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Merge pull request #48 from rusty1s/graph_saint
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2 parents a1ae903 + a597b82 commit 6b4d97f

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13 files changed

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13 files changed

+378
-51
lines changed

‎csrc/cpu/rw_cpu.cpp

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#include "rw_cpu.h"
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#include "utils.h"
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torch::Tensor random_walk_cpu(torch::Tensor rowptr, torch::Tensor col,
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torch::Tensor start, int64_t walk_length) {
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CHECK_CPU(rowptr);
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CHECK_CPU(col);
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CHECK_CPU(start);
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CHECK_INPUT(rowptr.dim() == 1);
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CHECK_INPUT(col.dim() == 1);
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CHECK_INPUT(start.dim() == 1);
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auto rand = torch::rand({start.size(0), walk_length},
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start.options().dtype(torch::kFloat));
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auto L = walk_length + 1;
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auto out = torch::full({start.size(0), L}, -1, start.options());
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auto rowptr_data = rowptr.data_ptr<int64_t>();
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auto col_data = col.data_ptr<int64_t>();
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auto start_data = start.data_ptr<int64_t>();
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auto rand_data = rand.data_ptr<float>();
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auto out_data = out.data_ptr<int64_t>();
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for (auto n = 0; n < start.size(0); n++) {
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auto cur = start_data[n];
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out_data[n * L] = cur;
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int64_t row_start, row_end;
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for (auto l = 0; l < walk_length; l++) {
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row_start = rowptr_data[cur];
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row_end = rowptr_data[cur + 1];
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cur = col_data[row_start + int64_t(rand_data[n * walk_length + l] *
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(row_end - row_start))];
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out_data[n * L + l + 1] = cur;
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}
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}
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return out;
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}

‎csrc/cpu/rw_cpu.h

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#pragma once
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#include <torch/extension.h>
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torch::Tensor random_walk_cpu(torch::Tensor rowptr, torch::Tensor col,
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torch::Tensor start, int64_t walk_length);

‎csrc/cpu/saint_cpu.cpp

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#include "saint_cpu.h"
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#include "utils.h"
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std::tuple<torch::Tensor, torch::Tensor, torch::Tensor>
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subgraph_cpu(torch::Tensor idx, torch::Tensor rowptr, torch::Tensor row,
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torch::Tensor col) {
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CHECK_CPU(idx);
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CHECK_CPU(rowptr);
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CHECK_CPU(col);
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CHECK_INPUT(idx.dim() == 1);
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CHECK_INPUT(rowptr.dim() == 1);
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CHECK_INPUT(col.dim() == 1);
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auto assoc = torch::full({rowptr.size(0) - 1}, -1, idx.options());
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assoc.index_copy_(0, idx, torch::arange(idx.size(0), idx.options()));
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auto idx_data = idx.data_ptr<int64_t>();
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auto rowptr_data = rowptr.data_ptr<int64_t>();
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auto col_data = col.data_ptr<int64_t>();
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auto assoc_data = assoc.data_ptr<int64_t>();
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std::vector<int64_t> rows, cols, indices;
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int64_t v, w, w_new, row_start, row_end;
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for (int64_t v_new = 0; v_new < idx.size(0); v_new++) {
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v = idx_data[v_new];
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row_start = rowptr_data[v];
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row_end = rowptr_data[v + 1];
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for (int64_t j = row_start; j < row_end; j++) {
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w = col_data[j];
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w_new = assoc_data[w];
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if (w_new > -1) {
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rows.push_back(v_new);
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cols.push_back(w_new);
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indices.push_back(j);
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}
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}
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}
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int64_t length = rows.size();
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row = torch::from_blob(rows.data(), {length}, row.options()).clone();
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col = torch::from_blob(cols.data(), {length}, row.options()).clone();
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idx = torch::from_blob(indices.data(), {length}, row.options()).clone();
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return std::make_tuple(row, col, idx);
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}

‎csrc/cpu/saint_cpu.h

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#pragma once
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#include <torch/extension.h>
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std::tuple<torch::Tensor, torch::Tensor, torch::Tensor>
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subgraph_cpu(torch::Tensor idx, torch::Tensor rowptr, torch::Tensor row,
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torch::Tensor col);

‎csrc/cuda/rw_cuda.cu

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#include "rw_cuda.h"
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#include <ATen/cuda/CUDAContext.h>
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#include "utils.cuh"
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#define THREADS 1024
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#define BLOCKS(N) (N + THREADS - 1) / THREADS
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__global__ void uniform_random_walk_kernel(const int64_t *rowptr,
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const int64_t *col,
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const int64_t *start,
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const float *rand, int64_t *out,
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int64_t walk_length, int64_t numel) {
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const int64_t thread_idx = blockIdx.x * blockDim.x + threadIdx.x;
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if (thread_idx < numel) {
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int64_t cur = start[thread_idx];
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out[thread_idx] = cur;
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int64_t row_start, row_end;
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for (int64_t l = 0; l < walk_length; l++) {
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row_start = rowptr[cur], row_end = rowptr[cur + 1];
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cur = col[row_start +
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int64_t(rand[l * numel + thread_idx] * (row_end - row_start))];
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out[(l + 1) * numel + thread_idx] = cur;
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}
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}
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}
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torch::Tensor random_walk_cuda(torch::Tensor rowptr, torch::Tensor col,
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torch::Tensor start, int64_t walk_length) {
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CHECK_CUDA(rowptr);
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CHECK_CUDA(col);
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CHECK_CUDA(start);
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cudaSetDevice(rowptr.get_device());
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CHECK_INPUT(rowptr.dim() == 1);
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CHECK_INPUT(col.dim() == 1);
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CHECK_INPUT(start.dim() == 1);
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auto rand = torch::rand({walk_length, start.size(0)},
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start.options().dtype(torch::kFloat));
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auto out = torch::full({walk_length + 1, start.size(0)}, -1, start.options());
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auto stream = at::cuda::getCurrentCUDAStream();
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uniform_random_walk_kernel<<<BLOCKS(start.numel()), THREADS, 0, stream>>>(
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rowptr.data_ptr<int64_t>(), col.data_ptr<int64_t>(),
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start.data_ptr<int64_t>(), rand.data_ptr<float>(),
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out.data_ptr<int64_t>(), walk_length, start.numel());
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return out.t().contiguous();
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}

‎csrc/cuda/rw_cuda.h

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#pragma once
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#include <torch/extension.h>
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torch::Tensor random_walk_cuda(torch::Tensor rowptr, torch::Tensor col,
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torch::Tensor start, int64_t walk_length);

‎csrc/rw.cpp

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#include <Python.h>
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#include <torch/script.h>
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#include "cpu/rw_cpu.h"
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#ifdef WITH_CUDA
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#include "cuda/rw_cuda.h"
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#endif
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#ifdef _WIN32
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PyMODINIT_FUNC PyInit__rw(void) { return NULL; }
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#endif
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torch::Tensor random_walk(torch::Tensor rowptr, torch::Tensor col,
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torch::Tensor start, int64_t walk_length) {
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if (rowptr.device().is_cuda()) {
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#ifdef WITH_CUDA
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return random_walk_cuda(rowptr, col, start, walk_length);
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#else
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AT_ERROR("Not compiled with CUDA support");
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#endif
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} else {
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return random_walk_cpu(rowptr, col, start, walk_length);
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}
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}
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static auto registry =
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torch::RegisterOperators().op("torch_sparse::random_walk", &random_walk);

‎csrc/saint.cpp

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#include <Python.h>
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#include <torch/script.h>
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#include "cpu/saint_cpu.h"
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#ifdef _WIN32
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PyMODINIT_FUNC PyInit__saint(void) { return NULL; }
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#endif
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std::tuple<torch::Tensor, torch::Tensor, torch::Tensor>
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subgraph(torch::Tensor idx, torch::Tensor rowptr, torch::Tensor row,
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torch::Tensor col) {
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if (idx.device().is_cuda()) {
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#ifdef WITH_CUDA
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AT_ERROR("No CUDA version supported");
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#else
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AT_ERROR("Not compiled with CUDA support");
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#endif
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} else {
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return subgraph_cpu(idx, rowptr, row, col);
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}
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}
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static auto registry =
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torch::RegisterOperators().op("torch_sparse::saint_subgraph", &subgraph);

‎test/test_saint.py

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import torch
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from torch_sparse.tensor import SparseTensor
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def test_saint_subgraph():
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row = torch.tensor([0, 0, 1, 1, 2, 2, 2, 3, 3, 4])
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col = torch.tensor([1, 2, 0, 2, 0, 1, 3, 2, 4, 3])
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adj = SparseTensor(row=row, col=col)
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node_idx = torch.tensor([0, 1, 2])
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adj, edge_index = adj.saint_subgraph(node_idx)

‎torch_sparse/__init__.py

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try:
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for library in [
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'_version', '_convert', '_diag', '_spmm', '_spspmm', '_metis'
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'_version', '_convert', '_diag', '_spmm', '_spspmm', '_metis',
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'_rw', '_saint'
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]:
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torch.ops.load_library(importlib.machinery.PathFinder().find_spec(
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library, [osp.dirname(__file__)]).origin)
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from .reduce import sum, mean, min, max # noqa
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from .matmul import matmul # noqa
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from .cat import cat, cat_diag # noqa
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from .rw import random_walk # noqa
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from .metis import partition # noqa
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from .saint import saint_subgraph # noqa
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from .convert import to_torch_sparse, from_torch_sparse # noqa
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from .convert import to_scipy, from_scipy # noqa
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'matmul',
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'cat',
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'cat_diag',
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'random_walk',
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'partition',
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'saint_subgraph',
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'to_torch_sparse',
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'from_torch_sparse',
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'to_scipy',

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