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v3.cu
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#include <stdio.h>
#include <cmath>
#include <iostream>
#include <vector>
#include <unordered_map>
#include <fstream>
#include <string>
#include <sstream>
#include <cstdlib> // for rand() and srand()
#include <ctime> // for time()
#include <stdexcept>
using namespace std;
#define CHECK(call) \
do \
{ \
const cudaError_t error_code = call; \
if (error_code != cudaSuccess) \
{ \
printf("CUDA Error:\n"); \
printf(" File: %s\n", __FILE__); \
printf(" Line: %d\n", __LINE__); \
printf(" Error code: %d\n", error_code); \
printf(" Error text: %s\n", \
cudaGetErrorString(error_code)); \
exit(1); \
} \
} while (0)
template <typename DataType>
class Kmeans
{
public:
Kmeans(int num_clusters, int num_features, DataType *clusters, int num_samples);
Kmeans(int num_clusters, int num_features, DataType *clusters, int num_samples, int max_iters, float eplison);
virtual ~Kmeans();
void getDistance(const DataType *v_data);
void updateClusters(const DataType *v_data);
virtual void fit(const DataType *v_data);
float accuracy(int *v_label);
DataType *m_clusters; //[num_clusters, num_features]
int m_num_clusters;
int m_num_features;
float *m_distances; // [num_samples, num_clusters]
int *m_sampleClasses; // [num_samples, ]
int m_num_samples;
float m_optTarget;
int m_max_iters;
float m_epsilon;
private:
Kmeans(const Kmeans &model);
Kmeans &operator=(const Kmeans &model);
};
template <typename DataType>
Kmeans<DataType>::Kmeans(int numClusters, int numFeatures, DataType *clusters, int nsamples) : m_num_clusters(numClusters), m_num_features(numFeatures), m_max_iters(50),
m_optTarget(1e7), m_epsilon(0.001), m_num_samples(nsamples)
{
m_clusters = new float[numClusters * numFeatures];
for (int i = 0; i < this->m_num_clusters * this->m_num_features; ++i)
{
this->m_clusters[i] = clusters[i];
}
m_distances = new float[nsamples * numClusters]{0.0};
m_sampleClasses = new int[nsamples]{0};
}
template <typename DataType>
Kmeans<DataType>::Kmeans(int numClusters, int numFeatures, DataType *clusters, int nsamples,
int maxIters, float epsilon) : m_num_clusters(numClusters), m_num_features(numFeatures), m_max_iters(maxIters),
m_optTarget(1e7), m_epsilon(epsilon), m_num_samples(nsamples)
{
m_clusters = new float[numClusters * numFeatures];
for (int i = 0; i < this->m_num_clusters * this->m_num_features; ++i)
{
this->m_clusters[i] = clusters[i];
}
m_distances = new float[nsamples * numClusters]{0.0};
m_sampleClasses = new int[nsamples]{0};
}
template <typename DataType>
Kmeans<DataType>::~Kmeans()
{
if (m_clusters)
delete[] m_clusters;
if (m_distances)
delete[] m_distances;
if (m_sampleClasses)
delete[] m_sampleClasses;
}
template <typename DataType>
void Kmeans<DataType>::getDistance(const DataType *v_data)
{
/*
v_data: [nsamples, numFeatures, ]
*/
float loss = 0.0;
for (int i = 0; i < m_num_samples; ++i)
{
float minDist = 1e8;
int minIdx = -1;
for (int j = 0; j < m_num_clusters; ++j)
{
float sum = 0.0;
for (int k = 0; k < m_num_features; ++k)
{
sum += (v_data[i * m_num_features + k] - m_clusters[j * m_num_features + k]) *
(v_data[i * m_num_features + k] - m_clusters[j * m_num_features + k]);
}
this->m_distances[i * m_num_clusters + j] = sqrt(sum);
if (sum <= minDist)
{
minDist = sum;
minIdx = j;
}
}
m_sampleClasses[i] = minIdx;
loss += m_distances[i * m_num_clusters + minIdx];
}
m_optTarget = loss;
}
template <typename DataType>
void Kmeans<DataType>::updateClusters(const DataType *v_data)
{
for (int i = 0; i < m_num_clusters * m_num_features; ++i)
this->m_clusters[i] = 0.0;
for (int i = 0; i < m_num_clusters; ++i)
{
int cnt = 0;
for (int j = 0; j < m_num_samples; ++j)
{
if (i != m_sampleClasses[j])
continue;
for (int k = 0; k < m_num_features; ++k)
{
this->m_clusters[i * m_num_features + k] += v_data[j * m_num_features + k];
}
cnt++;
}
for (int ii = 0; ii < m_num_features; ii++)
this->m_clusters[i * m_num_features + ii] /= cnt;
}
}
template <typename DataType>
void Kmeans<DataType>::fit(const DataType *v_data)
{
float lastLoss = this->m_optTarget;
for (int i = 0; i < m_max_iters; ++i)
{
this->getDistance(v_data);
this->updateClusters(v_data);
if (std::abs(lastLoss - this->m_optTarget) < this->m_epsilon)
{
std::cout << "迭代步长已经小于epsilon!!!" << std::endl;
break;
}
lastLoss = this->m_optTarget;
std::cout << "Iters: " << i + 1 << " current loss : " << m_optTarget << std::endl;
}
}
template <typename DataType>
float Kmeans<DataType>::accuracy(int *v_label)
{
// map clusters to labels
int *mappedLabels = new int[this->m_num_samples];
for (int clusterNum = 0; clusterNum < this->m_num_clusters; clusterNum++)
{
std::vector<int> clusterIndices;
// 找到属于当前簇的数据点的索引
for (size_t i = 0; i < this->m_num_samples; ++i)
{
if (this->m_sampleClasses[i] == clusterNum)
{
clusterIndices.push_back(i);
}
}
// 统计当前簇中真实标签出现的频率
std::unordered_map<int, int> labelFreq;
for (int index : clusterIndices)
{
++labelFreq[v_label[index]];
}
// 找到当前簇中出现频率最高的真实标签
int mostFrequentLabel = -1;
int maxFreq = 0;
for (const auto &pair : labelFreq)
{
if (pair.second > maxFreq)
{
mostFrequentLabel = pair.first;
maxFreq = pair.second;
}
}
// 将当前簇中的标签映射为出现频率最高的真实标签
for (int index : clusterIndices)
{
mappedLabels[index] = mostFrequentLabel;
}
}
int count = 0;
for (int i = 0; i < this->m_num_samples; i++)
{
// if(i < 100){
// std::cout << "--------------------------------------------------------" << std:: endl;
// std::cout << "m_sampleClasses[i]: " << m_sampleClasses[i] << std::endl;
// std::cout << "v_label[i]: " << v_label[i] << std::endl;
// }
if (v_label[i] == mappedLabels[i])
count++;
}
float res = float(count) / float(this->m_num_samples);
return res;
}
template <typename DataType>
class KmeansGPUV3 : public Kmeans<DataType>
{
public:
KmeansGPUV3(int num_clusters, int num_features, DataType *clusters, int num_samples);
KmeansGPUV3(int num_clusters, int num_features, DataType *clusters, int num_samples,
int max_iters, float eplison);
virtual ~KmeansGPUV3();
void fit(const DataType *v_data);
DataType *d_data; // [num_samples, num_features]
DataType *d_clusters; // [num_clusters, num_features]
int *d_sampleClasses; // [num_samples, ]
float *d_min_dist; // [num_samples, ]
float *d_loss; // [num_samples, ]
int *d_cluster_size; //[num_clusters, ]
cudaStream_t calculate_stream;
cudaStream_t update_stream;
cudaEvent_t calculate_event;
cudaEvent_t update_event;
private:
KmeansGPUV3(const Kmeans<DataType> &model);
KmeansGPUV3 &operator=(const Kmeans<DataType> &model);
};
template <typename DataType>
KmeansGPUV3<DataType>::KmeansGPUV3(int num_clusters, int num_features, DataType *clusters, int num_samples,
int max_iters, float eplison)
: Kmeans<DataType>(num_clusters, num_features, clusters, num_samples, max_iters, eplison)
{
CHECK(cudaStreamCreate(&calculate_stream));
CHECK(cudaStreamCreate(&update_stream));
CHECK(cudaEventCreate(&calculate_event));
CHECK(cudaEventCreate(&update_event));
int data_buf_size = this->m_num_samples * this->m_num_features;
int cluster_buf_size = this->m_num_clusters * this->m_num_features;
int mem_size = sizeof(DataType) * (data_buf_size + cluster_buf_size) + sizeof(int) * (this->m_num_samples) +
sizeof(float) * (this->m_num_samples + this->m_num_samples) + sizeof(int) * this->m_num_clusters;
CHECK(cudaMallocAsync((void **)&d_data, mem_size, calculate_stream));
d_clusters = (DataType *)(d_data + data_buf_size);
d_sampleClasses = (int *)(d_clusters + cluster_buf_size);
d_min_dist = (float *)(d_sampleClasses + this->m_num_samples);
d_loss = (float *)(d_min_dist + this->m_num_samples);
d_cluster_size = (int *)(d_loss + this->m_num_samples);
CHECK(cudaMemcpyAsync(d_clusters, this->m_clusters, sizeof(DataType) * cluster_buf_size, cudaMemcpyHostToDevice, update_stream));
CHECK(cudaEventRecord(update_event, update_stream));
printf("num_samples: %d num_clusters: %d num_features: %d\n", num_samples, num_clusters, num_features);
}
template <typename DataType>
KmeansGPUV3<DataType>::~KmeansGPUV3()
{
CHECK(cudaFreeAsync(d_data, calculate_stream));
CHECK(cudaStreamDestroy(calculate_stream));
CHECK(cudaStreamDestroy(update_stream));
CHECK(cudaEventDestroy(calculate_event));
CHECK(cudaEventDestroy(update_event));
}
template <typename DataType>
__global__ void initV2(DataType *x, const DataType value, const int N)
{
const int n = threadIdx.x + blockIdx.x * blockDim.x;
if (n < N)
x[n] = value;
}
template <typename T>
struct SumOp
{
__device__ __forceinline__ T operator()(const T &a, const T &b) const { return a + b; }
};
template <template <typename> class ReductionOp, typename T>
__inline__ __device__ T WarpReduce(T val)
{
auto func = ReductionOp<T>();
#pragma unroll
for (int mask = 16; mask > 0; mask >>= 1)
{
val = func(val, __shfl_xor_sync(0xffffffff, val, mask, 32));
}
return val;
}
template <template <typename> class ReductionOp, typename T>
__inline__ __device__
T
blockReduce(T val)
{
static __shared__ T shared[32];
int lane = threadIdx.x & 0x1f;
int wid = threadIdx.x >> 5;
val = WarpReduce<ReductionOp, T>(val);
if (lane == 0)
shared[wid] = val;
__syncthreads();
val = (threadIdx.x < (blockDim.x >> 5)) ? shared[lane] : (T)0.0f;
val = WarpReduce<ReductionOp, T>(val);
return val;
}
template <template <typename> class ReductionOp>
__global__ void vec1DReduce(float *vec, float *reduce, const int N)
{
int n = blockDim.x * blockIdx.x + threadIdx.x;
float val = 0.0f;
auto func = ReductionOp<float>();
#pragma unroll
for (; n < N; n += blockDim.x * gridDim.x)
val = func(val, vec[n]);
__syncthreads();
float block_sum = blockReduce<ReductionOp, float>(val);
if (threadIdx.x == 0)
reduce[blockIdx.x] = block_sum;
}
template <typename DataType>
__global__ void update(
const DataType *d_data,
DataType *d_clusters,
int *d_sampleClasses,
int *d_cluster_size,
const int num_samples,
const int num_features)
{
// grid_size = num_samples, block_size = block_size
int clusterId = d_sampleClasses[blockIdx.x];
int clustercnt = d_cluster_size[clusterId];
#pragma unroll
for (int i = threadIdx.x; i < num_features; i += blockDim.x)
{
atomicAdd(&(d_clusters[clusterId * num_features + i]), d_data[num_features * blockIdx.x + i] / clustercnt);
}
}
constexpr int kMaxPackBytes = 128 / 8; // CUDA 最多支持 128 个 bit 的访问粒度
constexpr int kMaxPackSize = 8; // half 类型占 2 个字节,也就是 16 个 bit,所以最大可以 Pack 的数量为 128 / 16 = 8
constexpr int Min(int a, int b)
{
return a < b ? a : b;
}
template <typename T>
constexpr int PackSize()
{
return Min(kMaxPackBytes / sizeof(T), kMaxPackSize);
}
template <typename T, typename U, typename... Args>
constexpr int PackSize()
{
return Min(PackSize<T>(), PackSize<U, Args...>());
}
template <typename T, int N>
struct GetPackType
{
using type = typename std::aligned_storage<N * sizeof(T), N * sizeof(T)>::type;
};
template <typename T, int N>
using PackType = typename GetPackType<T, N>::type;
template <typename T, int pack_size>
struct alignas(sizeof(T) * pack_size) Packed
{
__device__ Packed()
{
// do nothing
}
union
{
PackType<T, pack_size> storage;
T elem[pack_size];
};
};
template <typename DataType, int pack_size>
__device__ float calDistPacked(const DataType *d_data,
const DataType *d_clusters, // [num_clusters, num_features]
const int clusterNo, const int num_features)
{
// grid_size = num_samples, block_size = 128
const int sample_offset = num_features * blockIdx.x;
const int cluster_offset = num_features * clusterNo;
const PackType<DataType, pack_size> *buf = reinterpret_cast<const PackType<DataType, pack_size> *>(d_data + sample_offset);
const PackType<DataType, pack_size> *cluster_buf = reinterpret_cast<const PackType<DataType, pack_size> *>(d_clusters + cluster_offset);
int num_packs = num_features / pack_size;
float distance = 0.0f;
float sub_val;
Packed<DataType, pack_size> data_pack;
Packed<DataType, pack_size> cluster_pack;
#pragma unroll
for (int pack_id = threadIdx.x; pack_id < num_packs; pack_id += blockDim.x)
{
data_pack.storage = *(buf + pack_id);
cluster_pack.storage = *(cluster_buf + pack_id);
#pragma unroll
for (int elem_id = 0; elem_id < pack_size; ++elem_id)
{
sub_val = (float)(data_pack.elem[elem_id] - cluster_pack.elem[elem_id]);
distance += sub_val * sub_val;
}
}
__syncthreads();
distance = blockReduce<SumOp, float>(distance);
return distance;
}
template <typename DataType, int pack_size>
__global__ void calClustersDistPackedkernel(const DataType *d_data,
const DataType *d_clusters, // [num_clusters, num_features]
int *d_sample_classes, // [nsamples, ]
float *d_min_dist, // [nsamples, ]
int *d_clusterSize, // [nsamples, ]
const int num_features,
const int num_clusters)
{
// grid_size = num_samples, block_size = 256
float min_dist = 1e9f;
float dist;
int min_idx;
#pragma unroll
for (int i = 0; i < num_clusters; ++i)
{
dist = calDistPacked<DataType, pack_size>(d_data, d_clusters, i, num_features);
if (dist < min_dist)
{
min_dist = dist;
min_idx = i;
}
}
if (threadIdx.x == 0)
{
d_sample_classes[blockIdx.x] = min_idx;
d_min_dist[blockIdx.x] = sqrtf(min_dist);
atomicAdd(&(d_clusterSize[min_idx]), 1);
}
}
template <typename DataType>
void launchFit(const DataType *d_data, DataType *d_clusters, int *d_sample_classes,
int *d_cluster_size, float *d_min_dist, float *d_loss, const int num_clusters,
const int num_samples, const int num_features, cudaStream_t calculate_stream,
cudaStream_t update_stream, cudaEvent_t calculate_event, cudaEvent_t update_event)
{
CHECK(cudaStreamWaitEvent(calculate_stream, update_event));
initV2<int><<<1, 1024, 0, calculate_stream>>>(d_cluster_size, 0.0f, num_clusters);
const int block_size = 32;
if (num_features % 4)
{
calClustersDistPackedkernel<DataType, 1><<<num_samples, block_size, 0, calculate_stream>>>(d_data, d_clusters,
d_sample_classes, d_min_dist, d_cluster_size, num_features, num_clusters);
}
else
{
calClustersDistPackedkernel<DataType, 4><<<num_samples, block_size, 0, calculate_stream>>>(d_data, d_clusters,
d_sample_classes, d_min_dist, d_cluster_size, num_features, num_clusters);
}
CHECK(cudaEventRecord(calculate_event, calculate_stream));
vec1DReduce<SumOp><<<block_size, block_size, 0, calculate_stream>>>(d_min_dist, d_loss, num_samples);
vec1DReduce<SumOp><<<1, block_size, 0, calculate_stream>>>(d_loss, d_loss, block_size);
CHECK(cudaStreamWaitEvent(update_stream, calculate_event));
initV2<DataType><<<1, 1024, 0, update_stream>>>(d_clusters, 0.0f, num_clusters * num_features);
update<DataType><<<num_samples, block_size, 0, update_stream>>>(d_data, d_clusters,
d_sample_classes, d_cluster_size, num_samples, num_features);
CHECK(cudaEventRecord(update_event, update_stream));
}
template <typename DataType>
void KmeansGPUV3<DataType>::fit(const DataType *v_data)
{
float *h_loss = new float[this->m_num_samples]{0.0};
CHECK(cudaMemcpyAsync(d_data, v_data, sizeof(DataType) * this->m_num_samples * this->m_num_features, cudaMemcpyHostToDevice, calculate_stream));
float lastLoss = 0;
for (int i = 0; i < this->m_max_iters; ++i)
{
launchFit<DataType>(d_data, d_clusters, d_sampleClasses, d_cluster_size, d_min_dist, d_loss,
this->m_num_clusters, this->m_num_samples, this->m_num_features, calculate_stream, update_stream,
calculate_event, update_event);
CHECK(cudaMemcpyAsync(h_loss, d_loss, sizeof(float) * this->m_num_samples, cudaMemcpyDeviceToHost, calculate_stream));
CHECK(cudaStreamSynchronize(calculate_stream));
this->m_optTarget = h_loss[0];
// if (std::abs(lastLoss - this->m_optTarget) < this->m_epsilon)
// {
// std::cout << "迭代步长已经小于epsilon!!!" << std::endl;
// break;
// }
lastLoss = this->m_optTarget;
std::cout << "Iters: " << i + 1 << " current loss : " << this->m_optTarget << std::endl;
}
CHECK(cudaMemcpyAsync(this->m_clusters, d_clusters, sizeof(DataType) * this->m_num_clusters * this->m_num_features, cudaMemcpyDeviceToHost, calculate_stream));
CHECK(cudaMemcpyAsync(this->m_sampleClasses, d_sampleClasses, sizeof(int) * this->m_num_samples, cudaMemcpyDeviceToHost, calculate_stream));
delete[] h_loss;
}
void readCoordinate(float *data, int *label, const int n_features, int &n, string file)
{
std::ifstream ifs;
ifs.open(file, std::ios::in);
if (ifs.fail())
{
std::cout << "No such file or directory: " << file << std::endl;
exit(1);
}
std::string line;
while (std::getline(ifs, line))
{
std::stringstream sstream(line);
if (line.empty())
continue;
int m = 0;
std::string s_fea;
while (std::getline(sstream, s_fea, ','))
{
if (m < n_features)
data[n * n_features + m] = std::stod(s_fea);
else
label[n] = std::stoi(s_fea);
m++;
}
n++;
}
ifs.close();
}
template <typename T>
void printVecInVec(const T *vecInVec, int rows, int cols, const std::string &title)
{
std::cout << title << ":" << std::endl;
for (int i = 0; i < rows; ++i)
{
for (int j = 0; j < cols; ++j)
{
std::cout << vecInVec[i * cols + j] << " ";
}
std::cout << std::endl;
}
}
template <typename DataType>
void timing(
DataType *data,
int *label,
DataType *clusters,
const int numClusters,
const int n_features,
const int n_samples,
const int method)
{
Kmeans<DataType> *model;
switch (method)
{
case 0:
model = new Kmeans<DataType>(numClusters, n_features, clusters, n_samples, 50, 1e-5);
break;
case 1:
model = new KmeansGPUV3<DataType>(numClusters, n_features, clusters, n_samples, 50, 1e-5);
break;
default:
break;
}
std::cout << "*********starting fitting*********" << std::endl;
cudaEvent_t start, stop;
CHECK(cudaEventCreate(&start));
CHECK(cudaEventCreate(&stop));
CHECK(cudaEventRecord(start));
cudaEventQuery(start);
model->fit(data);
CHECK(cudaEventRecord(stop));
CHECK(cudaEventSynchronize(stop));
float elapsedTime;
CHECK(cudaEventElapsedTime(&elapsedTime, start, stop));
CHECK(cudaEventDestroy(start));
CHECK(cudaEventDestroy(stop));
printf("Time = %g ms.\n", elapsedTime);
// std::cout << "********* final clusters**********" << std::endl;
// printVecInVec<float>(model->m_clusters, numClusters, n_features, "clusters");
std::cout << "********* accuracy **********" << std::endl;
std::cout << "model accuracy : " << model->accuracy(label) << std::endl;
printVecInVec<int>(model->m_sampleClasses, 1, 10, "sampleClasses_10");
delete model;
}
void launch_kmeans(
float *data,
const int n_clusters,
const int n_samples,
const int n_features
)
{
int* cidx = new int[n_clusters];
float* centroids = new float[n_clusters * n_features];
srand(time(NULL));
for (int i = 0; i < n_clusters; i++)
cidx[i] = rand() % n_samples;
for (int i = 0; i < n_clusters; i++)
{
for (int j = 0; j < n_features; j++)
{
centroids[i * n_features + j] = data[cidx[i] * n_features + j];
}
}
Kmeans<float> *model = new KmeansGPUV3<float>(n_clusters, n_features, centroids, n_samples, 50, 1e-5);
cudaEvent_t start, stop;
CHECK(cudaEventCreate(&start));
CHECK(cudaEventCreate(&stop));
CHECK(cudaEventRecord(start));
cudaEventQuery(start);
model->fit(data);
CHECK(cudaEventRecord(stop));
CHECK(cudaEventSynchronize(stop));
float elapsedTime;
CHECK(cudaEventElapsedTime(&elapsedTime, start, stop));
CHECK(cudaEventDestroy(start));
CHECK(cudaEventDestroy(stop));
printf("Time = %g ms.\n", elapsedTime);
delete model;
}
int main()
{
string file = "/home/gg/Desktop/kmeans/data/test_samples.csv";
int N = 0; // 实际读取的样本数量
const int n_nums = 100; // 数据中,有100个样本
const int n_features = 256; // 每个样本有4个特征
const int n_classes = 256;
float *data = new float[n_features * n_nums];
int *label = new int[n_nums];
readCoordinate(data, label, n_features, N, file);
std::cout << "num of samples : " << N << std::endl;
// 数据初始化
int cidx[n_classes] = {0};
srand(time(NULL));
for (int i = 0; i < n_classes; i++)
cidx[i] = rand() % n_nums;
float clusters[n_classes * n_features] = {0};
for (int i = 0; i < n_classes; i++)
{
for (int j = 0; j < n_features; j++)
{
clusters[i * n_features + j] = data[cidx[i] * n_features + j];
}
}
// printVecInVec<float>(clusters, n_classes, n_features, "clusters");
// std::cout << "Using CPU:" << std::endl;
// timing<float>(data, label, clusters, n_classes, n_features, N, 0);
std::cout << "Using CUDA:" << std::endl;
timing<float>(data, label, clusters, n_classes, n_features, N, 1);
delete[] data;
delete[] label;
return 0;
}