diff --git a/.gitignore b/.gitignore index d4e726d..5b158d8 100644 --- a/.gitignore +++ b/.gitignore @@ -285,3 +285,8 @@ ipython_config.py # Remove previous ipynb_checkpoints # git rm -r .ipynb_checkpoints/ + +# We do not include any matrix data since it can be quite large. +# Instead there are urls to where to download the data in the repo +*.bin +*.mtx diff --git a/go.sum b/go.sum index d45948d..540c822 100644 --- a/go.sum +++ b/go.sum @@ -1,2 +1,49 @@ +dmitri.shuralyov.com/gpu/mtl v0.0.0-20201218220906-28db891af037/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU= +github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo= +github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af/go.mod h1:K08gAheRH3/J6wwsYMMT4xOr94bZjxIelGM0+d/wbFw= +github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90/go.mod h1:R/bRT+9gY/C5z7JzPU0zXsXHKM4/ayA+zqcVNZzPa1k= +github.com/go-gl/glfw/v3.3/glfw 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v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= +golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= +gonum.org/v1/gonum v0.0.0-20180816165407-929014505bf4/go.mod h1:Y+Yx5eoAFn32cQvJDxZx5Dpnq+c3wtXuadVZAcxbbBo= +gonum.org/v1/gonum v0.8.2/go.mod h1:oe/vMfY3deqTw+1EZJhuvEW2iwGF1bW9wwu7XCu0+v0= gonum.org/v1/gonum v0.17.0 h1:VbpOemQlsSMrYmn7T2OUvQ4dqxQXU+ouZFQsZOx50z4= gonum.org/v1/gonum v0.17.0/go.mod h1:El3tOrEuMpv2UdMrbNlKEh9vd86bmQ6vqIcDwxEOc1E= +gonum.org/v1/netlib v0.0.0-20190313105609-8cb42192e0e0/go.mod h1:wa6Ws7BG/ESfp6dHfk7C6KdzKA7wR7u/rKwOGE66zvw= +gonum.org/v1/plot v0.0.0-20190515093506-e2840ee46a6b/go.mod h1:Wt8AAjI+ypCyYX3nZBvf6cAIx93T+c/OS2HFAYskSZc= +rsc.io/pdf v0.1.1/go.mod h1:n8OzWcQ6Sp37PL01nO98y4iUCRdTGarVfzxY20ICaU4= diff --git a/src/main.go b/src/main.go index 4f1a6ce..370f87b 100644 --- a/src/main.go +++ b/src/main.go @@ -3,88 +3,104 @@ package main import ( "bufio" "fmt" - "io" "os" "strconv" "strings" + "time" "github.com/james-bowman/sparse" - "gonum.org/v1/gonum/mat" ) -func matrix_read_market(path string) (*sparse.CSR, error) { +// The "SuiteSparse" collection of matrices come in a format called +// "market matrix" and so we parse and load them to a sparse.COO format here. +func matrix_load_market(path string) *sparse.COO { f, err := os.Open(path) if err != nil { - return nil, fmt.Errorf("open %q: %w", path, err) + panic(err) } - defer f.Close() - sc := bufio.NewScanner(f) + scanner := bufio.NewScanner(f) - const maxCapacity = 1024 * 1024 // Long lines - buf := make([]byte, 64*1024) - sc.Buffer(buf, maxCapacity) + // skip header + scanner.Scan() - if !sc.Scan() { - if err := sc.Err(); err != nil { - return nil, fmt.Errorf("read header: %w", err) + // skip comments + for scanner.Scan() { + line := scanner.Text() + if !strings.HasPrefix(line, "%") { + break } - return nil, fmt.Errorf("empty file!") } - header := strings.Fields(strings.TrimSpace(sc.Text())) - if len(header) != 5 || header[0] != "%%MatrixMarket" { - return nil, fmt.Errorf("invalid matrix martket header: %q", sc.Text()) + fields := strings.Fields(scanner.Text()) + + rows, _ := strconv.Atoi(fields[0]) + cols, _ := strconv.Atoi(fields[1]) + nnz, _ := strconv.Atoi(fields[2]) + + r := make([]int, nnz) + c := make([]int, nnz) + v := make([]float64, nnz) + + i := 0 + + for scanner.Scan() { + f := strings.Fields(scanner.Text()) + + ri, _ := strconv.Atoi(f[0]) + ci, _ := strconv.Atoi(f[1]) + val, _ := strconv.ParseFloat(f[2], 64) + + r[i] = ri - 1 + c[i] = ci - 1 + v[i] = val + i++ } - object := strings.ToLower(header[1]) - format := strings.ToLower(header[2]) - field := strings.ToLower(header[3]) - symmetry := strings.ToLower(header[4]) + coo := sparse.NewCOO(rows, cols, r, c, v) - if object != "matrix" { - return nil, fmt.Errorf("unsupported object: %q", object) - } - if format != "coordinate" { - return nil, fmt.Errorf("unsupported format %q (need coordinate)", format) - } - - switch field { - case "real", "integer", "pattern": - default: - return nil, fmt.Errorf("unsupported field %q", field) - } - - switch symmetry { - case "general", "symmetric": - default: - return nil, fmt.Errorf("unsupported symmetry %q", symmetry) - } - - // Skip comments and then read the size line - var size_line string - for sc.Scan() { - line := strings.TrimSpace(sc.Text()) - if line == "" || strings.HasPrefix(line, "%") { - continue // skip comment - } - sizeLine + return coo } func main() { - A := mat.NewDense(2, 2, []float64{ - 1, 2, - 3, 4, - }) + // small_test_matrix_path := "suitesparse_test_matrices/1138_bus.mtx" + big_8mill_nnz_matrix_path := "suitesparse_test_matrices/thermal2.mtx" + m := matrix_load_market(big_8mill_nnz_matrix_path) + rows, cols := m.Dims() + fmt.Printf("matrix size: %d x %d \n", rows, cols) - B := mat.NewDense(2, 2, []float64{ - 5, 6, - 7, 8, - }) + if rows != cols { + panic("sparse matmul benchmark assumes square matrix") + } - var C mat.Dense - C.Mul(A, B) + // Convert to Compressed-Sparse-Row-storage + m_csr := m.ToCSR() + // Warm up caches to not include "first call" effects + var warm sparse.CSR + for i := 0; i < 3; i += 1 { + warm.Mul(m_csr, m_csr) + } - fmt.Printf("%v\n", mat.Formatted(&C)) + // The CSR x CSR matrix multiplication is supposed to have a specific optimised + // path for matmuls + var out sparse.CSR + number_of_mults := 100 + + time_begin := time.Now() + for i := 0; i < number_of_mults; i += 1 { + out.Mul(m_csr, m_csr) + } + + elapsed := time.Since(time_begin) + elapsed_ms := elapsed.Milliseconds() + + time_per_matmul := float32(elapsed_ms) / float32(number_of_mults) + + out_rows, out_cols := out.Dims() + if out_rows != rows || out_cols != cols { + panic("Output matrix dimensions not same as input. We are supposed to matmul square matrices") + } + + fmt.Printf("Elapsed time per mat mul: %.4f ms\n", time_per_matmul) } diff --git a/suitesparse_test_matrices/urls.txt b/suitesparse_test_matrices/urls.txt new file mode 100644 index 0000000..aabe188 --- /dev/null +++ b/suitesparse_test_matrices/urls.txt @@ -0,0 +1,6 @@ +# This is just a small matrix for debugging / validating code +https://suitesparse-collection-website.herokuapp.com/MM/HB/1138_bus.tar.gz + + +# This is a real large (not really, but ok) sparse matrix with 8.5 million non-zero elements +https://suitesparse-collection-website.herokuapp.com/MM/Schmid/thermal2.tar.gz