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Temporary commit for testing on yona.

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This commit is contained in:
W. Michael Brown
2011-03-27 12:31:18 -04:00
parent 04f1dc492e
commit 092ee2eea8
7 changed files with 160 additions and 29 deletions
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13
lib/gpu/Nvidia.makefile
View File

@ -58,7 +58,8 @@ OBJS = $(OBJ_DIR)/pair_gpu_atom.o $(OBJ_DIR)/pair_gpu_ans.o \
$(OBJ_DIR)/cmmc_long_gpu_memory.o $(OBJ_DIR)/cmmc_long_gpu.o \
$(OBJ_DIR)/cmmc_msm_gpu_memory.o $(OBJ_DIR)/cmmc_msm_gpu.o \
$(CUDPP)
PTXS = $(OBJ_DIR)/pair_gpu_atom_kernel.ptx $(OBJ_DIR)/pair_gpu_atom_ptx.h \
PTXS = $(OBJ_DIR)/pair_gpu_dev_kernel.ptx \
$(OBJ_DIR)/pair_gpu_atom_kernel.ptx $(OBJ_DIR)/pair_gpu_atom_ptx.h \
$(OBJ_DIR)/pair_gpu_nbor_kernel.ptx $(OBJ_DIR)/pair_gpu_nbor_ptx.h \
$(OBJ_DIR)/pair_gpu_build_kernel.ptx $(OBJ_DIR)/pair_gpu_build_ptx.h \
$(OBJ_DIR)/pppm_gpu_kernel.ptx $(OBJ_DIR)/pppm_gpu_ptx.h \
@ -125,8 +126,14 @@ $(OBJ_DIR)/pair_gpu_nbor_shared.o: pair_gpu_nbor_shared.cpp pair_gpu_nbor_shared
$(OBJ_DIR)/pair_gpu_nbor.o: pair_gpu_nbor.cpp pair_gpu_nbor.h pair_gpu_nbor_shared.h $(NVD_H)
$(CUDR) -o $@ -c pair_gpu_nbor.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/pair_gpu_device.o: pair_gpu_device.cpp pair_gpu_device.h $(ALL_H)
$(CUDR) -o $@ -c pair_gpu_device.cpp
$(OBJ_DIR)/pair_gpu_dev_kernel.ptx: pair_gpu_dev_kernel.cu
$(CUDA) --ptx -DNV_KERNEL -o $@ pair_gpu_dev_kernel.cu
$(OBJ_DIR)/pair_gpu_dev_ptx.h: $(OBJ_DIR)/pair_gpu_dev_kernel.ptx
$(BSH) ./geryon/file_to_cstr.sh $(OBJ_DIR)/pair_gpu_dev_kernel.ptx $(OBJ_DIR)/pair_gpu_dev_ptx.h
$(OBJ_DIR)/pair_gpu_device.o: pair_gpu_device.cpp pair_gpu_device.h $(ALL_H) $(OBJ_DIR)/pair_gpu_dev_ptx.h
$(CUDR) -o $@ -c pair_gpu_device.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/atomic_gpu_memory.o: $(ALL_H) atomic_gpu_memory.h atomic_gpu_memory.cpp
$(CUDR) -o $@ -c atomic_gpu_memory.cpp

11
lib/gpu/Opencl.makefile
View File

@ -46,8 +46,8 @@ OBJS = $(OBJ_DIR)/pair_gpu_atom.o $(OBJ_DIR)/pair_gpu_ans.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)/pppm_gpu_cl.h \
KERS = $(OBJ_DIR)/pair_gpu_dev_cl.h $(OBJ_DIR)/pair_gpu_atom_cl.h \
$(OBJ_DIR)/pair_gpu_nbor_cl.h $(OBJ_DIR)/pppm_gpu_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)/lj_expand_gpu_cl.h $(OBJ_DIR)/ljc_cut_gpu_cl.h \
@ -74,8 +74,11 @@ $(OBJ_DIR)/pair_gpu_nbor_shared.o: pair_gpu_nbor_shared.cpp pair_gpu_nbor_shared
$(OBJ_DIR)/pair_gpu_nbor.o: pair_gpu_nbor.cpp pair_gpu_nbor.h $(OCL_H) pair_gpu_nbor_shared.h
$(OCL) -o $@ -c pair_gpu_nbor.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/pair_gpu_device.o: pair_gpu_device.cpp pair_gpu_device.h $(ALL_H)
$(OCL) -o $@ -c pair_gpu_device.cpp
$(OBJ_DIR)/pair_gpu_dev_cl.h: pair_gpu_dev_kernel.cu
$(BSH) ./geryon/file_to_cstr.sh pair_gpu_dev_kernel.cu $(OBJ_DIR)/pair_gpu_dev_cl.h
$(OBJ_DIR)/pair_gpu_device.o: pair_gpu_device.cpp pair_gpu_device.h $(ALL_H) $(OBJ_DIR)/pair_gpu_dev_cl.h
$(OCL) -o $@ -c pair_gpu_device.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/atomic_gpu_memory.o: $(OCL_H) atomic_gpu_memory.h atomic_gpu_memory.cpp
$(OCL) -o $@ -c atomic_gpu_memory.cpp

2
lib/gpu/lj_cut_gpu.cpp
View File

@ -89,6 +89,8 @@ bool ljl_gpu_init(const int ntypes, double **cutsq,
}
if (message)
fprintf(screen,"\n");
LJLMF.device->estimate_gpu_overhead();
return true;
}

6
lib/gpu/pair_gpu_atom.h
View File

@ -81,6 +81,12 @@ class PairGPUAtom {
bool add_fields(const bool charge, const bool rot, const bool gpu_nbor,
const bool bonds);
/// Returns true if GPU is using charges
bool charge() { return _charge; }
/// Returns true if GPU is using quaternions
bool quat() { return _rot; }
/// Only free matrices of length inum or nall for resizing
void clear_resize();

39
lib/gpu/pair_gpu_balance.h
View File

@ -53,7 +53,7 @@ class PairGPUBalance {
if (gpu_split>0)
host_nlocal=static_cast<int>(ceil((1.0-gpu_split)*nlocal));
else
host_nlocal=static_cast<int>(ceil(0.1*nlocal));
host_nlocal=static_cast<int>(ceil(0.05*nlocal));
}
return host_nlocal;
}
@ -130,7 +130,7 @@ void PairGPUBalanceT::init(PairGPUDevice<numtyp, acctyp> *gpu,
if (split<0.0) {
_load_balance=true;
_desired_split=0.9;
_desired_split=0.90;
} else {
_load_balance=false;
_desired_split=split;
@ -162,31 +162,27 @@ int PairGPUBalanceT::get_gpu_count(const int ago, const int inum_full) {
template <class numtyp, class acctyp>
void PairGPUBalanceT::balance(const double cpu_time) {
if (_measure_this_step) {
_measure_this_step=false;
double gpu_time=_device_time.seconds();
double max_gpu_time;
MPI_Allreduce(&gpu_time,&max_gpu_time,1,MPI_DOUBLE,MPI_MAX,
_device->gpu_comm());
if (_inum_full==_inum) {
_desired_split=1.0;
return;
}
_measure_this_step=false;
double gpu_time=_device_time.seconds();
double cpu_time_per_atom=cpu_time/(_inum_full-_inum);
double cpu_other_time=_device->host_time()-cpu_time;
int host_inum=static_cast<int>((max_gpu_time-cpu_other_time)/
cpu_time_per_atom);
double cpu_gpu_time[3], max_times[3];
cpu_gpu_time[0]=cpu_time/(_inum_full-_inum);
cpu_gpu_time[1]=gpu_time/_inum;
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());
double split=(max_times[0]+max_times[2])/(max_times[0]+max_times[1]);
split*=_HD_BALANCE_GAP;
if (split>1.0)
split=1.0;
if (_avg_count<10)
_desired_split=(_desired_split*_avg_count+split)/(_avg_count+1);
else
_desired_split=_desired_split*(1.0-_HD_BALANCE_WEIGHT)+
_HD_BALANCE_WEIGHT*split;
double split=static_cast<double>(_inum_full-host_inum)/_inum_full;
_desired_split=split*_HD_BALANCE_GAP;
if (_desired_split<0.0)
_desired_split=0.0;
if (!_gpu_nbor) {
if (_desired_split<_max_split)
@ -194,6 +190,7 @@ void PairGPUBalanceT::balance(const double cpu_time) {
else
_actual_split=_max_split;
}
//std::cout << gpu_time << " " << max_gpu_time << " " << cpu_other_time << " " << cpu_time_per_atom << " " << cpu_time << " " << _desired_split << " " << host_inum << std::endl;
}
_avg_split+=_desired_split;
_avg_count++;

99
lib/gpu/pair_gpu_device.cpp
View File

@ -23,12 +23,19 @@
#include <omp.h>
#endif
#ifdef USE_OPENCL
#include "pair_gpu_dev_cl.h"
#else
#include "pair_gpu_dev_ptx.h"
#endif
#define BLOCK_1D 64
#define PairGPUDeviceT PairGPUDevice<numtyp, acctyp>
template <class numtyp, class acctyp>
PairGPUDeviceT::PairGPUDevice() : _init_count(0), _device_init(false),
_gpu_mode(GPU_FORCE), _first_device(0),
_last_device(0) {
_last_device(0), _compiled(false) {
}
template <class numtyp, class acctyp>
@ -113,6 +120,11 @@ bool PairGPUDeviceT::init_device(MPI_Comm world, MPI_Comm replica,
return false;
gpu->set(my_gpu);
_block_size=BLOCK_1D;
if (static_cast<size_t>(_block_size)>gpu->group_size())
_block_size=gpu->group_size();
return true;
}
@ -139,6 +151,7 @@ bool PairGPUDeviceT::init(PairGPUAns<numtyp,acctyp> &ans, const bool charge,
// Initialize atom and nbor data
if (!atom.init(nall,charge,rot,*gpu,gpu_nbor,gpu_nbor && maxspecial>0))
return false;
compile_kernels();
} else
atom.add_fields(charge,rot,gpu_nbor,gpu_nbor && maxspecial);
@ -149,6 +162,7 @@ bool PairGPUDeviceT::init(PairGPUAns<numtyp,acctyp> &ans, const bool charge,
*gpu,gpu_nbor,gpu_host,pre_cut))
return false;
nbor->cell_size(cell_size);
_gpu_overhead=0.0;
_init_count++;
return true;
@ -164,6 +178,7 @@ bool PairGPUDeviceT::init(PairGPUAns<numtyp,acctyp> &ans, const int nlocal,
// Initialize atom and nbor data
if (!atom.init(nall,true,false,*gpu,false,false))
return false;
compile_kernels();
} else
atom.add_fields(true,false,false,false);
@ -214,6 +229,71 @@ void PairGPUDeviceT::init_message(FILE *screen, const char *name,
}
}
template <class numtyp, class acctyp>
void PairGPUDeviceT::estimate_gpu_overhead() {
UCL_H_Vec<int> h_sample_x(1,*gpu), h_sample_q(1,*gpu);
UCL_H_Vec<int> h_sample_quat(1,*gpu), h_sample_ans(1,*gpu);
UCL_D_Vec<int> d_sample_x(1,*gpu), d_sample_q(1,*gpu);
UCL_D_Vec<int> d_sample_quat(1,*gpu), d_sample_ans(1,*gpu);
UCL_Timer x_timer(*gpu), q_timer(*gpu);
UCL_Timer quat_timer(*gpu), ans_timer(*gpu), kernel_timer(*gpu);
UCL_Timer over_timer(*gpu);
h_sample_x[0]=1;
h_sample_q[0]=1;
h_sample_quat[0]=1;
_gpu_overhead=0.0;
for (int i=0; i<10; i++) {
gpu->sync();
gpu_barrier();
over_timer.start();
gpu->sync();
gpu_barrier();
/*
x_timer.start();
ucl_copy(d_sample_x,h_sample_x,true);
x_timer.stop();
if (atom.charge()) {
q_timer.start();
ucl_copy(d_sample_q,h_sample_q,true);
q_timer.stop();
}
if (atom.quat()) {
quat_timer.start();
ucl_copy(d_sample_quat,h_sample_quat,true);
quat_timer.stop();
}
*/
kernel_timer.start();
zero(d_sample_ans,1);
kernel_timer.stop();
ans_timer.start();
ucl_copy(h_sample_ans,d_sample_ans,true);
ans_timer.stop();
over_timer.stop();
/* x_timer.add_to_total();
if (atom.charge())
q_timer.add_to_total();
if (atom.quat())
quat_timer.add_to_total();
*/ kernel_timer.add_to_total();
ans_timer.add_to_total();
double time, mpi_time;
time = over_timer.seconds();
MPI_Allreduce(&time,&mpi_time,1,MPI_DOUBLE,MPI_MAX,gpu_comm());
_gpu_overhead+=mpi_time;
}
if (world_me()==0)
std::cout << "Estimated overhead per timestep: " << _gpu_overhead/10.0
<< " seconds.\n";
}
template <class numtyp, class acctyp>
void PairGPUDeviceT::output_times(UCL_Timer &time_pair,
PairGPUAns<numtyp,acctyp> &ans,
@ -326,6 +406,11 @@ void PairGPUDeviceT::clear() {
if (_init_count==0) {
atom.clear();
_nbor_shared.clear();
if (_compiled) {
k_zero.clear();
delete dev_program;
_compiled=false;
}
}
}
}
@ -340,6 +425,18 @@ void PairGPUDeviceT::clear_device() {
}
}
template <class numtyp, class acctyp>
void PairGPUDeviceT::compile_kernels() {
if (_compiled)
return;
std::string flags="-cl-mad-enable";
dev_program=new UCL_Program(*gpu);
dev_program->load_string(pair_gpu_dev_kernel,flags.c_str());
k_zero.set_function(*dev_program,"kernel_zero");
_compiled=true;
}
template <class numtyp, class acctyp>
double PairGPUDeviceT::host_memory_usage() const {
return atom.host_memory_usage()+4*sizeof(numtyp)+

19
lib/gpu/pair_gpu_device.h
View File

@ -67,6 +67,9 @@ class PairGPUDevice {
void init_message(FILE *screen, const char *name,
const int first_gpu, const int last_gpu);
/// Esimate the overhead from GPU calls from multiple procs
void estimate_gpu_overhead();
/// Output a message with timing information
void output_times(UCL_Timer &time_pair, PairGPUAns<numtyp,acctyp> &ans,
PairGPUNbor &nbor, const double avg_split,
@ -157,6 +160,15 @@ class PairGPUDevice {
/// Return the initialization count for the device
inline int init_count() const { return _init_count; }
// -------------------- SHARED DEVICE ROUTINES --------------------
// Perform asynchronous zero of integer array
void zero(UCL_D_Vec<int> &mem, const int numel) {
int num_blocks=static_cast<int>(ceil(static_cast<double>(numel)/
_block_size));
k_zero.set_size(num_blocks,_block_size);
k_zero.run(&mem.begin(),&numel);
}
// -------------------------- DEVICE DATA -------------------------
/// Geryon Device
@ -184,6 +196,13 @@ class PairGPUDevice {
int _gpu_mode, _first_device, _last_device, _nthreads;
double _particle_split;
double _cpu_full;
double _gpu_overhead;
int _block_size;
UCL_Program *dev_program;
UCL_Kernel k_zero;
bool _compiled;
void compile_kernels();
template <class t>
inline std::string toa(const t& in) {