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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5537 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-01-12 15:24:04 +00:00
parent 9cd3b0f28d
commit 8f2257ecbf
41 changed files with 351 additions and 244 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
lib/gpu/Makefile.fermi
View File

@ -30,7 +30,7 @@ CUDR_CPP = mpic++ -DMPI_GERYON -I$(CUDA_HOME)/include
CUDR_OPTS = -O3 -ffast-math -funroll-loops -DMPI_GERYON
BIN_DIR = ./
OBJ_DIR = ./obj
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh

4
lib/gpu/Makefile.lens
View File

@ -26,11 +26,11 @@ 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
CUDR_CPP = mpic++ -DMPI_GERYON -openmp
CUDR_OPTS = -O2 -xSSE2 -ip -use-intel-optimized-headers -fno-alias
BIN_DIR = ./
OBJ_DIR = ./obj
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh

2
lib/gpu/Makefile.lincoln
View File

@ -28,7 +28,7 @@ CUDR_CPP = mpic++ -DMPI_GERYON
CUDR_OPTS = -O3 -DMPI_GERYON -ffast-math -funroll-loops
BIN_DIR = ./
OBJ_DIR = ./obj
OBJ_DIR = ./
LIB_DIR = ./
AR = ar

2
lib/gpu/Makefile.linux
View File

@ -30,7 +30,7 @@ CUDR_CPP = mpic++ -DMPI_GERYON -DMPICH_IGNORE_CXX_SEEK
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
BIN_DIR = ./
OBJ_DIR = ./obj
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh

2
lib/gpu/Makefile.linux_opencl
View File

@ -22,7 +22,7 @@ OCL_LINK = -lOpenCL
OCL_PREC = -D_SINGLE_SINGLE
BIN_DIR = ./
OBJ_DIR = ./ocl_obj
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh

2
lib/gpu/Makefile.longhorn
View File

@ -27,7 +27,7 @@ CUDR_CPP = mpicxx -DMPI_GERYON -DMPICH_IGNORE_CXX_SEEK
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
BIN_DIR = ./
OBJ_DIR = ./obj
OBJ_DIR = ./
LIB_DIR = ./
AR = ar

2
lib/gpu/Makefile.mac
View File

@ -30,7 +30,7 @@ CUDR_CPP = mpic++
CUDR_OPTS = -O2 -m32 -g
BIN_DIR = ./
OBJ_DIR = ./obj
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh

2
lib/gpu/Makefile.mac_opencl
View File

@ -22,7 +22,7 @@ OCL_LINK = -framework OpenCL
OCL_PREC = -D_SINGLE_SINGLE
BIN_DIR = ./
OBJ_DIR = ./ocl_obj
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh

16
lib/gpu/Nvidia.makefile
View File

@ -47,6 +47,7 @@ OBJS = $(OBJ_DIR)/pair_gpu_atom.o $(OBJ_DIR)/pair_gpu_nbor.o \
$(OBJ_DIR)/lj96_cut_gpu_memory.o $(OBJ_DIR)/lj96_cut_gpu.o \
$(OBJ_DIR)/ljc_cut_gpu_memory.o $(OBJ_DIR)/ljc_cut_gpu.o \
$(OBJ_DIR)/ljcl_cut_gpu_memory.o $(OBJ_DIR)/ljcl_cut_gpu.o \
$(OBJ_DIR)/crml_gpu_memory.o $(OBJ_DIR)/crml_gpu.o \
$(OBJ_DIR)/cmm_cut_gpu_memory.o $(OBJ_DIR)/cmm_cut_gpu.o \
$(OBJ_DIR)/cmmc_long_gpu_memory.o $(OBJ_DIR)/cmmc_long_gpu.o \
$(CUDPP)
@ -59,8 +60,9 @@ PTXS = $(OBJ_DIR)/pair_gpu_atom_kernel.ptx $(OBJ_DIR)/pair_gpu_atom_ptx.h \
$(OBJ_DIR)/lj96_cut_gpu_kernel.ptx $(OBJ_DIR)/lj96_cut_gpu_ptx.h \
$(OBJ_DIR)/ljc_cut_gpu_kernel.ptx $(OBJ_DIR)/ljc_cut_gpu_ptx.h \
$(OBJ_DIR)/ljcl_cut_gpu_kernel.ptx $(OBJ_DIR)/ljcl_cut_gpu_ptx.h \
$(OBJ_DIR)/crml_cut_gpu_kernel.ptx $(OBJ_DIR)/crml_cut_gpu_ptx.h \
$(OBJ_DIR)/cmm_cut_gpu_kernel.ptx $(OBJ_DIR)/cmm_cut_gpu_ptx.h \
$(OBJ_DIR)/cmmc_long_gpu_kernel.ptx $(OBJ_DIR)/cmmc_long_gpu_ptx.h
$(OBJ_DIR)/cmmc_long_gpu_kernel.ptx $(OBJ_DIR)/cmmc_long_gpu_ptx.h
all: $(GPU_LIB) $(EXECS)
@ -169,6 +171,18 @@ $(OBJ_DIR)/ljcl_cut_gpu_memory.o: $(ALL_H) ljcl_cut_gpu_memory.h ljcl_cut_gpu_me
$(OBJ_DIR)/ljcl_cut_gpu.o: $(ALL_H) ljcl_cut_gpu_memory.h ljcl_cut_gpu.cpp
$(CUDR) -o $@ -c ljcl_cut_gpu.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/crml_gpu_kernel.ptx: crml_gpu_kernel.cu pair_gpu_precision.h
$(CUDA) --ptx -DNV_KERNEL -o $@ crml_gpu_kernel.cu
$(OBJ_DIR)/crml_gpu_ptx.h: $(OBJ_DIR)/crml_gpu_kernel.ptx $(OBJ_DIR)/crml_gpu_kernel.ptx
$(BSH) ./geryon/file_to_cstr.sh $(OBJ_DIR)/crml_gpu_kernel.ptx $(OBJ_DIR)/crml_gpu_ptx.h
$(OBJ_DIR)/crml_gpu_memory.o: $(ALL_H) crml_gpu_memory.h crml_gpu_memory.cpp $(OBJ_DIR)/crml_gpu_ptx.h $(OBJ_DIR)/charge_gpu_memory.o
$(CUDR) -o $@ -c crml_gpu_memory.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/crml_gpu.o: $(ALL_H) crml_gpu_memory.h crml_gpu.cpp
$(CUDR) -o $@ -c crml_gpu.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/lj96_cut_gpu_kernel.ptx: lj96_cut_gpu_kernel.cu pair_gpu_precision.h
$(CUDA) --ptx -DNV_KERNEL -o $@ lj96_cut_gpu_kernel.cu

11
lib/gpu/Opencl.makefile
View File

@ -37,12 +37,14 @@ OBJS = $(OBJ_DIR)/pair_gpu_atom.o $(OBJ_DIR)/pair_gpu_nbor.o \
$(OBJ_DIR)/lj96_cut_gpu_memory.o $(OBJ_DIR)/lj96_cut_gpu.o \
$(OBJ_DIR)/ljc_cut_gpu_memory.o $(OBJ_DIR)/ljc_cut_gpu.o \
$(OBJ_DIR)/ljcl_cut_gpu_memory.o $(OBJ_DIR)/ljcl_cut_gpu.o \
$(OBJ_DIR)/crml_gpu_memory.o $(OBJ_DIR)/crml_gpu.o \
$(OBJ_DIR)/cmm_cut_gpu_memory.o $(OBJ_DIR)/cmm_cut_gpu.o \
$(OBJ_DIR)/cmmc_long_gpu_memory.o $(OBJ_DIR)/cmmc_long_gpu.o
KERS = $(OBJ_DIR)/pair_gpu_atom_cl.h $(OBJ_DIR)/pair_gpu_nbor_cl.h \
$(OBJ_DIR)/gb_gpu_nbor_cl.h $(OBJ_DIR)/gb_gpu_cl.h \
$(OBJ_DIR)/lj_cut_gpu_cl.h $(OBJ_DIR)/lj96_cut_gpu_cl.h \
$(OBJ_DIR)/ljc_cut_gpu_cl.h $(OBJ_DIR)/ljcl_cut_gpu_cl.h \
$(OBJ_DIR)/crml_gpu_cl.h \
$(OBJ_DIR)/cmm_cut_gpu_cl.h $(OBJ_DIR)/cmmc_long_gpu_cl.h
OCL_EXECS = $(BIN_DIR)/ocl_get_devices
@ -112,6 +114,15 @@ $(OBJ_DIR)/ljcl_cut_gpu_memory.o: $(ALL_H) ljcl_cut_gpu_memory.h ljcl_cut_gpu_me
$(OBJ_DIR)/ljcl_cut_gpu.o: $(ALL_H) ljcl_cut_gpu_memory.h ljcl_cut_gpu.cpp
$(OCL) -o $@ -c ljcl_cut_gpu.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/crml_gpu_cl.h: crml_gpu_kernel.cu
$(BSH) ./geryon/file_to_cstr.sh crml_gpu_kernel.cu $(OBJ_DIR)/crml_gpu_cl.h;
$(OBJ_DIR)/crml_gpu_memory.o: $(ALL_H) crml_gpu_memory.h crml_gpu_memory.cpp $(OBJ_DIR)/crml_gpu_cl.h $(OBJ_DIR)/pair_gpu_nbor_cl.h $(OBJ_DIR)/crml_gpu_cl.h $(OBJ_DIR)/charge_gpu_memory.o
$(OCL) -o $@ -c crml_gpu_memory.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/crml_gpu.o: $(ALL_H) crml_gpu_memory.h crml_gpu.cpp
$(OCL) -o $@ -c crml_gpu.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/lj96_cut_gpu_cl.h: lj96_cut_gpu_kernel.cu
$(BSH) ./geryon/file_to_cstr.sh lj96_cut_gpu_kernel.cu $(OBJ_DIR)/lj96_cut_gpu_cl.h;

8
lib/gpu/cmm_cut_gpu.cpp
View File

@ -46,7 +46,7 @@ bool cmm_gpu_init(const int ntypes, double **cutsq, int **cg_types,
CMMMF.device->init_message(screen,"cg/cmm",first_gpu,last_gpu);
bool message=false;
if (world_me==0 && screen)
if (CMMMF.device->replica_me()==0 && screen)
message=true;
if (message) {
@ -62,14 +62,14 @@ bool cmm_gpu_init(const int ntypes, double **cutsq, int **cg_types,
return false;
}
MPI_Barrier(MPI_COMM_WORLD);
CMMMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing GPU %d on core %d...",gpu_rank,i);
fprintf(screen,"Initializing GPU %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing GPUs %d-%d on core %d...",first_gpu,
last_gpu,i);
@ -83,7 +83,7 @@ bool cmm_gpu_init(const int ntypes, double **cutsq, int **cg_types,
if (!init_ok)
return false;
}
MPI_Barrier(CMMMF.device->gpu_comm);
CMMMF.device->gpu_barrier();
if (message)
fprintf(screen,"Done.\n");
}

20
lib/gpu/cmm_cut_gpu_kernel.cu
View File

@ -91,14 +91,14 @@ __kernel void kernel_pair(__global numtyp4 *x_, __global numtyp4 *lj1,
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;
@ -203,14 +203,14 @@ __kernel void kernel_pair_fast(__global numtyp4 *x_, __global numtyp4 *lj1_in,
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;

8
lib/gpu/cmmc_long_gpu.cpp
View File

@ -48,7 +48,7 @@ bool cmml_gpu_init(const int ntypes, double **cutsq, int **cg_type,
CMMLMF.device->init_message(screen,"cg/cmm/coul/long",first_gpu,last_gpu);
bool message=false;
if (world_me==0 && screen)
if (CMMLMF.device->replica_me()==0 && screen)
message=true;
if (message) {
@ -66,14 +66,14 @@ bool cmml_gpu_init(const int ntypes, double **cutsq, int **cg_type,
return false;
}
MPI_Barrier(MPI_COMM_WORLD);
CMMLMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing GPU %d on core %d...",gpu_rank,i);
fprintf(screen,"Initializing GPU %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing GPUs %d-%d on core %d...",first_gpu,
last_gpu,i);
@ -88,7 +88,7 @@ bool cmml_gpu_init(const int ntypes, double **cutsq, int **cg_type,
if (!init_ok)
return false;
}
MPI_Barrier(CMMLMF.device->gpu_comm);
CMMLMF.device->gpu_barrier();
if (message)
fprintf(screen,"Done.\n");
}

24
lib/gpu/cmmc_long_gpu_kernel.cu
View File

@ -114,15 +114,15 @@ __kernel void kernel_pair(__global numtyp4 *x_, __global numtyp4 *lj1,
sp_lj[7]=sp_lj_in[7];
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp e_coul=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp e_coul=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;
@ -256,15 +256,15 @@ __kernel void kernel_pair_fast(__global numtyp4 *x_, __global numtyp4 *lj1_in,
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp e_coul=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp e_coul=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;

8
lib/gpu/gb_gpu.cpp
View File

@ -69,7 +69,7 @@ bool gb_gpu_init(const int ntypes, const double gamma,
GBMF.device->init_message(screen,"gayberne",first_gpu,last_gpu);
bool message=false;
if (world_me==0 && screen)
if (GBMF.device->replica_me()==0 && screen)
message=true;
if (message) {
@ -86,14 +86,14 @@ bool gb_gpu_init(const int ntypes, const double gamma,
return false;
}
MPI_Barrier(MPI_COMM_WORLD);
GBMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing GPU %d on core %d...",gpu_rank,i);
fprintf(screen,"Initializing GPU %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing GPUs %d-%d on core %d...",first_gpu,
last_gpu,i);
@ -108,7 +108,7 @@ bool gb_gpu_init(const int ntypes, const double gamma,
if (!init_ok)
return false;
}
MPI_Barrier(GBMF.device->gpu_comm);
GBMF.device->gpu_barrier();
if (message)
fprintf(screen,"Done.\n");
}

16
lib/gpu/gb_gpu_kernel.cu
View File

@ -105,18 +105,18 @@ __kernel void kernel_gayberne(__global numtyp4* x_,__global numtyp4 *q,
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp4 tor;
tor.x=(numtyp)0;
tor.y=(numtyp)0;
tor.z=(numtyp)0;
tor.x=(acctyp)0;
tor.y=(acctyp)0;
tor.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;

30
lib/gpu/gb_gpu_kernel_lj.cu
View File

@ -42,14 +42,14 @@ __kernel void kernel_sphere_gb(__global numtyp4 *x_,__global numtyp4 *q,
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;
@ -276,14 +276,14 @@ __kernel void kernel_lj(__global numtyp4 *x_, __global numtyp4 *lj1,
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_ij+ii;
int i=*nbor;
@ -385,14 +385,14 @@ __kernel void kernel_lj_fast(__global numtyp4 *x_, __global numtyp4 *lj1_in,
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_ij+ii;
int i=*nbor;

23
lib/gpu/gb_gpu_memory.cpp
View File

@ -222,7 +222,7 @@ void GB_GPU_MemoryT::clear() {
single[4]=0;
single[5]=atom->cast_time();
MPI_Reduce(single,times,6,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD);
MPI_Reduce(single,times,6,MPI_DOUBLE,MPI_SUM,0,device->replica());
double avg_split=hd_balancer.all_avg_split();
_max_bytes+=dev_error.row_bytes()+lj1.row_bytes()+lj3.row_bytes()+
@ -230,12 +230,13 @@ void GB_GPU_MemoryT::clear() {
shape.row_bytes()+well.row_bytes()+lshape.row_bytes()+
gamma_upsilon_mu.row_bytes();
double mpi_max_bytes;
MPI_Reduce(&_max_bytes,&mpi_max_bytes,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD);
MPI_Reduce(&_max_bytes,&mpi_max_bytes,1,MPI_DOUBLE,MPI_MAX,0,
device->replica());
double max_mb=mpi_max_bytes/(1024*1024);
if (device->world_me()==0)
if (device->replica_me()==0)
if (screen && times[3]>0.0) {
int world_size=device->world_size();
int replica_size=device->replica_size();
fprintf(screen,"\n\n-------------------------------------");
fprintf(screen,"--------------------------------\n");
@ -244,15 +245,15 @@ void GB_GPU_MemoryT::clear() {
fprintf(screen,"--------------------------------\n");
if (device->procs_per_gpu()==1) {
fprintf(screen,"Data Transfer: %.4f s.\n",times[0]/world_size);
fprintf(screen,"Data Cast/Pack: %.4f s.\n",times[5]/world_size);
fprintf(screen,"Neighbor copy: %.4f s.\n",times[1]/world_size);
fprintf(screen,"Data Transfer: %.4f s.\n",times[0]/replica_size);
fprintf(screen,"Data Cast/Pack: %.4f s.\n",times[5]/replica_size);
fprintf(screen,"Neighbor copy: %.4f s.\n",times[1]/replica_size);
if (nbor->gpu_nbor())
fprintf(screen,"Neighbor build: %.4f s.\n",times[2]/world_size);
fprintf(screen,"Neighbor build: %.4f s.\n",times[2]/replica_size);
else
fprintf(screen,"Neighbor unpack: %.4f s.\n",times[2]/world_size);
fprintf(screen,"Force calc: %.4f s.\n",times[3]/world_size);
fprintf(screen,"LJ calc: %.4f s.\n",times[4]/world_size);
fprintf(screen,"Neighbor unpack: %.4f s.\n",times[2]/replica_size);
fprintf(screen,"Force calc: %.4f s.\n",times[3]/replica_size);
fprintf(screen,"LJ calc: %.4f s.\n",times[4]/replica_size);
}
fprintf(screen,"Average split: %.4f.\n",avg_split);
fprintf(screen,"Max Mem / Proc: %.2f MB.\n",max_mb);

6
lib/gpu/geryon/nvc_device.h
View File

@ -13,7 +13,7 @@
copyright : (C) 2009 by W. Michael Brown
email : brownw@ornl.gov
***************************************************************************/
/* -----------------------------------------------------------------------
Copyright (2009) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -95,7 +95,7 @@ class UCL_Device {
/** \note You cannot delete the default stream **/
inline void pop_command_queue() {
if (_cq.size()<2) return;
CUDA_SAFE_CALL_NS(cudaStreamDestroy(_cq.back()));
CUDA_DESTRUCT_CALL_NS(cudaStreamDestroy(_cq.back()));
_cq.pop_back();
}
@ -290,7 +290,7 @@ inline void UCL_Device::print_all(std::ostream &out) {
else
out << "Unknown\n";
#endif
#if CUDART_VERSION >= 3000
#if CUDART_VERSION >= 3010
out << " Concurrent kernel execution: ";
if (_properties[i].concurrentKernels)
out << "Yes\n";

21
lib/gpu/geryon/nvc_macros.h
View File

@ -6,7 +6,7 @@
#undef _GLIBCXX_ATOMIC_BUILTINS
#endif // _GLIBCXX_ATOMIC_BUILTINS
#endif // __APPLE__
#include <stdio.h>
#include <cassert>
#include <cuda_runtime.h>
@ -18,6 +18,11 @@
#define NVC_GERYON_EXIT assert(0==1)
#endif
#ifdef UCL_DEBUG
#define UCL_SYNC_DEBUG
#define UCL_DESTRUCT_CHECK
#endif
#ifndef UCL_NO_API_CHECK
#define CUDA_SAFE_CALL_NS( call) do { \
@ -32,7 +37,7 @@
#define CUDA_SAFE_CALL( call) do { \
CUDA_SAFE_CALL_NS( call); \
cudaError err=cudaThreadSynchronize(); \
cudaError err=cudaThreadSynchronize(); \
if( cudaSuccess != err) { \
fprintf(stderr, "Cuda error in file '%s' in line %i : %s.\n", \
__FILE__, __LINE__, cudaGetErrorString( err) ); \
@ -53,5 +58,17 @@
#endif
#ifdef UCL_DESTRUCT_CHECK
#define CUDA_DESTRUCT_CALL( call) CUDA_SAFE_CALL( call)
#define CUDA_DESTRUCT_CALL_NS( call) CUDA_SAFE_CALL_NS( call)
#else
#define CUDA_DESTRUCT_CALL( call) call
#define CUDA_DESTRUCT_CALL_NS( call) call
#endif
#endif

6
lib/gpu/geryon/nvd_device.h
View File

@ -20,7 +20,7 @@
certain rights in this software. This software is distributed under
the Simplified BSD License.
----------------------------------------------------------------------- */
#ifndef NVD_DEVICE
#define NVD_DEVICE
@ -233,7 +233,7 @@ inline UCL_Device::UCL_Device() {
&_properties.back().canMapHostMemory,
CU_DEVICE_ATTRIBUTE_CAN_MAP_HOST_MEMORY, dev));
#endif
#if CUDA_VERSION >= 3000
#if CUDA_VERSION >= 3010
CU_SAFE_CALL_NS(cuDeviceGetAttribute(
&_properties.back().concurrentKernels,
CU_DEVICE_ATTRIBUTE_CONCURRENT_KERNELS, dev));
@ -339,7 +339,7 @@ inline void UCL_Device::print_all(std::ostream &out) {
else
out << "No\n";
#endif
#if CUDA_VERSION >= 3000
#if CUDA_VERSION >= 3010
out << " Concurrent kernel execution: ";
if (_properties[i].concurrentKernels)
out << "Yes\n";

19
lib/gpu/geryon/nvd_macros.h
View File

@ -1,6 +1,6 @@
#ifndef NVD_MACROS_H
#define NVD_MACROS_H
#include <stdio.h>
#include <cassert>
#include <cuda.h>
@ -18,6 +18,11 @@
#define NVD_GERYON_EXIT assert(0==1)
#endif
#ifdef UCL_DEBUG
#define UCL_SYNC_DEBUG
#define UCL_DESTRUCT_CHECK
#endif
#ifndef UCL_NO_API_CHECK
#define CU_SAFE_CALL_NS( call ) do { \
@ -53,5 +58,17 @@
#endif
#ifdef UCL_DESTRUCT_CHECK
#define CU_DESTRUCT_CALL( call) CU_SAFE_CALL( call)
#define CU_DESTRUCT_CALL_NS( call) CU_SAFE_CALL_NS( call)
#else
#define CU_DESTRUCT_CALL( call) call
#define CU_DESTRUCT_CALL_NS( call) call
#endif
#endif

6
lib/gpu/geryon/nvd_memory.h
View File

@ -20,7 +20,7 @@
certain rights in this software. This software is distributed under
the Simplified BSD License.
----------------------------------------------------------------------- */
#ifndef NVD_MEMORY_H
#define NVD_MEMORY_H
@ -78,7 +78,7 @@ inline int _host_alloc(mat_type &mat, UCL_Device &dev, const size_t n,
template <class mat_type>
inline void _host_free(mat_type &mat, const enum UCL_MEMOPT kind) {
if (kind!=UCL_NOT_PINNED)
CU_SAFE_CALL(cuMemFreeHost(mat.begin()));
CU_DESTRUCT_CALL(cuMemFreeHost(mat.begin()));
else
free(mat.begin());
}
@ -134,7 +134,7 @@ inline int _device_alloc(mat_type &mat, UCL_Device &d, const size_t rows,
template <class mat_type>
inline void _device_free(mat_type &mat) {
CU_SAFE_CALL(cuMemFree(mat.cbegin()));
CU_DESTRUCT_CALL(cuMemFree(mat.cbegin()));
}
inline void _device_view(CUdeviceptr *ptr, CUdeviceptr &in) {

6
lib/gpu/geryon/nvd_timer.h
View File

@ -20,7 +20,7 @@
certain rights in this software. This software is distributed under
the Simplified BSD License.
----------------------------------------------------------------------- */
#ifndef NVD_TIMER_H
#define NVD_TIMER_H
@ -41,8 +41,8 @@ class UCL_Timer {
/** \note init() must be called to reuse timer after a clear() **/
inline void clear() {
if (_initialized) {
CU_SAFE_CALL(cuEventDestroy(start_event));
CU_SAFE_CALL(cuEventDestroy(stop_event));
CU_DESTRUCT_CALL(cuEventDestroy(start_event));
CU_DESTRUCT_CALL(cuEventDestroy(stop_event));
_initialized=false;
_total_time=0.0;
}

6
lib/gpu/geryon/ocl_device.h
View File

@ -20,7 +20,7 @@
certain rights in this software. This software is distributed under
the Simplified BSD License.
----------------------------------------------------------------------- */
#ifndef OCL_DEVICE
#define OCL_DEVICE
@ -265,10 +265,10 @@ inline UCL_Device::UCL_Device() {
inline UCL_Device::~UCL_Device() {
if (_device>-1) {
for (size_t i=0; i<_cq.size(); i++) {
CL_SAFE_CALL(clReleaseCommandQueue(_cq.back()));
CL_DESTRUCT_CALL(clReleaseCommandQueue(_cq.back()));
_cq.pop_back();
}
CL_SAFE_CALL(clReleaseContext(_context));
CL_DESTRUCT_CALL(clReleaseContext(_context));
}
}

8
lib/gpu/geryon/ocl_kernel.h
View File

@ -13,7 +13,7 @@
copyright : (C) 2010 by W. Michael Brown
email : brownw@ornl.gov
***************************************************************************/
/* -----------------------------------------------------------------------
Copyright (2010) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -51,9 +51,9 @@ class UCL_Program {
/** \note Must call init() after each clear **/
inline void clear() {
if (_init_done) {
CL_SAFE_CALL(clReleaseProgram(_program));
CL_SAFE_CALL(clReleaseContext(_context));
CL_SAFE_CALL(clReleaseCommandQueue(_cq));
CL_DESTRUCT_CALL(clReleaseProgram(_program));
CL_DESTRUCT_CALL(clReleaseContext(_context));
CL_DESTRUCT_CALL(clReleaseCommandQueue(_cq));
_init_done=false;
}
}

4
lib/gpu/geryon/ocl_timer.h
View File

@ -20,7 +20,7 @@
certain rights in this software. This software is distributed under
the Simplified BSD License.
----------------------------------------------------------------------- */
#ifndef OCL_TIMER_H
#define OCL_TIMER_H
@ -41,7 +41,7 @@ class UCL_Timer {
/** \note init() must be called to reuse timer after a clear() **/
inline void clear() {
if (_initialized) {
CL_SAFE_CALL(clReleaseCommandQueue(_cq));
CL_DESTRUCT_CALL(clReleaseCommandQueue(_cq));
clReleaseEvent(start_event);
clReleaseEvent(stop_event);
_initialized=false;

8
lib/gpu/lj96_cut_gpu.cpp
View File

@ -45,7 +45,7 @@ bool lj96_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
LJ96MF.device->init_message(screen,"lj96/cut",first_gpu,last_gpu);
bool message=false;
if (world_me==0 && screen)
if (LJ96MF.device->replica_me()==0 && screen)
message=true;
if (message) {
@ -61,14 +61,14 @@ bool lj96_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
return false;
}
MPI_Barrier(MPI_COMM_WORLD);
LJ96MF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing GPU %d on core %d...",gpu_rank,i);
fprintf(screen,"Initializing GPU %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing GPUs %d-%d on core %d...",first_gpu,
last_gpu,i);
@ -82,7 +82,7 @@ bool lj96_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
if (!init_ok)
return false;
}
MPI_Barrier(LJ96MF.device->gpu_comm);
LJ96MF.device->gpu_barrier();
if (message)
fprintf(screen,"Done.\n");
}

20
lib/gpu/lj96_cut_gpu_kernel.cu
View File

@ -91,14 +91,14 @@ __kernel void kernel_pair(__global numtyp4 *x_, __global numtyp4 *lj1,
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;
@ -196,14 +196,14 @@ __kernel void kernel_pair_fast(__global numtyp4 *x_, __global numtyp4 *lj1_in,
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;

8
lib/gpu/lj_cut_gpu.cpp
View File

@ -46,7 +46,7 @@ bool ljl_gpu_init(const int ntypes, double **cutsq,
LJLMF.device->init_message(screen,"lj/cut",first_gpu,last_gpu);
bool message=false;
if (world_me==0 && screen)
if (LJLMF.device->replica_me()==0 && screen)
message=true;
if (message) {
@ -62,14 +62,14 @@ bool ljl_gpu_init(const int ntypes, double **cutsq,
return false;
}
MPI_Barrier(MPI_COMM_WORLD);
LJLMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing GPU %d on core %d...",gpu_rank,i);
fprintf(screen,"Initializing GPU %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing GPUs %d-%d on core %d...",first_gpu,
last_gpu,i);
@ -83,7 +83,7 @@ bool ljl_gpu_init(const int ntypes, double **cutsq,
if (!init_ok)
return false;
}
MPI_Barrier(LJLMF.device->gpu_comm);
LJLMF.device->gpu_barrier();
if (message)
fprintf(screen,"Done.\n");
}

20
lib/gpu/lj_cut_gpu_kernel.cu
View File

@ -91,14 +91,14 @@ __kernel void kernel_pair(__global numtyp4 *x_, __global numtyp4 *lj1,
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;
@ -195,14 +195,14 @@ __kernel void kernel_pair_fast(__global numtyp4 *x_, __global numtyp4 *lj1_in,
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;

8
lib/gpu/ljc_cut_gpu.cpp
View File

@ -47,7 +47,7 @@ bool ljc_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
LJCMF.device->init_message(screen,"lj/cut/coul/cut",first_gpu,last_gpu);
bool message=false;
if (world_me==0 && screen)
if (LJCMF.device->replica_me()==0 && screen)
message=true;
if (message) {
@ -65,14 +65,14 @@ bool ljc_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
return false;
}
MPI_Barrier(MPI_COMM_WORLD);
LJCMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing GPU %d on core %d...",gpu_rank,i);
fprintf(screen,"Initializing GPU %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing GPUs %d-%d on core %d...",first_gpu,
last_gpu,i);
@ -87,7 +87,7 @@ bool ljc_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
if (!init_ok)
return false;
}
MPI_Barrier(LJCMF.device->gpu_comm);
LJCMF.device->gpu_barrier();
if (message)
fprintf(screen,"Done.\n");
}

24
lib/gpu/ljc_cut_gpu_kernel.cu
View File

@ -106,15 +106,15 @@ __kernel void kernel_pair(__global numtyp4 *x_, __global numtyp4 *lj1,
sp_lj[7]=sp_lj_in[7];
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp e_coul=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp e_coul=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;
@ -234,15 +234,15 @@ __kernel void kernel_pair_fast(__global numtyp4 *x_, __global numtyp4 *lj1_in,
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp e_coul=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp e_coul=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;

8
lib/gpu/ljcl_cut_gpu.cpp
View File

@ -48,7 +48,7 @@ bool ljcl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
LJCLMF.device->init_message(screen,"lj/cut/coul/long",first_gpu,last_gpu);
bool message=false;
if (world_me==0 && screen)
if (LJCLMF.device->replica_me()==0 && screen)
message=true;
if (message) {
@ -66,14 +66,14 @@ bool ljcl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
return false;
}
MPI_Barrier(MPI_COMM_WORLD);
LJCLMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing GPU %d on core %d...",gpu_rank,i);
fprintf(screen,"Initializing GPU %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing GPUs %d-%d on core %d...",first_gpu,
last_gpu,i);
@ -88,7 +88,7 @@ bool ljcl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
if (!init_ok)
return false;
}
MPI_Barrier(LJCLMF.device->gpu_comm);
LJCLMF.device->gpu_barrier();
if (message)
fprintf(screen,"Done.\n");
}

24
lib/gpu/ljcl_cut_gpu_kernel.cu
View File

@ -114,15 +114,15 @@ __kernel void kernel_pair(__global numtyp4 *x_, __global numtyp4 *lj1,
sp_lj[7]=sp_lj_in[7];
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp e_coul=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp e_coul=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;
@ -248,15 +248,15 @@ __kernel void kernel_pair_fast(__global numtyp4 *x_, __global numtyp4 *lj1_in,
if (ii<inum) {
acctyp energy=(numtyp)0;
acctyp e_coul=(numtyp)0;
acctyp energy=(acctyp)0;
acctyp e_coul=(acctyp)0;
acctyp4 f;
f.x=(numtyp)0;
f.y=(numtyp)0;
f.z=(numtyp)0;
f.x=(acctyp)0;
f.y=(acctyp)0;
f.z=(acctyp)0;
acctyp virial[6];
for (int i=0; i<6; i++)
virial[i]=(numtyp)0;
virial[i]=(acctyp)0;
__global int *nbor=dev_nbor+ii;
int i=*nbor;

74
lib/gpu/pair_gpu_atom.cpp
View File

@ -30,7 +30,8 @@ __win_sort _win_sort;
template <class numtyp, class acctyp>
PairGPUAtomT::PairGPUAtom() : _compiled(false),_allocated(false),_eflag(false),
_vflag(false),_inum(0),_ilist(NULL) {
_vflag(false),_inum(0),_ilist(NULL),
_newton(false) {
#ifndef USE_OPENCL
sort_config.op = CUDPP_ADD;
sort_config.datatype = CUDPP_UINT;
@ -64,7 +65,13 @@ int PairGPUAtomT::bytes_per_atom() const {
}
template <class numtyp, class acctyp>
bool PairGPUAtomT::alloc(const int max_atoms) {
bool PairGPUAtomT::alloc(const int inum, const int nall) {
_max_atoms=static_cast<int>(static_cast<double>(nall)*1.10);
if (_newton)
_max_local=_max_atoms;
else
_max_local=static_cast<int>(static_cast<double>(inum)*1.10);
bool success=true;
int ans_elements=4;
@ -79,10 +86,10 @@ bool PairGPUAtomT::alloc(const int max_atoms) {
// Allocate storage for CUDPP sort
#ifndef USE_OPENCL
#ifdef WINDLL
_win_sort_alloc(max_atoms);
_win_sort_alloc(_max_atoms);
#else
if (_gpu_nbor) {
CUDPPResult result = cudppPlan(&sort_plan, sort_config, max_atoms, 1, 0);
CUDPPResult result = cudppPlan(&sort_plan, sort_config, _max_atoms, 1, 0);
if (CUDPP_SUCCESS != result)
return false;
}
@ -92,23 +99,23 @@ bool PairGPUAtomT::alloc(const int max_atoms) {
// -------------------------- Host allocations
// Get a host write only buffer
#ifdef GPU_CAST
success=success && (host_x_cast.alloc(max_atoms*3,*dev,
success=success && (host_x_cast.alloc(_max_atoms*3,*dev,
UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);
success=success && (host_type_cast.alloc(max_atoms,*dev,
success=success && (host_type_cast.alloc(_max_atoms,*dev,
UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);
#else
success=success && (host_x.alloc(max_atoms*4,*dev,
success=success && (host_x.alloc(_max_atoms*4,*dev,
UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);
#endif
success=success && (host_ans.alloc(ans_elements*max_atoms,*dev)==UCL_SUCCESS);
success=success && (host_engv.alloc(_ev_fields*max_atoms,*dev)==UCL_SUCCESS);
success=success &&(host_ans.alloc(ans_elements*_max_local,*dev)==UCL_SUCCESS);
success=success &&(host_engv.alloc(_ev_fields*_max_local,*dev)==UCL_SUCCESS);
// Buffer for casting only if different precisions
if (_charge)
success=success && (host_q.alloc(max_atoms,*dev,
success=success && (host_q.alloc(_max_atoms,*dev,
UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);
// Buffer for casting only if different precisions
if (_rot)
success=success && (host_quat.alloc(max_atoms*4,*dev,
success=success && (host_quat.alloc(_max_atoms*4,*dev,
UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);
@ -128,43 +135,44 @@ bool PairGPUAtomT::alloc(const int max_atoms) {
dev_q.view(host_q);
} else {
#ifdef GPU_CAST
success=success && (UCL_SUCCESS==dev_x.alloc(max_atoms*4,*dev));
success=success && (UCL_SUCCESS==dev_x.alloc(_max_atoms*4,*dev));
success=success && (UCL_SUCCESS==
dev_x_cast.alloc(max_atoms*3,*dev,UCL_READ_ONLY));
dev_x_cast.alloc(_max_atoms*3,*dev,UCL_READ_ONLY));
success=success && (UCL_SUCCESS==
dev_type_cast.alloc(max_atoms,*dev,UCL_READ_ONLY));
dev_type_cast.alloc(_max_atoms,*dev,UCL_READ_ONLY));
_gpu_bytes+=dev_x_cast.row_bytes()+dev_type_cast.row_bytes();
#else
success=success && (UCL_SUCCESS==
dev_x.alloc(max_atoms*4,*dev,UCL_READ_ONLY));
dev_x.alloc(_max_atoms*4,*dev,UCL_READ_ONLY));
#endif
success=success && (dev_engv.alloc(_ev_fields*max_atoms,*dev,
success=success && (dev_engv.alloc(_ev_fields*_max_local,*dev,
UCL_WRITE_ONLY)==UCL_SUCCESS);
success=success && (dev_ans.alloc(ans_elements*max_atoms,
success=success && (dev_ans.alloc(ans_elements*_max_local,
*dev,UCL_WRITE_ONLY)==UCL_SUCCESS);
if (_charge) {
success=success && (dev_q.alloc(max_atoms,*dev,
success=success && (dev_q.alloc(_max_atoms,*dev,
UCL_READ_ONLY)==UCL_SUCCESS);
_gpu_bytes+=dev_q.row_bytes();
}
if (_rot) {
success=success && (dev_quat.alloc(max_atoms*4,*dev,
success=success && (dev_quat.alloc(_max_atoms*4,*dev,
UCL_READ_ONLY)==UCL_SUCCESS);
_gpu_bytes+=dev_quat.row_bytes();
}
}
if (_gpu_nbor) {
success=success && (dev_cell_id.alloc(max_atoms,*dev)==UCL_SUCCESS);
success=success && (dev_particle_id.alloc(max_atoms,*dev)==UCL_SUCCESS);
success=success && (dev_cell_id.alloc(_max_atoms,*dev)==UCL_SUCCESS);
success=success && (dev_particle_id.alloc(_max_atoms,*dev)==UCL_SUCCESS);
_gpu_bytes+=dev_cell_id.row_bytes()+dev_particle_id.row_bytes();
if (_bonds) {
success=success && (dev_tag.alloc(max_atoms,*dev)==UCL_SUCCESS);
success=success && (dev_tag.alloc(_max_atoms,*dev)==UCL_SUCCESS);
_gpu_bytes+=dev_tag.row_bytes();
}
}
_gpu_bytes+=dev_x.row_bytes()+dev_engv.row_bytes()+dev_ans.row_bytes();
_allocated=true;
return success;
}
@ -188,14 +196,13 @@ bool PairGPUAtomT::init(const int inum, const int nall, const bool charge,
_ev_fields=6+_e_fields;
// Initialize atom and nbor data
int max_local=static_cast<int>(static_cast<double>(inum)*1.10);
if (max_local==0)
max_local=1000;
if (nall<=inum)
_max_atoms=max_local*2;
else
_max_atoms=static_cast<int>(static_cast<double>(nall)*1.10);
int ef_inum=inum;
if (ef_inum==0)
ef_inum=1000;
int ef_nall=nall;
if (ef_nall<=ef_inum)
ef_nall=ef_inum*2;
// Initialize timers for the selected device
time_pos.init(*dev);
time_other.init(*dev);
@ -209,8 +216,7 @@ bool PairGPUAtomT::init(const int inum, const int nall, const bool charge,
compile_kernels(*dev);
#endif
_allocated=true;
return success && alloc(_max_atoms);
return success && alloc(ef_inum,ef_nall);
}
template <class numtyp, class acctyp>
@ -285,7 +291,7 @@ double PairGPUAtomT::host_memory_usage() const {
atom_bytes+=4;
int ans_bytes=atom_bytes+_ev_fields;
return _max_atoms*atom_bytes*sizeof(numtyp)+
ans_bytes*(_max_atoms)*sizeof(acctyp)+
ans_bytes*(_max_local)*sizeof(acctyp)+
sizeof(PairGPUAtom<numtyp,acctyp>);
}

25
lib/gpu/pair_gpu_atom.h
View File

@ -77,11 +77,9 @@ class PairGPUAtom {
inline bool resize(const int inum, const int nall, bool &success) {
_inum=inum;
_nall=nall;
if (nall>_max_atoms) {
if (inum>_max_local || nall>_max_atoms) {
clear_resize();
_max_atoms=static_cast<int>(static_cast<double>(nall)*1.10);
_allocated=true;
success = success && alloc(_max_atoms);
success = success && alloc(inum,nall);
return true;
}
return false;
@ -203,6 +201,19 @@ class PairGPUAtom {
ucl_copy(dev_v,view,false);
}
/// Pack LAMMPS atom "self" type constants into 2 vectors and copy to device
template <class dev_typ, class t1, class t2>
inline void self_pack2(const int n, UCL_D_Vec<dev_typ> &dev_v,
UCL_H_Vec<numtyp> &buffer, t1 **one, t2 **two) {
for (int i=0; i<n; i++) {
buffer[i*2]=static_cast<numtyp>(one[i][i]);
buffer[i*2+1]=static_cast<numtyp>(two[i][i]);
}
UCL_H_Vec<dev_typ> view;
view.view((dev_typ*)buffer.begin(),n,*dev);
ucl_copy(dev_v,view,false);
}
// -------------------------COPY TO GPU ----------------------------------
/// Cast positions and types to write buffer
@ -386,15 +397,17 @@ class PairGPUAtom {
bool _compiled;
bool alloc(const int max_atoms);
bool alloc(const int inum, const int nall);
bool _allocated, _eflag, _vflag, _ef_atom, _vf_atom, _rot, _charge, _other;
int _max_atoms, _nall, _inum, _e_fields, _ev_fields;
int _max_local, _max_atoms, _nall, _inum, _e_fields, _ev_fields;
bool _gpu_nbor, _bonds;
int *_ilist;
double _time_cast;
double _gpu_bytes;
bool _newton;
#ifndef USE_OPENCL
CUDPPConfiguration sort_config;

12
lib/gpu/pair_gpu_balance.h
View File

@ -65,11 +65,9 @@ class PairGPUBalance {
inline double all_avg_split() {
if (_load_balance) {
double _all_avg_split=0.0;
int nprocs;
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
MPI_Reduce(&_avg_split,&_all_avg_split,1,MPI_DOUBLE,MPI_SUM,0,
MPI_COMM_WORLD);
_all_avg_split/=nprocs;
_device->replica());
_all_avg_split/=_device->replica_size();
return _all_avg_split/_avg_count;
} else
return _actual_split;
@ -83,10 +81,10 @@ class PairGPUBalance {
inline void start_timer() {
if (_measure_this_step) {
_device->gpu->sync();
MPI_Barrier(_device->gpu_comm);
_device->gpu_barrier();
_device_time.start();
_device->gpu->sync();
MPI_Barrier(_device->gpu_comm);
_device->gpu_barrier();
_device->start_host_timer();
}
}
@ -178,7 +176,7 @@ void PairGPUBalanceT::balance(const double cpu_time, const bool gpu_nbor) {
cpu_gpu_time[2]=(_device->host_time()-cpu_time)/_inum_full;
MPI_Allreduce(cpu_gpu_time,max_times,3,MPI_DOUBLE,MPI_MAX,
_device->gpu_comm);
_device->gpu_comm());
double split=(max_times[0]+max_times[2])/(max_times[0]+max_times[1]);
split*=_HD_BALANCE_GAP;

66
lib/gpu/pair_gpu_device.cpp
View File

@ -10,7 +10,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Mike Brown (ORNL), brownw@ornl.gov
------------------------------------------------------------------------- */
@ -34,19 +34,28 @@ PairGPUDeviceT::~PairGPUDevice() {
}
template <class numtyp, class acctyp>
bool PairGPUDeviceT::init_device(const int first_gpu, const int last_gpu,
const int gpu_mode, const double p_split) {
bool PairGPUDeviceT::init_device(MPI_Comm world, MPI_Comm replica,
const int first_gpu, const int last_gpu,
const int gpu_mode, const double p_split,
const int nthreads) {
_nthreads=nthreads;
if (_device_init)
return true;
_device_init=true;
_comm_world=world;
_comm_replica=replica;
_first_device=first_gpu;
_last_device=last_gpu;
_gpu_mode=gpu_mode;
_particle_split=p_split;
// Get the rank within the world
MPI_Comm_rank(MPI_COMM_WORLD,&_world_me);
MPI_Comm_size(MPI_COMM_WORLD,&_world_size);
// Get the rank/size within the world
MPI_Comm_rank(_comm_world,&_world_me);
MPI_Comm_size(_comm_world,&_world_size);
// Get the rank/size within the replica
MPI_Comm_rank(_comm_replica,&_replica_me);
MPI_Comm_size(_comm_replica,&_replica_size);
// Get the names of all nodes
int name_length;
@ -54,7 +63,7 @@ bool PairGPUDeviceT::init_device(const int first_gpu, const int last_gpu,
char node_names[MPI_MAX_PROCESSOR_NAME*_world_size];
MPI_Get_processor_name(node_name,&name_length);
MPI_Allgather(&node_name,MPI_MAX_PROCESSOR_NAME,MPI_CHAR,&node_names,
MPI_MAX_PROCESSOR_NAME,MPI_CHAR,MPI_COMM_WORLD);
MPI_MAX_PROCESSOR_NAME,MPI_CHAR,_comm_world);
std::string node_string=std::string(node_name);
// Get the number of procs per node
@ -80,7 +89,7 @@ bool PairGPUDeviceT::init_device(const int first_gpu, const int last_gpu,
// Set up a per node communicator and find rank within
MPI_Comm node_comm;
MPI_Comm_split(MPI_COMM_WORLD, split_id, 0, &node_comm);
MPI_Comm_split(_comm_world, split_id, 0, &node_comm);
int node_rank;
MPI_Comm_rank(node_comm,&node_rank);
@ -90,8 +99,8 @@ bool PairGPUDeviceT::init_device(const int first_gpu, const int last_gpu,
int my_gpu=node_rank/_procs_per_gpu;
// Set up a per device communicator
MPI_Comm_split(node_comm,my_gpu,0,&gpu_comm);
MPI_Comm_rank(gpu_comm,&_gpu_rank);
MPI_Comm_split(node_comm,my_gpu,0,&_comm_gpu);
MPI_Comm_rank(_comm_gpu,&_gpu_rank);
gpu=new UCL_Device();
if (my_gpu>=gpu->num_devices())
@ -111,10 +120,13 @@ bool PairGPUDeviceT::init(const bool charge, const bool rot, const int nlocal,
return false;
if (_init_count==0) {
// Initialize atom and nbor data
if (!atom.init(nlocal,nall,charge,rot,*gpu,gpu_nbor,
int ef_nlocal=nlocal;
if (_particle_split<1.0 && _particle_split>0.0)
ef_nlocal=static_cast<int>(_particle_split*nlocal);
if (!atom.init(ef_nlocal,nall,charge,rot,*gpu,gpu_nbor,
gpu_nbor && maxspecial>0))
return false;
if (!nbor.init(nlocal,host_nlocal,max_nbors,maxspecial,*gpu,gpu_nbor,
if (!nbor.init(ef_nlocal,host_nlocal,max_nbors,maxspecial,*gpu,gpu_nbor,
gpu_host,pre_cut))
return false;
nbor.cell_size(cell_size);
@ -136,7 +148,7 @@ void PairGPUDeviceT::init_message(FILE *screen, const char *name,
std::string fs=toa(gpu->free_gigabytes())+"/";
#endif
if (_world_me == 0 && screen) {
if (_replica_me == 0 && screen) {
fprintf(screen,"\n-------------------------------------");
fprintf(screen,"-------------------------------------\n");
fprintf(screen,"- Using GPGPU acceleration for %s:\n",name);
@ -175,14 +187,14 @@ void PairGPUDeviceT::output_times(UCL_Timer &time_pair, const double avg_split,
single[3]=time_pair.total_seconds();
single[4]=atom.cast_time();
MPI_Reduce(single,times,5,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD);
MPI_Reduce(single,times,5,MPI_DOUBLE,MPI_SUM,0,_comm_replica);
double my_max_bytes=max_bytes;
double mpi_max_bytes;
MPI_Reduce(&my_max_bytes,&mpi_max_bytes,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD);
MPI_Reduce(&my_max_bytes,&mpi_max_bytes,1,MPI_DOUBLE,MPI_MAX,0,_comm_replica);
double max_mb=mpi_max_bytes/(1024.0*1024.0);
if (world_me()==0)
if (replica_me()==0)
if (screen && times[3]>0.0) {
fprintf(screen,"\n\n-------------------------------------");
fprintf(screen,"--------------------------------\n");
@ -191,14 +203,14 @@ void PairGPUDeviceT::output_times(UCL_Timer &time_pair, const double avg_split,
fprintf(screen,"--------------------------------\n");
if (procs_per_gpu()==1) {
fprintf(screen,"Data Transfer: %.4f s.\n",times[0]/_world_size);
fprintf(screen,"Data Cast/Pack: %.4f s.\n",times[4]/_world_size);
fprintf(screen,"Neighbor copy: %.4f s.\n",times[1]/_world_size);
fprintf(screen,"Data Transfer: %.4f s.\n",times[0]/_replica_size);
fprintf(screen,"Data Cast/Pack: %.4f s.\n",times[4]/_replica_size);
fprintf(screen,"Neighbor copy: %.4f s.\n",times[1]/_replica_size);
if (nbor.gpu_nbor())
fprintf(screen,"Neighbor build: %.4f s.\n",times[2]/_world_size);
fprintf(screen,"Neighbor build: %.4f s.\n",times[2]/_replica_size);
else
fprintf(screen,"Neighbor unpack: %.4f s.\n",times[2]/_world_size);
fprintf(screen,"Force calc: %.4f s.\n",times[3]/_world_size);
fprintf(screen,"Neighbor unpack: %.4f s.\n",times[2]/_replica_size);
fprintf(screen,"Force calc: %.4f s.\n",times[3]/_replica_size);
}
fprintf(screen,"Average split: %.4f.\n",avg_split);
fprintf(screen,"Max Mem / Proc: %.2f MB.\n",max_mb);
@ -239,10 +251,11 @@ double PairGPUDeviceT::host_memory_usage() const {
template class PairGPUDevice<PRECISION,ACC_PRECISION>;
PairGPUDevice<PRECISION,ACC_PRECISION> pair_gpu_device;
bool lmp_init_device(const int first_gpu, const int last_gpu,
const int gpu_mode, const double particle_split) {
return pair_gpu_device.init_device(first_gpu,last_gpu,gpu_mode,
particle_split);
bool lmp_init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu,
const int last_gpu, const int gpu_mode,
const double particle_split, const int nthreads) {
return pair_gpu_device.init_device(world,replica,first_gpu,last_gpu,gpu_mode,
particle_split,nthreads);
}
void lmp_clear_device() {
@ -261,3 +274,4 @@ double lmp_gpu_forces(double **f, double **tor, double *eatom,
}
return 0.0;
}

33
lib/gpu/pair_gpu_device.h
View File

@ -10,7 +10,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Mike Brown (ORNL), brownw@ornl.gov
------------------------------------------------------------------------- */
@ -34,8 +34,9 @@ class PairGPUDevice {
/// Initialize the device for use by this process
/** Sets up a per-device MPI communicator for load balancing and initializes
* the device (>=first_gpu and <=last_gpu) that this proc will be using **/
bool init_device(const int first_gpu, const int last_gpu,
const int gpu_mode, const double particle_split);
bool init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu,
const int last_gpu, const int gpu_mode,
const double particle_split, const int nthreads);
/// Initialize the device for Atom and Neighbor storage
/** \param rot True if quaternions need to be stored
@ -83,12 +84,26 @@ class PairGPUDevice {
/// Return the number of procs sharing a device (size of device commincator)
inline int procs_per_gpu() const { return _procs_per_gpu; }
/// Return my rank in the device communicator
inline int gpu_rank() const { return _gpu_rank; }
/// Return the number of threads per proc
inline int num_threads() const { return _nthreads; }
/// My rank within all processes
inline int world_me() const { return _world_me; }
/// Total number of processes
inline int world_size() const { return _world_size; }
/// MPI Barrier for world
inline void world_barrier() { MPI_Barrier(_comm_world); }
/// Return the replica MPI communicator
inline MPI_Comm & replica() { return _comm_replica; }
/// My rank within replica communicator
inline int replica_me() const { return _replica_me; }
/// Number of procs in replica communicator
inline int replica_size() const { return _replica_size; }
/// Return the per-GPU MPI communicator
inline MPI_Comm & gpu_comm() { return _comm_gpu; }
/// Return my rank in the device communicator
inline int gpu_rank() const { return _gpu_rank; }
/// MPI Barrier for gpu
inline void gpu_barrier() { MPI_Barrier(_comm_gpu); }
/// Return the 'mode' for acceleration: GPU_FORCE or GPU_NEIGH
inline int gpu_mode() const { return _gpu_mode; }
/// Index of first device used by a node
@ -104,8 +119,6 @@ class PairGPUDevice {
/// Geryon Device
UCL_Device *gpu;
/// Device communicator
MPI_Comm gpu_comm;
enum{GPU_FORCE, GPU_NEIGH};
@ -122,8 +135,10 @@ class PairGPUDevice {
private:
int _init_count;
bool _device_init;
int _procs_per_gpu, _gpu_rank, _world_me, _world_size;
int _gpu_mode, _first_device, _last_device;
MPI_Comm _comm_world, _comm_replica, _comm_gpu;
int _procs_per_gpu, _gpu_rank, _world_me, _world_size, _replica_me,
_replica_size;
int _gpu_mode, _first_device, _last_device, _nthreads;
double _particle_split;
double _cpu_full;

1
lib/gpu/pair_gpu_precision.h
View File

@ -85,6 +85,7 @@ inline std::ostream & operator<<(std::ostream &out, const _lgpu_double4 &v) {
#endif
#define MAX_SHARED_TYPES 8
#define MAX_BIO_SHARED_TYPES 128
enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_SPHERE,ELLIPSE_ELLIPSE};
#endif