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2026-07-13 13:35:51 +08:00

1526 lines
59 KiB
Python

import gc
import logging
import math
import os
import sys
from datetime import timedelta
from timeit import default_timer as timer
import constants
import dgl
import numpy as np
import torch
import torch.distributed as dist
import torch.multiprocessing as mp
from convert_partition import create_graph_object, create_metadata_json
from dataset_utils import get_dataset
from dist_lookup import DistLookupService
from globalids import (
assign_shuffle_global_nids_edges,
assign_shuffle_global_nids_nodes,
lookup_shuffle_global_nids_edges,
)
from gloo_wrapper import allgather_sizes, alltoallv_cpu, gather_metadata_json
from utils import (
augment_edge_data,
DATA_TYPE_ID,
get_edge_types,
get_etype_featnames,
get_gid_offsets,
get_gnid_range_map,
get_idranges,
get_node_types,
get_ntype_counts_map,
get_ntype_featnames,
map_partid_rank,
memory_snapshot,
read_json,
read_ntype_partition_files,
REV_DATA_TYPE_ID,
write_dgl_objects,
write_metadata_json,
)
def gen_node_data(
rank, world_size, num_parts, id_lookup, ntid_ntype_map, schema_map
):
"""
For this data processing pipeline, reading node files is not needed. All the needed information about
the nodes can be found in the metadata json file. This function generates the nodes owned by a given
process, using metis partitions.
Parameters:
-----------
rank : int
rank of the process
world_size : int
total no. of processes
num_parts : int
total no. of partitions
id_lookup : instance of class DistLookupService
Distributed lookup service used to map global-nids to respective partition-ids and
shuffle-global-nids
ntid_ntype_map :
a dictionary where keys are node_type ids(integers) and values are node_type names(strings).
schema_map:
dictionary formed by reading the input metadata json file for the input dataset.
Please note that, it is assumed that for the input graph files, the nodes of a particular node-type are
split into `p` files (because of `p` partitions to be generated). On a similar node, edges of a particular
edge-type are split into `p` files as well.
#assuming m nodetypes present in the input graph
"num_nodes_per_chunk" : [
[a0, a1, a2, ... a<p-1>],
[b0, b1, b2, ... b<p-1>],
...
[m0, m1, m2, ... m<p-1>]
]
Here, each sub-list, corresponding a nodetype in the input graph, has `p` elements. For instance [a0, a1, ... a<p-1>]
where each element represents the number of nodes which are to be processed by a process during distributed partitioning.
In addition to the above key-value pair for the nodes in the graph, the node-features are captured in the
"node_data" key-value pair. In this dictionary the keys will be nodetype names and value will be a dictionary which
is used to capture all the features present for that particular node-type. This is shown in the following example:
"node_data" : {
"paper": { # node type
"feat": { # feature key
"format": {"name": "numpy"},
"data": ["node_data/paper-feat-part1.npy", "node_data/paper-feat-part2.npy"]
},
"label": { # feature key
"format": {"name": "numpy"},
"data": ["node_data/paper-label-part1.npy", "node_data/paper-label-part2.npy"]
},
"year": { # feature key
"format": {"name": "numpy"},
"data": ["node_data/paper-year-part1.npy", "node_data/paper-year-part2.npy"]
}
}
}
In the above textual description we have a node-type, which is paper, and it has 3 features namely feat, label and year.
Each feature has `p` files whose location in the filesystem is the list for the key "data" and "foramt" is used to
describe storage format.
Returns:
--------
dictionary :
dictionary where keys are column names and values are numpy arrays, these arrays are generated by
using information present in the metadata json file
"""
local_node_data = {}
for local_part_id in range(num_parts // world_size):
local_node_data[constants.GLOBAL_NID + "/" + str(local_part_id)] = []
local_node_data[constants.NTYPE_ID + "/" + str(local_part_id)] = []
local_node_data[
constants.GLOBAL_TYPE_NID + "/" + str(local_part_id)
] = []
# Note that `get_idranges` always returns two dictionaries. Keys in these
# dictionaries are type names for nodes and edges and values are
# `num_parts` number of tuples indicating the range of type-ids in first
# dictionary and range of global-nids in the second dictionary.
type_nid_dict, global_nid_dict = get_idranges(
schema_map[constants.STR_NODE_TYPE],
get_ntype_counts_map(
schema_map[constants.STR_NODE_TYPE],
schema_map[constants.STR_NUM_NODES_PER_TYPE],
),
num_chunks=num_parts,
)
for ntype_id, ntype_name in ntid_ntype_map.items():
# No. of nodes in each process can differ significantly in lopsided distributions
# Synchronize on a per ntype basis
dist.barrier()
type_start, type_end = (
type_nid_dict[ntype_name][0][0],
type_nid_dict[ntype_name][-1][1],
)
gnid_start, gnid_end = (
global_nid_dict[ntype_name][0, 0],
global_nid_dict[ntype_name][0, 1],
)
node_partid_slice = id_lookup.get_partition_ids(
np.arange(gnid_start, gnid_end, dtype=np.int64)
) # exclusive
for local_part_id in range(num_parts // world_size):
cond = node_partid_slice == (rank + local_part_id * world_size)
own_gnids = np.arange(gnid_start, gnid_end, dtype=np.int64)
own_gnids = own_gnids[cond]
own_tnids = np.arange(type_start, type_end, dtype=np.int64)
own_tnids = own_tnids[cond]
local_node_data[
constants.NTYPE_ID + "/" + str(local_part_id)
].append(np.ones(own_gnids.shape, dtype=np.int64) * ntype_id)
local_node_data[
constants.GLOBAL_NID + "/" + str(local_part_id)
].append(own_gnids)
local_node_data[
constants.GLOBAL_TYPE_NID + "/" + str(local_part_id)
].append(own_tnids)
for k in local_node_data.keys():
local_node_data[k] = np.concatenate(local_node_data[k])
return local_node_data
def exchange_edge_data(rank, world_size, num_parts, edge_data, id_lookup):
"""
Exchange edge_data among processes in the world.
Prepare list of sliced data targeting each process and trigger
alltoallv_cpu to trigger messaging api
Parameters:
-----------
rank : int
rank of the process
world_size : int
total no. of processes
edge_data : dictionary
edge information, as a dicitonary which stores column names as keys and values
as column data. This information is read from the edges.txt file.
id_lookup : DistLookupService instance
this object will be used to retrieve ownership information of nodes
Returns:
--------
dictionary :
the input argument, edge_data, is updated with the edge data received by other processes
in the world.
"""
# Synchronize at the beginning of this function
dist.barrier()
# Prepare data for each rank in the cluster.
timer_start = timer()
CHUNK_SIZE = 100 * 1000 * 1000 # 100 * 8 * 5 = 1 * 4 = 8 GB/message/node
num_edges = edge_data[constants.GLOBAL_SRC_ID].shape[0]
all_counts = allgather_sizes(
[num_edges], world_size, num_parts, return_sizes=True
)
max_edges = np.amax(all_counts)
all_edges = np.sum(all_counts)
num_chunks = (max_edges // CHUNK_SIZE) + (
0 if (max_edges % CHUNK_SIZE == 0) else 1
)
LOCAL_CHUNK_SIZE = (num_edges // num_chunks) + (
0 if (num_edges % num_chunks == 0) else 1
)
logging.debug(
f"[Rank: {rank} Edge Data Shuffle - max_edges: {max_edges}, \
local_edges: {num_edges} and num_chunks: {num_chunks} \
Total edges: {all_edges} Local_CHUNK_SIZE: {LOCAL_CHUNK_SIZE}"
)
for local_part_id in range(num_parts // world_size):
local_src_ids = []
local_dst_ids = []
local_type_eids = []
local_etype_ids = []
local_eids = []
for chunk in range(num_chunks):
chunk_start = chunk * LOCAL_CHUNK_SIZE
chunk_end = (chunk + 1) * LOCAL_CHUNK_SIZE
logging.debug(
f"[Rank: {rank}] EdgeData Shuffle: processing \
local_part_id: {local_part_id} and chunkid: {chunk}"
)
cur_src_id = edge_data[constants.GLOBAL_SRC_ID][
chunk_start:chunk_end
]
cur_dst_id = edge_data[constants.GLOBAL_DST_ID][
chunk_start:chunk_end
]
cur_type_eid = edge_data[constants.GLOBAL_TYPE_EID][
chunk_start:chunk_end
]
cur_etype_id = edge_data[constants.ETYPE_ID][chunk_start:chunk_end]
cur_eid = edge_data[constants.GLOBAL_EID][chunk_start:chunk_end]
input_list = []
owner_ids = id_lookup.get_partition_ids(cur_dst_id)
for idx in range(world_size):
send_idx = owner_ids == (idx + local_part_id * world_size)
send_idx = send_idx.reshape(cur_src_id.shape[0])
filt_data = np.column_stack(
(
cur_src_id[send_idx == 1],
cur_dst_id[send_idx == 1],
cur_type_eid[send_idx == 1],
cur_etype_id[send_idx == 1],
cur_eid[send_idx == 1],
)
)
if filt_data.shape[0] <= 0:
input_list.append(torch.empty((0, 5), dtype=torch.int64))
else:
input_list.append(torch.from_numpy(filt_data))
# Now send newly formed chunk to others.
dist.barrier()
output_list = alltoallv_cpu(
rank, world_size, input_list, retain_nones=False
)
# Replace the values of the edge_data, with the received data from all the other processes.
rcvd_edge_data = torch.cat(output_list).numpy()
local_src_ids.append(rcvd_edge_data[:, 0])
local_dst_ids.append(rcvd_edge_data[:, 1])
local_type_eids.append(rcvd_edge_data[:, 2])
local_etype_ids.append(rcvd_edge_data[:, 3])
local_eids.append(rcvd_edge_data[:, 4])
edge_data[
constants.GLOBAL_SRC_ID + "/" + str(local_part_id)
] = np.concatenate(local_src_ids)
edge_data[
constants.GLOBAL_DST_ID + "/" + str(local_part_id)
] = np.concatenate(local_dst_ids)
edge_data[
constants.GLOBAL_TYPE_EID + "/" + str(local_part_id)
] = np.concatenate(local_type_eids)
edge_data[
constants.ETYPE_ID + "/" + str(local_part_id)
] = np.concatenate(local_etype_ids)
edge_data[
constants.GLOBAL_EID + "/" + str(local_part_id)
] = np.concatenate(local_eids)
# Check if the data was exchanged correctly
local_edge_count = 0
for local_part_id in range(num_parts // world_size):
local_edge_count += edge_data[
constants.GLOBAL_SRC_ID + "/" + str(local_part_id)
].shape[0]
shuffle_edge_counts = allgather_sizes(
[local_edge_count], world_size, num_parts, return_sizes=True
)
shuffle_edge_total = np.sum(shuffle_edge_counts)
assert shuffle_edge_total == all_edges
timer_end = timer()
logging.info(
f"[Rank: {rank}] Time to send/rcv edge data: {timedelta(seconds=timer_end-timer_start)}"
)
# Clean up.
edge_data.pop(constants.GLOBAL_SRC_ID)
edge_data.pop(constants.GLOBAL_DST_ID)
edge_data.pop(constants.GLOBAL_TYPE_EID)
edge_data.pop(constants.ETYPE_ID)
edge_data.pop(constants.GLOBAL_EID)
return edge_data
def exchange_feature(
rank,
data,
id_lookup,
feat_type,
feat_key,
featdata_key,
gid_start,
gid_end,
type_id_start,
type_id_end,
local_part_id,
world_size,
num_parts,
cur_features,
cur_global_ids,
):
"""This function is used to send/receive one feature for either nodes or
edges of the input graph dataset.
Parameters:
-----------
rank : int
integer, unique id assigned to the current process
data: dicitonary
dictionry in which node or edge features are stored and this information
is read from the appropriate node features file which belongs to the
current process
id_lookup : instance of DistLookupService
instance of an implementation of dist. lookup service to retrieve values
for keys
feat_type : string
this is used to distinguish which features are being exchanged. Please
note that for nodes ownership is clearly defined and for edges it is
always assumed that destination end point of the edge defines the
ownership of that particular edge
feat_key : string
this string is used as a key in the dictionary to store features, as
tensors, in local dictionaries
featdata_key : numpy array
features associated with this feature key being processed
gid_start : int
starting global_id, of either node or edge, for the feature data
gid_end : int
ending global_if, of either node or edge, for the feature data
type_id_start : int
starting type_id for the feature data
type_id_end : int
ending type_id for the feature data
local_part_id : int
integers used to the identify the local partition id used to locate
data belonging to this partition
world_size : int
total number of processes created
num_parts : int
total number of partitions
cur_features : dictionary
dictionary to store the feature data which belongs to the current
process
cur_global_ids : dictionary
dictionary to store global ids, of either nodes or edges, for which
the features stored in the cur_features dictionary
Returns:
-------
dictionary :
a dictionary is returned where keys are type names and
feature data are the values
list :
a dictionary of global_ids either nodes or edges whose features are
received during the data shuffle process
"""
# type_ids for this feature subset on the current rank
gids_feat = np.arange(gid_start, gid_end)
local_idx = np.arange(0, type_id_end - type_id_start)
feats_per_rank = []
global_id_per_rank = []
tokens = feat_key.split("/")
assert len(tokens) == 3
local_feat_key = "/".join(tokens[:-1]) + "/" + str(local_part_id)
logging.debug(
f"[Rank: {rank} feature: {feat_key}, gid_start - {gid_start} and gid_end - {gid_end}"
)
# Get the partition ids for the range of global nids.
if feat_type == constants.STR_NODE_FEATURES:
# Retrieve the partition ids for the node features.
# Each partition id will be in the range [0, num_parts).
partid_slice = id_lookup.get_partition_ids(
np.arange(gid_start, gid_end, dtype=np.int64)
)
else:
# Edge data case.
# Ownership is determined by the destination node.
assert data is not None
global_eids = np.arange(gid_start, gid_end, dtype=np.int64)
if data[constants.GLOBAL_EID].shape[0] > 0:
logging.debug(
f"[Rank: {rank} disk read global eids - min - {np.amin(data[constants.GLOBAL_EID])}, max - {np.amax(data[constants.GLOBAL_EID])}, count - {data[constants.GLOBAL_EID].shape}"
)
# Now use `data` to extract destination nodes' global id
# and use that to get the ownership
common, idx1, idx2 = np.intersect1d(
data[constants.GLOBAL_EID], global_eids, return_indices=True
)
assert (
common.shape[0] == idx2.shape[0]
), f"Rank {rank}: {common.shape[0]} != {idx2.shape[0]}"
assert (
common.shape[0] == global_eids.shape[0]
), f"Rank {rank}: {common.shape[0]} != {global_eids.shape[0]}"
global_dst_nids = data[constants.GLOBAL_DST_ID][idx1]
assert np.all(global_eids == data[constants.GLOBAL_EID][idx1])
partid_slice = id_lookup.get_partition_ids(global_dst_nids)
# determine the shape of the feature-data
# this is needed to so that ranks where feature-data is not present
# should use the correct shape for sending the padded vector.
# exchange length here.
feat_dim_len = 0
if featdata_key is not None:
feat_dim_len = len(featdata_key.shape)
all_lens = allgather_sizes(
[feat_dim_len], world_size, num_parts, return_sizes=True
)
if all_lens[0] <= 0:
logging.debug(
f"[Rank: {rank} No process has any feature data to shuffle for {local_feat_key}"
)
return cur_features, cur_global_ids
rank0_shape_len = all_lens[0]
for idx in range(1, world_size):
assert (all_lens[idx] == 0) or (all_lens[idx] == rank0_shape_len), (
f"feature: {local_feat_key} shapes does not match "
f"at rank - {idx} and rank - 0"
)
# exchange actual data here.
if featdata_key is not None:
logging.debug(f"Rank: {rank} {featdata_key.shape=}")
feat_dims_dtype = list(featdata_key.shape)
assert (
len(featdata_key.shape) == 2 or len(featdata_key.shape) == 1
), f"We expect 1D or 2D tensors for features, got shape {featdata_key.shape}"
# When a feature is 2-dim, the shape should match the feature dimension.
if len(featdata_key.shape) == 2:
feature_dimension = feat_dims_dtype[1]
else:
feature_dimension = 0
feat_dims_dtype.append(DATA_TYPE_ID[featdata_key.dtype])
else:
feat_dims_dtype = list(np.zeros((rank0_shape_len), dtype=np.int64))
feat_dims_dtype.append(DATA_TYPE_ID[torch.float32])
feature_dimension = 0
feature_dimension_tensor = torch.tensor([feature_dimension])
dist.all_reduce(feature_dimension_tensor, op=dist.ReduceOp.MAX)
feature_dimension = feature_dimension_tensor.item()
logging.debug(f"Sending the feature shape information - {feat_dims_dtype}")
all_dims_dtype = allgather_sizes(
feat_dims_dtype, world_size, num_parts, return_sizes=True
)
for idx in range(world_size):
cond = partid_slice == (idx + local_part_id * world_size)
gids_per_partid = gids_feat[cond]
local_idx_partid = local_idx[cond]
if gids_per_partid.shape[0] == 0:
assert len(all_dims_dtype) % world_size == 0
dim_len = int(len(all_dims_dtype) / world_size)
rank0_shape = list(np.zeros((dim_len - 1), dtype=np.int32))
assert (
len(rank0_shape) == 2 or len(rank0_shape) == 1
), f"We expect 1D or 2D tensors for features, got shape {rank0_shape}"
# When a feature is 2-dim, the shape[1] (number of columns) should match the feature dimension.
if len(rank0_shape) == 2:
rank0_shape[1] = feature_dimension
rank0_dtype = REV_DATA_TYPE_ID[
all_dims_dtype[(dim_len - 1) : (dim_len)][0]
]
data = torch.empty(rank0_shape, dtype=rank0_dtype)
feats_per_rank.append(data)
global_id_per_rank.append(torch.empty((0,), dtype=torch.int64))
else:
feats_per_rank.append(featdata_key[local_idx_partid])
global_id_per_rank.append(
torch.from_numpy(gids_per_partid).type(torch.int64)
)
for idx, tt in enumerate(feats_per_rank):
logging.debug(
f"[Rank: {rank} features shape - {tt.shape} and ids - {global_id_per_rank[idx].shape}"
)
# features (and global nids) per rank to be sent out are ready
# for transmission, perform alltoallv here.
output_feat_list = alltoallv_cpu(
rank, world_size, feats_per_rank, retain_nones=False
)
output_id_list = alltoallv_cpu(
rank, world_size, global_id_per_rank, retain_nones=False
)
logging.debug(
f"[Rank : {rank} feats - {output_feat_list}, ids - {output_id_list}"
)
assert len(output_feat_list) == len(output_id_list), (
"Length of feature list and id list are expected to be equal while "
f"got {len(output_feat_list)} and {len(output_id_list)}."
)
# stitch node_features together to form one large feature tensor
if len(output_feat_list) > 0:
output_feat_list = torch.cat(output_feat_list)
output_id_list = torch.cat(output_id_list)
if local_feat_key in cur_features:
temp = cur_features[local_feat_key]
cur_features[local_feat_key] = torch.cat([temp, output_feat_list])
temp = cur_global_ids[local_feat_key]
cur_global_ids[local_feat_key] = torch.cat([temp, output_id_list])
else:
cur_features[local_feat_key] = output_feat_list
cur_global_ids[local_feat_key] = output_id_list
else:
cur_features[local_feat_key] = torch.empty(
(0, feature_dimension), dtype=torch.float32
)
cur_global_ids[local_feat_key] = torch.empty((0,), dtype=torch.int64)
return cur_features, cur_global_ids
def exchange_features(
rank,
world_size,
num_parts,
feature_tids,
type_id_map,
id_lookup,
feature_data,
feat_type,
data,
):
"""
This function is used to shuffle node features so that each process will receive
all the node features whose corresponding nodes are owned by the same process.
The mapping procedure to identify the owner process is not straight forward. The
following steps are used to identify the owner processes for the locally read node-
features.
a. Compute the global_nids for the locally read node features. Here metadata json file
is used to identify the corresponding global_nids. Please note that initial graph input
nodes.txt files are sorted based on node_types.
b. Using global_nids and metis partitions owner processes can be easily identified.
c. Now each process sends the global_nids for which shuffle_global_nids are needed to be
retrieved.
d. After receiving the corresponding shuffle_global_nids these ids are added to the
node_data and edge_data dictionaries
This pipeline assumes all the input data in numpy format, except node/edge features which
are maintained as tensors throughout the various stages of the pipeline execution.
Parameters:
-----------
rank : int
rank of the current process
world_size : int
total no. of participating processes.
feature_tids : dictionary
dictionary with keys as node-type names with suffixes as feature names
and value is a dictionary. This dictionary contains information about
node-features associated with a given node-type and value is a list.
This list contains a of indexes, like [starting-idx, ending-idx) which
can be used to index into the node feature tensors read from
corresponding input files.
type_id_map : dictionary
mapping between type names and global_ids, of either nodes or edges,
which belong to the keys in this dictionary
id_lookup : instance of class DistLookupService
Distributed lookup service used to map global-nids to respective
partition-ids and shuffle-global-nids
feat_type : string
this is used to distinguish which features are being exchanged. Please
note that for nodes ownership is clearly defined and for edges it is
always assumed that destination end point of the edge defines the
ownership of that particular edge
data: dicitonary
dictionry in which node or edge features are stored and this information
is read from the appropriate node features file which belongs to the
current process
Returns:
--------
dictionary :
a dictionary is returned where keys are type names and
feature data are the values
list :
a dictionary of global_ids either nodes or edges whose features are
received during the data shuffle process
"""
start = timer()
own_features = {}
own_global_ids = {}
# To iterate over the node_types and associated node_features
for feat_key, type_info in feature_tids.items():
# To iterate over the feature data, of a given (node or edge )type
# type_info is a list of 3 elements (as shown below):
# [feature-name, starting-idx, ending-idx]
# feature-name is the name given to the feature-data,
# read from the input metadata file
# [starting-idx, ending-idx) specifies the range of indexes
# associated with the features data
# Determine the owner process for these features.
# Note that the keys in the node features (and similarly edge features)
# dictionary is of the following format:
# `node_type/feature_name/local_part_id`:
# where node_type and feature_name are self-explanatory and
# local_part_id denotes the partition-id, in the local process,
# which will be used a suffix to store all the information of a
# given partition which is processed by the current process. Its
# values start from 0 onwards, for instance 0, 1, 2 ... etc.
# local_part_id can be easily mapped to global partition id very
# easily, using cyclic ordering. All local_part_ids = 0 from all
# processes will form global partition-ids between 0 and world_size-1.
# Similarly all local_part_ids = 1 from all processes will form
# global partition ids in the range [world_size, 2*world_size-1] and
# so on.
tokens = feat_key.split("/")
assert len(tokens) == 3
type_name = tokens[0]
feat_name = tokens[1]
logging.debug(f"[Rank: {rank}] processing feature: {feat_key}")
for feat_info in type_info:
# Compute the global_id range for this feature data
type_id_start = int(feat_info[0])
type_id_end = int(feat_info[1])
begin_global_id = type_id_map[type_name][0]
gid_start = begin_global_id + type_id_start
gid_end = begin_global_id + type_id_end
# Check if features exist for this type_name + feat_name.
# This check should always pass, because feature_tids are built
# by reading the input metadata json file for existing features.
assert feat_key in feature_data
for local_part_id in range(num_parts // world_size):
featdata_key = feature_data[feat_key]
# Synchronize for each feature
dist.barrier()
own_features, own_global_ids = exchange_feature(
rank,
data,
id_lookup,
feat_type,
feat_key,
featdata_key,
gid_start,
gid_end,
type_id_start,
type_id_end,
local_part_id,
world_size,
num_parts,
own_features,
own_global_ids,
)
end = timer()
logging.info(
f"[Rank: {rank}] Total time for feature exchange: {timedelta(seconds = end - start)}"
)
for k, v in own_features.items():
logging.debug(f"Rank: {rank}] Key - {k} Value - {v.shape}")
return own_features, own_global_ids
def exchange_graph_data(
rank,
world_size,
num_parts,
node_features,
edge_features,
node_feat_tids,
edge_feat_tids,
edge_data,
id_lookup,
ntypes_ntypeid_map,
ntypes_gnid_range_map,
etypes_geid_range_map,
ntid_ntype_map,
schema_map,
):
"""
Wrapper function which is used to shuffle graph data on all the processes.
Parameters:
-----------
rank : int
rank of the current process
world_size : int
total no. of participating processes.
num_parts : int
total no. of graph partitions.
node_feautres : dicitonary
dictionry where node_features are stored and this information is read from the appropriate
node features file which belongs to the current process
edge_features : dictionary
dictionary where edge_features are stored. This information is read from the appropriate
edge feature files whose ownership is assigned to the current process
node_feat_tids: dictionary
in which keys are node-type names and values are triplets. Each triplet has node-feature name
and the starting and ending type ids of the node-feature data read from the corresponding
node feature data file read by current process. Each node type may have several features and
hence each key may have several triplets.
edge_feat_tids : dictionary
a dictionary in which keys are edge-type names and values are triplets of the format
<feat-name, start-per-type-idx, end-per-type-idx>. This triplet is used to identify
the chunk of feature data for which current process is responsible for
edge_data : dictionary
dictionary which is used to store edge information as read from appropriate files assigned
to each process.
id_lookup : instance of class DistLookupService
Distributed lookup service used to map global-nids to respective partition-ids and
shuffle-global-nids
ntypes_ntypeid_map : dictionary
mappings between node type names and node type ids
ntypes_gnid_range_map : dictionary
mapping between node type names and global_nids which belong to the keys in this dictionary
etypes_geid_range_map : dictionary
mapping between edge type names and global_eids which are assigned to the edges of this
edge_type
ntid_ntype_map : dictionary
mapping between node type id and no of nodes which belong to each node_type_id
schema_map : dictionary
is the data structure read from the metadata json file for the input graph
Returns:
--------
dictionary :
the input argument, node_data dictionary, is updated with the node data received from other processes
in the world. The node data is received by each rank in the process of data shuffling.
dictionary :
node features dictionary which has node features for the nodes which are owned by the current
process
dictionary :
list of global_nids for the nodes whose node features are received when node features shuffling was
performed in the `exchange_features` function call
dictionary :
the input argument, edge_data dictionary, is updated with the edge data received from other processes
in the world. The edge data is received by each rank in the process of data shuffling.
dictionary :
edge features dictionary which has edge features. These destination end points of these edges
are owned by the current process
dictionary :
list of global_eids for the edges whose edge features are received when edge features shuffling
was performed in the `exchange_features` function call
"""
memory_snapshot("ShuffleNodeFeaturesBegin: ", rank)
logging.debug(f"[Rank: {rank} - node_feat_tids - {node_feat_tids}")
rcvd_node_features, rcvd_global_nids = exchange_features(
rank,
world_size,
num_parts,
node_feat_tids,
ntypes_gnid_range_map,
id_lookup,
node_features,
constants.STR_NODE_FEATURES,
None,
)
dist.barrier()
memory_snapshot("ShuffleNodeFeaturesComplete: ", rank)
logging.debug(f"[Rank: {rank}] Done with node features exchange.")
rcvd_edge_features, rcvd_global_eids = exchange_features(
rank,
world_size,
num_parts,
edge_feat_tids,
etypes_geid_range_map,
id_lookup,
edge_features,
constants.STR_EDGE_FEATURES,
edge_data,
)
dist.barrier()
logging.debug(f"[Rank: {rank}] Done with edge features exchange.")
node_data = gen_node_data(
rank, world_size, num_parts, id_lookup, ntid_ntype_map, schema_map
)
dist.barrier()
memory_snapshot("NodeDataGenerationComplete: ", rank)
edge_data = exchange_edge_data(
rank, world_size, num_parts, edge_data, id_lookup
)
dist.barrier()
memory_snapshot("ShuffleEdgeDataComplete: ", rank)
return (
node_data,
rcvd_node_features,
rcvd_global_nids,
edge_data,
rcvd_edge_features,
rcvd_global_eids,
)
def read_dataset(rank, world_size, id_lookup, params, schema_map, ntype_counts):
"""
This function gets the dataset and performs post-processing on the data which is read from files.
Additional information(columns) are added to nodes metadata like owner_process, global_nid which
are later used in processing this information. For edge data, which is now a dictionary, we add new columns
like global_edge_id and owner_process. Augmenting these data structure helps in processing these data structures
when data shuffling is performed.
Parameters:
-----------
rank : int
rank of the current process
world_size : int
total no. of processes instantiated
id_lookup : instance of class DistLookupService
Distributed lookup service used to map global-nids to respective partition-ids and
shuffle-global-nids
params : argparser object
argument parser object to access command line arguments
schema_map : dictionary
dictionary created by reading the input graph metadata json file
Returns :
---------
dictionary
in which keys are node-type names and values are are tuples representing the range of ids
for nodes to be read by the current process
dictionary
node features which is a dictionary where keys are feature names and values are feature
data as multi-dimensional tensors
dictionary
in which keys are node-type names and values are triplets. Each triplet has node-feature name
and the starting and ending type ids of the node-feature data read from the corresponding
node feature data file read by current process. Each node type may have several features and
hence each key may have several triplets.
dictionary
edge data information is read from edges.txt and additional columns are added such as
owner process for each edge.
dictionary
edge features which is also a dictionary, similar to node features dictionary
dictionary
a dictionary in which keys are edge-type names and values are tuples indicating the range of ids
for edges read by the current process.
dictionary
a dictionary in which keys are edge-type names and values are triplets,
(edge-feature-name, start_type_id, end_type_id). These type_ids are indices in the edge-features
read by the current process. Note that each edge-type may have several edge-features.
"""
edge_features = {}
(
node_features,
node_feat_tids,
edge_data,
edge_typecounts,
edge_tids,
edge_features,
edge_feat_tids,
) = get_dataset(
params.input_dir,
params.graph_name,
rank,
world_size,
params.num_parts,
schema_map,
ntype_counts,
)
# Synchronize so that everybody completes reading dataset from disk
dist.barrier()
logging.info(f"[Rank: {rank}] Done reading dataset {params.input_dir}")
edge_data = augment_edge_data(
edge_data, id_lookup, edge_tids, rank, world_size, params.num_parts
)
dist.barrier() # SYNCH
logging.debug(
f"[Rank: {rank}] Done augmenting edge_data: {len(edge_data)}, {edge_data[constants.GLOBAL_SRC_ID].shape}"
)
return (
node_features,
node_feat_tids,
edge_data,
edge_typecounts,
edge_features,
edge_feat_tids,
)
def reorder_data(num_parts, world_size, data, key):
"""
Auxiliary function used to sort node and edge data for the input graph.
Parameters:
-----------
num_parts : int
total no. of partitions
world_size : int
total number of nodes used in this execution
data : dictionary
which is used to store the node and edge data for the input graph
key : string
specifies the column which is used to determine the sort order for
the remaining columns
Returns:
--------
dictionary
same as the input dictionary, but with reordered columns (values in
the dictionary), as per the np.argsort results on the column specified
by the ``key`` column
"""
for local_part_id in range(num_parts // world_size):
sorted_idx = data[key + "/" + str(local_part_id)].argsort()
for k, v in data.items():
tokens = k.split("/")
assert len(tokens) == 2
if tokens[1] == str(local_part_id):
data[k] = v[sorted_idx]
sorted_idx = None
gc.collect()
return data
def gen_dist_partitions(rank, world_size, params):
"""
Function which will be executed by all Gloo processes to begin execution of the pipeline.
This function expects the input dataset is split across multiple file format.
Input dataset and its file structure is described in metadata json file which is also part of the
input dataset. On a high-level, this metadata json file contains information about the following items
a) Nodes metadata, It is assumed that nodes which belong to each node-type are split into p files
(wherer `p` is no. of partitions).
b) Similarly edge metadata contains information about edges which are split into p-files.
c) Node and Edge features, it is also assumed that each node (and edge) feature, if present, is also
split into `p` files.
For example, a sample metadata json file might be as follows: :
(In this toy example, we assume that we have "m" node-types, "k" edge types, and for node_type = ntype0-name
we have two features namely feat0-name and feat1-name. Please note that the node-features are also split into
`p` files. This will help in load-balancing during data-shuffling phase).
Terminology used to identify any particular "id" assigned to nodes, edges or node features. Prefix "global" is
used to indicate that this information is either read from the input dataset or autogenerated based on the information
read from input dataset files. Prefix "type" is used to indicate a unique id assigned to either nodes or edges.
For instance, type_node_id means that a unique id, with a given node type, assigned to a node. And prefix "shuffle"
will be used to indicate a unique id, across entire graph, assigned to either a node or an edge. For instance,
SHUFFLE_GLOBAL_NID means a unique id which is assigned to a node after the data shuffle is completed.
Some high-level notes on the structure of the metadata json file.
1. path(s) mentioned in the entries for nodes, edges and node-features files can be either absolute or relative.
if these paths are relative, then it is assumed that they are relative to the folder from which the execution is
launched.
2. The id_startx and id_endx represent the type_node_id and type_edge_id respectively for nodes and edge data. This
means that these ids should match the no. of nodes/edges read from any given file. Since these are type_ids for
the nodes and edges in any given file, their global_ids can be easily computed as well.
{
"graph_name" : xyz,
"node_type" : ["ntype0-name", "ntype1-name", ....], #m node types
"num_nodes_per_chunk" : [
[a0, a1, ...a<p-1>], #p partitions
[b0, b1, ... b<p-1>],
....
[c0, c1, ..., c<p-1>] #no, of node types
],
"edge_type" : ["src_ntype:edge_type:dst_ntype", ....], #k edge types
"num_edges_per_chunk" : [
[a0, a1, ...a<p-1>], #p partitions
[b0, b1, ... b<p-1>],
....
[c0, c1, ..., c<p-1>] #no, of edge types
],
"node_data" : {
"ntype0-name" : {
"feat0-name" : {
"format" : {"name": "numpy"},
"data" : [ #list of lists
["<path>/feat-0.npy", 0, id_end0],
["<path>/feat-1.npy", id_start1, id_end1],
....
["<path>/feat-<p-1>.npy", id_start<p-1>, id_end<p-1>]
]
},
"feat1-name" : {
"format" : {"name": "numpy"},
"data" : [ #list of lists
["<path>/feat-0.npy", 0, id_end0],
["<path>/feat-1.npy", id_start1, id_end1],
....
["<path>/feat-<p-1>.npy", id_start<p-1>, id_end<p-1>]
]
}
}
},
"edges": { #k edge types
"src_ntype:etype0-name:dst_ntype" : {
"format": {"name" : "csv", "delimiter" : " "},
"data" : [
["<path>/etype0-name-0.txt", 0, id_end0], #These are type_edge_ids for edges of this type
["<path>/etype0-name-1.txt", id_start1, id_end1],
...,
["<path>/etype0-name-<p-1>.txt", id_start<p-1>, id_end<p-1>]
]
},
...,
"src_ntype:etype<k-1>-name:dst_ntype" : {
"format": {"name" : "csv", "delimiter" : " "},
"data" : [
["<path>/etype<k-1>-name-0.txt", 0, id_end0],
["<path>/etype<k-1>-name-1.txt", id_start1, id_end1],
...,
["<path>/etype<k-1>-name-<p-1>.txt", id_start<p-1>, id_end<p-1>]
]
},
},
}
The function performs the following steps:
1. Reads the metis partitions to identify the owner process of all the nodes in the entire graph.
2. Reads the input data set, each partitipating process will map to a single file for the edges,
node-features and edge-features for each node-type and edge-types respectively. Using nodes metadata
information, nodes which are owned by a given process are generated to optimize communication to some
extent.
3. Now each process shuffles the data by identifying the respective owner processes using metis
partitions.
a. To identify owner processes for nodes, metis partitions will be used.
b. For edges, the owner process of the destination node will be the owner of the edge as well.
c. For node and edge features, identifying the owner process is a little bit involved.
For this purpose, graph metadata json file is used to first map the locally read node features
to their global_nids. Now owner process is identified using metis partitions for these global_nids
to retrieve shuffle_global_nids. A similar process is used for edge_features as well.
d. After all the data shuffling is done, the order of node-features may be different when compared to
their global_type_nids. Node- and edge-data are ordered by node-type and edge-type respectively.
And now node features and edge features are re-ordered to match the order of their node- and edge-types.
4. Last step is to create the DGL objects with the data present on each of the processes.
a. DGL objects for nodes, edges, node- and edge- features.
b. Metadata is gathered from each process to create the global metadata json file, by process rank = 0.
Parameters:
----------
rank : int
integer representing the rank of the current process in a typical distributed implementation
world_size : int
integer representing the total no. of participating processes in a typical distributed implementation
params : argparser object
this object, key value pairs, provides access to the command line arguments from the runtime environment
"""
global_start = timer()
logging.info(
f"[Rank: {rank}] Starting distributed data processing pipeline..."
)
memory_snapshot("Pipeline Begin: ", rank)
# init processing
schema_map = read_json(os.path.join(params.input_dir, params.schema))
# The resources, which are node-id to partition-id mappings, are split
# into `world_size` number of parts, where each part can be mapped to
# each physical node.
id_lookup = DistLookupService(
os.path.join(params.input_dir, params.partitions_dir),
schema_map[constants.STR_NODE_TYPE],
rank,
world_size,
params.num_parts,
)
# get the id to name mappings here.
ntypes_ntypeid_map, ntypes, ntypeid_ntypes_map = get_node_types(schema_map)
etypes_etypeid_map, etypes, etypeid_etypes_map = get_edge_types(schema_map)
logging.info(
f"[Rank: {rank}] Initialized metis partitions and node_types map..."
)
# Initialize distributed lookup service for partition-id and shuffle-global-nids mappings
# for global-nids
_, global_nid_ranges = get_idranges(
schema_map[constants.STR_NODE_TYPE],
get_ntype_counts_map(
schema_map[constants.STR_NODE_TYPE],
schema_map[constants.STR_NUM_NODES_PER_TYPE],
),
)
id_map = dgl.distributed.id_map.IdMap(global_nid_ranges)
id_lookup.set_idMap(id_map)
# read input graph files and augment these datastructures with
# appropriate information (global_nid and owner process) for node and edge data
(
node_features,
node_feat_tids,
edge_data,
edge_typecounts,
edge_features,
edge_feat_tids,
) = read_dataset(
rank,
world_size,
id_lookup,
params,
schema_map,
get_ntype_counts_map(
schema_map[constants.STR_NODE_TYPE],
schema_map[constants.STR_NUM_NODES_PER_TYPE],
),
)
logging.info(
f"[Rank: {rank}] Done augmenting file input data with auxilary columns"
)
memory_snapshot("DatasetReadComplete: ", rank)
# send out node and edge data --- and appropriate features.
# this function will also stitch the data recvd from other processes
# and return the aggregated data
# ntypes_gnid_range_map = get_gnid_range_map(node_tids)
# etypes_geid_range_map = get_gnid_range_map(edge_tids)
ntypes_gnid_range_map = get_gid_offsets(
schema_map[constants.STR_NODE_TYPE],
get_ntype_counts_map(
schema_map[constants.STR_NODE_TYPE],
schema_map[constants.STR_NUM_NODES_PER_TYPE],
),
)
etypes_geid_range_map = get_gid_offsets(
schema_map[constants.STR_EDGE_TYPE], edge_typecounts
)
(
node_data,
rcvd_node_features,
rcvd_global_nids,
edge_data,
rcvd_edge_features,
rcvd_global_eids,
) = exchange_graph_data(
rank,
world_size,
params.num_parts,
node_features,
edge_features,
node_feat_tids,
edge_feat_tids,
edge_data,
id_lookup,
ntypes_ntypeid_map,
ntypes_gnid_range_map,
etypes_geid_range_map,
ntypeid_ntypes_map,
schema_map,
)
gc.collect()
logging.debug(f"[Rank: {rank}] Done with data shuffling...")
memory_snapshot("DataShuffleComplete: ", rank)
# sort node_data by ntype
node_data = reorder_data(
params.num_parts, world_size, node_data, constants.NTYPE_ID
)
logging.debug(f"[Rank: {rank}] Sorted node_data by node_type")
memory_snapshot("NodeDataSortComplete: ", rank)
# resolve global_ids for nodes
# Synchronize before assigning shuffle-global-ids to nodes
dist.barrier()
assign_shuffle_global_nids_nodes(
rank, world_size, params.num_parts, node_data
)
logging.debug(f"[Rank: {rank}] Done assigning global-ids to nodes...")
memory_snapshot("ShuffleGlobalID_Nodes_Complete: ", rank)
# shuffle node feature according to the node order on each rank.
for ntype_name in ntypes:
featnames = get_ntype_featnames(ntype_name, schema_map)
for featname in featnames:
# if a feature name exists for a node-type, then it should also have
# feature data as well. Hence using the assert statement.
for local_part_id in range(params.num_parts // world_size):
feature_key = (
ntype_name + "/" + featname + "/" + str(local_part_id)
)
assert feature_key in rcvd_global_nids
global_nids = rcvd_global_nids[feature_key]
_, idx1, _ = np.intersect1d(
node_data[constants.GLOBAL_NID + "/" + str(local_part_id)],
global_nids,
return_indices=True,
)
shuffle_global_ids = node_data[
constants.SHUFFLE_GLOBAL_NID + "/" + str(local_part_id)
][idx1]
feature_idx = shuffle_global_ids.argsort()
rcvd_node_features[feature_key] = rcvd_node_features[
feature_key
][feature_idx]
memory_snapshot("ReorderNodeFeaturesComplete: ", rank)
# Sort edge_data by etype
edge_data = reorder_data(
params.num_parts, world_size, edge_data, constants.ETYPE_ID
)
logging.debug(f"[Rank: {rank}] Sorted edge_data by edge_type")
memory_snapshot("EdgeDataSortComplete: ", rank)
# Synchronize before assigning shuffle-global-nids for edges end points.
dist.barrier()
shuffle_global_eid_offsets = assign_shuffle_global_nids_edges(
rank, world_size, params.num_parts, edge_data
)
logging.debug(f"[Rank: {rank}] Done assigning global_ids to edges ...")
memory_snapshot("ShuffleGlobalID_Edges_Complete: ", rank)
# Shuffle edge features according to the edge order on each rank.
for etype_name in etypes:
featnames = get_etype_featnames(etype_name, schema_map)
for featname in featnames:
for local_part_id in range(params.num_parts // world_size):
feature_key = (
etype_name + "/" + featname + "/" + str(local_part_id)
)
assert feature_key in rcvd_global_eids
global_eids = rcvd_global_eids[feature_key]
_, idx1, _ = np.intersect1d(
edge_data[constants.GLOBAL_EID + "/" + str(local_part_id)],
global_eids,
return_indices=True,
)
shuffle_global_ids = edge_data[
constants.SHUFFLE_GLOBAL_EID + "/" + str(local_part_id)
][idx1]
feature_idx = shuffle_global_ids.argsort()
rcvd_edge_features[feature_key] = rcvd_edge_features[
feature_key
][feature_idx]
# determine global-ids for edge end-points
# Synchronize before retrieving shuffle-global-nids for edges end points.
dist.barrier()
edge_data = lookup_shuffle_global_nids_edges(
rank, world_size, params.num_parts, edge_data, id_lookup, node_data
)
logging.debug(
f"[Rank: {rank}] Done resolving orig_node_id for local node_ids..."
)
memory_snapshot("ShuffleGlobalID_Lookup_Complete: ", rank)
def prepare_local_data(src_data, local_part_id):
local_data = {}
for k, v in src_data.items():
tokens = k.split("/")
if tokens[len(tokens) - 1] == str(local_part_id):
local_data["/".join(tokens[:-1])] = v
return local_data
# create dgl objects here
output_meta_json = {}
start = timer()
graph_formats = None
if params.graph_formats:
graph_formats = params.graph_formats.split(",")
prev_last_ids = {}
for local_part_id in range(params.num_parts // world_size):
# Synchronize for each local partition of the graph object.
dist.barrier()
num_edges = shuffle_global_eid_offsets[local_part_id]
node_count = len(
node_data[constants.NTYPE_ID + "/" + str(local_part_id)]
)
edge_count = len(
edge_data[constants.ETYPE_ID + "/" + str(local_part_id)]
)
local_node_data = prepare_local_data(node_data, local_part_id)
local_edge_data = prepare_local_data(edge_data, local_part_id)
tot_node_count = sum(schema_map["num_nodes_per_type"])
tot_edge_count = sum(schema_map["num_edges_per_type"])
(
graph_obj,
ntypes_map_val,
etypes_map_val,
ntypes_map,
etypes_map,
orig_nids,
orig_eids,
) = create_graph_object(
tot_node_count,
tot_edge_count,
node_count,
edge_count,
params.num_parts,
schema_map,
rank + local_part_id * world_size,
local_node_data,
local_edge_data,
num_edges,
get_ntype_counts_map(
schema_map[constants.STR_NODE_TYPE],
schema_map[constants.STR_NUM_NODES_PER_TYPE],
),
edge_typecounts,
prev_last_ids,
return_orig_nids=params.save_orig_nids,
return_orig_eids=params.save_orig_eids,
use_graphbolt=params.use_graphbolt,
store_inner_node=params.store_inner_node,
store_inner_edge=params.store_inner_edge,
store_eids=params.store_eids,
)
sort_etypes = len(etypes_map) > 1
local_node_features = prepare_local_data(
rcvd_node_features, local_part_id
)
local_edge_features = prepare_local_data(
rcvd_edge_features, local_part_id
)
write_dgl_objects(
graph_obj,
local_node_features,
local_edge_features,
params.output,
rank + (local_part_id * world_size),
orig_nids,
orig_eids,
graph_formats,
sort_etypes,
params.use_graphbolt,
)
if params.use_graphbolt:
memory_snapshot("DiskWriteGrapgboltObjectsComplete: ", rank)
else:
memory_snapshot("DiskWriteDGLObjectsComplete: ", rank)
# get the meta-data
json_metadata = create_metadata_json(
params.graph_name,
node_count,
edge_count,
local_part_id * world_size + rank,
params.num_parts,
ntypes_map_val,
etypes_map_val,
ntypes_map,
etypes_map,
params.output,
params.use_graphbolt,
)
output_meta_json[
"local-part-id-" + str(local_part_id * world_size + rank)
] = json_metadata
memory_snapshot("MetadataCreateComplete: ", rank)
last_id_tensor = torch.tensor(
[prev_last_ids[rank + (local_part_id * world_size)]],
dtype=torch.int64,
)
gather_list = [
torch.zeros(1, dtype=torch.int64) for _ in range(world_size)
]
dist.all_gather(gather_list, last_id_tensor)
for rank_id, last_id in enumerate(gather_list):
prev_last_ids[
rank_id + (local_part_id * world_size)
] = last_id.item()
if rank == 0:
# get meta-data from all partitions and merge them on rank-0
metadata_list = gather_metadata_json(output_meta_json, rank, world_size)
metadata_list[0] = output_meta_json
write_metadata_json(
metadata_list,
params.output,
params.graph_name,
world_size,
params.num_parts,
)
else:
# send meta-data to Rank-0 process
gather_metadata_json(output_meta_json, rank, world_size)
end = timer()
logging.info(
f"[Rank: {rank}] Time to create dgl objects: {timedelta(seconds = end - start)}"
)
memory_snapshot("MetadataWriteComplete: ", rank)
global_end = timer()
logging.info(
f"[Rank: {rank}] Total execution time of the program: {timedelta(seconds = global_end - global_start)}"
)
memory_snapshot("PipelineComplete: ", rank)
def single_machine_run(params):
"""Main function for distributed implementation on a single machine
Parameters:
-----------
params : argparser object
Argument Parser structure with pre-determined arguments as defined
at the bottom of this file.
"""
processes = []
mp.set_start_method("spawn")
# Invoke `target` function from each of the spawned process for distributed
# implementation
for rank in range(params.world_size):
p = mp.Process(
target=run,
args=(rank, params.world_size, gen_dist_partitions, params),
)
p.start()
processes.append(p)
for p in processes:
p.join()
def run(rank, world_size, func_exec, params, backend="gloo"):
"""
Init. function which is run by each process in the Gloo ProcessGroup
Parameters:
-----------
rank : integer
rank of the process
world_size : integer
number of processes configured in the Process Group
proc_exec : function name
function which will be invoked which has the logic for each process in the group
params : argparser object
argument parser object to access the command line arguments
backend : string
string specifying the type of backend to use for communication
"""
os.environ["MASTER_ADDR"] = "127.0.0.1"
os.environ["MASTER_PORT"] = "29500"
# create Gloo Process Group
dist.init_process_group(
backend,
rank=rank,
world_size=world_size,
timeout=timedelta(seconds=5 * 60),
)
# Invoke the main function to kick-off each process
func_exec(rank, world_size, params)
def multi_machine_run(params):
"""
Function to be invoked when executing data loading pipeline on multiple machines
Parameters:
-----------
params : argparser object
argparser object providing access to command line arguments.
"""
rank = int(os.environ["RANK"])
# init the gloo process group here.
dist.init_process_group(
backend="gloo",
rank=rank,
world_size=params.world_size,
timeout=timedelta(seconds=params.process_group_timeout),
)
logging.info(f"[Rank: {rank}] Done with process group initialization...")
# invoke the main function here.
gen_dist_partitions(rank, params.world_size, params)
logging.info(
f"[Rank: {rank}] Done with Distributed data processing pipeline processing."
)