ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

patch 13Dec16: neighbor refactor, Stan pppm/disp bug fix, M Brown INTEL package updates

Browse Source
This commit is contained in:
Steve Plimpton
2016-12-13 17:14:28 -07:00
parent 624c57e9da
commit f509f133af
14 changed files with 484 additions and 32 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
doc/src/Manual.txt
View File

@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="30 Nov 2016 version"> <META NAME="docnumber" CONTENT="13 Dec 2016 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<H1></H1> <H1></H1>
LAMMPS Documentation :c,h3 LAMMPS Documentation :c,h3
30 Nov 2016 version :c,h4 13 Dec 2016 version :c,h4
Version info: :h4 Version info: :h4

127
src/MAKE/MACHINES/Makefile.cori2 Executable file
View File

@ -0,0 +1,127 @@
# cori2 = NERSC Cori II KNL, static build, FFTW (single precision)
# ---------------------------------------------------------------------
# module swap craype-haswell craype-mic-knl
# module load fftw
# module load craype-hugepages2M
# Recommend using #SBATCH -S 2 for core specialization
# ---------------------------------------------------------------------
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = CC
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -qno-offload \
-fno-alias -ansi-alias -restrict $(OPTFLAGS) -DLMP_INTEL_NO_TBB
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = CC
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB =
SIZE = size
ARCHIVE = ar
ARFLAGS = -rc
SHLIBFLAGS = -shared
# ---------------------------------------------------------------------
# LAMMPS-specific settings, all OPTIONAL
# specify settings for LAMMPS features you will use
# if you change any -D setting, do full re-compile after "make clean"
# LAMMPS ifdef settings
# see possible settings in Section 2.2 (step 4) of manual
LMP_INC = #-DLAMMPS_GZIP -DLAMMPS_JPEG
# MPI library
# see discussion in Section 2.2 (step 5) of manual
# MPI wrapper compiler/linker can provide this info
# can point to dummy MPI library in src/STUBS as in Makefile.serial
# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
# INC = path for mpi.h, MPI compiler settings
# PATH = path for MPI library
# LIB = name of MPI library
MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1
MPI_PATH =
MPI_LIB =
# FFT library
# see discussion in Section 2.2 (step 6) of manaul
# 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_FFTW3 -DFFT_SINGLE
FFT_PATH =
FFT_LIB = -lfftw3f
# JPEG and/or PNG library
# see discussion in Section 2.2 (step 7) of manual
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
# INC = path(s) for jpeglib.h and/or png.h
# PATH = path(s) for JPEG library and/or PNG library
# LIB = name(s) of JPEG library and/or PNG library
JPG_INC =
JPG_PATH =
JPG_LIB = #-ljpeg
# ---------------------------------------------------------------------
# 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)
# 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) $< > $@
%.o:%.cu
$(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

123
src/MAKE/OPTIONS/Makefile.intel_cpu Executable file
View File

@ -0,0 +1,123 @@
# intel_cpu_intelmpi = USER-INTEL package, Intel MPI, MKL FFT
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpiicpc
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
-fno-alias -ansi-alias -restrict $(OPTFLAGS)
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpiicpc
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc -ltbbmalloc_proxy
SIZE = size
ARCHIVE = ar
ARFLAGS = -rc
SHLIBFLAGS = -shared
# ---------------------------------------------------------------------
# LAMMPS-specific settings, all OPTIONAL
# specify settings for LAMMPS features you will use
# if you change any -D setting, do full re-compile after "make clean"
# LAMMPS ifdef settings
# see possible settings in Section 2.2 (step 4) of manual
LMP_INC = -DLAMMPS_GZIP -DLAMMPS_JPEG
# MPI library
# see discussion in Section 2.2 (step 5) of manual
# MPI wrapper compiler/linker can provide this info
# can point to dummy MPI library in src/STUBS as in Makefile.serial
# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
# INC = path for mpi.h, MPI compiler settings
# PATH = path for MPI library
# LIB = name of MPI library
MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1
MPI_PATH =
MPI_LIB =
# FFT library
# see discussion in Section 2.2 (step 6) of manaul
# can be left blank to use provided KISS FFT library
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
# PATH = path for FFT library
# LIB = name of FFT library
FFT_INC = -DFFT_MKL -DFFT_SINGLE
FFT_PATH =
FFT_LIB = -L$MKLROOT/lib/intel64/ -lmkl_intel_ilp64 \
-lmkl_sequential -lmkl_core
# JPEG and/or PNG library
# see discussion in Section 2.2 (step 7) of manual
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
# INC = path(s) for jpeglib.h and/or png.h
# PATH = path(s) for JPEG library and/or PNG library
# LIB = name(s) of JPEG library and/or PNG library
JPG_INC =
JPG_PATH =
JPG_LIB = -ljpeg
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
include Makefile.package.settings
include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)
# Path to src files
vpath %.cpp ..
vpath %.h ..
# Link target
$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library targets
lib: $(OBJ) $(EXTRA_LINK_DEPENDS)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
shlib: $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
$(OBJ) $(EXTRA_LIB) $(LIB)
# Compilation rules
%.o:%.cpp $(EXTRA_CPP_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp $(EXTRA_CPP_DEPENDS)
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
%.o:%.cu $(EXTRA_CPP_DEPENDS)
$(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

123
src/MAKE/OPTIONS/Makefile.intel_knl_coprocessor Normal file
View File

@ -0,0 +1,123 @@
# intel_phi = USER-INTEL with Phi x200 (KNL) offload support,Intel MPI,MKL FFT
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpiicpc
MIC_OPT = -qoffload-arch=mic-avx512 -fp-model fast=2
CCFLAGS = -g -O3 -qopenmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64 \
-xHost -fno-alias -ansi-alias -restrict \
-qoverride-limits $(MIC_OPT)
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpiicpc
LINKFLAGS = -g -O3 -xHost -qopenmp -qoffload $(MIC_OPT)
LIB = -ltbbmalloc
SIZE = size
ARCHIVE = ar
ARFLAGS = -rc
SHLIBFLAGS = -shared
# ---------------------------------------------------------------------
# LAMMPS-specific settings, all OPTIONAL
# specify settings for LAMMPS features you will use
# if you change any -D setting, do full re-compile after "make clean"
# LAMMPS ifdef settings
# see possible settings in Section 2.2 (step 4) of manual
LMP_INC = -DLAMMPS_GZIP -DLAMMPS_JPEG
# MPI library
# see discussion in Section 2.2 (step 5) of manual
# MPI wrapper compiler/linker can provide this info
# can point to dummy MPI library in src/STUBS as in Makefile.serial
# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
# INC = path for mpi.h, MPI compiler settings
# PATH = path for MPI library
# LIB = name of MPI library
MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1
MPI_PATH =
MPI_LIB =
# FFT library
# see discussion in Section 2.2 (step 6) of manaul
# can be left blank to use provided KISS FFT library
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
# PATH = path for FFT library
# LIB = name of FFT library
FFT_INC = -DFFT_MKL -DFFT_SINGLE
FFT_PATH =
FFT_LIB = -L$(MKLROOT)/lib/intel64/ -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core
# JPEG and/or PNG library
# see discussion in Section 2.2 (step 7) of manual
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
# INC = path(s) for jpeglib.h and/or png.h
# PATH = path(s) for JPEG library and/or PNG library
# LIB = name(s) of JPEG library and/or PNG library
JPG_INC =
JPG_PATH =
JPG_LIB = -ljpeg
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
include Makefile.package.settings
include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)
# Path to src files
vpath %.cpp ..
vpath %.h ..
# Link target
$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library targets
lib: $(OBJ) $(EXTRA_LINK_DEPENDS)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
shlib: $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
$(OBJ) $(EXTRA_LIB) $(LIB)
# Compilation rules
%.o:%.cpp $(EXTRA_CPP_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp $(EXTRA_CPP_DEPENDS)
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
%.o:%.cu $(EXTRA_CPP_DEPENDS)
$(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

32
src/USER-INTEL/fix_intel.cpp
View File

@ -63,7 +63,7 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
_nbor_pack_width = 1; _nbor_pack_width = 1;
_precision_mode = PREC_MODE_MIXED; _precision_mode = PREC_MODE_MIXED;
_offload_balance = 1.0; _offload_balance = -1.0;
_overflow_flag[LMP_OVERFLOW] = 0; _overflow_flag[LMP_OVERFLOW] = 0;
_off_overflow_flag[LMP_OVERFLOW] = 0; _off_overflow_flag[LMP_OVERFLOW] = 0;
@ -189,10 +189,18 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
offload_cores = omp_get_num_procs(); offload_cores = omp_get_num_procs();
omp_set_num_threads(offload_cores); omp_set_num_threads(offload_cores);
max_offload_threads = omp_get_max_threads(); max_offload_threads = omp_get_max_threads();
#ifdef __AVX512F__
if ( (offload_cores / 4) % 2 == 1) {
offload_cores += 4;
max_offload_threads += 4;
}
#endif
} }
_max_offload_threads = max_offload_threads; _max_offload_threads = max_offload_threads;
_offload_cores = offload_cores; _offload_cores = offload_cores;
if (_offload_threads == 0) _offload_threads = offload_cores; if (_offload_threads == 0) _offload_threads = offload_cores;
if (_offload_cores > 244 && _offload_tpc > 2)
_offload_tpc = 2;
} }
#endif #endif
@ -317,6 +325,8 @@ void FixIntel::init()
error->all(FLERR, error->all(FLERR,
"Currently, cannot use more than one intel style with hybrid."); "Currently, cannot use more than one intel style with hybrid.");
neighbor->fix_intel = (void *)this;
check_neighbor_intel(); check_neighbor_intel();
if (_precision_mode == PREC_MODE_SINGLE) if (_precision_mode == PREC_MODE_SINGLE)
_single_buffers->zero_ev(); _single_buffers->zero_ev();
@ -1004,8 +1014,10 @@ void FixIntel::set_offload_affinity()
int offload_threads = _offload_threads; int offload_threads = _offload_threads;
int offload_tpc = _offload_tpc; int offload_tpc = _offload_tpc;
int offload_affinity_balanced = _offload_affinity_balanced; int offload_affinity_balanced = _offload_affinity_balanced;
int offload_cores = _offload_cores;
#pragma offload target(mic:_cop) mandatory \ #pragma offload target(mic:_cop) mandatory \
in(node_rank,offload_threads,offload_tpc,offload_affinity_balanced) in(node_rank,offload_threads,offload_tpc,offload_affinity_balanced, \
offload_cores)
{ {
omp_set_num_threads(offload_threads); omp_set_num_threads(offload_threads);
#pragma omp parallel #pragma omp parallel
@ -1013,20 +1025,24 @@ void FixIntel::set_offload_affinity()
int tnum = omp_get_thread_num(); int tnum = omp_get_thread_num();
kmp_affinity_mask_t mask; kmp_affinity_mask_t mask;
kmp_create_affinity_mask(&mask); kmp_create_affinity_mask(&mask);
int proc; int proc = offload_threads * node_rank + tnum;
if (offload_affinity_balanced) { #ifdef __AVX512F__
proc = offload_threads * node_rank + tnum; proc = (proc / offload_tpc) + (proc % offload_tpc) *
((offload_cores) / 4);
proc += 68;
#else
if (offload_affinity_balanced)
proc = proc * 4 - (proc / 60) * 240 + proc / 60 + 1; proc = proc * 4 - (proc / 60) * 240 + proc / 60 + 1;
} else { else
proc = offload_threads * node_rank + tnum;
proc += (proc / 4) * (4 - offload_tpc) + 1; proc += (proc / 4) * (4 - offload_tpc) + 1;
} #endif
kmp_set_affinity_mask_proc(proc, &mask); kmp_set_affinity_mask_proc(proc, &mask);
if (kmp_set_affinity(&mask) != 0) if (kmp_set_affinity(&mask) != 0)
printf("Could not set affinity on rank %d thread %d to %d\n", printf("Could not set affinity on rank %d thread %d to %d\n",
node_rank, tnum, proc); node_rank, tnum, proc);
} }
} }
if (_precision_mode == PREC_MODE_SINGLE) if (_precision_mode == PREC_MODE_SINGLE)
_single_buffers->set_off_params(offload_threads, _cop, _separate_buffers); _single_buffers->set_off_params(offload_threads, _cop, _separate_buffers);
else if (_precision_mode == PREC_MODE_MIXED) else if (_precision_mode == PREC_MODE_MIXED)

2
src/USER-INTEL/intel_intrinsics.h
View File

@ -28,7 +28,7 @@
// implementations. // implementations.
// Vector classes provided with the intel compiler // Vector classes provided with the intel compiler
#ifdef __MIC__ #if defined(__MIC__) && !defined(__AVX512F__)
#include <mic/micvec.h> #include <mic/micvec.h>
#else #else
#include <dvec.h> // icc-mmic hates generating movq #include <dvec.h> // icc-mmic hates generating movq

15
src/USER-INTEL/intel_preprocess.h
View File

@ -22,6 +22,11 @@
#ifdef __INTEL_OFFLOAD #ifdef __INTEL_OFFLOAD
#ifdef LMP_INTEL_OFFLOAD #ifdef LMP_INTEL_OFFLOAD
#define _LMP_INTEL_OFFLOAD #define _LMP_INTEL_OFFLOAD
#ifdef __TARGET_ARCH_MIC
#ifndef __MIC__
#define __MIC__ 1
#endif
#endif
#endif #endif
#endif #endif
@ -62,6 +67,7 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
#define INTEL_MAX_STENCIL_CHECK 4096 #define INTEL_MAX_STENCIL_CHECK 4096
#define INTEL_P3M_MAXORDER 5 #define INTEL_P3M_MAXORDER 5
#ifdef __INTEL_COMPILER
#ifdef __AVX__ #ifdef __AVX__
#undef INTEL_VECTOR_WIDTH #undef INTEL_VECTOR_WIDTH
#define INTEL_VECTOR_WIDTH 8 #define INTEL_VECTOR_WIDTH 8
@ -90,6 +96,13 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
#endif #endif
#endif #endif
#else
#undef INTEL_VECTOR_WIDTH
#define INTEL_VECTOR_WIDTH 1
#endif
#define INTEL_DATA_ALIGN 64 #define INTEL_DATA_ALIGN 64
#define INTEL_ONEATOM_FACTOR 2 #define INTEL_ONEATOM_FACTOR 2
#define INTEL_MIC_NBOR_PAD INTEL_MIC_VECTOR_WIDTH #define INTEL_MIC_NBOR_PAD INTEL_MIC_VECTOR_WIDTH
@ -97,7 +110,7 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
#define INTEL_LB_MEAN_WEIGHT 0.1 #define INTEL_LB_MEAN_WEIGHT 0.1
#define INTEL_BIGP 1e15 #define INTEL_BIGP 1e15
#define INTEL_MAX_HOST_CORE_COUNT 512 #define INTEL_MAX_HOST_CORE_COUNT 512
#define INTEL_MAX_COI_CORES 2 #define INTEL_MAX_COI_CORES 36
#define IP_PRE_get_stride(stride, n, datasize, torque) \ #define IP_PRE_get_stride(stride, n, datasize, torque) \
{ \ { \

15
src/USER-INTEL/verlet_lrt_intel.cpp
View File

@ -43,7 +43,20 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
VerletLRTIntel::VerletLRTIntel(LAMMPS *lmp, int narg, char **arg) : VerletLRTIntel::VerletLRTIntel(LAMMPS *lmp, int narg, char **arg) :
Verlet(lmp, narg, arg) {} Verlet(lmp, narg, arg) {
#if defined(_LMP_INTEL_LRT_PTHREAD)
pthread_mutex_init(&_kmutex,NULL);
#endif
}
/* ---------------------------------------------------------------------- */
VerletLRTIntel::~VerletLRTIntel()
{
#if defined(_LMP_INTEL_LRT_PTHREAD)
pthread_mutex_destroy(&_kmutex);
#endif
}
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
initialization before run initialization before run

2
src/USER-INTEL/verlet_lrt_intel.h
View File

@ -40,7 +40,7 @@ namespace LAMMPS_NS {
class VerletLRTIntel : public Verlet { class VerletLRTIntel : public Verlet {
public: public:
VerletLRTIntel(class LAMMPS *, int, char **); VerletLRTIntel(class LAMMPS *, int, char **);
virtual ~VerletLRTIntel() {} virtual ~VerletLRTIntel();
virtual void init(); virtual void init();
virtual void setup(); virtual void setup();
virtual void run(int); virtual void run(int);

30
src/force.cpp
View File

@ -237,7 +237,10 @@ Pair *Force::new_pair(const char *style, int trysuffix, int &sflag)
return pair_creator(lmp); return pair_creator(lmp);
} }
error->all(FLERR,"Unknown pair style"); char str[128];
sprintf(str,"Unknown pair style %s",style);
error->all(FLERR,str);
return NULL; return NULL;
} }
@ -362,7 +365,10 @@ Bond *Force::new_bond(const char *style, int trysuffix, int &sflag)
return bond_creator(lmp); return bond_creator(lmp);
} }
error->all(FLERR,"Unknown bond style"); char str[128];
sprintf(str,"Unknown bond style %s",style);
error->all(FLERR,str);
return NULL; return NULL;
} }
@ -440,7 +446,10 @@ Angle *Force::new_angle(const char *style, int trysuffix, int &sflag)
return angle_creator(lmp); return angle_creator(lmp);
} }
error->all(FLERR,"Unknown angle style"); char str[128];
sprintf(str,"Unknown angle style %s",style);
error->all(FLERR,str);
return NULL; return NULL;
} }
@ -519,7 +528,10 @@ Dihedral *Force::new_dihedral(const char *style, int trysuffix, int &sflag)
return dihedral_creator(lmp); return dihedral_creator(lmp);
} }
error->all(FLERR,"Unknown dihedral style"); char str[128];
sprintf(str,"Unknown dihedral style %s",style);
error->all(FLERR,str);
return NULL; return NULL;
} }
@ -597,7 +609,10 @@ Improper *Force::new_improper(const char *style, int trysuffix, int &sflag)
return improper_creator(lmp); return improper_creator(lmp);
} }
error->all(FLERR,"Unknown improper style"); char str[128];
sprintf(str,"Unknown improper style %s",style);
error->all(FLERR,str);
return NULL; return NULL;
} }
@ -679,7 +694,10 @@ KSpace *Force::new_kspace(int narg, char **arg, int trysuffix, int &sflag)
return kspace_creator(lmp, narg-1, &arg[1]); return kspace_creator(lmp, narg-1, &arg[1]);
} }
error->all(FLERR,"Unknown kspace style"); char str[128];
sprintf(str,"Unknown kspace style %s",arg[0]);
error->all(FLERR,str);
return NULL; return NULL;
} }

15
src/memory.cpp
View File

@ -18,12 +18,12 @@
#include "error.h" #include "error.h"
#if defined(LMP_USER_INTEL) && defined(__INTEL_COMPILER) #if defined(LMP_USER_INTEL) && defined(__INTEL_COMPILER)
#ifndef LMP_INTEL_NO_TBB
#define LMP_USE_TBB_ALLOCATOR #define LMP_USE_TBB_ALLOCATOR
#include "tbb/scalable_allocator.h" #include "tbb/scalable_allocator.h"
#else
#include <malloc.h>
#endif #endif
#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN)
#define LAMMPS_MEMALIGN 64
#endif #endif
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -75,6 +75,15 @@ void *Memory::srealloc(void *ptr, bigint nbytes, const char *name)
#if defined(LMP_USE_TBB_ALLOCATOR) #if defined(LMP_USE_TBB_ALLOCATOR)
ptr = scalable_aligned_realloc(ptr, nbytes, LAMMPS_MEMALIGN); ptr = scalable_aligned_realloc(ptr, nbytes, LAMMPS_MEMALIGN);
#elif defined(LMP_INTEL_NO_TBB) && defined(LAMMPS_MEMALIGN)
ptr = realloc(ptr, nbytes);
uintptr_t offset = ((uintptr_t)(const void *)(ptr)) % LAMMPS_MEMALIGN;
if (offset) {
void *optr = ptr;
ptr = smalloc(nbytes, name);
memcpy(ptr, optr, MIN(nbytes,malloc_usable_size(optr)));
free(optr);
}
#else #else
ptr = realloc(ptr,nbytes); ptr = realloc(ptr,nbytes);
#endif #endif

15
src/modify.cpp
View File

@ -767,7 +767,8 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
if (strcmp(estyle,fix[ifix]->style) == 0) match = 1; if (strcmp(estyle,fix[ifix]->style) == 0) match = 1;
} }
} }
if (!match) error->all(FLERR,"Replacing a fix, but new style != old style"); if (!match) error->all(FLERR,
"Replacing a fix, but new style != old style");
if (fix[ifix]->igroup != igroup && comm->me == 0) if (fix[ifix]->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Replacing a fix, but new group != old group"); error->warning(FLERR,"Replacing a fix, but new group != old group");
@ -812,7 +813,11 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
fix[ifix] = fix_creator(lmp,narg,arg); fix[ifix] = fix_creator(lmp,narg,arg);
} }
if (fix[ifix] == NULL) error->all(FLERR,"Unknown fix style"); if (fix[ifix] == NULL) {
char str[128];
sprintf(str,"Unknown fix style %s",arg[2]);
error->all(FLERR,str);
}
// check if Fix is in restart_global list // check if Fix is in restart_global list
// if yes, pass state info to the Fix so it can reset itself // if yes, pass state info to the Fix so it can reset itself
@ -994,7 +999,11 @@ void Modify::add_compute(int narg, char **arg, int trysuffix)
compute[ncompute] = compute_creator(lmp,narg,arg); compute[ncompute] = compute_creator(lmp,narg,arg);
} }
if (compute[ncompute] == NULL) error->all(FLERR,"Unknown compute style"); if (compute[ncompute] == NULL) {
char str[128];
sprintf(str,"Unknown compute style %s",arg[2]);
error->all(FLERR,str);
}
ncompute++; ncompute++;
} }

11
src/neighbor.cpp
View File

@ -890,7 +890,8 @@ void Neighbor::init_pair()
for (i = 0; i < nstencil; i++) { for (i = 0; i < nstencil; i++) {
flag = 0; flag = 0;
for (j = 0; j < npair_perpetual; j++) for (j = 0; j < npair_perpetual; j++)
if (lists[plist[j]]->stencil_method == neigh_stencil[i]->istyle) flag = 1; if (lists[plist[j]]->stencil_method == neigh_stencil[i]->istyle)
flag = 1;
if (flag) slist[nstencil_perpetual++] = i; if (flag) slist[nstencil_perpetual++] = i;
} }
@ -1139,8 +1140,8 @@ void Neighbor::print_pairwise_info()
} else { } else {
sprintf(str," (%d) command %s",i+1,requests[i]->command_style); sprintf(str," (%d) command %s",i+1,requests[i]->command_style);
} }
fprintf(out,"%s\n",str); fprintf(out,"%s",str);
if (requests[i]->half) kind = "half"; if (requests[i]->half) kind = "half";
else if (requests[i]->full) kind = "full"; else if (requests[i]->full) kind = "full";
else if (requests[i]->gran) kind = "size"; else if (requests[i]->gran) kind = "size";
@ -1328,7 +1329,6 @@ int Neighbor::choose_stencil(NeighRequest *rq)
if (style == BIN && !(mask & NS_BIN)) continue; if (style == BIN && !(mask & NS_BIN)) continue;
if (style == MULTI && !(mask & NS_MULTI)) continue; if (style == MULTI && !(mask & NS_MULTI)) continue;
if (dimension == 2 && !(mask & NS_2D)) continue; if (dimension == 2 && !(mask & NS_2D)) continue;
if (dimension == 3 && !(mask & NS_3D)) continue; if (dimension == 3 && !(mask & NS_3D)) continue;
@ -1389,7 +1389,8 @@ int Neighbor::choose_pair(NeighRequest *rq)
// triclinic = orthgonal/triclinic box // triclinic = orthgonal/triclinic box
int copyflag,skipflag,halfflag,fullflag,halffullflag,sizeflag,respaflag, int copyflag,skipflag,halfflag,fullflag,halffullflag,sizeflag,respaflag,
ghostflag,off2onflag,onesideflag,ssaflag,ompflag,intelflag,kokkos_device_flag,kokkos_host_flag; ghostflag,off2onflag,onesideflag,ssaflag,ompflag,intelflag,
kokkos_device_flag,kokkos_host_flag;
copyflag = skipflag = halfflag = fullflag = halffullflag = sizeflag = copyflag = skipflag = halfflag = fullflag = halffullflag = sizeflag =
ghostflag = respaflag = off2onflag = onesideflag = ssaflag = ghostflag = respaflag = off2onflag = onesideflag = ssaflag =

2
src/version.h
View File

@ -1 +1 @@
#define LAMMPS_VERSION "30 Nov 2016" #define LAMMPS_VERSION "13 Dec 2016"