[Feature] Add removed edges in distributed graph partitioning to handle heterogeneous graph (#3137)

* Added code for Rectifying (TypeError: unhashable type: 'slice') when copying file

* 1) added distributed preprocessing code to create ParMetis Input from CSV files
2) add code to run pm_dglpart on multiple machines
3) added support for recreating heteregenous graph from homo geneous graph based on dropped edges, as ParMetis currently only supports homogeneous graphs

* move to pandas

* Added comments and remove drop_duplicates as it was redundant

* Addressed Pr Comments

* Rename variable

* Added comment

* Added comment

* updated ReadMe
Co-authored-by: Ankit Garg <gaank@amazon.com>
Co-authored-by: Da Zheng <zhengda1936@gmail.com>

README.md

@@ -37,6 +37,8 @@ DGL provides a plenty of learning materials for all kinds of users from ML resea
 
 It is convenient to train models using DGL on large-scale graphs across multiple GPUs or multiple machines. DGL extensively optimizes the whole stack to reduce the overhead in communication, memory consumption and synchronization. As a result, DGL can easily scale to billion-sized graphs. See the [system performance note](https://docs.dgl.ai/performance.html) for the comparison with the other tools.
 
+Now DistDGL ParMETIS implementation also provides support for hetero graph by adding back the dropped edges back into the partitioned graph thus handling parMetis hetero graph usecase.
+
 ## Get Started
 
 Users can install DGL from [pip and conda](https://www.dgl.ai/pages/start.html). Advanced users can follow the [instructions](https://docs.dgl.ai/install/index.html#install-from-source) to install from source.

examples/pytorch/rgcn/experimental/preprocessing_dist_training/edges/identity1/sample.csv

+identity1,0,0,1
+identity1,1,0,2
+

examples/pytorch/rgcn/experimental/preprocessing_dist_training/edges/identity2/sample.csv

+identity2,0,1,2
+identity2,1,0,2
+

examples/pytorch/rgcn/experimental/preprocessing_dist_training/edges/identity3/sample.csv

+identity3,0,0,2

examples/pytorch/rgcn/experimental/preprocessing_dist_training/metis_creation.py

+import pandas as pd
+import os
+import glob
+import json
+import argparse
+from collections import defaultdict
+
+path = os.getcwd()
+
+parser = argparse.ArgumentParser()
+parser.add_argument("-n", "--name", help="name of graph to create", default="order")
+parser.add_argument("-nc", "--node_column", nargs="+", default=['order_id', 'entity_index', 'order_datetime', 'cid'])
+parser.add_argument("-nk", "--node_key", default='entity_index')
+parser.add_argument("-ec", "--edge_column", nargs="+", default=['predicate_type', 'predicate_index', 'entity_index', 'entity_index_y'])
+parser.add_argument("-es", "--edge_start", default="entity_index")
+parser.add_argument("-en", "--edge_end", default="entity_index_y")
+args = parser.parse_args()
+
+
+#Store all types of node in nodes folder
+nodes_list = sorted(glob.glob(os.path.join(path, "nodes/*")))
+
+if os.path.exists("{}_nodes.txt".format(args.name)):
+    os.remove("{}_nodes.txt".format(args.name))
+
+schema_dict = defaultdict(dict)
+
+node_type_id = 0
+all_nodes_count = 0
+for node_type_name in nodes_list:
+    nodes_count = 0
+    csv_files = sorted(glob.glob(os.path.join(node_type_name, "*.csv")))
+    for file_name in csv_files:
+        df = pd.read_csv(file_name, error_bad_lines=False, escapechar='\\', names=args.node_column, usecols=[*range(len(args.node_column))])
+        df_entity = pd.DataFrame(df[args.node_key], columns=[args.node_key])
+        df_entity['type'] = node_type_id
+        column_list = ['type']
+        for weight_index in range(len(nodes_list)):
+            weight_num = "weight{}".format(weight_index)
+            column_list.append(weight_num)
+            if weight_index == node_type_id:
+                df_entity[weight_num] = 1
+            else:
+                df_entity[weight_num] = 0
+        nodes_count += len(df_entity.index)
+        column_list.append(args.node_key)
+        #This loop is trying to create file which servers as an input for Metis Algorithm.
+        #More details about metis input can been found here : https://docs.dgl.ai/en/0.6.x/guide/distributed-preprocessing.html#input-format-for-parmetis
+        df_entity.to_csv("{}_nodes.txt".format(args.name), columns=column_list, sep=" ", index=False, header=False, mode='a')
+    schema_dict['nid'][os.path.basename(node_type_name)] = [all_nodes_count, nodes_count + all_nodes_count]
+    all_nodes_count += nodes_count
+    node_type_id += 1
+
+
+if os.path.exists("{}_edges.txt".format(args.name)):
+    os.remove("{}_edges.txt".format(args.name))
+
+#Store all types of edge in edges folder
+edges_list = sorted(glob.glob(os.path.join(path, "edges/*")))
+
+
+all_edges_count = 0
+edge_type_id = 0
+for edge_type_name in edges_list:
+    edge_count = 0
+    csv_files = sorted(glob.glob(os.path.join(edge_type_name, "*.csv")))
+    for file_name in csv_files:
+        df = pd.read_csv(file_name, error_bad_lines=False, escapechar='\\', names=args.edge_column, usecols=[*range(len(args.edge_column))])
+        df_entity = pd.DataFrame(df[[args.edge_start, args.edge_end]], columns=[args.edge_start, args.edge_end])
+        df_entity['type'] = edge_type_id
+        df_entity = df_entity.reset_index()
+        df_entity['number'] = df_entity.index + edge_count
+        edge_count += len(df_entity.index)
+        #This loop is trying to create file which servers as an input for Metis Algorithm.
+        #More details about metis input can been found here : https://docs.dgl.ai/en/0.6.x/guide/distributed-preprocessing.html#input-format-for-parmetis
+        df_entity.to_csv("{}_edges.txt".format(args.name), columns=[args.edge_start, args.edge_end, 'number', 'type'], sep=" ", index=False, header=False, mode='a')
+    schema_dict['eid'][os.path.basename(edge_type_name)] = [all_edges_count, all_edges_count + edge_count]
+    edge_type_id += 1
+    all_edges_count += edge_count
+
+if os.path.exists("{}_stats.txt".format(args.name)):
+    os.remove("{}_stats.txt".format(args.name))
+
+
+df = pd.DataFrame([[all_nodes_count, all_edges_count, len(nodes_list)]], columns=['nodes_count', 'edges_count', 'weight_count'])
+df.to_csv("{}_stats.txt".format(args.name), columns=['nodes_count', 'edges_count', 'weight_count'], sep=" ", index=False, header=False)
+
+if os.path.exists("{}.json".format(args.name)):
+    os.remove("{}.json".format(args.name))
+
+with open("{}.json".format(args.name), "w", encoding="utf8") as json_file:
+    json.dump(schema_dict, json_file, ensure_ascii=False)
+

examples/pytorch/rgcn/experimental/preprocessing_dist_training/nodes/order/sample.csv

+171-0000102-1785122,0,2021-06-01 21:15:33,18604601535
+171-0000550-1206725,1,2021-06-08 12:53:53,19613747325
+171-0000784-4201160,2,2021-06-05 16:27:42,8348611025

examples/pytorch/rgcn/experimental/preprocessing_dist_training/pre_process_dist_training.sh

+#!/bin/bash
+
+
+cur_dir=$(pwd)
+host_count=`cat hostfile | wc -l`
+graph_name="order"
+perhost_part=2
+current_host=`ifconfig | grep -Eo 'inet (addr:)?([0-9]*\.){3}[0-9]*' | grep -Eo '([0-9]*\.){3}[0-9]*' | grep -v '127.0.0.1'`
+
+echo "metis creation start"
+
+##Nodes 
+`python3 metis_creation.py -n ${graph_name}`
+
+echo "metis creation ends"
+
+echo "directory creation starts"
+while read p; do
+  if [ "$p" != "$current_host" ]; then
+    `ssh ${p} "mkdir -p ${cur_dir}" < /dev/null`
+  fi
+done <hostfile
+
+echo "directory creation ends"
+
+echo "partioning starts"
+`mpirun --hostfile hostfile -np ${host_count} pm_dglpart ${graph_name} ${perhost_part} > mpirun.out`
+echo "partioning ends"
+
+
+echo "scp starts"
+while read p; do
+  if [ "$p" != "$current_host" ]; then
+    `scp ${p}:${cur_dir}/* ./ < /dev/null`
+  fi
+done <hostfile
+echo "scp ends"
+
+echo "fetching removed edges starts"
+`cat mpirun.out | grep "Duplicate edges with metadata" | awk -F'[][]' '{print $4}' > remove.csv`
+echo "fetching removed edges ends"
+
+echo "homo graph to herto graph starts"
+`python3 substitute_to_hetero.py -n order -r remove.csv`
+echo "homo graph to herto graph ends"

tools/convert_partition.py

@@ -6,8 +6,10 @@ import numpy as np
 import dgl
 import torch as th
 import pyarrow
+import pandas as pd
 from pyarrow import csv
 
+
 parser = argparse.ArgumentParser(description='Construct graph partitions')
 parser.add_argument('--input-dir', required=True, type=str,
                     help='The directory path that contains the partition results.')
@@ -27,6 +29,8 @@ parser.add_argument('--edge-attr-dtype', type=str, default=None,
                     help='The data type of the edge attributes')
 parser.add_argument('--output', required=True, type=str,
                     help='The output directory of the partitioned results')
+parser.add_argument('--removed-edges', help='file where we have edges that were dropped', default=None, type=str)
+
 args = parser.parse_args()
 
 input_dir = args.input_dir
@@ -38,6 +42,29 @@ edge_attr_dtype = args.edge_attr_dtype
 workspace_dir = args.workspace
 output_dir = args.output
 
+
+if args.removed_edges is not None:
+    removed_file = '{}/{}'.format(input_dir, args.removed_edges)
+    remove_column_index = [0, 1, 2, 3]
+    remove_column_name = ["distributed_src_id", "distributed_dest_id", "src_id", "dest_id"]
+    removed_df = pd.read_csv(removed_file, sep=" ", header=None)
+    removed_df.rename(columns = {0: "src_id", 1: "dest_id"}, inplace=True)
+
+    # We are adding removed edges back into the partitioned file, so that all the edges
+    # that were removed during ParMETIS gets retained back into the partioned file, so that
+    # no edges were lost.
+
+    print('Adding removed edges back into the partitioned file, that way all edges that were removed during ParMETIS gets retained back into the partioned file')
+
+    for part_id in range(num_parts):
+        edge_file = '{}/p{:03}-{}_edges.txt'.format(input_dir, part_id, graph_name)
+        part_df = pd.read_csv(edge_file, sep=" ", usecols=remove_column_index, names=remove_column_name)
+        merge_df = pd.merge(part_df, removed_df, how='inner', on=["src_id", "dest_id"])
+        merge_df.to_csv(edge_file, mode='a', header=False, index=False, sep=" ")
+
+    print('All dropped edges were retained back into the partitioned files. Now partitioned files has all edges in them')
+
+
 with open(args.schema) as json_file:
     schema = json.load(json_file)
 nid_ranges = schema['nid']
@@ -222,4 +249,4 @@ for part_id in range(num_parts):
                                                 'edge_feats': edge_feat_file,
                                                 'part_graph': part_graph_file}
 with open('{}/{}.json'.format(output_dir, graph_name), 'w') as outfile:
-    json.dump(part_metadata, outfile, sort_keys=True, indent=4)
+    json.dump(part_metadata, outfile, sort_keys=True, indent=4)
\ No newline at end of file