
Neigh time (%) = 0.122991 (17.8349)
Comm time (%) = 0.25264 (36.6353)
Outpt time (%) = 0.000259042 (0.0375636)
Other time (%) = 0.102765 (14.9019)
Nlocal: 16000 ave 16001 max 15999 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 13632.5 ave 13635 max 13630 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
FullNghs: 1.20283e+06 ave 1.20347e+06 max 1.2022e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 2405666
Ave neighs/atom = 75.1771
Neighbor list builds = 5
Dangerous builds = 0

68
examples/accelerate/log.lj.1Feb14.kokkos.omp.1
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LAMMPS (27 May 2014)
KOKKOS mode is enabled (../lammps.cpp:468)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
package kokkos neigh half
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100
Memory usage per processor = 7.79551 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 2.29105 on 1 procs (1 MPI x 1 OpenMP) for 100 steps with 32000 atoms
Pair time (%) = 1.82425 (79.6249)
Neigh time (%) = 0.338632 (14.7806)
Comm time (%) = 0.0366232 (1.59853)
Outpt time (%) = 0.000144005 (0.00628553)
Other time (%) = 0.0914049 (3.98965)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19657 ave 19657 max 19657 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1202833
Ave neighs/atom = 37.5885
Neighbor list builds = 5
Dangerous builds = 0

68
examples/accelerate/log.lj.1Feb14.kokkos.omp.4
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LAMMPS (27 May 2014)
KOKKOS mode is enabled (../lammps.cpp:468)
using 4 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100
Memory usage per processor = 13.2888 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 0.983697 on 4 procs (1 MPI x 4 OpenMP) for 100 steps with 32000 atoms
Pair time (%) = 0.767155 (77.9869)
Neigh time (%) = 0.14734 (14.9782)
Comm time (%) = 0.041466 (4.21532)
Outpt time (%) = 0.000172138 (0.0174991)
Other time (%) = 0.0275636 (2.80204)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19657 ave 19657 max 19657 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.40567e+06 ave 2.40567e+06 max 2.40567e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2405666
Ave neighs/atom = 75.1771
Neighbor list builds = 5
Dangerous builds = 0

80
examples/accelerate/log.lj.5.0.1Feb14.gpu.1
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LAMMPS (1 Feb 2014)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1 threads_per_atom 8
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut/gpu 5.0
pair_coeff 1 1 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 58.5717 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -7.1616931 0 -5.0017016 -5.6743465
100 0.75998441 -6.1430228 0 -5.0030506 -0.43702263
200 0.75772859 -6.1397321 0 -5.0031437 -0.40563811
300 0.75030002 -6.1286578 0 -5.0032122 -0.33104717
400 0.73999054 -6.1132463 0 -5.0032649 -0.24001424
500 0.73224838 -6.1016938 0 -5.0033255 -0.16524979
600 0.72455889 -6.0902001 0 -5.003366 -0.099949772
700 0.71911385 -6.0820798 0 -5.0034133 -0.046759186
800 0.71253787 -6.0722342 0 -5.0034316 0.0019671065
900 0.70835425 -6.0659819 0 -5.0034546 0.037482543
1000 0.70648171 -6.0631852 0 -5.0034668 0.057159495
Loop time of 53.1575 on 1 procs for 1000 steps with 256000 atoms
Pair time (%) = 45.4859 (85.5682)
Neigh time (%) = 7.9155e-05 (0.000148907)
Comm time (%) = 1.40304 (2.63941)
Outpt time (%) = 0.00999498 (0.0188026)
Other time (%) = 6.25847 (11.7734)
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 141542 ave 141542 max 141542 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

80
examples/accelerate/log.lj.5.0.1Feb14.gpu.4
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LAMMPS (1 Feb 2014)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1 threads_per_atom 8
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut/gpu 5.0
pair_coeff 1 1 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 20.382 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -7.1616931 0 -5.0017016 -5.6743465
100 0.75998441 -6.1430228 0 -5.0030506 -0.43702263
200 0.75772859 -6.1397321 0 -5.0031437 -0.40563811
300 0.75030002 -6.1286578 0 -5.0032122 -0.33104718
400 0.73999055 -6.1132463 0 -5.0032649 -0.24001425
500 0.73224835 -6.1016938 0 -5.0033256 -0.16524973
600 0.72455878 -6.0902 0 -5.0033661 -0.099949172
700 0.71911606 -6.0820833 0 -5.0034134 -0.046771469
800 0.71253754 -6.0722337 0 -5.0034316 0.0019725827
900 0.70832904 -6.0659437 0 -5.0034543 0.03758241
1000 0.70634002 -6.062973 0 -5.0034671 0.057951142
Loop time of 26.0448 on 4 procs for 1000 steps with 256000 atoms
Pair time (%) = 18.6673 (71.674)
Neigh time (%) = 6.55651e-05 (0.00025174)
Comm time (%) = 5.797 (22.2578)
Outpt time (%) = 0.0719919 (0.276416)
Other time (%) = 1.50839 (5.79152)
Nlocal: 64000 ave 64092 max 63823 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 64384.2 ave 64490 max 64211 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

80
examples/accelerate/log.phosphate.1Feb14.gpu.1
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LAMMPS (1 Feb 2014)
# GI-System
units metal
newton off
package gpu force/neigh 0 1 1
atom_style charge
read_data data.phosphate
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
1 by 1 by 1 MPI processor grid
reading atoms ...
10950 atoms
reading velocities ...
10950 velocities
replicate 3 3 3
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
1 by 1 by 1 MPI processor grid
295650 atoms
pair_style lj/cut/coul/long/gpu 15.0
pair_coeff 1 1 0.0 0.29
pair_coeff 1 2 0.0 0.29
pair_coeff 1 3 0.000668 2.5738064
pair_coeff 2 2 0.0 0.29
pair_coeff 2 3 0.004251 1.91988674
pair_coeff 3 3 0.012185 2.91706967
kspace_style pppm/gpu 1e-5
neighbor 2.0 bin
thermo 100
timestep 0.001
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
run 200
PPPM initialization ...
G vector (1/distance) = 0.210051
grid = 108 108 108
stencil order = 5
estimated absolute RMS force accuracy = 0.000178801
estimated relative force accuracy = 1.24171e-05
using double precision FFTs
3d grid and FFT values/proc = 1520875 1259712
Memory usage per processor = 266.927 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 400.30257 -2381941.6 0 -2366643.8 -449.96842 4242016.4
100 411.69681 -2392428.5 0 -2376695.3 7046.698 4308883.5
200 401.28392 -2394152.5 0 -2378817.2 3243.2685 4334284.4
Loop time of 154.943 on 1 procs for 200 steps with 295650 atoms
Pair time (%) = 12.0178 (7.75625)
Kspce time (%) = 80.3771 (51.8753)
Neigh time (%) = 0.0138304 (0.00892614)
Comm time (%) = 0.348981 (0.225232)
Outpt time (%) = 0.00180006 (0.00116176)
Other time (%) = 62.1834 (40.1331)
FFT time (% of Kspce) = 56.9885 (70.9013)
FFT Gflps 3d (1d only) = 1.24196 3.00739
Nlocal: 295650 ave 295650 max 295650 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 226982 ave 226982 max 226982 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 6
Dangerous builds = 0
unfix 1
Please see the log.cite file for references relevant to this simulation

80
examples/accelerate/log.phosphate.1Feb14.gpu.4
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LAMMPS (1 Feb 2014)
# GI-System
units metal
newton off
package gpu force/neigh 0 1 1
atom_style charge
read_data data.phosphate
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
1 by 2 by 2 MPI processor grid
reading atoms ...
10950 atoms
reading velocities ...
10950 velocities
replicate 3 3 3
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
2 by 1 by 2 MPI processor grid
295650 atoms
pair_style lj/cut/coul/long/gpu 15.0
pair_coeff 1 1 0.0 0.29
pair_coeff 1 2 0.0 0.29
pair_coeff 1 3 0.000668 2.5738064
pair_coeff 2 2 0.0 0.29
pair_coeff 2 3 0.004251 1.91988674
pair_coeff 3 3 0.012185 2.91706967
kspace_style pppm/gpu 1e-5
neighbor 2.0 bin
thermo 100
timestep 0.001
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
run 200
PPPM initialization ...
G vector (1/distance) = 0.210051
grid = 108 108 108
stencil order = 5
estimated absolute RMS force accuracy = 0.000178801
estimated relative force accuracy = 1.24171e-05
using double precision FFTs
3d grid and FFT values/proc = 427915 314928
Memory usage per processor = 80.0769 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 400.30257 -2381941.6 0 -2366643.8 -449.96842 4242016.4
100 411.69681 -2392428.5 0 -2376695.3 7046.698 4308883.5
200 401.28392 -2394152.5 0 -2378817.2 3243.2685 4334284.4
Loop time of 56.1151 on 4 procs for 200 steps with 295650 atoms
Pair time (%) = 4.55937 (8.12503)
Kspce time (%) = 34.5442 (61.5596)
Neigh time (%) = 0.00624901 (0.0111361)
Comm time (%) = 0.470437 (0.838343)
Outpt time (%) = 0.000446558 (0.000795789)
Other time (%) = 16.5344 (29.4651)
FFT time (% of Kspce) = 22.6526 (65.5758)
FFT Gflps 3d (1d only) = 3.12448 11.5533
Nlocal: 73912.5 ave 74223 max 73638 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nghost: 105257 ave 105797 max 104698 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 6
Dangerous builds = 0
unfix 1
Please see the log.cite file for references relevant to this simulation

135
examples/accelerate/log.rhodo.1Feb14.gpu.1
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LAMMPS (1 Feb 2014)
# Rhodopsin model
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long/gpu 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm/gpu 1e-4
read_data data.rhodo
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
18 = max angles/atom
scanning dihedrals ...
40 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
27723 bonds
reading angles ...
40467 angles
reading dihedrals ...
56829 dihedrals
reading impropers ...
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
replicate $x $y $z
replicate 2 $y $z
replicate 2 2 $z
replicate 2 2 2
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
1 by 1 by 1 MPI processor grid
256000 atoms
221784 bonds
323736 angles
454632 dihedrals
8272 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
12936 = # of size 2 clusters
29064 = # of size 3 clusters
5976 = # of size 4 clusters
33864 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 100
thermo_style multi
timestep 2.0
run 200
PPPM initialization ...
G vector (1/distance) = 0.245959
grid = 48 64 60
stencil order = 5
estimated absolute RMS force accuracy = 0.0410392
estimated relative force accuracy = 0.000123588
using double precision FFTs
3d grid and FFT values/proc = 237705 184320
Memory usage per processor = 760.048 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 157024.0504 KinEng = 172792.6155 Temp = 301.1796
PotEng = -15768.5651 E_bond = 28164.9917 E_angle = 117224.0742
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6323
E_coul = 1894295.6635 E_long = -2130488.8032 Press = 9562.1557
Volume = 2457390.7959
---------------- Step 100 ----- CPU = 36.3779 (sec) ----------------
TotEng = -233301.6813 KinEng = 123222.9259 Temp = 214.7790
PotEng = -356524.6072 E_bond = 13098.4672 E_angle = 56766.9111
E_dihed = 45556.8240 E_impro = 1313.9378 E_vdwl = -40863.9278
E_coul = 1705084.7672 E_long = -2137481.5867 Press = -1634.3912
Volume = 2522232.6302
---------------- Step 200 ----- CPU = 70.7784 (sec) ----------------
TotEng = -308342.0030 KinEng = 108937.4160 Temp = 189.8792
PotEng = -417279.4189 E_bond = 9579.0134 E_angle = 47373.6274
E_dihed = 39847.4817 E_impro = 967.6755 E_vdwl = -23635.2960
E_coul = 1646633.4711 E_long = -2138045.3918 Press = -1185.9327
Volume = 2554683.1533
Loop time of 70.7784 on 1 procs for 200 steps with 256000 atoms
Pair time (%) = 10.0374 (14.1815)
Bond time (%) = 27.2471 (38.4963)
Kspce time (%) = 7.19169 (10.1608)
Neigh time (%) = 5.43951 (7.68527)
Comm time (%) = 0.681534 (0.962912)
Outpt time (%) = 0.00139809 (0.0019753)
Other time (%) = 20.1798 (28.5112)
FFT time (% of Kspce) = 5.17983 (72.0253)
FFT Gflps 3d (1d only) = 1.72575 2.95071
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 161662 ave 161662 max 161662 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 7.43187
Neighbor list builds = 31
Dangerous builds = 12
Please see the log.cite file for references relevant to this simulation

135
examples/accelerate/log.rhodo.1Feb14.gpu.4
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LAMMPS (1 Feb 2014)
# Rhodopsin model
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long/gpu 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm/gpu 1e-4
read_data data.rhodo
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
18 = max angles/atom
scanning dihedrals ...
40 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
27723 bonds
reading angles ...
40467 angles
reading dihedrals ...
56829 dihedrals
reading impropers ...
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
replicate $x $y $z
replicate 2 $y $z
replicate 2 2 $z
replicate 2 2 2
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
1 by 2 by 2 MPI processor grid
256000 atoms
221784 bonds
323736 angles
454632 dihedrals
8272 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
12936 = # of size 2 clusters
29064 = # of size 3 clusters
5976 = # of size 4 clusters
33864 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 100
thermo_style multi
timestep 2.0
run 200
PPPM initialization ...
G vector (1/distance) = 0.245959
grid = 48 64 60
stencil order = 5
estimated absolute RMS force accuracy = 0.0410392
estimated relative force accuracy = 0.000123588
using double precision FFTs
3d grid and FFT values/proc = 68635 46080
Memory usage per processor = 250.358 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 157024.0504 KinEng = 172792.6155 Temp = 301.1796
PotEng = -15768.5651 E_bond = 28164.9917 E_angle = 117224.0742
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6323
E_coul = 1894295.6635 E_long = -2130488.8032 Press = 9562.1557
Volume = 2457390.7959
---------------- Step 100 ----- CPU = 12.3409 (sec) ----------------
TotEng = -233301.6797 KinEng = 123222.9259 Temp = 214.7790
PotEng = -356524.6057 E_bond = 13098.4672 E_angle = 56766.9111
E_dihed = 45556.8240 E_impro = 1313.9378 E_vdwl = -40863.9278
E_coul = 1705084.7688 E_long = -2137481.5867 Press = -1634.3910
Volume = 2522232.6302
---------------- Step 200 ----- CPU = 23.6590 (sec) ----------------
TotEng = -308341.9699 KinEng = 108937.4196 Temp = 189.8792
PotEng = -417279.3895 E_bond = 9579.0134 E_angle = 47373.6274
E_dihed = 39847.4807 E_impro = 967.6755 E_vdwl = -23635.2996
E_coul = 1646633.5046 E_long = -2138045.3916 Press = -1185.9299
Volume = 2554683.1519
Loop time of 23.6591 on 4 procs for 200 steps with 256000 atoms
Pair time (%) = 4.81669 (20.3587)
Bond time (%) = 6.52579 (27.5826)
Kspce time (%) = 4.48765 (18.968)
Neigh time (%) = 1.3238 (5.5953)
Comm time (%) = 0.490551 (2.07342)
Outpt time (%) = 0.000454485 (0.00192098)
Other time (%) = 6.01414 (25.42)
FFT time (% of Kspce) = 1.77734 (39.6051)
FFT Gflps 3d (1d only) = 5.02949 11.6654
Nlocal: 64000 ave 64001 max 63999 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 70656.5 ave 70660 max 70654 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 7.43187
Neighbor list builds = 31
Dangerous builds = 12
Please see the log.cite file for references relevant to this simulation

118
src/MAKE/MACHINES/Makefile.astra_gcc
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@ -1,118 +0,0 @@
# astra_gcc = ThunderX2 GCC/OpenMPI Based, FFTW
# need to load the following modules:
# 1) arm-based developer pack
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpicxx
CCFLAGS = -O3 -funroll-loops -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
DEPFLAGS = -M
LINK = mpicxx
LINKFLAGS = -O3 -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
LIB = -lstdc++
ARCHIVE = ar
ARFLAGS = -rcsv
SIZE = size
# ---------------------------------------------------------------------
# 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 3.5 of the manual
LMP_INC = -DLAMMPS_GZIP
# MPI library
# see discussion in Section 3.4 of the 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 =
MPI_PATH =
MPI_LIB =
# FFT library
# see discussion in Section 3.5.2 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_FFTW2 -I${FFTW_INC}
FFT_PATH = -I${FFTW_INC}
FFT_LIB = -L${FFTW_LIB} -lfftw3
# JPEG and/or PNG library
# see discussion in Section 3.5.4 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): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
$(SIZE) $@
# Library targets
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
@rm -f ../$(ARLIB)
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
@rm -f $(ARLIB)
@ln -s ../$(ARLIB) $(ARLIB)
$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
$(OBJ) $(EXTRA_LIB) $(LIB)
@rm -f $(SHLIB)
@ln -s ../$(SHLIB) $(SHLIB)
# 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

125
src/MAKE/MACHINES/Makefile.bgl
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@ -1,125 +0,0 @@
# bgl = LLNL Blue Gene Light machine, xlC, native MPI, FFTW
SHELL = /bin/sh
.SUFFIXES: .cpp .u
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = /opt/ibmcmp/vacpp/7.0/bin/blrts_xlC
CCFLAGS = -O3
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = /opt/ibmcmp/vacpp/7.0/bin/blrts_xlC
LINKFLAGS = -O \
-L/opt/ibmcmp/xlf/9.1/blrts_lib \
-L/opt/ibmcmp/vacpp/7.0/blrts_lib \
-L/bgl/local/lib \
-L/bgl/local/bglfftwgel-2.1.5.pre5/lib
LIB = -lxlopt -lxlomp_ser -lxl -lxlfmath -lm \
-lmsglayer.rts -lrts.rts -ldevices.rts -lmassv
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 3.5 of the manual
LMP_INC = -DLAMMPS_GZIP
# MPI library
# see discussion in Section 3.4 of the 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 = -DMPICH_SKIP_MPICXX
MPI_PATH =
MPI_LIB = -lmpich.rts
# FFT library
# see discussion in Section 3.5.2 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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library
# see discussion in Section 3.5.4 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): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
$(SIZE) $@
# Library targets
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
@rm -f ../$(ARLIB)
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
@rm -f $(ARLIB)
@ln -s ../$(ARLIB) $(ARLIB)
$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
$(OBJ) $(EXTRA_LIB) $(LIB)
@rm -f $(SHLIB)
@ln -s ../$(SHLIB) $(SHLIB)
# 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

119
src/MAKE/MACHINES/Makefile.chama
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@ -1,119 +0,0 @@
# chama = Intel SandyBridge, mpic++, openmpi, no FFTW
# need to load the following modules:
# 1) intel/12.1
# 2) openmpi-intel/1.4
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpic++
CCFLAGS = -O3 -axAVX -funroll-loops -fstrict-aliasing -openmp
DEPFLAGS = -M
LINK = mpic++
LINKFLAGS = -O3 -axAVX -openmp
LIB = -lstdc++
ARCHIVE = ar
ARFLAGS = -rcsv
SIZE = size
# ---------------------------------------------------------------------
# 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 3.5 of the manual
LMP_INC = -DLAMMPS_GZIP
# MPI library
# see discussion in Section 3.4 of the 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 = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1
MPI_PATH =
MPI_LIB =
# FFT library
# see discussion in Section 3.5.2 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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library
# see discussion in Section 3.5.4 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): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
$(SIZE) $@
# Library targets
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
@rm -f ../$(ARLIB)
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
@rm -f $(ARLIB)
@ln -s ../$(ARLIB) $(ARLIB)
$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
$(OBJ) $(EXTRA_LIB) $(LIB)
@rm -f $(SHLIB)
@ln -s ../$(SHLIB) $(SHLIB)
# 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

136
src/MAKE/MACHINES/Makefile.glory
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@ -1,136 +0,0 @@
# glory = Linux cluster with 4-way quad cores, Intel mpicxx, native MPI, FFTW
SHELL = /bin/sh
# this Makefile builds LAMMPS for mvapich running on Glory
# to invoke this Makefile, you need these modules loaded:
# compilers/intel-11.1-f064-c064
# mpi/mvapich-1.1_intel-11.1-f064-c064
# libraries/fftw-2.1.5
# you can determine which modules are loaded by typing:
# module list
# these modules are not the default ones, but can be enabled by
# lines like this in your .cshrc or other start-up shell file
# or by typing them before you build LAMMPS:
# module swap mpi misc/env-mvapich
# module load compilers/intel-11.1-f064-c064
# module load mpi/mvapich-1.1_intel-11.1-f064-c064
# module load libraries/fftw-2.1.5
# these same modules need to be loaded to submit a LAMMPS job,
# either interactively or via a batch script
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpicxx
CCFLAGS = -O
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpicxx
LINKFLAGS = -O
LIB = -lstdc++ -lm
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 3.5 of the manual
LMP_INC = -DLAMMPS_GZIP
# MPI library
# see discussion in Section 3.4 of the 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 =
MPI_PATH =
MPI_LIB =
# FFT library
# see discussion in Section 3.5.2 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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library
# see discussion in Section 3.5.4 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): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
$(SIZE) $@
# Library targets
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
@rm -f ../$(ARLIB)
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
@rm -f $(ARLIB)
@ln -s ../$(ARLIB) $(ARLIB)
$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
$(OBJ) $(EXTRA_LIB) $(LIB)
@rm -f $(SHLIB)
@ln -s ../$(SHLIB) $(SHLIB)
# 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

121
src/MAKE/MACHINES/Makefile.icex
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@ -1,121 +0,0 @@
# icex = unknown 64-bit x86_64 machine
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpicxx
CCFLAGS = -g -O3 -Wall -Wextra -frounding-math -fsignaling-nans -march=native
SHFLAGS = -shared -MD -mcmodel=medium -fpic -fPIC
DEPFLAGS = -M
LINK = mpicxx
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 3.5 of the manual
LMP_INC = -DLAMMPS_GZIP
#LMP_INC += -DLAMMPS_JPEG
LMP_INC += -DLAMMPS_MEMALIGN=64
# MPI library
# see discussion in Section 3.4 of the 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 = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1
MPI_PATH =
MPI_LIB =
# FFT library
# see discussion in Section 3.5.2 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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library
# see discussion in Section 3.5.4 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): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
$(SIZE) $@
# Library targets
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
@rm -f ../$(ARLIB)
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
@rm -f $(ARLIB)
@ln -s ../$(ARLIB) $(ARLIB)
$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
$(OBJ) $(EXTRA_LIB) $(LIB)
@rm -f $(SHLIB)
@ln -s ../$(SHLIB) $(SHLIB)
# 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

119
src/MAKE/MACHINES/Makefile.myrinet
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@ -1,119 +0,0 @@
# myrinet = cluster, g++, myrinet MPI, no FFTs
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = g++
CCFLAGS = -O
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = g++
LINKFLAGS = -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 3.5 of the manual
LMP_INC = -DLAMMPS_GZIP
# MPI library
# see discussion in Section 3.4 of the 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/opt/mpich-mx/include
MPI_PATH = -L/opt/mpich-mx/lib -L/opt/mx/lib
MPI_LIB = -lmpich -lmyriexpress
# FFT library
# see discussion in Section 3.5.2 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_NONE
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library
# see discussion in Section 3.5.4 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): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
$(SIZE) $@
# Library targets
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
@rm -f ../$(ARLIB)
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
@rm -f $(ARLIB)
@ln -s ../$(ARLIB) $(ARLIB)
$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
$(OBJ) $(EXTRA_LIB) $(LIB)
@rm -f $(SHLIB)
@ln -s ../$(SHLIB) $(SHLIB)
# 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

139
src/MAKE/MACHINES/Makefile.redsky
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@ -1,139 +0,0 @@
# redsky - SUN X6275 nodes, Nehalem procs, mpic++, openmpi, OpenMP, no FFTW
SHELL = /bin/sh
# This Makefile builds LAMMPS for RedSky with OpenMPI.
# To use this Makefile, you need appropriate modules loaded.
# You can determine which modules are loaded by typing:
# module list
# These modules can be enabled by lines like this in your .cshrc or
# other start-up shell file or by typing them before you build LAMMPS:
# module load mpi/openmpi-1.4.2_oobpr_intel-11.1-f064-c064
# module load libraries/intel-mkl-11.1.064
# module load libraries/fftw-2.1.5_openmpi-1.4.2_oobpr_intel-11.1-f064-c064
# These same modules need to be loaded to submit a LAMMPS job,
# either interactively or via a batch script.
# IMPORTANT NOTE:
# to run efficiently on RedSky, use the "numa_wrapper" mpiexec option,
# to insure processes and their memory are locked to specific cores
# e.g. in your batch script:
# nodes=$SLURM_JOB_NUM_NODES
# cores=8
# mpiexec --npernode $cores numa_wrapper --ppn $cores lmp_redsky < in > out
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpic++ -fopenmp
CCFLAGS = -O2 -xsse4.2 -funroll-loops -fstrict-aliasing
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpic++ -fopenmp
LINKFLAGS = -O -xsse4.2
LIB = -lstdc++
SIZE = size
ARCHIVE = ar
ARFLAGS = -rcsv
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 3.5 of the manual
LMP_INC = -DLAMMPS_GZIP
# MPI library
# see discussion in Section 3.4 of the 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 =
MPI_PATH =
MPI_LIB =
# FFT library
# see discussion in Section 3.5.2 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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library
# see discussion in Section 3.5.4 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): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
$(SIZE) $@
# Library targets
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
@rm -f ../$(ARLIB)
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
@rm -f $(ARLIB)
@ln -s ../$(ARLIB) $(ARLIB)
$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
$(OBJ) $(EXTRA_LIB) $(LIB)
@rm -f $(SHLIB)
@ln -s ../$(SHLIB) $(SHLIB)
# 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

120
src/MAKE/MACHINES/Makefile.storm
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@ -1,120 +0,0 @@
# storm = Cray Red Storm XT3, Cray CC, native MPI, FFTW
SHELL = /bin/sh
.SUFFIXES: .cpp .d
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = CC
CCFLAGS = -fastsse
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = CC
LINKFLAGS = -O
LIB = -lstdc++
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 3.5 of the manual
LMP_INC = -DLAMMPS_GZIP
# MPI library
# see discussion in Section 3.4 of the 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 = -DMPICH_SKIP_MPICXX
MPI_PATH =
MPI_LIB =
# FFT library
# see discussion in Section 3.5.2 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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library
# see discussion in Section 3.5.4 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): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
$(SIZE) $@
# Library targets
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
@rm -f ../$(ARLIB)
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
@rm -f $(ARLIB)
@ln -s ../$(ARLIB) $(ARLIB)
$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
$(OBJ) $(EXTRA_LIB) $(LIB)
@rm -f $(SHLIB)
@ln -s ../$(SHLIB) $(SHLIB)
# 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

119
src/MAKE/MACHINES/Makefile.tacc
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@ -1,119 +0,0 @@
# tacc = UT Lonestar TACC machine, mpiCC, MPI, FFTW
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpiCC
CCFLAGS = -O
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpiCC
LINKFLAGS = -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 3.5 of the manual
LMP_INC = -DLAMMPS_GZIP
# MPI library
# see discussion in Section 3.4 of the 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 = -DMPICH_SKIP_MPICXX
MPI_PATH =
MPI_LIB = -lmpich -lpthread
# FFT library
# see discussion in Section 3.5.2 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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library
# see discussion in Section 3.5.4 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): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
$(SIZE) $@
# Library targets
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
@rm -f ../$(ARLIB)
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
@rm -f $(ARLIB)
@ln -s ../$(ARLIB) $(ARLIB)
$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
$(OBJ) $(EXTRA_LIB) $(LIB)
@rm -f $(SHLIB)
@ln -s ../$(SHLIB) $(SHLIB)
# 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

121
src/MAKE/MACHINES/Makefile.xt3
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@ -1,121 +0,0 @@
# xt3 = PSC BigBen Cray XT3, CC, native MPI, FFTW
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = CC
CCFLAGS = -O3 --target=catamount \
-fomit-frame-pointer -finline-functions \
-Wall -Wno-unused -funroll-all-loops
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = CC
LINKFLAGS = --target=catamount -O
LIB = -lgmalloc
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 3.5 of the manual
LMP_INC = -DLAMMPS_GZIP -DLAMMPS_XDR
# MPI library
# see discussion in Section 3.4 of the 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 = -DMPICH_SKIP_MPICXX
MPI_PATH =
MPI_LIB = -lmpich -lpthread
# FFT library
# see discussion in Section 3.5.2 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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library
# see discussion in Section 3.5.4 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): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
$(SIZE) $@
# Library targets
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
@rm -f ../$(ARLIB)
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
@rm -f $(ARLIB)
@ln -s ../$(ARLIB) $(ARLIB)
$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
$(OBJ) $(EXTRA_LIB) $(LIB)
@rm -f $(SHLIB)
@ln -s ../$(SHLIB) $(SHLIB)
# 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

120
src/MAKE/MACHINES/Makefile.xt5
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@ -1,120 +0,0 @@
# xt5 = Cray XT5, Cray CC, native MPI, FFTW
SHELL = /bin/sh
.SUFFIXES: .cpp .d
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = CC
CCFLAGS = -fastsse
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = CC
LINKFLAGS = -O
LIB = -lstdc++
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 3.5 of the manual
LMP_INC = -DLAMMPS_GZIP
# MPI library
# see discussion in Section 3.4 of the 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 = -DMPICH_SKIP_MPICXX
MPI_PATH =
MPI_LIB =
# FFT library
# see discussion in Section 3.5.2 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 =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library
# see discussion in Section 3.5.4 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): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
$(SIZE) $@
# Library targets
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
@rm -f ../$(ARLIB)
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
@rm -f $(ARLIB)
@ln -s ../$(ARLIB) $(ARLIB)
$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
$(OBJ) $(EXTRA_LIB) $(LIB)
@rm -f $(SHLIB)
@ln -s ../$(SHLIB) $(SHLIB)
# 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

79
tools/lammps-shell/README
View File

@ -1,7 +1,7 @@
The LAMMPS Shell. An enhanced LAMMPS executable for interactive sessions.
Overview
========
^^^^^^^^
This is a program that functions very similar to the regular LAMMPS
executable but has several modifications and additions that make it
@ -27,7 +27,7 @@ These enhancements makes the LAMMPS shell an attractive choice for
interactive LAMMPS sessions in graphical user interfaces.
TAB-expansion
=============
^^^^^^^^^^^^^
When writing commands interactively at the shell prompt, you can hit
the TAB key at any time to try and complete the text. This completion
@ -48,10 +48,11 @@ available in that executable.
to known compute/fix IDs and variable names. Variable name expansion
is also available for the ${name} variable syntax.
- In all other cases, expansion will be performed on filenames.
- In all other cases TAB expansion will complete to names of files
and directories.
Command line editing and history
================================
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
When typing commands, command line editing similar to what BASH
provides is available. Thus it is possible to move around the
@ -79,7 +80,7 @@ readline, please see the available documentation at:
http://www.gnu.org/s/readline/#Documentation
Additional commands
===================
^^^^^^^^^^^^^^^^^^^
The followind commands are added to the LAMMPS shell on top of the
regular LAMMPS commands:
@ -87,14 +88,24 @@ regular LAMMPS commands:
- help (or ?) print a brief help message
- history display the current command history list
- clear_history wipe out the current command history list
- save_history <range> <file>
write commands from the history to file.
The range is given as <from>-<to>, where <from> and <to>
may be empty. Example: save_history 100- in.recent
- source <file> read commands from file (same as "include")
- pwd print current working directory
- cd <directory> change current working directory (same as pwd if no directory)
- mem print current and maximum memory usage
- |<command> execute <command> as a shell command and return to the command prompt
- exit exit the LAMMPS shell cleanly (unlike the "quit" command)
Please note that some known shell operations are implemented in the
LAMMPS "shell" command in a platform neutral fashion, while using
the '\|' character will always pass the following text to the
operating system's shell command.
Compilation
===========
^^^^^^^^^^^
Compilation of the LAMMPS shell can be enabled by setting the CMake
variable BUILD_LAMMPS_SHELL to "on" or using the makefile in the
@ -104,7 +115,61 @@ customization depending on the features and settings used for
compiling LAMMPS.
Limitations
===========
^^^^^^^^^^^
The LAMMPS shell was not designed for use with MPI parallelization
via "mpirun" or "mpiexec" or "srun".
Readline customization
^^^^^^^^^^^^^^^^^^^^^^
The behavior of the readline functionality can be customized in the
"${HOME}/.inputrc" file. This can be used to alter the default
settings or change the key-bindings. The LAMMPS Shell sets the
application name "lammps-shell", so customizations can be either
global or specific for the LAMMPS shell by bracketing them between
"$if lammps-shell" and "$endif" like in the following example:
$if lammps-shell
# disable "beep" or "screen flash"
set bell-style none
# bind the "Insert" key to toggle overwrite mode
"\e[2~": overwrite-mode
$endif
More details about this are in the readline documentation https://tiswww.cwru.edu/php/chet/readline/rluserman.html#SEC9
LAMMPS Shell tips and tricks
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Enable tilde expansion
""""""""""""""""""""""
Adding "set expand-tilde on" to "${HOME}/.inputrc" is recommended as
this will change the filename expansion behavior to replace any text
starting with "~" by the full path to the corresponding user's home
directory. While the expansion of filenames **will** happen on all
arguments where the context is not known (e.g. "~/compile/lamm<TAB>"
will expand to "~/compile/lammps/"), it will not replace the tilde by
default. But since LAMMPS does not do tilde expansion itself (unlike a
shell), this will result in errors. Instead the tilde-expression should
be expanded into a valid path, where the plain "~/" stands for the
current user's home directory and "~someuser/" stands for
"/home/someuser" or whatever the full path to that user's home directory
is.
File extension association
""""""""""""""""""""""""""
Since the LAMMPS shell (unlike the regular LAMMPS executable) does not
exit when an input file is passed on the command line with the "-in" or
"-i" flag (the behavior is like for "python -i <filename>"), it makes
the LAMMPS shell suitable for associating it with input files based on
their filename extension (e.g. ".lmp"). Since "lammps-shell" is a
console application, you have to run it inside a terminal program with a
command line like this:
xterm -title "LAMMPS Shell" -e /path/to/lammps-shell -i in.file.lmp

109
tools/lammps-shell/lammps-shell.cpp
View File

@ -12,6 +12,7 @@
#include <cstdlib>
#include <cstring>
#include <ctime>
#include <fstream>
#include <iostream>
#include <string>
#include <vector>
@ -32,14 +33,20 @@
#include <signal.h>
#endif
#if defined(_OPENMP)
#include <omp.h>
#endif
#include <readline/history.h>
#include <readline/readline.h>
using namespace LAMMPS_NS;
const int buflen = 512;
char *omp_threads = nullptr;
const int buflen = 512;
char buf[buflen];
void *lmp = nullptr;
enum {
ATOM_STYLE,
INTEGRATE_STYLE,
@ -145,6 +152,57 @@ static char *dupstring(const std::string &text)
return copy;
}
static int save_history(std::string range, std::string file)
{
int from = history_base;
int to = from + history_length - 1;
if (!range.empty()) {
std::size_t found = range.find_first_of("-");
if (found == std::string::npos) { // only a single number
int num = strtol(range.c_str(), NULL, 10);
if ((num >= from) && (num <= to)) {
from = to = num;
} else
return 1;
} else { // range of numbers
if (found > 0) { // get number before '-'
int num = strtol(range.substr(0, found).c_str(), NULL, 10);
if ((num >= from) && (num <= to)) {
from = num;
} else
return 1;
}
if (range.size() > found + 1) { // get number after '-'
int num = strtol(range.substr(found + 1).c_str(), NULL, 10);
if ((num >= from) && (num <= to)) {
to = num;
} else
return 1;
}
}
std::ofstream out(file, std::ios::out | std::ios::trunc);
if (out.fail()) {
std::cerr << "'" << utils::getsyserror() << "' error when "
<< "trying to open file '" << file << "' for writing.\n";
return 0;
}
out << "# saved LAMMPS Shell history\n";
for (int i = from; i <= to; ++i) {
HIST_ENTRY *item = history_get(i);
if (item == nullptr) {
out.close();
return 1;
}
out << item->line << "\n";
}
out.close();
}
return 0;
}
template <int STYLE> char *style_generator(const char *text, int state)
{
static int idx, num, len;
@ -229,7 +287,7 @@ static char *cmd_generator(const char *text, int state)
len = strlen(text);
do {
if ((len == 0) || (commands[idx].substr(0, len) == text))
if ((idx < commands.size()) && ((len == 0) || (commands[idx].substr(0, len) == text)))
return dupstring(commands[idx++]);
else
++idx;
@ -464,23 +522,27 @@ static void init_commands()
commands.push_back("pwd");
commands.push_back("cd");
commands.push_back("mem");
commands.push_back("source");
commands.push_back("history");
commands.push_back("clear_history");
commands.push_back("save_history");
// set name so there can be specific entries in ~/.inputrc
rl_readline_name = "lammps-shell";
rl_basic_word_break_characters = " \t\n\"\\'`@><=;|&(";
// attempt completions only if we are connected to a tty,
// attempt completions only if we are connected to a tty or are running tests.
// otherwise any tabs in redirected input will cause havoc.
if (isatty(fileno(stdin))) {
const char *test_mode = getenv("LAMMPS_SHELL_TESTING");
if (test_mode) std::cout << "*TESTING* using LAMMPS Shell in test mode *TESTING*\n";
if (isatty(fileno(stdin)) || test_mode) {
rl_attempted_completion_function = cmd_completion;
} else {
rl_bind_key('\t', rl_insert);
}
// read old history
read_history(".lammps_history");
// read saved history, but not in test mode.
if (!test_mode) read_history(".lammps_history");
#if !defined(_WIN32)
signal(SIGINT, ctrl_c_handler);
@ -553,6 +615,10 @@ static int shell_cmd(const std::string &cmd)
} else if (words[0] == "exit") {
free(text);
return shell_end();
} else if (words[0] == "source") {
lammps_file(lmp, words[1].c_str());
free(text);
return 0;
} else if ((words[0] == "pwd") || ((words[0] == "cd") && (words.size() == 1))) {
if (getcwd(buf, buflen)) std::cout << buf << "\n";
free(text);
@ -565,7 +631,7 @@ static int shell_cmd(const std::string &cmd)
return 0;
} else if (words[0] == "mem") {
double meminfo[3];
lammps_memory_usage(lmp,meminfo);
lammps_memory_usage(lmp, meminfo);
std::cout << "Memory usage. Current: " << meminfo[0] << " MByte, "
<< "Maximum : " << meminfo[2] << " MByte\n";
free(text);
@ -581,6 +647,20 @@ static int shell_cmd(const std::string &cmd)
free(text);
clear_history();
return 0;
} else if (words[0] == "save_history") {
free(text);
if (words.size() == 3) {
if (save_history(words[1], words[2]) != 0) {
int from = history_base;
int to = from + history_length - 1;
std::cerr << "Range error: min = " << from << " max = " << to << "\n";
return 1;
}
} else {
std::cerr << "Usage: save_history <range> <filename>\n";
return 1;
}
return 0;
}
lammps_command(lmp, text);
@ -593,13 +673,24 @@ int main(int argc, char **argv)
char *line;
std::string trimmed;
lammps_get_os_info(buf,buflen);
std::cout << "LAMMPS Shell version 1.0 OS: " << buf;
lammps_get_os_info(buf, buflen);
std::cout << "LAMMPS Shell version 1.1 OS: " << buf;
if (!lammps_config_has_exceptions())
std::cout << "WARNING: LAMMPS was compiled without exceptions\n"
"WARNING: The shell will terminate on errors.\n";
#if defined(_OPENMP)
int nthreads = omp_get_max_threads();
#else
int nthreads = 1;
#endif
// avoid OMP_NUM_THREADS warning and change the default behavior
// to use the maximum number of threads available since this is
// not intended to be run with MPI.
omp_threads = dupstring(std::string("OMP_NUM_THREADS=" + std::to_string(nthreads)));
putenv(omp_threads);
lmp = lammps_open_no_mpi(argc, argv, nullptr);
if (lmp == nullptr) return 1;

1
unittest/CMakeLists.txt
View File

@ -7,6 +7,7 @@ add_subdirectory(c-library)
add_subdirectory(cplusplus)
add_subdirectory(fortran)
add_subdirectory(python)
add_subdirectory(tools)
add_subdirectory(force-styles)
find_package(ClangFormat 8.0)

20
unittest/tools/CMakeLists.txt Normal file
View File

@ -0,0 +1,20 @@
# we use python 3's subprocess module to run the tools and check the output
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp 3.5) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
find_package(Python3 COMPONENTS Interpreter)
endif()
if(Python_EXECUTABLE)
if(BUILD_LAMMPS_SHELL)
add_test(NAME LammpsShell
COMMAND ${Python_EXECUTABLE} -u ${CMAKE_CURRENT_SOURCE_DIR}/test_lammps_shell.py -v
WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
endif()
else()
message(STATUS "Skipping Tests for LAMMPS tools: no suitable Python interpreter")
endif()

64
unittest/tools/test_lammps_shell.py Normal file
View File

@ -0,0 +1,64 @@
import os, re, subprocess, unittest
# enable test mode
os.putenv('LAMMPS_SHELL_TESTING','1')
shell_prompt_re = r"([^>]*LAMMPS Shell> ([a-z0-9_]+) *([a-z0-9_\.]+)?.*\n)+"
#
class LammpsShell(unittest.TestCase):
def setUp(self):
self.proc = subprocess.Popen('./lammps-shell',
stdin=subprocess.PIPE, stdout=subprocess.PIPE)
def tearDown(self):
self.proc.kill()
def InputRunner(self,text):
"""Test tab expansions"""
try:
[outs,errs] = self.proc.communicate(input=text, timeout=1)
except TimeoutExpired:
proc.kill()
[outs,errs] = proc.communicate()
return outs.decode('UTF-8')
def testExpandClear(self):
"""Test expansion of a shell specific command"""
matches = re.findall(shell_prompt_re, self.InputRunner(b'cle\t\n'), re.MULTILINE)
self.assertEqual(matches[0][1],"clear")
def testExpandSource(self):
"""Test expansion of a shell command and a file name"""
with open('.tmp.in.source', 'w') as out:
print('units real', file=out)
out.close()
matches = re.findall(shell_prompt_re, self.InputRunner(b'sour\t.tmp.in.sou\t\n'), re.MULTILINE)
os.remove('.tmp.in.source')
self.assertEqual(matches[0][1],"source")
self.assertEqual(matches[0][2],".tmp.in.source")
def testHistory(self):
"""Test history expansion"""
out = self.InputRunner(b'clear_history\nunits real\ndimension 2\n!!:p\n!-3:p\n!dim:p\n!uni:p\nprint !!:$\nprint !dim:1\n')
idx = 0
lines = out.splitlines()
for line in lines:
if line.startswith('LAMMPS Shell>'): break
idx += 1
self.assertEqual(lines[idx+4],"dimension 2")
self.assertEqual(lines[idx+6],"units real")
self.assertEqual(lines[idx+8],"dimension 2")
self.assertEqual(lines[idx+10],"units real")
self.assertEqual(lines[idx+12],"real")
self.assertEqual(lines[idx+14],"2")
###########################
if __name__ == "__main__":
unittest.main()