diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index 40288268a1..ab6aa91b7c 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation :c,h3 -30 Nov 2016 version :c,h4 +13 Dec 2016 version :c,h4 Version info: :h4 diff --git a/src/MAKE/MACHINES/Makefile.cori2 b/src/MAKE/MACHINES/Makefile.cori2 new file mode 100755 index 0000000000..a367d54080 --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.cori2 @@ -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 diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu b/src/MAKE/OPTIONS/Makefile.intel_cpu new file mode 100755 index 0000000000..b34ff47761 --- /dev/null +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu @@ -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 diff --git a/src/MAKE/OPTIONS/Makefile.intel_knl_coprocessor b/src/MAKE/OPTIONS/Makefile.intel_knl_coprocessor new file mode 100644 index 0000000000..b7f3cd6846 --- /dev/null +++ b/src/MAKE/OPTIONS/Makefile.intel_knl_coprocessor @@ -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 diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index 06bd23abcc..84f4994901 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -63,7 +63,7 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) _nbor_pack_width = 1; _precision_mode = PREC_MODE_MIXED; - _offload_balance = 1.0; + _offload_balance = -1.0; _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(); omp_set_num_threads(offload_cores); 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; _offload_cores = offload_cores; if (_offload_threads == 0) _offload_threads = offload_cores; + if (_offload_cores > 244 && _offload_tpc > 2) + _offload_tpc = 2; } #endif @@ -317,6 +325,8 @@ void FixIntel::init() error->all(FLERR, "Currently, cannot use more than one intel style with hybrid."); + neighbor->fix_intel = (void *)this; + check_neighbor_intel(); if (_precision_mode == PREC_MODE_SINGLE) _single_buffers->zero_ev(); @@ -1004,8 +1014,10 @@ void FixIntel::set_offload_affinity() int offload_threads = _offload_threads; int offload_tpc = _offload_tpc; int offload_affinity_balanced = _offload_affinity_balanced; + int offload_cores = _offload_cores; #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); #pragma omp parallel @@ -1013,20 +1025,24 @@ void FixIntel::set_offload_affinity() int tnum = omp_get_thread_num(); kmp_affinity_mask_t mask; kmp_create_affinity_mask(&mask); - int proc; - if (offload_affinity_balanced) { - proc = offload_threads * node_rank + tnum; + int proc = offload_threads * node_rank + tnum; + #ifdef __AVX512F__ + 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; - } else { - proc = offload_threads * node_rank + tnum; + else proc += (proc / 4) * (4 - offload_tpc) + 1; - } + #endif kmp_set_affinity_mask_proc(proc, &mask); if (kmp_set_affinity(&mask) != 0) printf("Could not set affinity on rank %d thread %d to %d\n", node_rank, tnum, proc); } } + if (_precision_mode == PREC_MODE_SINGLE) _single_buffers->set_off_params(offload_threads, _cop, _separate_buffers); else if (_precision_mode == PREC_MODE_MIXED) diff --git a/src/USER-INTEL/intel_intrinsics.h b/src/USER-INTEL/intel_intrinsics.h index 754b390722..44a9605961 100644 --- a/src/USER-INTEL/intel_intrinsics.h +++ b/src/USER-INTEL/intel_intrinsics.h @@ -28,7 +28,7 @@ // implementations. // Vector classes provided with the intel compiler -#ifdef __MIC__ +#if defined(__MIC__) && !defined(__AVX512F__) #include #else #include // icc-mmic hates generating movq diff --git a/src/USER-INTEL/intel_preprocess.h b/src/USER-INTEL/intel_preprocess.h index 48378d3840..ad07dfd7c2 100644 --- a/src/USER-INTEL/intel_preprocess.h +++ b/src/USER-INTEL/intel_preprocess.h @@ -22,6 +22,11 @@ #ifdef __INTEL_OFFLOAD #ifdef LMP_INTEL_OFFLOAD #define _LMP_INTEL_OFFLOAD +#ifdef __TARGET_ARCH_MIC +#ifndef __MIC__ +#define __MIC__ 1 +#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_P3M_MAXORDER 5 +#ifdef __INTEL_COMPILER #ifdef __AVX__ #undef INTEL_VECTOR_WIDTH #define INTEL_VECTOR_WIDTH 8 @@ -90,6 +96,13 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR, #endif #endif +#else + +#undef INTEL_VECTOR_WIDTH +#define INTEL_VECTOR_WIDTH 1 + +#endif + #define INTEL_DATA_ALIGN 64 #define INTEL_ONEATOM_FACTOR 2 #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_BIGP 1e15 #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) \ { \ diff --git a/src/USER-INTEL/verlet_lrt_intel.cpp b/src/USER-INTEL/verlet_lrt_intel.cpp index fcd9dff08a..afb7852f98 100644 --- a/src/USER-INTEL/verlet_lrt_intel.cpp +++ b/src/USER-INTEL/verlet_lrt_intel.cpp @@ -43,7 +43,20 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ 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 diff --git a/src/USER-INTEL/verlet_lrt_intel.h b/src/USER-INTEL/verlet_lrt_intel.h index 112b299cd1..a699c20796 100644 --- a/src/USER-INTEL/verlet_lrt_intel.h +++ b/src/USER-INTEL/verlet_lrt_intel.h @@ -40,7 +40,7 @@ namespace LAMMPS_NS { class VerletLRTIntel : public Verlet { public: VerletLRTIntel(class LAMMPS *, int, char **); - virtual ~VerletLRTIntel() {} + virtual ~VerletLRTIntel(); virtual void init(); virtual void setup(); virtual void run(int); diff --git a/src/force.cpp b/src/force.cpp index 3154139d54..95a6ff4f6d 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -237,7 +237,10 @@ Pair *Force::new_pair(const char *style, int trysuffix, int &sflag) 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; } @@ -362,7 +365,10 @@ Bond *Force::new_bond(const char *style, int trysuffix, int &sflag) 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; } @@ -440,7 +446,10 @@ Angle *Force::new_angle(const char *style, int trysuffix, int &sflag) 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; } @@ -519,7 +528,10 @@ Dihedral *Force::new_dihedral(const char *style, int trysuffix, int &sflag) 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; } @@ -597,7 +609,10 @@ Improper *Force::new_improper(const char *style, int trysuffix, int &sflag) 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; } @@ -679,7 +694,10 @@ KSpace *Force::new_kspace(int narg, char **arg, int trysuffix, int &sflag) 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; } diff --git a/src/memory.cpp b/src/memory.cpp index 1ab5074079..ed0993202b 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -18,12 +18,12 @@ #include "error.h" #if defined(LMP_USER_INTEL) && defined(__INTEL_COMPILER) +#ifndef LMP_INTEL_NO_TBB #define LMP_USE_TBB_ALLOCATOR #include "tbb/scalable_allocator.h" +#else +#include #endif - -#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) -#define LAMMPS_MEMALIGN 64 #endif using namespace LAMMPS_NS; @@ -75,6 +75,15 @@ void *Memory::srealloc(void *ptr, bigint nbytes, const char *name) #if defined(LMP_USE_TBB_ALLOCATOR) 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 ptr = realloc(ptr,nbytes); #endif diff --git a/src/modify.cpp b/src/modify.cpp index 6370998a23..2e5bd78504 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -767,7 +767,8 @@ void Modify::add_fix(int narg, char **arg, int trysuffix) 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) 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); } - 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 // 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); } - 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++; } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index d014f1c8d0..f968be1dd0 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -890,7 +890,8 @@ void Neighbor::init_pair() for (i = 0; i < nstencil; i++) { flag = 0; 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; } @@ -1139,8 +1140,8 @@ void Neighbor::print_pairwise_info() } else { 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"; else if (requests[i]->full) kind = "full"; 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 == MULTI && !(mask & NS_MULTI)) continue; - if (dimension == 2 && !(mask & NS_2D)) continue; if (dimension == 3 && !(mask & NS_3D)) continue; @@ -1389,7 +1389,8 @@ int Neighbor::choose_pair(NeighRequest *rq) // triclinic = orthgonal/triclinic box 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 = ghostflag = respaflag = off2onflag = onesideflag = ssaflag = diff --git a/src/version.h b/src/version.h index 1562ca3d95..c7c630c699 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "30 Nov 2016" +#define LAMMPS_VERSION "13 Dec 2016"