[Feature] Gather mm (#3641)

* init

* init

* working cublasGemm

* benchmark high-mem/low-mem, err gather_mm output

* cuda kernel for bmm like kernel

* removed cpu copy for E_per_Rel

* benchmark code from Minjie

* fixed cublas results in gathermm sorted

* use GPU shared mem in unsorted gather mm

* minor

* Added an optimal version of gather_mm_unsorted

* lint

* init gather_mm_scatter

* cublas transpose added

* fixed h_offset for multiple rel

* backward unittest

* cublas support to transpose W

* adding missed file

* forgot to add header file

* lint

* lint

* cleanup

* lint

* docstring

* lint

* added unittest

* lint

* lint

* unittest

* changed err type

* skip cpu test

* skip CPU code

* move in-len loop inside

* lint

* added check different dim length for B

* w_per_len is optional now

* moved gather_mm to pytorch/backend with backward support

* removed a_/b_trans support

* transpose op inside GEMM call

* removed out alloc from API, changed W 2D to 3D

* Added se_gather_mm, Separate API for sortedE

* Fixed gather_mm (unsorted) user interface

* unsorted gmm backward + separate CAPI for un/sorted A

* typecast to float to support atomicAdd

* lint typecast

* lint

* added gather_mm_scatter

* minor

* const

* design changes

* Added idx_a, idx_b support gmm_scatter

* dgl doc

* lint

* adding gather_mm in ops

* lint

* lint

* minor

* removed benchmark files

* minor

* empty commit
Co-authored-by: Israt Nisa <nisisrat@amazon.com>

docs/source/api/python/dgl.ops.rst

@@ -246,6 +246,19 @@ DGL provide operators to reduce value tensor along the first dimension by segmen
 
    segment_reduce
 
+GatherMM and SegmentMM Module
+-----------------------------
+
+SegmentMM: DGL provide operators to perform matrix multiplication according to segments.
+
+GatherMM: DGL provide operators to gather data according to the given indices and perform matrix multiplication.
+
+.. autosummary::
+   :toctree: ../../generated/
+
+   gather_mm
+   segment_mm
+
 Supported Data types
 --------------------
 Operators defined in ``dgl.ops`` support floating point data types, i.e. the operands

python/dgl/backend/backend.py

@@ -1827,6 +1827,51 @@ def csrmask(A, A_weights, B):
     """
     pass
 
+def gather_mm(A, B, idx_a, idx_b):
+    r""" Dense Matrix Multiplication interface. It multiplies 2D dense tensor A
+    and 3D dense tensor B according to their relation types. A is unsorted and
+    the relation type is fetched from idx_b.
+
+    Parameters
+    ----------
+    A : tensor
+        2-D tensor of shape (N, D1)
+    B : tensor
+        3-D tensor of shape (R, D1, D2)
+    idx_a : Tensor, optional
+        If specified, must be a 1-D integer tensor of shape (K,).
+    idx_b : Tensor, optional
+        If specified, must be a 1-D integer tensor of shape (K,).
+
+    Returns
+    -------
+    Tensor
+        The output dense matrix of shape (N, D2)
+    """
+    pass
+
+def segment_mm(A, B, seglen_A):
+    r""" Dense Matrix Multiplication interface. It multiplies dense tensor A
+    and dense tensor B according to relation types. A is sorted and concatenated
+    according to relation types.
+
+    Parameters
+    ----------
+    A : tensor
+        2-D tensor of shape (N, D1)
+    B : tensor
+        3-D tensor of shape (R, D1, D2)
+    seglen_A : Tensor
+        An integer tensor of shape (R,). Each element is the length of segments
+        of input ``A``. The summation of all elements must be equal to N.
+
+    Returns
+    -------
+    Tensor
+        The output dense matrix of shape (N, D2)
+    """
+    pass
+
 
 ###############################################################################
 # Other interfaces

python/dgl/backend/pytorch/sparse.py

 import torch as th
 from distutils.version import LooseVersion
 from ...base import is_all, ALL
+from ...sparse import _gspmm, _gspmm_hetero, _gsddmm, _gsddmm_hetero, _segment_reduce, _bwd_segment_cmp
+from ...sparse import _csrmm, _csrsum, _csrmask, _scatter_add, _update_grad_minmax_hetero, _gather_mm, _gather_mm_scatter, _segment_mm
 from ...sparse import _gspmm, _gspmm_hetero, _gsddmm, _gsddmm_hetero, _segment_reduce, _bwd_segment_cmp, _edge_softmax_forward, _edge_softmax_backward
 from ...sparse import _csrmm, _csrsum, _csrmask, _scatter_add, _update_grad_minmax_hetero
 from ...heterograph_index import create_unitgraph_from_csr
@@ -27,7 +29,7 @@ else:
         return decorate_bwd
 
 __all__ = ['gspmm', 'gsddmm', 'gspmm_hetero', 'gsddmm_hetero', 'edge_softmax', 'edge_softmax_hetero',
-           'segment_reduce', 'scatter_add', 'csrmm', 'csrsum', 'csrmask']
+           'segment_reduce', 'scatter_add', 'csrmm', 'csrsum', 'csrmask', 'gather_mm', 'segment_mm']
 
 
 def _reduce_grad(grad, shape):
@@ -691,6 +693,70 @@ class CSRMask(th.autograd.Function):
         return None, csrmask(gidxB, dB_weights, gidxA), None
 
 
+class SEGMENTMM(th.autograd.Function):
+    @staticmethod
+    @custom_fwd(cast_inputs=th.float16)
+    def forward(ctx, A, B, seglen_A):
+        if A.shape[0] != th.sum(seglen_A):
+            raise Exception("The summation of the elements of seglen_A must be equal to " +
+                "dimension 0 of A. Expected "+ str(A.shape[0]) + "got" + str(th.sum(seglen_A)))
+        if B.dim() != 3:
+            raise Exception("Expected dimension of B is 3. Got " + str(B.dim()))
+        # Reshaping B form 3D to 2D
+        B_3D_shape = B.shape
+        B = B.reshape(B.shape[0] * B.shape[1], B.shape[2])
+        C = th.zeros((A.shape[0], B.shape[1]), device=A.device, dtype=A.dtype)
+        C = _segment_mm(A, B, C, seglen_A)
+        ctx.backward_cache = A, B, seglen_A, B_3D_shape
+        return C
+
+    @staticmethod
+    def backward(ctx, dZ):
+        A, B, seglen_A, B_3D_shape = ctx.backward_cache
+        A_grad = B_grad = None
+        if ctx.needs_input_grad[0]:
+            #  Compute A_grad = Out_grad * B^T
+            A_grad = th.zeros(A.shape, device=A.device, dtype=A.dtype)
+            A_grad = _segment_mm(dZ, B, A_grad, seglen_A, b_trans=True)
+        if ctx.needs_input_grad[1]:
+            #  Compute B_grad = A^T * Out_grad
+            B_grad = th.zeros(B.shape, device=B.device, dtype=B.dtype)
+            B_grad = _segment_mm(A, dZ, B_grad, seglen_A, a_trans=True)
+            B_grad = B_grad.reshape(B_3D_shape[0], B_3D_shape[1], B_3D_shape[2])
+        return A_grad, B_grad, None, None, None, None, None, None
+
+
+class GATHERMM(th.autograd.Function):
+    @staticmethod
+    @custom_fwd(cast_inputs=th.float16)
+    def forward(ctx, A, B, idx_a, idx_b):
+        if B.dim() != 3:
+            raise Exception("Expected dimension of B is 3. Got " + str(B.dim()))
+        # Reshaping B form 3D to 2D
+        B_3D_shape = B.shape
+        B = B.reshape(B.shape[0] * B.shape[1], B.shape[2])
+        C = th.zeros((A.shape[0], B.shape[1]), device=A.device, dtype=A.dtype)
+        C = _gather_mm(A, B, C, B_3D_shape[0], idx_a, idx_b)
+        ctx.backward_cache = A, B, idx_a, idx_b, B_3D_shape
+        return C
+
+    @staticmethod
+    def backward(ctx, dZ):
+        A, B, idx_a, idx_b, B_3D_shape = ctx.backward_cache
+        A_grad = B_grad = None
+        if ctx.needs_input_grad[0]:
+            #  Compute A_grad = Out_grad * B^T
+            A_grad = th.zeros(A.shape, device=A.device, dtype=A.dtype)
+            A_grad = _gather_mm_scatter(dZ, B, A_grad, B_3D_shape[0],
+                idx_b=idx_b, idx_c=idx_a, b_trans=True)
+        if ctx.needs_input_grad[1]:
+            #  Compute B_grad = A^T * Out_grad
+            B_grad = th.zeros(B.shape, device=B.device, dtype=B.dtype)
+            B_grad = _gather_mm_scatter(A, dZ, B_grad, B_3D_shape[0],
+                idx_a=idx_a, idx_c=idx_b)
+            B_grad = B_grad.reshape(B_3D_shape[0], B_3D_shape[1], B_3D_shape[2])
+        return A_grad, B_grad, None, None, None, None, None, None
+
 def gspmm(gidx, op, reduce_op, lhs_data, rhs_data):
     if op == 'sub':
         op = 'add'
@@ -766,3 +832,9 @@ def csrsum(gidxs, weights):
 
 def csrmask(gidxA, A_weights, gidxB):
     return CSRMask.apply(gidxA, A_weights, gidxB)
+
+def segment_mm(A, B, seglen_A):
+    return SEGMENTMM.apply(A, B, seglen_A)
+
+def gather_mm(A, B, idx_a = None, idx_b = None):
+    return GATHERMM.apply(A, B, idx_a, idx_b)

python/dgl/ops/__init__.py

@@ -3,3 +3,4 @@ from .spmm import *
 from .sddmm import *
 from .edge_softmax import *
 from .segment import *
+from .gather_mm import *

python/dgl/ops/gather_mm.py

+"""dgl gather_mm operator module."""
+from ..backend import gather_mm as gather_mm_internal
+from ..backend import segment_mm as segment_mm_internal
+
+__all__ = ['gather_mm', 'segment_mm']
+
+def segment_mm(lhs_data, rhs_data, seglen_lhs):
+    r""" Performs matrix multiplication according to segments.
+    Suppose ``seglen_lhs == [10, 5, 0, 3]``, the operator will perform
+    four matrix multiplications:
+    lhs_data[0:10] @ rhs_data[0], lhs_data[10:15] @ rhs_data[1],
+    lhs_data[15:15] @ rhs_data[2], lhs_data[15:18] @ rhs_data[3]
+
+    Parameters
+    ----------
+    lhs_data : tensor
+        The left operand, 2-D tensor of shape (N, D1)
+    rhs_data : tensor
+        The right operand, 2-D tensor of shape (R * D1, D2)
+    seglen_lhs : tensor
+        An integer tensor of shape (R,). Each element is the length of segments
+        of input ``lhs_data``. The summation of all elements must be equal to N.
+
+    Returns
+    -------
+    tensor
+        The output dense matrix of shape (N, D2)
+    """
+    return segment_mm_internal(lhs_data, rhs_data, seglen_lhs)
+
+def gather_mm(lhs_data, rhs_data, idx_lhs = None, idx_rhs = None):
+    r"""Gather data according to the given indices and perform matrix multiplication.
+
+    Let the result tensor be C, the operator conducts the following computation:
+
+    If both idx_lhs and idx_rhs are not none:
+
+      c[i] = lhs_data[idx_lhs[i]] @ rhs_data[idx_rhs[i]]
+      , where len(C) == len(idx_lhs) == len(idx_rhs)
+
+    If idx_lhs is given but not idx_rhs:
+
+      c[i] = rhs_data[idx_lhs[i]] @ rhs_data[i]
+      , where len(C) == len(idx_lhs)
+
+    If idx_rhs is given but not idx_lhs:
+
+      c[i] = lhs_data[i] @ rhs_data[idx_rhs[i]]
+      , where len(C) == len(idx_rhs)
+
+
+    Parameters
+    ----------
+    lhs_data : tensor
+        2-D tensor of shape (N, D1)
+    rhs_data : tensor
+        3-D tensor of shape (R, D1, D2)
+    idx_lhs : Tensor, optional
+        If specified, must be a 1-D integer tensor of shape (K,).
+    idx_rhs : Tensor, optional
+        If specified, must be a 1-D integer tensor of shape (K,).
+
+    Returns
+    -------
+    Tensor
+        The output dense matrix of shape (N, D2)
+    """
+    return gather_mm_internal(lhs_data, rhs_data, idx_lhs, idx_rhs)

python/dgl/sparse.py

@@ -389,6 +389,111 @@ def _gspmm_hetero(gidx, op, reduce_op, u_len, u_and_e_tuple):
     return out, (list_arg_u, list_arg_e, list_arg_u_ntype, list_arg_e_etype)
 
 
+def _segment_mm(A, B, out, seglen_A, a_trans=False, b_trans=False):
+    r""" Dense Matrix Multiplication interface. It multiplies dense tensor A
+    and dense tensor B according to relation types. A is sorted and concatenated
+    according to relation types.
+
+    Parameters
+    ----------
+    A : tensor
+        2-D tensor of shape (N, D1)
+    B : tensor
+        2-D tensor of shape (R * D1, D2)
+    seglen_A : Tensor
+        An integer tensor of shape (R,). Each element is the length of segments
+        of input ``A``. The summation of all elements must be equal to N.
+    a_trans : bool
+        Indicates whether matrix A needs to be tranposed
+    b_trans : bool
+        Indicates whether matrix B needs to be tranposed
+
+    Returns
+    -------
+    Tensor
+        The output dense matrix of shape (N, D2)
+    """
+    # TODO(Israt): Add CPU support. Currently, only handles GPU code
+    _CAPI_DGLKernelSEGMENTMM(to_dgl_nd(A),
+                            to_dgl_nd(B),
+                            to_dgl_nd_for_write(out),
+                            to_dgl_nd(seglen_A),
+                            a_trans, b_trans)
+    return out
+
+
+def _gather_mm(A, B, out, num_rel, idx_a=None, idx_b=None):
+    r""" Generalized Dense Matrix Multiplication interface. It multiplies
+    tensor A and B according to relation types and outputs in out. B is a
+    concatenated tensor across relation types. A is unsorted and the
+    relation type is fetched from param etypes.
+
+    Parameters
+    ----------
+    A : tensor
+        2-D tensor of shape (N, D1)
+    B : tensor
+        2-D tensor of shape (R * D1, D2)
+    idx_a : Tensor, optional
+        If specified, must be a 1-D integer tensor of shape (K,)
+    idx_b : Tensor, optional
+        If specified, must be a 1-D integer tensor of shape (N,)
+
+    Returns
+    -------
+    Tensor
+        The output dense matrix of shape (N, D2)
+    """
+    # TODO(Israt): Add CPU support. Currently, only handles GPU code
+    _CAPI_DGLKernelGATHERMM(to_dgl_nd(A),
+                            to_dgl_nd(B),
+                            to_dgl_nd_for_write(out),
+                            to_dgl_nd(idx_a),
+                            to_dgl_nd(idx_b),
+                            num_rel)
+    return out
+
+
+def _gather_mm_scatter(A, B, out, num_rel, idx_a=None, idx_b=None, idx_c=None,
+                       a_trans=False, b_trans=False):
+    r""" Generalized Dense Matrix Multiplication interface. It multiplies
+    tensor A and B according to relation types and outputs in out. B is a
+    concatenated tensor across relation types. A is unsorted and the
+    relation type is fetched from param etypes.
+
+    Parameters
+    ----------
+    A : tensor
+        2-D tensor of shape (N, D1)
+    B : tensor
+        2-D tensor of shape (R * D1, D2)
+    idx_a : Tensor, optional
+        If specified, must be a 1-D integer tensor of shape (K,)
+    idx_b : Tensor, optional
+        If specified, must be a 1-D integer tensor of shape (N,)
+    idx_c : Tensor, optional
+        If specified, must be a 1-D integer tensor of shape (N,)
+    A_trans : bool
+        Indicates whether matrix A needs to be tranposed
+    B_trans : bool
+        Indicates whether matrix B needs to be tranposed
+
+    Returns
+    -------
+    Tensor
+        The output dense matrix of shape (N, D2)
+    """
+    # TODO(Israt): Add CPU support. Currently, only handles GPU code
+    _CAPI_DGLKernelGATHERMMSCATTER(to_dgl_nd(A),
+                            to_dgl_nd(B),
+                            to_dgl_nd_for_write(out),
+                            to_dgl_nd(idx_a),
+                            to_dgl_nd(idx_b),
+                            to_dgl_nd(idx_c),
+                            num_rel, a_trans, b_trans)
+    return out
+
+
 def _gsddmm(gidx, op, lhs, rhs, lhs_target='u', rhs_target='v'):
     r""" Generalized Sampled-Dense-Dense Matrix Multiplication interface. It
     takes the result of :attr:`op` on source node feature and destination node

src/array/cpu/gather_mm.cc

+ /*!
+ *  Copyright (c) 2020 by Contributors
+ * \file kernel/cpu/gaher_mm.cc
+ * \brief GatherMM C APIs and definitions.
+ */
+#include "./gather_mm.h"
+#include <dgl/array.h>
+
+namespace dgl {
+namespace aten {
+
+#define SWITCH_BITS(bits, DType, ...)                           \
+  do {                                                          \
+    if ((bits) == 16 || (bits) == 32) {                         \
+      typedef float DType;                                      \
+      { __VA_ARGS__ }                                           \
+    } else if ((bits) == 64) {                                  \
+      typedef double DType;                                     \
+      { __VA_ARGS__ }                                           \
+    } else {                                                    \
+      LOG(FATAL) << "Data type not recognized with bits " << bits; \
+    }                                                           \
+  } while (0)
+
+
+/*! \brief Generalized segmentMM. */
+template <int XPU, typename IdType, int bits>
+void segmentMM(const NDArray A,
+          const NDArray B,
+          NDArray C,
+          const NDArray seglen_A,
+          bool a_trans, bool b_trans) {
+    SWITCH_BITS(bits, DType, {
+        LOG(FATAL) << "Unsupported CPU kernel for SegmentMM.";
+  });
+}
+
+/*! \brief Generalized GatherMM. */
+template <int XPU, typename IdType, int bits>
+void gatherMM(const NDArray A,
+          const NDArray B,
+          NDArray C,
+          const NDArray idx_a,
+          const NDArray idx_b,
+          const int num_rel) {
+    SWITCH_BITS(bits, DType, {
+        LOG(FATAL) << "Unsupported CPU kernel for GatherMM.";
+  });
+}
+
+/*! \brief Generalized GatherMM_scatter. */
+template <int XPU, typename IdType, int bits>
+void gatherMM_scatter(const NDArray A,
+          const NDArray B,
+          NDArray C,
+          const NDArray idx_a,
+          const NDArray idx_b,
+          const NDArray idx_c,
+          const int num_rel,
+          bool a_trans, bool b_trans) {
+    SWITCH_BITS(bits, DType, {
+        LOG(FATAL) << "Unsupported CPU kernel for GatherMM.";
+  });
+}
+
+template void gatherMM<kDLCPU, int32_t, 16>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray idx_a, const NDArray idx_b, const int num_rel);
+template void gatherMM<kDLCPU, int64_t, 16>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray idx_a, const NDArray idx_b, const int num_rel);
+template void gatherMM<kDLCPU, int32_t, 32>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray idx_a, const NDArray idx_b, const int num_rel);
+template void gatherMM<kDLCPU, int64_t, 32>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray idx_a, const NDArray idx_b, const int num_rel);
+template void gatherMM<kDLCPU, int32_t, 64>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray idx_a, const NDArray idx_b, const int num_rel);
+template void gatherMM<kDLCPU, int64_t, 64>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray idx_a, const NDArray idx_b, const int num_rel);
+
+template void gatherMM_scatter<kDLCPU, int32_t, 16>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray idx_a, const NDArray idx_b, const NDArray idx_c,
+    const int num_rel, bool a_trans, bool b_trans);
+template void gatherMM_scatter<kDLCPU, int64_t, 16>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray idx_a, const NDArray idx_b, const NDArray idx_c,
+    const int num_rel, bool a_trans, bool b_trans);
+template void gatherMM_scatter<kDLCPU, int32_t, 32>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray idx_a, const NDArray idx_b, const NDArray idx_c,
+    const int num_rel, bool a_trans, bool b_trans);
+template void gatherMM_scatter<kDLCPU, int64_t, 32>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray idx_a, const NDArray idx_b, const NDArray idx_c,
+    const int num_rel, bool a_trans, bool b_trans);
+template void gatherMM_scatter<kDLCPU, int32_t, 64>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray idx_a, const NDArray idx_b, const NDArray idx_c,
+    const int num_rel, bool a_trans, bool b_trans);
+template void gatherMM_scatter<kDLCPU, int64_t, 64>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray idx_a, const NDArray idx_b, const NDArray idx_c,
+    const int num_rel, bool a_trans, bool b_trans);
+
+template void segmentMM<kDLCPU, int32_t, 16>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray seglen_A, bool a_trans, bool b_trans);
+template void segmentMM<kDLCPU, int64_t, 16>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray seglen_A, bool a_trans, bool b_trans);
+template void segmentMM<kDLCPU, int32_t, 32>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray seglen_A, bool a_trans, bool b_trans);
+template void segmentMM<kDLCPU, int64_t, 32>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray seglen_A, bool a_trans, bool b_trans);
+template void segmentMM<kDLCPU, int32_t, 64>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray seglen_A, bool a_trans, bool b_trans);
+template void segmentMM<kDLCPU, int64_t, 64>(
+    const NDArray A, const NDArray B, NDArray C,
+    const NDArray seglen_A, bool a_trans, bool b_trans);
+
+}  // namespace aten
+}  // namespace dgl

src/array/cpu/gather_mm.h

+/*!
+ *  Copyright (c) 2022 by Contributors
+ * \file array/cpu/gather_mm.h
+ * \brief GATHER_MM CPU kernel function header.
+ */
+#ifndef DGL_ARRAY_CPU_GATHER_MM_H_
+#define DGL_ARRAY_CPU_GATHER_MM_H_
+
+#include <dgl/array.h>
+#include <dgl/bcast.h>
+#include <utility>
+
+namespace dgl {
+namespace aten {
+namespace cpu {
+
+template <typename DType>
+void transpose(const DType *in, DType *out, const int N, const int M) {
+#pragma omp parallel for
+    for (int n = 0; n < N * M; n++) {
+        int i = n / N;
+        int j = n % N;
+        out[n] = in[M * j + i];
+    }
+}
+
+template <typename DType>
+void matmul(const DType *A, const DType *B,
+    DType *C, const int M, const int N, const int K) {
+#pragma omp parallel
+    {
+        int i, j, k;
+#pragma omp for
+        for (i = 0; i < M; i++) {
+            for (j = 0; j < N; j++) {
+                DType local_accum = 0;
+                for (k = 0; k < K; k++) {
+                    local_accum += A[i * K + k] * B[k * N + j];
+                }
+                C[i * N + j] = local_accum;
+            }
+        }
+    }
+}
+
+/*!
+ * \brief CPU kernel of Gather_mm. The input matrix A is expected to be
+ *        sorted according to relation type.
+ * \param A The input dense matrix of dimension m x k
+ * \param B The input dense matrix of dimension k x n
+ * \param C The output dense matrix od dimension m x n
+ * \param A_dim1_per_rel The number of rows in each relation in A
+ * \param B_dim1_per_rel The number of rows in each relation in B
+ * \param a_trans Matrix A to be transposed
+ * \param b_trans Matrix B to be transposed
+ */
+template <int XPU, typename IdType, typename DType>
+void gatherMM_SortedEtype(const NDArray A,
+              const NDArray B,
+              NDArray C,
+              const NDArray A_dim1_per_rel,
+              const NDArray B_dim1_per_rel,
+              bool a_trans, bool b_trans) {
+    assert(A_dim1_per_rel.NumElements() == B_dim1_per_rel.NumElements());
+    int64_t num_rel = A_dim1_per_rel.NumElements();
+    const DType *A_data = A.Ptr<DType>();
+    const DType *B_data = B.Ptr<DType>();
+    const IdType* A_rel_data = A_dim1_per_rel.Ptr<IdType>();
+    const IdType* B_rel_data = B_dim1_per_rel.Ptr<IdType>();
+    DType *C_data = C.Ptr<DType>();
+
+    int64_t A_offset = 0, B_offset = 0, C_offset = 0;
+    int64_t m, n, k, h_col, w_row;
+    for (int etype = 0; etype < num_rel; ++etype) {
+        assert((a_trans) ? A_rel_data[etype] : A->shape[1] ==  \
+            (b_trans) ? B->shape[1] : B_rel_data[etype]);
+        m = A_rel_data[etype];  // rows of A
+        n = B->shape[1];  // cols of B
+        k = B_rel_data[etype];  // rows of B == cols of A
+
+        NDArray A_trans, B_trans;
+        if (a_trans) {
+            A_trans = NDArray::Empty({m * k}, A->dtype, A->ctx);
+            transpose<DType>(A_data + A_offset, static_cast<DType *>(A_trans->data), m, k);
+        }
+        if (b_trans) {
+            B_trans = NDArray::Empty({k * n}, B->dtype, B->ctx);
+            transpose<DType>(B_data + B_offset, static_cast<DType *>(B_trans->data), k, n);
+        }
+        if (a_trans || b_trans) {
+            int64_t tmp = k;
+            if (a_trans)
+                std::swap(m, k);
+            if (b_trans) {
+                k = tmp;
+                std::swap(n, k);
+            }
+        }
+        matmul<DType>(
+            (a_trans) ? static_cast<DType *>(A_trans->data) : A_data + A_offset,
+            (b_trans) ? static_cast<DType *>(B_trans->data) : B_data + B_offset,
+            C_data + C_offset, m, n, k);
+        A_offset += m * k;
+        B_offset += k * n;
+        C_offset += m * n;
+    }
+}
+
+}  // namespace cpu
+}  // namespace aten
+}  // namespace dgl
+
+#endif  // DGL_ARRAY_CPU_GATHER_MM_H_

src/array/kernel.cc

@@ -52,6 +52,60 @@ void SpMM(const std::string& op, const std::string& reduce,
   });
 }
 
+
+/*! \brief Generalized segmented dense Matrix-Matrix Multiplication. */
+void SegmentMM(const NDArray A,
+          const NDArray B,
+          NDArray C,
+          const NDArray seglen_A,
+          bool A_trans, bool B_trans) {
+  ATEN_XPU_SWITCH_CUDA(A->ctx.device_type, XPU, "GatherMM", {
+    ATEN_ID_TYPE_SWITCH(seglen_A->dtype, IdType, {
+      ATEN_FLOAT_BITS_SWITCH(A->dtype, bits, "Feature data", {
+        segmentMM<XPU, IdType, bits>(A, B, C, seglen_A, A_trans, B_trans);
+      });
+    });
+  });
+}
+
+
+/*! \brief Generalized Dense Matrix-Matrix Multiplication according to relation types. */
+void GatherMM(const NDArray A,
+          const NDArray B,
+          NDArray C,
+          const NDArray idx_a,
+          const NDArray idx_b,
+          const int num_rel) {
+  ATEN_XPU_SWITCH_CUDA(A->ctx.device_type, XPU, "GatherMM", {
+    ATEN_ID_TYPE_SWITCH(idx_b->dtype, IdType, {
+      ATEN_FLOAT_BITS_SWITCH(A->dtype, bits, "Feature data", {
+        gatherMM<XPU, IdType, bits>(A, B, C, idx_a, idx_b, num_rel);
+      });
+    });
+  });
+}
+
+
+/*! \brief Generalized Dense Matrix-Matrix Multiplication according to relation types. */
+void GatherMM_scatter(const NDArray A,
+          const NDArray B,
+          NDArray C,
+          const NDArray idx_a,
+          const NDArray idx_b,
+          const NDArray idx_c,
+          const int num_rel,
+          bool A_trans, bool B_trans) {
+  ATEN_XPU_SWITCH_CUDA(A->ctx.device_type, XPU, "GatherMM", {
+    ATEN_ID_TYPE_SWITCH(idx_b->dtype, IdType, {
+      ATEN_FLOAT_BITS_SWITCH(A->dtype, bits, "Feature data", {
+        gatherMM_scatter<XPU, IdType, bits>(A, B, C, idx_a, idx_b, idx_c,
+           num_rel, A_trans, B_trans);
+      });
+    });
+  });
+}
+
+
 /*! \brief Generalized Sparse Matrix-Matrix Multiplication with hetero-graph support. */
 void SpMMHetero(const std::string& op, const std::string& reduce,
           HeteroGraphPtr graph,
@@ -390,6 +444,42 @@ DGL_REGISTER_GLOBAL("sparse._CAPI_DGLKernelSpMM")
     SpMM(op, reduce_op, graph.sptr(), U, E, V, {ArgU, ArgE});
   });
 
+DGL_REGISTER_GLOBAL("sparse._CAPI_DGLKernelGATHERMM")
+.set_body([] (DGLArgs args, DGLRetValue* rv) {
+    NDArray A = args[0];
+    NDArray B = args[1];
+    NDArray C = args[2];
+    NDArray idx_a = args[3];
+    NDArray idx_b = args[4];
+    int num_rel = args[5];
+    GatherMM(A, B, C, idx_a, idx_b, num_rel);
+  });
+
+DGL_REGISTER_GLOBAL("sparse._CAPI_DGLKernelGATHERMMSCATTER")
+.set_body([] (DGLArgs args, DGLRetValue* rv) {
+    NDArray A = args[0];
+    NDArray B = args[1];
+    NDArray C = args[2];
+    NDArray idx_a = args[3];
+    NDArray idx_b = args[4];
+    NDArray idx_c = args[5];
+    int num_rel = args[6];
+    bool A_trans = args[7];
+    bool B_trans = args[8];
+    GatherMM_scatter(A, B, C, idx_a, idx_b, idx_c, num_rel, A_trans, B_trans);
+  });
+
+DGL_REGISTER_GLOBAL("sparse._CAPI_DGLKernelSEGMENTMM")
+.set_body([] (DGLArgs args, DGLRetValue* rv) {
+    NDArray A = args[0];
+    NDArray B = args[1];
+    NDArray C = args[2];
+    NDArray seglen_A = args[3];
+    bool A_trans = args[4];
+    bool B_trans = args[5];
+    SegmentMM(A, B, C, seglen_A, A_trans, B_trans);
+  });
+
 DGL_REGISTER_GLOBAL("sparse._CAPI_DGLKernelEdge_softmax_forward")
 .set_body([] (DGLArgs args, DGLRetValue* rv) {
     HeteroGraphRef graph = args[0];

src/array/kernel_decl.h

@@ -112,6 +112,39 @@ void SDDMMCooHetero(const std::string& op,
               const std::vector<dgl_type_t>& lhs_eid,
               const std::vector<dgl_type_t>& rhs_eid);
 
+/*!
+ * \brief Generalized Dense Matrix-Matrix Multiplication according to relation types.
+ */
+template <int XPU, typename IdType, int bits>
+void gatherMM(const NDArray A,
+          const NDArray B,
+          NDArray out,
+          const NDArray idx_a,
+          const NDArray idx_b,
+          const int num_rel);
+
+/*!
+ * \brief Generalized Dense Matrix-Matrix Multiplication according to relation types.
+ */
+template <int XPU, typename IdType, int bits>
+void gatherMM_scatter(const NDArray A,
+          const NDArray B,
+          NDArray out,
+          const NDArray idx_a,
+          const NDArray idx_b,
+          const NDArray idx_c,
+          const int num_rel, bool a_trans, bool b_trans);
+
+/*!
+ * \brief Generalized segmented dense Matrix-Matrix Multiplication.
+ */
+template <int XPU, typename IdType, int bits>
+void segmentMM(const NDArray A,
+          const NDArray B,
+          NDArray out,
+          const NDArray seglen_A,
+          bool a_trans, bool b_trans);
+
 /*!
  * \brief Segment reduce.
  */

tests/compute/test_gatherMM.py

+from timeit import default_timer
+import dgl
+import backend as F
+import dgl.function as fn
+import time
+import numpy as np
+import unittest, pytest
+from test_utils import parametrize_dtype, get_cases
+
+iters = 5
+n_edge_scale = 1
+num_rel_scale = 1
+
+@unittest.skipIf(dgl.backend.backend_name != 'pytorch', reason='Only support PyTorch for now')
+@unittest.skipIf(F._default_context_str == 'cpu', reason="Not implemented.")
+
+@parametrize_dtype
+def test_gathermm(idtype):
+    def _test(feat_scale):
+        in_feat = 16 * feat_scale
+        out_feat = 8 * feat_scale
+        print("in/out feat", in_feat, out_feat)
+        E_per_rel = F.copy_to(F.tensor([50, 100, 20, 284, 89, 10, 82, 9200, 10, 20, 30, 100,
+            128, 20, 284, 89, 10, 82, 92, 10, 20, 30, 100, 1280, 20, 284, 89, 1000, 82,
+            92, 10, 2000, 30, 100, 128, 20, 284, 89, 10, 82, 92, 10, 20, 30]), F.cpu())
+
+        E_per_rel *= n_edge_scale
+        num_rel = len(E_per_rel)
+        print('num_rel', num_rel)
+        W_per_len = F.copy_to(F.full((num_rel,) ,in_feat, dtype=F.dtype(E_per_rel)), F.cpu())
+
+        H_arr = []
+        W_arr = []
+        Out_arr = []
+        Out_grad_arr = []
+
+        for eid in range(num_rel):
+            H_arr.append(F.randn((E_per_rel[eid], in_feat)))
+            W_arr.append(F.randn((in_feat, out_feat)))
+            Out_arr.append(F.zeros((E_per_rel[eid], out_feat)))
+            Out_grad_arr.append(F.ones((E_per_rel[eid], out_feat)))
+
+        H = F.cat([h for h in H_arr], 0)
+        W = F.cat([w for w in W_arr], 0)
+        W_3D = W.reshape(num_rel, in_feat, out_feat)
+        Out = F.cat([out for out in Out_arr], 0)
+        Out_grad = F.cat([o for o in Out_grad_arr], 0)
+
+        print('H.shape', H.shape)
+        print('W.shape', W.shape)
+        print('W_3D.shape', W_3D.shape)
+        print('Out.shape', Out.shape)
+
+        etype_arr = []
+        for eid in range(num_rel):
+            etype_arr.append(F.full((E_per_rel[eid],), eid, dtype=F.dtype(E_per_rel)))
+        etypes = F.cat([etype for etype in etype_arr], 0)
+
+        #################################################################
+        #  low-mem version using PyTorch operator
+        #################################################################
+
+        # forward pass
+        out = []
+        for i in range(len(E_per_rel)):
+            Hi = H_arr[i]
+            Wi = W_arr[i]
+            out.append(F.matmul(Hi, Wi))
+        out_low_mem = F.cat(out, 0)
+
+        # backward pass
+        H_grad = []
+        W_grad = []
+        for i in range(len(E_per_rel)):
+            Hi = H_arr[i]
+            Wi = W_arr[i]
+            Out_gradi = Out_grad_arr[i]
+            H_grad.append(F.matmul(Out_gradi, Wi.transpose(0,1)))
+            W_grad.append(F.matmul(Hi.transpose(0,1), Out_gradi))
+        Hgrad_low_mem = F.cat(H_grad, 0)
+        Wgrad_low_mem = F.cat(W_grad, 0)
+        Wgrad_low_mem = Wgrad_low_mem.reshape(num_rel, in_feat, out_feat)
+
+        #################################################################
+        #  gather_mm where H sorted according to etype
+        #################################################################
+
+        seglen_A = E_per_rel
+        F.attach_grad(H)
+        F.attach_grad(W_3D)
+        with F.record_grad():
+            out_gmm_sorted = dgl.ops.segment_mm(H, W_3D, seglen_A)
+            F.backward(F.reduce_sum(out_gmm_sorted))
+            Hgrad_gmm_sorted = H.grad
+            Wgrad_gmm_sorted = W_3D.grad
+
+        #################################################################
+        #  gather_mm where H is not sorted (backward not supported yet)
+        #################################################################
+
+        F.attach_grad(H)
+        F.attach_grad(W_3D)
+        with F.record_grad():
+            out_gmm_unsorted = dgl.ops.gather_mm(H, W_3D, idx_rhs=etypes)
+            F.backward(F.reduce_sum(out_gmm_unsorted))
+            Hgrad_gmm_unsorted = H.grad
+            Wgrad_gmm_unsorted = W_3D.grad
+
+
+        # correctness check
+        assert F.allclose(out_low_mem, out_gmm_sorted, atol=1e-3, rtol=1e-3)
+        assert F.allclose(Hgrad_low_mem, Hgrad_gmm_sorted, atol=1e-3, rtol=1e-3)
+        assert F.allclose(Wgrad_low_mem, Wgrad_gmm_sorted, atol=1e-3, rtol=1e-3)
+        assert F.allclose(out_low_mem, out_gmm_unsorted, atol=1e-3, rtol=1e-3)
+        assert F.allclose(Hgrad_low_mem, Hgrad_gmm_unsorted, atol=1e-3, rtol=1e-3)
+        assert F.allclose(Wgrad_low_mem, Wgrad_gmm_unsorted, atol=1e-3, rtol=1e-3)
+
+    _test(1)
+    _test(4)
+    _test(16)
+    _test(32)
+
+if __name__ == '__main__':
+    test_gathermm()