[Distributed] fix docs for distributed training. (dmlc#2840)

* update distributed training doc.

* explain data split.

* fix message passing.

* id mapping.

* fix.

* test data reshuffling.

* fix a bug.

* fix test.

* Revert "fix test."

This reverts commit 907f1dd.

* Revert "fix a bug."

This reverts commit ff0a4d8.

* Revert "test data reshuffling."

This reverts commit 99bb2f6.

Co-authored-by: Zheng <[email protected]>

docs/source/guide/distributed-apis.rst

@@ -258,18 +258,22 @@ the same as single-process sampling.
 Split workloads
 ~~~~~~~~~~~~~~~
 
-Users need to split the training set so that each trainer works on its own subset. Similarly,
+To train a model, users first need to split the dataset into training, validation and test sets.
+For distributed training, this step is usually done before we invoke :func:`dgl.distributed.partition_graph`
+to partition a graph. We recommend to store the data split in boolean arrays as node data or edge data.
+For node classification tasks, the length of these boolean arrays is the number of nodes in a graph
+and each of their elements indicates the existence of a node in a training/validation/test set.
+Similar boolean arrays should be used for link prediction tasks.
+:func:`dgl.distributed.partition_graph` splits these boolean arrays (because they are stored as
+the node data or edge data of the graph) based on the graph partitioning
+result and store them with graph partitions.
+
+During distributed training, users need to assign training nodes/edges to each trainer. Similarly,
 we also need to split the validation and test set in the same way.
-
-For distributed training and evaluation, the recommended approach is to use boolean arrays to
-indicate the training/validation/test set. For node classification tasks, the length of these
-boolean arrays is the number of nodes in a graph and each of their elements indicates the existence
-of a node in a training/validation/test set. Similar boolean arrays should be used for
-link prediction tasks.
-
 DGL provides :func:`~dgl.distributed.node_split` and :func:`~dgl.distributed.edge_split` to
 split the training, validation and test set at runtime for distributed training. The two functions
-take the boolean arrays as input, split them and return a portion for the local trainer.
+take the boolean arrays constructed before graph partitioning as input, split them and
+return a portion for the local trainer.
 By default, they ensure that all portions have the same number of nodes/edges. This is
 important for synchronous SGD, which assumes each trainer has the same number of mini-batches.
 

docs/source/guide/distributed-preprocessing.rst

@@ -54,7 +54,7 @@ the graph structure of the partition as well as some metadata on nodes and edges
             |-- graph.dgl
 
 Load balancing
-^^^^^^^^^^^^^^
+~~~~~~~~~~~~~~
 
 When partitioning a graph, by default, Metis only balances the number of nodes in each partition.
 This can result in suboptimal configuration, depending on the task at hand. For example, in the case
@@ -79,9 +79,32 @@ the number of edges incident to the nodes of different types.
 The graph name will be used by :class:`dgl.distributed.DistGraph` to identify a distributed graph.
 A legal graph name should only contain alphabetic characters and underscores.
 
+ID mapping
+~~~~~~~~~~
+
+:func:`dgl.distributed.partition_graph` shuffles node IDs and edge IDs during the partitioning and shuffles
+node data and edge data accordingly. After training, we may need to save the computed node embeddings for
+any downstream tasks. Therefore, we need to reshuffle the saved node embeddings according to their original
+IDs.
+
+When `return_mapping=True`, :func:`dgl.distributed.partition_graph` returns the mappings between shuffled
+node/edge IDs and their original IDs. For a homogeneous graph, it returns two vectors. The first
+vector maps every shuffled node ID to its original ID; the second vector maps every shuffled edge ID to its
+original ID. For a heterogeneous graph, it returns two dictionaries of vectors. The first dictionary contains
+the mapping for each node type; the second dictionary contains the mapping for each edge type.
+
+.. code:: python
+
+    node_map, edge_map = dgl.distributed.partition_graph(g, 'graph_name', 4, '/tmp/test',
+                                                         balance_ntypes=g.ndata['train_mask'],
+                                                         return_mapping=True)
+    # Let's assume that node_emb is saved from the distributed training.
+    orig_node_emb = th.zeros(node_emb.shape, dtype=node_emb.dtype)
+    orig_labels[node_map] = node_emb
+
 
 7.1.1 Distributed partitioning
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 For a large graph, DGL uses `ParMetis <http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview>`__ to partition
 a graph in a cluster of machines. This solution requires users to prepare data for ParMETIS and use a DGL script
@@ -90,7 +113,7 @@ a graph in a cluster of machines. This solution requires users to prepare data f
 **Note**: `convert_partition.py` uses the `pyarrow` package to load csv files. Please install `pyarrow`.
 
 ParMETIS Installation
-^^^^^^^^^^^^^^^^^^^^^
+~~~~~~~~~~~~~~~~~~~~~
 
 ParMETIS requires METIS and GKLib. Please follow the instructions `here <https://github.com/KarypisLab/GKlib>`__
 to compile and install GKLib. For compiling and install METIS, please follow the instructions below to
@@ -124,7 +147,7 @@ Before running ParMETIS, we need to set two environment variables: `PATH` and `L
     export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/local/lib/
 
 Input format for ParMETIS
-^^^^^^^^^^^^^^^^^^^^^^^^^
+~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The input graph for ParMETIS is stored in three files with the following names: `xxx_nodes.txt`,
 `xxx_edges.txt` and `xxx_stats.txt`, where `xxx` is a graph name.
@@ -198,7 +221,7 @@ separated by whitespace:
 * `num_node_weights` stores the number of node weights in the node file.
 
 Run ParMETIS and output formats
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 ParMETIS contains a command called `pm_dglpart`, which loads the graph stored in the three
 files from the machine where `pm_dglpart` is invoked, distributes data to all machines in
@@ -247,7 +270,7 @@ processes to partition the graph named `xxx` into eight partitions (each process
     mpirun -np 4 pm_dglpart xxx 2
 
 Convert ParMETIS outputs to DGLGraph
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 DGL provides a script named `convert_partition.py`, located in the `tools` directory, to convert the data
 in the partition files into :class:`dgl.DGLGraph` objects and save them into files.
@@ -373,7 +396,7 @@ Below shows the demo code to construct the schema file.
         json.dump({'nid': nid_ranges, 'eid': eid_ranges}, outfile, indent=4)
 
 Construct node/edge features for a heterogeneous graph
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :class:`dgl.DGLGraph` output by `convert_partition.py` stores a heterogeneous graph partition
 as a homogeneous graph. Its node data contains a field called `orig_id` to store the node IDs

docs/source/guide/distributed.rst

@@ -67,8 +67,6 @@ to the cluster's machines and launch the training job on all machines.
 
 **Note**: The current distributed training API only supports the Pytorch backend.
 
-**Note**: The current implementation only supports graphs with one node type and one edge type.
-
 DGL implements a few distributed components to support distributed training. The figure below
 shows the components and their interactions.
 

docs/source/guide/message-efficient.rst

@@ -32,7 +32,7 @@ implementation would be like:
 
     linear = nn.Parameter(torch.FloatTensor(size=(1, node_feat_dim * 2)))
     def concat_message_function(edges):
-         return {'cat_feat': torch.cat([edges.src.ndata['feat'], edges.dst.ndata['feat']])}
+         return {'cat_feat': torch.cat([edges.src['feat'], edges.dst['feat']])}
     g.apply_edges(concat_message_function)
     g.edata['out'] = g.edata['cat_feat'] * linear