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convert_partition.py
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import copy
import gc
import logging
import os
import constants
import dgl
import dgl.backend as F
import dgl.graphbolt as gb
import numpy as np
import torch as th
import torch.distributed as dist
from dgl import EID, ETYPE, NID, NTYPE
from dgl.distributed.constants import DGL2GB_EID, GB_DST_ID
from dgl.distributed.partition import (
_cast_to_minimum_dtype,
_etype_str_to_tuple,
_etype_tuple_to_str,
cast_various_to_minimum_dtype_gb,
RESERVED_FIELD_DTYPE,
)
from utils import get_idranges, memory_snapshot
def _get_unique_invidx(srcids, dstids, nids, low_mem=True):
"""This function is used to compute a list of unique elements,
and their indices in the input list, which is the concatenation
of srcids, dstids and uniq_nids. In addition, this function will also
compute inverse indices, in the list of unique elements, for the
elements in srcids, dstids and nids arrays. srcids, dstids will be
over-written to contain the inverse indices. Basically, this function
is mimicing the functionality of numpy's unique function call.
The problem with numpy's unique function call is its high memory
requirement. For an input list of 3 billion edges it consumes about
550GB of systems memory, which is limiting the capability of the
partitioning pipeline.
Note: This function is a workaround solution for the high memory requirement
of numpy's unique function call. This function is not a general purpose
function and is only used in the context of the partitioning pipeline.
What's more, this function does not behave exactly the same as numpy's
unique function call. Namely, this function does not return the exact same
inverse indices as numpy's unique function call. However, for the current
use case, this function is sufficient.
Current numpy uniques function returns 3 return parameters, which are
. list of unique elements
. list of indices, in the input argument list, which are first
occurance of the corresponding element in the uniques list
. list of inverse indices, which are indices from the uniques list
and can be used to rebuild the original input array
Compared to the above numpy's return parameters, this work around
solution returns 4 values
. list of unique elements,
. list of indices, which may not be the first occurance of the
corresponding element from the uniques
. list of inverse indices, here we only build the inverse indices
for srcids and dstids input arguments. For the current use case,
only these two inverse indices are needed.
Parameters:
-----------
srcids : numpy array
a list of numbers, which are the src-ids of the edges
dstids : numpy array
a list of numbers, which are the dst-ids of the edges
nids : numpy array
a list of numbers, a list of unique shuffle-global-nids.
This list is guaranteed to be a list of sorted consecutive unique
list of numbers. Also, this list will be a `super set` for the
list of dstids. Current implementation of the pipeline guarantees
this assumption and is used to simplify the current implementation
of the workaround solution.
low_mem : bool, optional
Indicates whether to use the low memory version of the function. If
``False``, the function will use numpy's native ``unique`` function.
Otherwise, the function will use the low memory version of the
function.
Returns:
--------
numpy array :
a list of unique, sorted elements, computed from the input arguments
numpy array :
a list of integers. These are indices in the concatenated list
[srcids, dstids, uniq_nids], which are the input arguments to this function
numpy array :
a list of integers. These are inverse indices, which will be indices
from the unique elements list specifying the elements from the
input array, srcids
numpy array :
a list of integers. These are inverse indices, which will be indices
from the unique elements list specifying the elements from the
input array, dstids
"""
assert len(srcids) == len(
dstids
), f"Please provide the correct input parameters"
assert len(srcids) != 0, f"Please provide a non-empty edge-list."
if not low_mem:
logging.warning(
"Calling numpy's native function unique. This functions memory "
"overhead will limit size of the partitioned graph objects "
"processed by each node in the cluster."
)
uniques, idxes, inv_idxes = np.unique(
np.concatenate([srcids, dstids, nids]),
return_index=True,
return_inverse=True,
)
src_len = len(srcids)
dst_len = len(dstids)
return (
uniques,
idxes,
inv_idxes[:src_len],
inv_idxes[src_len : (src_len + dst_len)],
)
# find uniqes which appear only in the srcids list
mask = np.isin(srcids, nids, invert=True, kind="table")
srcids_only = srcids[mask]
srcids_idxes = np.where(mask == 1)[0]
# sort
uniques, unique_srcids_idx = np.unique(srcids_only, return_index=True)
idxes = srcids_idxes[unique_srcids_idx]
# build uniques and idxes, first and second return parameters
uniques = np.concatenate([uniques, nids])
idxes = np.concatenate(
[idxes, len(srcids) + len(dstids) + np.arange(len(nids))]
)
# sort and idxes
sort_idx = np.argsort(uniques)
uniques = uniques[sort_idx]
idxes = idxes[sort_idx]
# uniques and idxes are built
assert len(uniques) == len(idxes), f"Error building the idxes array."
srcids = np.searchsorted(uniques, srcids, side="left")
# process dstids now.
# dstids is guaranteed to be a subset of the `nids` list
# here we are computing index in the list of uniqes for
# each element in the list of dstids, in a two step process
# 1. locate the position of first element from nids in the
# list of uniques - dstids cannot appear to the left
# of this number, they are guaranteed to be on the right
# side of this number.
# 2. dstids = dstids - nids[0]
# By subtracting nids[0] from the list of dstids will make
# the list of dstids to be in the range of [0, max(nids)-1]
# 3. dstids = dstids - nids[0] + offset
# Now we move the list of dstids by `offset` which will be
# the starting position of the nids[0] element. Note that
# nids will ALWAYS be a SUPERSET of dstids.
offset = np.searchsorted(uniques, nids[0], side="left")
dstids = dstids - nids[0] + offset
# return the values
return uniques, idxes, srcids, dstids
# Utility functions.
def _is_homogeneous(ntypes, etypes):
"""Checks if the provided ntypes and etypes form a homogeneous graph."""
return len(ntypes) == 1 and len(etypes) == 1
def _coo2csc(src_ids, dst_ids):
src_ids, dst_ids = th.tensor(src_ids, dtype=th.int64), th.tensor(
dst_ids, dtype=th.int64
)
num_nodes = th.max(th.stack([src_ids, dst_ids], dim=0)).item() + 1
dst, idx = dst_ids.sort()
indptr = th.searchsorted(dst, th.arange(num_nodes + 1))
indices = src_ids[idx]
return indptr, indices, idx
def _create_edge_data(edgeid_offset, etype_ids, num_edges):
eid = th.arange(
edgeid_offset,
edgeid_offset + num_edges,
dtype=RESERVED_FIELD_DTYPE[dgl.EID],
)
etype = th.as_tensor(etype_ids, dtype=RESERVED_FIELD_DTYPE[dgl.ETYPE])
inner_edge = th.ones(num_edges, dtype=RESERVED_FIELD_DTYPE["inner_edge"])
return eid, etype, inner_edge
def _create_node_data(ntype, uniq_ids, reshuffle_nodes, inner_nodes):
node_type = th.as_tensor(ntype, dtype=RESERVED_FIELD_DTYPE[dgl.NTYPE])
node_id = th.as_tensor(uniq_ids[reshuffle_nodes])
inner_node = th.as_tensor(
inner_nodes[reshuffle_nodes],
dtype=RESERVED_FIELD_DTYPE["inner_node"],
)
return node_type, node_id, inner_node
def _compute_node_ntype(
global_src_id, global_dst_id, global_homo_nid, idx, reshuffle_nodes, id_map
):
global_ids = np.concatenate([global_src_id, global_dst_id, global_homo_nid])
part_global_ids = global_ids[idx]
part_global_ids = part_global_ids[reshuffle_nodes]
ntype, per_type_ids = id_map(part_global_ids)
return ntype, per_type_ids
def _graph_orig_ids(
return_orig_nids,
return_orig_eids,
ntypes_map,
etypes_map,
node_attr,
edge_attr,
per_type_ids,
type_per_edge,
global_edge_id,
):
orig_nids = None
orig_eids = None
if return_orig_nids:
orig_nids = {}
for ntype, ntype_id in ntypes_map.items():
mask = th.logical_and(
node_attr[dgl.NTYPE] == ntype_id,
node_attr["inner_node"],
)
orig_nids[ntype] = th.as_tensor(per_type_ids[mask])
if return_orig_eids:
orig_eids = {}
for etype, etype_id in etypes_map.items():
mask = th.logical_and(
type_per_edge == etype_id,
edge_attr["inner_edge"],
)
orig_eids[_etype_tuple_to_str(etype)] = th.as_tensor(
global_edge_id[mask]
)
return orig_nids, orig_eids
def _create_edge_attr_gb(
part_local_dst_id, edgeid_offset, etype_ids, ntypes, etypes, etypes_map
):
edge_attr = {}
# create edge data in graph.
num_edges = len(part_local_dst_id)
(
edge_attr[dgl.EID],
type_per_edge,
edge_attr["inner_edge"],
) = _create_edge_data(edgeid_offset, etype_ids, num_edges)
assert "inner_edge" in edge_attr
is_homo = _is_homogeneous(ntypes, etypes)
edge_type_to_id = (
{gb.etype_tuple_to_str(("_N", "_E", "_N")): 0}
if is_homo
else {
gb.etype_tuple_to_str(etype): etid
for etype, etid in etypes_map.items()
}
)
return edge_attr, type_per_edge, edge_type_to_id
def _create_node_attr(
idx,
global_src_id,
global_dst_id,
global_homo_nid,
uniq_ids,
reshuffle_nodes,
id_map,
inner_nodes,
):
# compute per_type_ids and ntype for all the nodes in the graph.
ntype, per_type_ids = _compute_node_ntype(
global_src_id,
global_dst_id,
global_homo_nid,
idx,
reshuffle_nodes,
id_map,
)
# create node data in graph.
node_attr = {}
(
node_attr[dgl.NTYPE],
node_attr[dgl.NID],
node_attr["inner_node"],
) = _create_node_data(ntype, uniq_ids, reshuffle_nodes, inner_nodes)
return node_attr, per_type_ids
def remove_attr_gb(
edge_attr, node_attr, store_inner_node, store_inner_edge, store_eids
):
edata, ndata = copy.deepcopy(edge_attr), copy.deepcopy(node_attr)
if not store_inner_edge:
assert "inner_edge" in edata
edata.pop("inner_edge")
if not store_eids:
assert dgl.EID in edata
edata.pop(dgl.EID)
if not store_inner_node:
assert "inner_node" in ndata
ndata.pop("inner_node")
return edata, ndata
def _process_partition_gb(
node_attr,
edge_attr,
type_per_edge,
src_ids,
dst_ids,
sort_etypes,
):
"""Preprocess partitions before saving:
1. format data types.
2. sort csc/csr by tag.
"""
for k, dtype in RESERVED_FIELD_DTYPE.items():
if k in node_attr:
node_attr[k] = F.astype(node_attr[k], dtype)
if k in edge_attr:
edge_attr[k] = F.astype(edge_attr[k], dtype)
indptr, indices, edge_ids = _coo2csc(src_ids, dst_ids)
if sort_etypes:
split_size = th.diff(indptr)
split_indices = th.split(type_per_edge, tuple(split_size), dim=0)
sorted_idxs = []
for split_indice in split_indices:
sorted_idxs.append(split_indice.sort()[1])
sorted_idx = th.cat(sorted_idxs, dim=0)
sorted_idx = (
th.repeat_interleave(indptr[:-1], split_size, dim=0) + sorted_idx
)
else:
sorted_idx = th.arange(len(edge_ids))
return indptr, indices[sorted_idx], edge_ids[sorted_idx]
def _update_node_map(node_map_val, end_ids_per_rank, id_ntypes, prev_last_id):
"""this function is modified from the function '_update_node_edge_map' in dgl.distributed.partition"""
# Update the node_map_val to be contiguous.
rank = dist.get_rank()
prev_end_id = (
end_ids_per_rank[rank - 1].item() if rank > 0 else prev_last_id
)
ntype_ids = {ntype: ntype_id for ntype_id, ntype in enumerate(id_ntypes)}
for ntype_id in list(ntype_ids.values()):
ntype = id_ntypes[ntype_id]
start_id = node_map_val[ntype][0][0]
end_id = node_map_val[ntype][0][1]
if not (start_id == -1 and end_id == -1):
continue
prev_ntype_id = (
ntype_ids[ntype] - 1
if ntype_ids[ntype] > 0
else max(ntype_ids.values())
)
prev_ntype = id_ntypes[prev_ntype_id]
if ntype_ids[ntype] == 0:
node_map_val[ntype][0][0] = prev_end_id
else:
node_map_val[ntype][0][0] = node_map_val[prev_ntype][0][1]
node_map_val[ntype][0][1] = node_map_val[ntype][0][0]
return node_map_val[ntype][0][-1]
def create_graph_object(
tot_node_count,
tot_edge_count,
node_count,
edge_count,
num_parts,
schema,
part_id,
node_data,
edge_data,
edgeid_offset,
node_typecounts,
edge_typecounts,
last_ids={},
return_orig_nids=False,
return_orig_eids=False,
use_graphbolt=False,
**kwargs,
):
"""
This function creates dgl objects for a given graph partition, as in function
arguments.
The "schema" argument is a dictionary, which contains the metadata related to node ids
and edge ids. It contains two keys: "nid" and "eid", whose value is also a dictionary
with the following structure.
1. The key-value pairs in the "nid" dictionary has the following format.
"ntype-name" is the user assigned name to this node type. "format" describes the
format of the contents of the files. and "data" is a list of lists, each list has
3 elements: file-name, start_id and end_id. File-name can be either absolute or
relative path to this file and starting and ending ids are type ids of the nodes
which are contained in this file. These type ids are later used to compute global ids
of these nodes which are used throughout the processing of this pipeline.
"ntype-name" : {
"format" : "csv",
"data" : [
[ <path-to-file>/ntype0-name-0.csv, start_id0, end_id0],
[ <path-to-file>/ntype0-name-1.csv, start_id1, end_id1],
...
[ <path-to-file>/ntype0-name-<p-1>.csv, start_id<p-1>, end_id<p-1>],
]
}
2. The key-value pairs in the "eid" dictionary has the following format.
As described for the "nid" dictionary the "eid" dictionary is similarly structured
except that these entries are for edges.
"etype-name" : {
"format" : "csv",
"data" : [
[ <path-to-file>/etype0-name-0, start_id0, end_id0],
[ <path-to-file>/etype0-name-1 start_id1, end_id1],
...
[ <path-to-file>/etype0-name-1 start_id<p-1>, end_id<p-1>]
]
}
In "nid" dictionary, the type_nids are specified that
should be assigned to nodes which are read from the corresponding nodes file.
Along the same lines dictionary for the key "eid" is used for edges in the
input graph.
These type ids, for nodes and edges, are used to compute global ids for nodes
and edges which are stored in the graph object.
Parameters:
-----------
tot_node_count : int
the number of all nodes
tot_edge_count : int
the number of all edges
node_count : int
the number of nodes in partition
edge_count : int
the number of edges in partition
graph_formats : str
the format of graph
num_parts : int
the number of parts
schame : json object
json object created by reading the graph metadata json file
part_id : int
partition id of the graph partition for which dgl object is to be created
node_data : numpy ndarray
node_data, where each row is of the following format:
<global_nid> <ntype_id> <global_type_nid>
edge_data : numpy ndarray
edge_data, where each row is of the following format:
<global_src_id> <global_dst_id> <etype_id> <global_type_eid>
edgeid_offset : int
offset to be used when assigning edge global ids in the current partition
return_orig_ids : bool, optional
Indicates whether to return original node/edge IDs.
Returns:
--------
dgl object
dgl object created for the current graph partition
dictionary
map between node types and the range of global node ids used
dictionary
map between edge types and the range of global edge ids used
dictionary
map between node type(string) and node_type_id(int)
dictionary
map between edge type(string) and edge_type_id(int)
dict of tensors
If `return_orig_nids=True`, return a dict of 1D tensors whose key is the node type
and value is a 1D tensor mapping between shuffled node IDs and the original node
IDs for each node type. Otherwise, ``None`` is returned.
dict of tensors
If `return_orig_eids=True`, return a dict of 1D tensors whose key is the edge type
and value is a 1D tensor mapping between shuffled edge IDs and the original edge
IDs for each edge type. Otherwise, ``None`` is returned.
"""
# create auxiliary data structures from the schema object
memory_snapshot("CreateDGLObj_Begin", part_id)
_, global_nid_ranges = get_idranges(
schema[constants.STR_NODE_TYPE], node_typecounts
)
_, global_eid_ranges = get_idranges(
schema[constants.STR_EDGE_TYPE], edge_typecounts
)
id_map = dgl.distributed.id_map.IdMap(global_nid_ranges)
ntypes = [(key, global_nid_ranges[key][0, 0]) for key in global_nid_ranges]
ntypes.sort(key=lambda e: e[1])
ntype_offset_np = np.array([e[1] for e in ntypes])
ntypes = [e[0] for e in ntypes]
ntypes_map = {e: i for i, e in enumerate(ntypes)}
etypes = [(key, global_eid_ranges[key][0, 0]) for key in global_eid_ranges]
etypes.sort(key=lambda e: e[1])
etypes = [e[0] for e in etypes]
etypes_map = {_etype_str_to_tuple(e): i for i, e in enumerate(etypes)}
node_map_val = {ntype: [] for ntype in ntypes}
edge_map_val = {_etype_str_to_tuple(etype): [] for etype in etypes}
memory_snapshot("CreateDGLObj_AssignNodeData", part_id)
shuffle_global_nids = node_data[constants.SHUFFLE_GLOBAL_NID]
node_data.pop(constants.SHUFFLE_GLOBAL_NID)
gc.collect()
ntype_ids = node_data[constants.NTYPE_ID]
node_data.pop(constants.NTYPE_ID)
gc.collect()
global_type_nid = node_data[constants.GLOBAL_TYPE_NID]
node_data.pop(constants.GLOBAL_TYPE_NID)
node_data = None
gc.collect()
global_homo_nid = ntype_offset_np[ntype_ids] + global_type_nid
assert np.all(shuffle_global_nids[1:] - shuffle_global_nids[:-1] == 1)
shuffle_global_nid_range = (shuffle_global_nids[0], shuffle_global_nids[-1])
# Determine the node ID ranges of different node types.
prev_last_id = last_ids.get(part_id - 1, 0)
for ntype_name in global_nid_ranges:
ntype_id = ntypes_map[ntype_name]
type_nids = shuffle_global_nids[ntype_ids == ntype_id]
if len(type_nids) == 0:
node_map_val[ntype_name].append([-1, -1])
else:
node_map_val[ntype_name].append(
[int(type_nids[0]), int(type_nids[-1]) + 1]
)
last_id = th.tensor(
[max(prev_last_id, int(type_nids[-1]) + 1)], dtype=th.int64
)
id_ntypes = list(global_nid_ranges.keys())
gather_last_ids = [
th.zeros(1, dtype=th.int64) for _ in range(dist.get_world_size())
]
dist.all_gather(gather_last_ids, last_id)
prev_last_id = _update_node_map(
node_map_val, gather_last_ids, id_ntypes, prev_last_id
)
last_ids[part_id] = prev_last_id
# process edges
memory_snapshot("CreateDGLObj_AssignEdgeData: ", part_id)
shuffle_global_src_id = edge_data[constants.SHUFFLE_GLOBAL_SRC_ID]
edge_data.pop(constants.SHUFFLE_GLOBAL_SRC_ID)
gc.collect()
shuffle_global_dst_id = edge_data[constants.SHUFFLE_GLOBAL_DST_ID]
edge_data.pop(constants.SHUFFLE_GLOBAL_DST_ID)
gc.collect()
global_src_id = edge_data[constants.GLOBAL_SRC_ID]
edge_data.pop(constants.GLOBAL_SRC_ID)
gc.collect()
global_dst_id = edge_data[constants.GLOBAL_DST_ID]
edge_data.pop(constants.GLOBAL_DST_ID)
gc.collect()
global_edge_id = edge_data[constants.GLOBAL_TYPE_EID]
edge_data.pop(constants.GLOBAL_TYPE_EID)
gc.collect()
etype_ids = edge_data[constants.ETYPE_ID]
edge_data.pop(constants.ETYPE_ID)
edge_data = None
gc.collect()
logging.info(
f"There are {len(shuffle_global_src_id)} edges in partition {part_id}"
)
# It's not guaranteed that the edges are sorted based on edge type.
# Let's sort edges and all attributes on the edges.
if not np.all(np.diff(etype_ids) >= 0):
sort_idx = np.argsort(etype_ids)
(
shuffle_global_src_id,
shuffle_global_dst_id,
global_src_id,
global_dst_id,
global_edge_id,
etype_ids,
) = (
shuffle_global_src_id[sort_idx],
shuffle_global_dst_id[sort_idx],
global_src_id[sort_idx],
global_dst_id[sort_idx],
global_edge_id[sort_idx],
etype_ids[sort_idx],
)
assert np.all(np.diff(etype_ids) >= 0)
else:
print(f"[Rank: {part_id} Edge data is already sorted !!!")
# Determine the edge ID range of different edge types.
edge_id_start = edgeid_offset
for etype_name in global_eid_ranges:
etype = _etype_str_to_tuple(etype_name)
assert len(etype) == 3
etype_id = etypes_map[etype]
edge_map_val[etype].append(
[edge_id_start, edge_id_start + np.sum(etype_ids == etype_id)]
)
edge_id_start += np.sum(etype_ids == etype_id)
memory_snapshot("CreateDGLObj_UniqueNodeIds: ", part_id)
# get the edge list in some order and then reshuffle.
# Here the order of nodes is defined by the sorted order.
uniq_ids, idx, part_local_src_id, part_local_dst_id = _get_unique_invidx(
shuffle_global_src_id,
shuffle_global_dst_id,
np.arange(shuffle_global_nid_range[0], shuffle_global_nid_range[1] + 1),
)
inner_nodes = th.as_tensor(
np.logical_and(
uniq_ids >= shuffle_global_nid_range[0],
uniq_ids <= shuffle_global_nid_range[1],
)
)
# get the list of indices, from inner_nodes, which will sort inner_nodes as [True, True, ...., False, False, ...]
# essentially local nodes will be placed before non-local nodes.
reshuffle_nodes = th.arange(len(uniq_ids))
reshuffle_nodes = th.cat(
[reshuffle_nodes[inner_nodes.bool()], reshuffle_nodes[inner_nodes == 0]]
)
"""
Following procedure is used to map the part_local_src_id, part_local_dst_id to account for
reshuffling of nodes (to order localy owned nodes prior to non-local nodes in a partition)
1. Form a node_map, in this case a numpy array, which will be used to map old node-ids (pre-reshuffling)
to post-reshuffling ids.
2. Once the map is created, use this map to map all the node-ids in the part_local_src_id
and part_local_dst_id list to their appropriate `new` node-ids (post-reshuffle order).
3. Since only the node's order is changed, we will have to re-order nodes related information when
creating dgl object: this includes dgl.NTYPE, dgl.NID and inner_node.
4. Edge's order is not changed. At this point in the execution path edges are still ordered by their etype-ids.
5. Create the dgl object appropriately and return the dgl object.
Here is a simple example to understand the above flow better.
part_local_nids = [0, 1, 2, 3, 4, 5]
part_local_src_ids = [0, 0, 0, 0, 2, 3, 4]
part_local_dst_ids = [1, 2, 3, 4, 4, 4, 5]
Assume that nodes {1, 5} are halo-nodes, which are not owned by this partition.
reshuffle_nodes = [0, 2, 3, 4, 1, 5]
A node_map, which maps node-ids from old to reshuffled order is as follows:
node_map = np.zeros((len(reshuffle_nodes,)))
node_map[reshuffle_nodes] = np.arange(len(reshuffle_nodes))
Using the above map, we have mapped part_local_src_ids and part_local_dst_ids as follows:
part_local_src_ids = [0, 0, 0, 0, 1, 2, 3]
part_local_dst_ids = [4, 1, 2, 3, 3, 3, 5]
In this graph above, note that nodes {0, 1, 2, 3} are inner_nodes and {4, 5} are NON-inner-nodes
Since the edge are re-ordered in any way, there is no reordering required for edge related data
during the DGL object creation.
"""
# create the mappings to generate mapped part_local_src_id and part_local_dst_id
# This map will map from unshuffled node-ids to reshuffled-node-ids (which are ordered to prioritize
# locally owned nodes).
nid_map = np.zeros(
(
len(
reshuffle_nodes,
)
)
)
nid_map[reshuffle_nodes] = np.arange(len(reshuffle_nodes))
# Now map the edge end points to reshuffled_values.
part_local_src_id, part_local_dst_id = (
nid_map[part_local_src_id],
nid_map[part_local_dst_id],
)
"""
Creating attributes for graphbolt and DGLGraph is as follows.
node attributes:
this part is implemented in _create_node_attr.
compute the ntype and per type ids for each node with global node type id.
create ntype, nid and inner node with orig ntype and inner nodes
this part is shared by graphbolt and DGLGraph.
the attributes created for graphbolt are as follows:
edge attributes:
this part is implemented in _create_edge_attr_gb.
create eid, type per edge and inner edge with edgeid_offset.
create edge_type_to_id with etypes_map.
The process to remove extra attribute is implemented in remove_attr_gb.
the unused attributes like inner_node, inner_edge, eids will be removed following the arguments in kwargs.
edge_attr, node_attr are the variable that have removed extra attributes to construct csc_graph.
edata, ndata are the variable that reserve extra attributes to be used to generate orig_nid and orig_eid.
the src_ids and dst_ids will be transformed into indptr and indices in _coo2csc.
all variable mentioned above will be casted to minimum data type in cast_various_to_minimum_dtype_gb.
orig_nids and orig_eids will be generated in _graph_orig_ids with ndata and edata.
"""
# create the graph here now.
ndata, per_type_ids = _create_node_attr(
idx,
global_src_id,
global_dst_id,
global_homo_nid,
uniq_ids,
reshuffle_nodes,
id_map,
inner_nodes,
)
if use_graphbolt:
edata, type_per_edge, edge_type_to_id = _create_edge_attr_gb(
part_local_dst_id,
edgeid_offset,
etype_ids,
ntypes,
etypes,
etypes_map,
)
assert edata is not None
assert ndata is not None
sort_etypes = len(etypes_map) > 1
indptr, indices, csc_edge_ids = _process_partition_gb(
ndata,
edata,
type_per_edge,
part_local_src_id,
part_local_dst_id,
sort_etypes,
)
edge_attr, node_attr = remove_attr_gb(
edge_attr=edata, node_attr=ndata, **kwargs
)
edge_attr = {
attr: edge_attr[attr][csc_edge_ids] for attr in edge_attr.keys()
}
cast_various_to_minimum_dtype_gb(
node_count=node_count,
edge_count=edge_count,
tot_node_count=tot_node_count,
tot_edge_count=tot_edge_count,
num_parts=num_parts,
indptr=indptr,
indices=indices,
type_per_edge=type_per_edge,
etypes=etypes,
ntypes=ntypes,
node_attributes=node_attr,
edge_attributes=edge_attr,
)
part_graph = gb.fused_csc_sampling_graph(
csc_indptr=indptr,
indices=indices,
node_type_offset=None,
type_per_edge=type_per_edge[csc_edge_ids],
node_attributes=node_attr,
edge_attributes=edge_attr,
node_type_to_id=ntypes_map,
edge_type_to_id=edge_type_to_id,
)
else:
num_edges = len(part_local_dst_id)
part_graph = dgl.graph(
data=(part_local_src_id, part_local_dst_id), num_nodes=len(uniq_ids)
)
# create edge data in graph.
(
part_graph.edata[dgl.EID],
part_graph.edata[dgl.ETYPE],
part_graph.edata["inner_edge"],
) = _create_edge_data(edgeid_offset, etype_ids, num_edges)
ndata, per_type_ids = _create_node_attr(
idx,
global_src_id,
global_dst_id,
global_homo_nid,
uniq_ids,
reshuffle_nodes,
id_map,
inner_nodes,
)
for attr_name, node_attributes in ndata.items():
part_graph.ndata[attr_name] = node_attributes
type_per_edge = part_graph.edata[dgl.ETYPE]
ndata, edata = part_graph.ndata, part_graph.edata
# get the original node ids and edge ids from original graph.
orig_nids, orig_eids = _graph_orig_ids(
return_orig_nids,
return_orig_eids,
ntypes_map,
etypes_map,
ndata,
edata,
per_type_ids,
type_per_edge,
global_edge_id,
)
return (
part_graph,
node_map_val,
edge_map_val,
ntypes_map,
etypes_map,
orig_nids,
orig_eids,
)
def create_metadata_json(
graph_name,
num_nodes,
num_edges,
part_id,
num_parts,
node_map_val,
edge_map_val,
ntypes_map,
etypes_map,
output_dir,
use_graphbolt,
):
"""
Auxiliary function to create json file for the graph partition metadata
Parameters:
-----------
graph_name : string
name of the graph
num_nodes : int
no. of nodes in the graph partition
num_edges : int
no. of edges in the graph partition
part_id : int
integer indicating the partition id
num_parts : int
total no. of partitions of the original graph
node_map_val : dictionary
map between node types and the range of global node ids used
edge_map_val : dictionary
map between edge types and the range of global edge ids used
ntypes_map : dictionary
map between node type(string) and node_type_id(int)
etypes_map : dictionary
map between edge type(string) and edge_type_id(int)
output_dir : string
directory where the output files are to be stored
use_graphbolt : bool
whether to use graphbolt or not
Returns:
--------
dictionary
map describing the graph information
"""
part_metadata = {
"graph_name": graph_name,
"num_nodes": num_nodes,
"num_edges": num_edges,
"part_method": "metis",
"num_parts": num_parts,
"halo_hops": 1,
"node_map": node_map_val,
"edge_map": edge_map_val,
"ntypes": ntypes_map,
"etypes": etypes_map,
}
part_dir = "part" + str(part_id)
node_feat_file = os.path.join(part_dir, "node_feat.dgl")
edge_feat_file = os.path.join(part_dir, "edge_feat.dgl")
if use_graphbolt:
part_graph_file = os.path.join(part_dir, "fused_csc_sampling_graph.pt")
else:
part_graph_file = os.path.join(part_dir, "graph.dgl")
part_graph_type = "part_graph_graphbolt" if use_graphbolt else "part_graph"
part_metadata["part-{}".format(part_id)] = {
"node_feats": node_feat_file,
"edge_feats": edge_feat_file,
part_graph_type: part_graph_file,
}
return part_metadata