[Sparse] add sparse tensor computation support (apache#1289)

python/tvm/autotvm/task/dispatcher.py

@@ -16,8 +16,8 @@
 
 import logging
 
-from decorator import decorate
 import numpy as np
+from decorator import decorate
 
 from tvm import target as _target
 

python/tvm/contrib/sparse.py

@@ -0,0 +1,163 @@
+"""Tensor and Operation class for computation declaration."""
+# pylint: disable=invalid-name
+from __future__ import absolute_import as _abs
+import numpy as _np
+from .. import expr as _expr
+from .. import api as _api
+from .. import tensor as _tensor
+from .. import ndarray as _nd
+
+float32 = "float32"
+itype = 'int32'
+
+class CSRNDArray(object):
+    """Sparse tensor object in CSR format."""
+    def __init__(self, arg1, ctx=None, shape=None):
+        """Construct a sparse matrix in CSR format.
+
+        Parameters
+        ----------
+        arg1 : numpy.ndarray or a tuple with (data, indices, indptr)
+            The corresponding a dense numpy array,
+            or a tuple for constructing a sparse matrix directly.
+
+        ctx: tvm.TVMContext
+            The corresponding context.
+
+        shape : tuple of int
+            The shape of the array
+        """
+        if isinstance(arg1, tuple):
+            assert len(arg1) == 3
+            self.data, self.indices, self.indptr = arg1
+            self.shape = shape
+        elif isinstance(arg1, _np.ndarray):
+            source_array = arg1
+            ridx, cidx = _np.nonzero(source_array)
+            data = source_array[ridx, cidx]
+            self.data = _nd.array(data, ctx)
+            indices = _np.nonzero(source_array)[1].astype(itype)
+            self.indices = _nd.array(indices, ctx)
+            indptr = [0]+_np.apply_along_axis(_np.count_nonzero, axis=1, arr=source_array).tolist()
+            indptr = _np.cumsum(_np.array(indptr, itype)).astype(itype)
+            self.indptr = _nd.array(indptr, ctx)
+            self.shape = source_array.shape
+        else:
+            raise RuntimeError("Construct CSRNDArray with either a tuple (data, indices, indptr) "
+                               "or a numpy.array, can't handle type %s." % (type(arg1),))
+        self.stype = 'csr'
+        self.dtype = self.data.dtype
+        assert self.shape is not None
+        assert isinstance(self.data, _nd.NDArray)
+        assert isinstance(self.indices, _nd.NDArray)
+        assert str(self.indices.dtype) == 'int32' or \
+            str(self.indices.dtype) == 'int64', str(self.indices.dtype)
+        assert isinstance(self.indptr, _nd.NDArray)
+        assert str(self.indptr.dtype) == 'int32' or \
+            str(self.indptr.dtype) == 'int64', str(self.indptr.dtype)
+
+    def asnumpy(self):
+        """Construct a full matrix and convert it to numpy array."""
+        full = _np.zeros(self.shape, self.dtype)
+        ridx = _np.diff(self.indptr.asnumpy())
+        ridx = _np.hstack((_np.ones((v,), itype)*i for i, v in enumerate(ridx)))
+        full[ridx, self.indices.asnumpy().astype(itype)] = self.data.asnumpy()
+        return full
+
+def array(source_array, ctx=None, shape=None, stype='csr'):
+    """Construct a sparse NDArray from numpy.ndarray"""
+    ret = None
+    if stype == 'csr':
+        ret = CSRNDArray(source_array, shape=shape, ctx=ctx)
+    else:
+        raise NotImplementedError('stype=%s is not supported yet.' % (stype,))
+    return ret
+
+class SparsePlaceholderOp(object):
+    """Placeholder class for sparse tensor representations."""
+    def __init__(self, shape, nonzeros, dtype, name):
+        # pylint: disable=unused-argument
+        """Contructing a bare bone structure for a sparse matrix
+
+        Parameters
+        ----------
+        shape: Tuple of Expr
+            The shape of the tensor
+
+        nonzeros: int
+            The number of non-zero values
+
+        dtype: str, optional
+            The data type of the tensor
+
+        name: str, optional
+            The name hint of the tensor
+        """
+        self.shape = shape
+        self.dtype = dtype
+        self.name = name
+        self.stype = 'unknown'
+
+class CSRPlaceholderOp(SparsePlaceholderOp):
+    """Placeholder class for CSR based sparse tensor representation."""
+    def __init__(self, shape, nonzeros, dtype, name):
+        """Contructing a bare bone structure for a csr_matrix
+
+        Parameters
+        ----------
+        shape: Tuple of Expr
+            The shape of the tensor
+
+        nonzeros: int
+            The number of non-zero values
+
+        dtype: str, optional
+            The data type of the tensor
+
+        name: str, optional
+            The name hint of the tensor
+        """
+        SparsePlaceholderOp.__init__(self, shape, nonzeros, dtype, name)
+        self.stype = 'csr'
+        self.data = _api.placeholder((nonzeros,), dtype=dtype, name=self.name+'_data')
+        self.indices = _api.placeholder((nonzeros,), dtype=itype, name=self.name+'_indices')
+        self.indptr = _api.placeholder((self.shape[0]+1,), dtype=itype, name=self.name+'_indptr')
+        assert isinstance(self.data, _tensor.Tensor)
+        assert isinstance(self.indices, _tensor.Tensor)
+        assert isinstance(self.indptr, _tensor.Tensor)
+
+def placeholder(shape, nonzeros=None, dtype=None, name="placeholder", stype=None):
+    """Construct an empty sparse tensor object.
+
+    Parameters
+    ----------
+    shape: Tuple of Expr
+        The shape of the tensor
+
+    nonzeros: int
+        The number of non-zero values
+
+    dtype: str, optional
+        The data type of the tensor
+
+    name: str, optional
+        The name hint of the tensor
+
+    stype: str, optional
+        The name storage type of the sparse tensor (e.g. csr, coo, ell)
+
+    Returns
+    -------
+    tensor: SparsePlaceholderOp
+        The created sparse tensor placeholder
+    """
+    shape = (shape,) if isinstance(shape, _expr.Expr) else shape
+    nonzeros = 0 if nonzeros is None else nonzeros
+    dtype = float32 if dtype is None else dtype
+    stype = 'csr' if stype is None else stype
+    ret = None
+    if stype == 'csr':
+        ret = CSRPlaceholderOp(shape=shape, nonzeros=nonzeros, dtype=dtype, name=name)
+    else:
+        raise NotImplementedError('stype=%s is not supported yet.' % (stype,))
+    return ret

tests/python/contrib/test_sparse.py

@@ -0,0 +1,100 @@
+import tvm
+import tvm.contrib.sparse as tvmsp
+import tvm.ndarray as _nd
+import numpy as np
+from collections import namedtuple
+
+def test_static_tensor():
+    dtype = 'float32'
+    stype = 'csr'
+    target = 'llvm'
+    ctx = tvm.context(target, 0)
+    m = tvm.var('m')
+    n = tvm.var('n')
+    A = tvmsp.placeholder(shape=(m, n), name='A', dtype=dtype)
+    assert(A.stype == 'csr')
+    n = 3
+    a = np.maximum(np.random.uniform(size=(n,n)).astype(dtype)-.6, 0.)
+    a = tvmsp.array(a, ctx)
+    A.data = tvm.placeholder(a.data.shape, dtype, name='A_data')
+    Ab = tvm.decl_buffer(a.data.shape, dtype, name='A_data')
+    binds = {A.data: Ab}
+    C = tvm.compute(A.data.shape, lambda i: A.data[i] * 2., tag='cs_scatter')
+    s = tvm.create_schedule(C.op)
+    f = tvm.build(s, [A.data, C], target, binds=binds)
+    c = tvmsp.array(np.zeros((n,n), dtype), ctx)
+    c.data = tvm.nd.empty(a.data.shape, dtype)
+    c.indices = a.indices
+    c.indptr = a.indptr
+    f(a.data, c.data)
+    np.testing.assert_allclose(c.asnumpy(), a.asnumpy() * 2., rtol=1e-5)
+
+def test_dynamic_tensor():
+    dtype = 'float32'
+    stype = 'csr'
+    target = 'llvm'
+    ctx = tvm.context(target, 0)
+    nr, nc, n = tvm.var('nr'), tvm.var('nc'), tvm.var('n')
+    A = tvmsp.placeholder(shape=(nr, nc), nonzeros=n, name='A', dtype=dtype)
+    assert(A.stype == 'csr')
+    C = tvm.compute(A.data.shape, lambda i: A.data[i] * 2., tag='cs_scatter')
+    s = tvm.create_schedule(C.op)
+    _nr, _nc = 3, 5
+    a = np.maximum(np.random.uniform(size=(_nr, _nc)).astype(dtype)-.6, 0.)
+    a = tvmsp.array(a, ctx)
+    assert a.data.dtype == a.dtype
+    Ab = namedtuple('CSRBuffer', ['data', 'indices', 'indptr'])
+    Ab.data = tvm.decl_buffer(a.data.shape, a.data.dtype, name='A_data')
+    Ab.indices = tvm.decl_buffer(a.data.shape, a.data.dtype, name='A_indices')
+    binds = {A.data: Ab.data, A.indices: Ab.indices}
+    f = tvm.build(s, [nr, A.data, C], target, binds=binds)
+    c = tvmsp.array(np.zeros((_nr, _nc), dtype), ctx)
+    c.data = tvm.nd.empty(a.data.shape, dtype)
+    c.indices = a.indices
+    c.indptr = a.indptr
+    f(a.data.shape[0], a.data, c.data)
+    np.testing.assert_allclose(c.asnumpy(), a.asnumpy() * 2., rtol=1e-5)
+
+def test_sparse_array_tuple():
+    dtype, itype = 'float32', 'int32'
+    stype = 'csr'
+    target = 'llvm'
+    ctx = tvm.context(target, 0)
+    nr, nc, n = tvm.var('nr'), tvm.var('nc'), tvm.var('n')
+    A = tvmsp.placeholder(shape=(nr, nc), nonzeros=n, name='A', dtype=dtype)
+    assert(A.stype == 'csr')
+    C = tvm.compute(A.data.shape, lambda i: A.data[i] * 2., tag='cs_scatter')
+    s = tvm.create_schedule(C.op)
+    _nr, _nc = 3, 5
+    a = np.maximum(np.random.uniform(size=(_nr, _nc)).astype(dtype)-.6, 0.)
+    # convert to sparse array tuple
+    source_array = a
+    ridx, cidx = np.nonzero(source_array)
+    data = source_array[ridx, cidx]
+    a_data = _nd.array(data, ctx)
+    indices = np.nonzero(source_array)[1].astype(itype)
+    a_indices = _nd.array(indices, ctx)
+    indptr = [0]+np.apply_along_axis(np.count_nonzero, axis=1, arr=source_array).tolist()
+    indptr = np.cumsum(np.array(indptr, itype)).astype(itype)
+    a_indptr = _nd.array(indptr, ctx)
+    a_init = (a_data, a_indices, a_indptr)
+    # construct tvm sparse array with tuple
+    a = tvmsp.array(a_init, shape=source_array.shape, ctx=ctx)
+    assert a.data.dtype == a.dtype
+    Ab = namedtuple('CSRBuffer', ['data', 'indices', 'indptr'])
+    Ab.data = tvm.decl_buffer(a.data.shape, a.data.dtype, name='A_data')
+    Ab.indices = tvm.decl_buffer(a.data.shape, a.data.dtype, name='A_indices')
+    binds = {A.data: Ab.data, A.indices: Ab.indices}
+    f = tvm.build(s, [nr, A.data, C], target, binds=binds)
+    c = tvmsp.array(np.zeros((_nr, _nc), dtype), ctx)
+    c.data = tvm.nd.empty(a.data.shape, dtype)
+    c.indices = a.indices
+    c.indptr = a.indptr
+    f(a.data.shape[0], a.data, c.data)
+    np.testing.assert_allclose(c.asnumpy(), a.asnumpy() * 2., rtol=1e-5)
+
+if __name__ == "__main__":
+    test_static_tensor()
+    test_dynamic_tensor()
+    test_sparse_array_tuple()
+

topi/python/topi/__init__.py

@@ -32,6 +32,7 @@
 from . import rocm
 from . import vision
 from . import image
+from . import sparse
 from . import hls
 # not import testing by default
 # because testing can have extra deps that are not necessary

topi/python/topi/sparse/__init__.py

@@ -0,0 +1,7 @@
+# pylint: disable=wildcard-import
+"""Sparse operators"""
+from __future__ import absolute_import as _abs
+
+from .csrmv import csrmv
+from .csrmm import csrmm
+from .dense import dense

topi/python/topi/sparse/csrmm.py

@@ -0,0 +1,94 @@
+"""TVM operator compute SpMM in CSR format."""
+from __future__ import absolute_import
+import tvm
+from .. import tag
+from ..util import simplify
+
+def csrmm_default(data, indices, indptr, weight, bias=None):
+    # pylint: disable=invalid-name
+    """The default implementation of csrmm in topi.
+
+    Parameters
+    ----------
+    data : tvm.Tensor
+        1-D with shape [nonzeros]
+
+    indices : tvm.Tensor
+        1-D with shape [nonzeros]
+
+    indptr : tvm.Tensor
+        1-D with shape [m+1]
+
+    weight : tvm.Tensor
+        2-D with shape [k, n]
+
+    bias : tvm.Tensor, optional
+        1-D with shape [m]
+
+    Returns
+    -------
+    output : tvm.Tensor
+        2-D with shape [m, n]
+    """
+    assert len(data.shape) == 1 and len(indices.shape) == 1 and len(indptr.shape) == 1 \
+        and len(weight.shape) == 2, "only support 2-dim csrmm"
+    assert isinstance(weight, tvm.tensor.Tensor), \
+        "weight matrix is assumed to be tvm.Tensor, but weight is `%s`" % (type(weight))
+    if bias is not None:
+        assert len(bias.shape) == 1
+    M = simplify(indptr.shape[0]-1)
+    _, N = weight.shape
+    def csrmm_default_ir(data, indices, indptr, weight, out):
+        """define ir for csrmm"""
+        irb = tvm.ir_builder.create()
+        data_ptr = irb.buffer_ptr(data)
+        indices_ptr = irb.buffer_ptr(indices)
+        indptr_ptr = irb.buffer_ptr(indptr)
+        weight_ptr = irb.buffer_ptr(weight)
+        out_ptr = irb.buffer_ptr(out)
+        M = simplify(indptr.shape[0]-1)
+        _, N = weight.shape
+        with irb.for_range(0, N, for_type="vectorize", name='n') as n:
+            with irb.for_range(0, M, for_type="parallel", name='row') as row:
+                dot = irb.allocate('float32', (1,), name='dot', scope='local')
+                out_ptr[row*N+n] = 0.
+                dot[0] = 0.
+                row_start = indptr_ptr[row]
+                row_end = indptr_ptr[row+1]
+                row_elems = row_end-row_start
+                with irb.for_range(0, row_elems, name='idx') as idx:
+                    elem = row_start+idx
+                    dot[0] += data_ptr[elem] * weight_ptr[indices_ptr[elem]*N+n]
+                out_ptr[row*N+n] += dot[0]
+        return irb.get()
+    oshape = (M, N)
+    matmul = tvm.extern(oshape, [data, indices, indptr, weight],
+                        lambda ins, outs: csrmm_default_ir(ins[0], ins[1], ins[2], ins[3], outs[0]),
+                        tag="csrmm", dtype='float32', name='out')
+    if bias is not None:
+        matmul = tvm.compute(oshape, lambda i, j: matmul[i, j] + bias[i], \
+                             tag=tag.BROADCAST)
+    return matmul
+
+
+def csrmm(a, b, c=None):
+    """The `csrmm` routine performs a matrix-matrix operation defined as :math:`C := A*B + C`,
+    where `B` and `C` are dense matrices, `A` is an m-by-k sparse matrix in the CSR format.
+
+    Parameters
+    ----------
+    a : tvm.contrib.sparse.CSRNDArray
+        2-D sparse matrix with shape [m, k]
+
+    b : tvm.Tensor
+        2-D dense matrix with shape [k, n]
+
+    c : tvm.Tensor, optional
+        1-D dense vector with shape [n]
+
+    Returns
+    -------
+    output : tvm.Tensor
+        2-D with shape [m, n]
+    """
+    return csrmm_default(a.data, a.indices, a.indptr, b, c)