Merge branch 'master' into 0.3.x

dmlc · Aug 28, 2019 · bac662c · bac662c
2 parents 6f665d2 + e17add5
commit bac662c
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -87,12 +87,15 @@ add_definitions(-DENABLE_PARTIAL_FRONTIER=0)  # disable minigun partial frontier
 # Source file lists
 file(GLOB DGL_SRC
   src/*.cc
+  src/array/*.cc
+  src/array/cpu/*.cc
   src/kernel/*.cc
   src/kernel/cpu/*.cc
   src/runtime/*.cc
 )
 
 file(GLOB_RECURSE DGL_SRC_1
+  src/api/*.cc
   src/graph/*.cc
   src/scheduler/*.cc
 )

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
@@ -17,10 +17,10 @@ Contributors
 * [Tianyi Zhang](https://github.com/Tiiiger): SGC in Pytorch
 * [Jun Chen](https://github.com/kitaev-chen): GIN in Pytorch
 * [Aymen Waheb](https://github.com/aymenwah): APPNP in Pytorch
+* [Chengqiang Lu](https://github.com/geekinglcq): MGCN, SchNet and MPNN in PyTorch
 
 Other improvement
 * [Brett Koonce](https://github.com/brettkoonce)
 * [@giuseppefutia](https://github.com/giuseppefutia)
 * [@mori97](https://github.com/mori97)
 * Hao Jin
-
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -94,14 +94,19 @@ def tutorial_test_linux(backend) {
 }
 
 pipeline {
-  agent none
+  agent any
   stages {
     stage("Lint Check") {
       agent { docker { image "dgllib/dgl-ci-lint" } }
       steps {
         init_git()
         sh "bash tests/scripts/task_lint.sh"
       }
+      post {
+        always {
+          cleanWs disableDeferredWipeout: true, deleteDirs: true
+        }
+      }
     }
     stage("Build") {
       parallel {
@@ -110,6 +115,11 @@ pipeline {
           steps {
             build_dgl_linux("cpu")
           }
+          post {
+            always {
+              cleanWs disableDeferredWipeout: true, deleteDirs: true
+            }
+          }
         }
         stage("GPU Build") {
           agent {
@@ -122,6 +132,11 @@ pipeline {
             sh "nvidia-smi"
             build_dgl_linux("gpu")
           }
+          post {
+            always {
+              cleanWs disableDeferredWipeout: true, deleteDirs: true
+            }
+          }
         }
         stage("CPU Build (Win64)") {
           // Windows build machines are manually added to Jenkins master with
@@ -130,6 +145,11 @@ pipeline {
           steps {
             build_dgl_win64("cpu")
           }
+          post {
+            always {
+              cleanWs disableDeferredWipeout: true, deleteDirs: true
+            }
+          }
         }
         // Currently we don't have Windows GPU build machines
       }
@@ -141,12 +161,22 @@ pipeline {
           steps {
             cpp_unit_test_linux()
           }
+          post {
+            always {
+              cleanWs disableDeferredWipeout: true, deleteDirs: true
+            }
+          }
         }
         stage("C++ CPU (Win64)") {
           agent { label "windows" }
           steps {
             cpp_unit_test_win64()
           }
+          post {
+            always {
+              cleanWs disableDeferredWipeout: true, deleteDirs: true
+            }
+          }
         }
         stage("Torch CPU") {
           agent { docker { image "dgllib/dgl-ci-cpu" } }
@@ -167,6 +197,11 @@ pipeline {
               }
             }
           }
+          post {
+            always {
+              cleanWs disableDeferredWipeout: true, deleteDirs: true
+            }
+          }
         }
         stage("Torch CPU (Win64)") {
           agent { label "windows" }
@@ -182,6 +217,11 @@ pipeline {
               }
             }
           }
+          post {
+            always {
+              cleanWs disableDeferredWipeout: true, deleteDirs: true
+            }
+          }
         }
         stage("Torch GPU") {
           agent {
@@ -203,6 +243,11 @@ pipeline {
               }
             }
           }
+          post {
+            always {
+              cleanWs disableDeferredWipeout: true, deleteDirs: true
+            }
+          }
         }
         stage("MXNet CPU") {
           agent { docker { image "dgllib/dgl-ci-cpu" } }
@@ -212,17 +257,17 @@ pipeline {
                 unit_test_linux("mxnet", "cpu")
               }
             }
-            //stage("Example test") {
-            //  steps {
-            //    unit_test_linux("pytorch", "cpu")
-            //  }
-            //}
             //stage("Tutorial test") {
             //  steps {
             //    tutorial_test_linux("mxnet")
             //  }
             //}
           }
+          post {
+            always {
+              cleanWs disableDeferredWipeout: true, deleteDirs: true
+            }
+          }
         }
         stage("MXNet GPU") {
           agent {
@@ -238,19 +283,21 @@ pipeline {
                 unit_test_linux("mxnet", "gpu")
               }
             }
-            //stage("Example test") {
-            //  steps {
-            //    unit_test_linux("pytorch", "cpu")
-            //  }
-            //}
-            //stage("Tutorial test") {
-            //  steps {
-            //    tutorial_test_linux("mxnet")
-            //  }
-            //}
+          }
+          post {
+            always {
+              cleanWs disableDeferredWipeout: true, deleteDirs: true
+            }
           }
         }
       }
     }
   }
+  post {
+    always {
+      node('windows') {
+        bat "rmvirtualenv ${BUILD_TAG}"
+      }
+    }
+  }
 }
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # Deep Graph Library (DGL)
 [![Build Status](http://ci.dgl.ai:80/buildStatus/icon?job=DGL/master)](http://ci.dgl.ai:80/job/DGL/job/master/)
-[![GitHub license](https://dmlc.github.io/img/apache2.svg)](./LICENSE)
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](./LICENSE)
 
 [Documentation](https://docs.dgl.ai) | [DGL at a glance](https://docs.dgl.ai/tutorials/basics/1_first.html#sphx-glr-tutorials-basics-1-first-py) |
 [Model Tutorials](https://docs.dgl.ai/tutorials/models/index.html) | [Discussion Forum](https://discuss.dgl.ai)
@@ -15,11 +15,11 @@ A summary of the model accuracy and training speed with the Pytorch backend (on
 
 | Model                                                            | Reported <br> Accuracy | DGL <br> Accuracy | Author's training speed (epoch time)                                          | DGL speed (epoch time) | Improvement |
 | -----                                                            | -----------------      | ------------      | ------------------------------------                                          | ---------------------- | ----------- |
-| [GCN](https://arxiv.org/abs/1609.02907)                          | 81.5%                  | 81.0%             | [0.0051s (TF)](https://github.com/tkipf/gcn)                                  | 0.0038s                | 1.34x       |
-| [GAT](https://arxiv.org/abs/1710.10903)                          | 83.0%                  | 83.9%             | [0.0982s (TF)](https://github.com/PetarV-/GAT)                                | 0.0076s                | 12.9x       |
+| [GCN](https://arxiv.org/abs/1609.02907)                          | 81.5%                  | 81.0%             | [0.0051s (TF)](https://github.com/tkipf/gcn)                                  | 0.0031s                | 1.64x       |
+| [GAT](https://arxiv.org/abs/1710.10903)                          | 83.0%                  | 83.9%             | [0.0982s (TF)](https://github.com/PetarV-/GAT)                                | 0.0113s                | 8.69x       |
 | [SGC](https://arxiv.org/abs/1902.07153)                          | 81.0%                  | 81.9%             | n/a                                                                           | 0.0008s                | n/a         |
 | [TreeLSTM](http://arxiv.org/abs/1503.00075)                      | 51.0%                  | 51.72%            | [14.02s (DyNet)](https://github.com/clab/dynet/tree/master/examples/treelstm) | 3.18s                  | 4.3x        |
-| [R-GCN <br> (classification)](https://arxiv.org/abs/1703.06103)  | 73.23%                 | 73.53%            | [0.2853s (Theano)](https://github.com/tkipf/relational-gcn)                   | 0.0097s                | 29.4x       |
+| [R-GCN <br> (classification)](https://arxiv.org/abs/1703.06103)  | 73.23%                 | 73.53%            | [0.2853s (Theano)](https://github.com/tkipf/relational-gcn)                   | 0.0075s                | 38.2x       |
 | [R-GCN <br> (link prediction)](https://arxiv.org/abs/1703.06103) | 0.158                  | 0.151             | [2.204s (TF)](https://github.com/MichSchli/RelationPrediction)                | 0.453s                 | 4.86x       |
 | [JTNN](https://arxiv.org/abs/1802.04364)                         | 96.44%                 | 96.44%            | [1826s (Pytorch)](https://github.com/wengong-jin/icml18-jtnn)                 | 743s                   | 2.5x        |
 | [LGNN](https://arxiv.org/abs/1705.08415)                         | 94%                    | 94%               | n/a                                                                           | 1.45s                  | n/a         |
@@ -34,13 +34,13 @@ We are currently in Beta stage.  More features and improvements are coming.
 
 ## News
 
+v0.3 has just been released! Huge performance improvement (up to 19x). See release note
+[here](https://github.com/dmlc/dgl/releases/tag/v0.3).
+
 We presented DGL at [GTC 2019](https://www.nvidia.com/en-us/gtc/) as an
 instructor-led training session. Check out our slides and tutorial materials
 [here](https://github.com/dglai/DGL-GTC2019)!!!
 
-v0.2 has just been released! Many features, bugfix and performance improvement. See release note
-[here](https://github.com/dmlc/dgl/releases/tag/v0.2).
-
 ## System requirements
 
 DGL should work on

diff --git a/cmake/modules/CUDA.cmake b/cmake/modules/CUDA.cmake
@@ -231,6 +231,8 @@ macro(dgl_config_cuda out_variable)
   add_definitions(-DDGL_USE_CUDA)
 
   file(GLOB_RECURSE DGL_CUDA_SRC
+    src/array/cuda/*.cc
+    src/array/cuda/*.cu
     src/kernel/cuda/*.cc
     src/kernel/cuda/*.cu
     src/runtime/cuda/*.cc

diff --git a/conda/dgl/meta.yaml b/conda/dgl/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: dgl{{ environ.get('DGL_PACKAGE_SUFFIX', '') }}
-  version: "0.3"
+  version: "0.4"
 
 source:
   git_rev: 0.3.x

diff --git a/docs/README.md b/docs/README.md
@@ -5,6 +5,7 @@ Requirements
 ------------
 * sphinx
 * sphinx-gallery
+* sphinx_rtd_theme
 * Both pytorch and mxnet installed.
 
 Build documents

diff --git a/docs/source/api/python/batch.rst b/docs/source/api/python/batch.rst
@@ -37,3 +37,9 @@ Graph Readout
     mean_edges
     max_nodes
     max_edges
+    topk_nodes
+    topk_edges
+    softmax_nodes
+    softmax_edges
+    broadcast_nodes
+    broadcast_edges
diff --git a/docs/source/api/python/function.rst b/docs/source/api/python/function.rst
@@ -14,6 +14,32 @@ Message functions
     copy_src
     copy_edge
     src_mul_edge
+    copy_u
+    copy_e
+    u_add_v
+    u_sub_v
+    u_mul_v
+    u_div_v
+    u_add_e
+    u_sub_e
+    u_mul_e
+    u_div_e
+    v_add_u
+    v_sub_u
+    v_mul_u
+    v_div_u
+    v_add_e
+    v_sub_e
+    v_mul_e
+    v_div_e
+    e_add_u
+    e_sub_u
+    e_mul_u
+    e_div_u
+    e_add_v
+    e_sub_v
+    e_mul_v
+    e_div_v
 
 Reduce functions
 ----------------
@@ -23,3 +49,6 @@ Reduce functions
 
     sum
     max
+    min
+    prod
+    mean
diff --git a/docs/source/api/python/graph.rst b/docs/source/api/python/graph.rst
@@ -95,6 +95,8 @@ Using Node/edge features
     DGLGraph.edge_attr_schemes
     DGLGraph.set_n_initializer
     DGLGraph.set_e_initializer
+    DGLGraph.local_var
+    DGLGraph.local_scope
 
 Computing with DGLGraph
 -----------------------

diff --git a/docs/source/api/python/nn.mxnet.rst b/docs/source/api/python/nn.mxnet.rst
@@ -11,3 +11,24 @@ dgl.nn.mxnet.conv
 .. autoclass:: dgl.nn.mxnet.conv.GraphConv
     :members: weight, bias, forward
     :show-inheritance:
+
+.. autoclass:: dgl.nn.mxnet.conv.RelGraphConv
+    :members: forward
+    :show-inheritance:
+
+.. autoclass:: dgl.nn.mxnet.conv.TAGConv
+    :members: forward
+    :show-inheritance:
+
+dgl.nn.mxnet.glob
+-----------------
+
+.. automodule:: dgl.nn.mxnet.glob
+    :members:
+    :show-inheritance:
+
+dgl.nn.mxnet.softmax
+--------------------
+
+.. automodule:: dgl.nn.mxnet.softmax
+    :members: edge_softmax