Merge branch 'cmy_dev' into doc-v2

CMakeLists.txt

@@ -110,19 +110,6 @@ if(WITH_MTMETIS)
     target_compile_definitions(mtmetis_partition PRIVATE -DMTMETIS_64BIT_PARTITIONS)
 endif()
 
-if (WITH_LDG)
-    # Imports neighbor-clustering based (e.g. LDG algorithm) graph partitioning implementation
-    add_definitions(-DWITH_LDG)
-    set(LDG_DIR "third_party/ldg_partition")
-    
-    add_library(ldg_partition SHARED "csrc/partition/ldg.cpp")
-    target_link_libraries(ldg_partition PRIVATE ${TORCH_LIBRARIES})
-
-    add_subdirectory(${LDG_DIR})
-    target_include_directories(ldg_partition PRIVATE ${LDG_DIR})
-    target_link_libraries(ldg_partition PRIVATE ldg-vertex-partition)
-endif ()
-
 include_directories("csrc/include")
 add_library(${PROJECT_NAME} SHARED csrc/export.cpp)
 

CMakeLists_.txt

+cmake_minimum_required(VERSION 3.15)
+
+project(starrygl VERSION 0.1)
+
+option(WITH_PYTHON "Link to Python when building" ON)
+option(WITH_CUDA "Link to CUDA when building" ON)
+option(WITH_METIS "Link to METIS when building" ON)
+option(WITH_MTMETIS "Link to multi-threaded METIS when building" ON)
+option(WITH_LDG "Link to (multi-threaded optionally) LDG when building" ON)
+message("third_party dir is ${CMAKE_SOURCE_DIR}")
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+set(CMAKE_CUDA_STANDARD 14)
+set(CMAKE_CUDA_STANDARD_REQUIRED ON)
+
+find_package(OpenMP REQUIRED)
+link_libraries(OpenMP::OpenMP_CXX)
+
+find_package(Torch REQUIRED)
+include_directories(${TORCH_INCLUDE_DIRS})
+add_compile_options(${TORCH_CXX_FLAGS})
+
+if(WITH_PYTHON)
+    add_definitions(-DWITH_PYTHON)
+    find_package(Python3 COMPONENTS Interpreter Development REQUIRED)
+    include_directories(${Python3_INCLUDE_DIRS})
+endif()
+
+if(WITH_CUDA)
+    add_definitions(-DWITH_CUDA)
+    add_definitions(-DWITH_UVM)
+
+    find_package(CUDA REQUIRED)
+    include_directories(${CUDA_INCLUDE_DIRS})
+    set(CUDA_LIBRARIES "${CUDA_TOOLKIT_ROOT_DIR}/lib64/libcudart.so")
+
+    file(GLOB_RECURSE UVM_SRCS "csrc/uvm/*.cpp")
+
+    add_library(uvm_ops SHARED ${UVM_SRCS})
+    target_link_libraries(uvm_ops PRIVATE ${TORCH_LIBRARIES})
+endif()
+
+if(WITH_METIS)
+    add_definitions(-DWITH_METIS)
+    set(GKLIB_DIR "${CMAKE_SOURCE_DIR}/third_party/GKlib")
+    set(METIS_DIR "${CMAKE_SOURCE_DIR}/third_party/METIS")
+
+    set(GKLIB_INCLUDE_DIRS "${GKLIB_DIR}/include")
+    file(GLOB_RECURSE GKLIB_LIBRARIES "${GKLIB_DIR}/lib/lib*.a")
+
+    set(METIS_INCLUDE_DIRS "${METIS_DIR}/include")
+    file(GLOB_RECURSE METIS_LIBRARIES "${METIS_DIR}/lib/lib*.a")
+
+    include_directories(${METIS_INCLUDE_DIRS})
+
+    add_library(metis_partition SHARED "csrc/partition/metis.cpp")
+    target_link_libraries(metis_partition PRIVATE ${TORCH_LIBRARIES})
+    target_link_libraries(metis_partition PRIVATE ${GKLIB_LIBRARIES})
+    target_link_libraries(metis_partition PRIVATE ${METIS_LIBRARIES})
+endif()
+
+if(WITH_MTMETIS)
+    add_definitions(-DWITH_MTMETIS)
+    set(MTMETIS_DIR "${CMAKE_SOURCE_DIR}/third_party/mt-metis")
+
+    set(MTMETIS_INCLUDE_DIRS "${MTMETIS_DIR}/include")
+    file(GLOB_RECURSE MTMETIS_LIBRARIES "${MTMETIS_DIR}/lib/lib*.a")
+
+    include_directories(${MTMETIS_INCLUDE_DIRS})
+    add_library(mtmetis_partition SHARED "csrc/partition/mtmetis.cpp")
+    target_link_libraries(mtmetis_partition PRIVATE ${TORCH_LIBRARIES})
+    target_link_libraries(mtmetis_partition PRIVATE ${MTMETIS_LIBRARIES})
+
+    target_compile_definitions(mtmetis_partition PRIVATE -DMTMETIS_64BIT_VERTICES)
+    target_compile_definitions(mtmetis_partition PRIVATE -DMTMETIS_64BIT_EDGES)
+    target_compile_definitions(mtmetis_partition PRIVATE -DMTMETIS_64BIT_WEIGHTS)
+    target_compile_definitions(mtmetis_partition PRIVATE -DMTMETIS_64BIT_PARTITIONS)
+endif()
+
+if (WITH_LDG)
+    # Imports neighbor-clustering based (e.g. LDG algorithm) graph partitioning implementation
+    add_definitions(-DWITH_LDG)
+    # set(LDG_DIR "csrc/partition/neighbor_clustering")
+    set(LDG_DIR "third_party/ldg_partition")
+    add_library(ldg_partition SHARED "csrc/partition/ldg.cpp")
+    target_link_libraries(ldg_partition PRIVATE ${TORCH_LIBRARIES})
+
+    # add_subdirectory(${LDG_DIR})
+    target_include_directories(ldg_partition PRIVATE ${LDG_DIR})
+    target_link_libraries(ldg_partition PRIVATE ldg-vertex-partition)
+endif ()
+
+include_directories("csrc/include")
+add_library(${PROJECT_NAME} SHARED csrc/export.cpp)
+
+target_link_libraries(${PROJECT_NAME} PRIVATE ${TORCH_LIBRARIES})
+target_compile_definitions(${PROJECT_NAME} PRIVATE -DTORCH_EXTENSION_NAME=lib${PROJECT_NAME})
+
+if(WITH_PYTHON)
+    find_library(TORCH_PYTHON_LIBRARY torch_python PATHS "${TORCH_INSTALL_PREFIX}/lib")
+    target_link_libraries(${PROJECT_NAME} PRIVATE ${TORCH_PYTHON_LIBRARY})
+endif()
+
+if (WITH_CUDA)
+    target_link_libraries(${PROJECT_NAME} PRIVATE uvm_ops)
+endif()
+
+if (WITH_METIS)
+    message(STATUS "Current project '${PROJECT_NAME}' uses METIS graph partitioning algorithm.")
+    target_link_libraries(${PROJECT_NAME} PRIVATE metis_partition)
+endif()
+
+if (WITH_MTMETIS)
+    message(STATUS "Current project '${PROJECT_NAME}' uses multi-threaded METIS graph partitioning algorithm.")
+    target_link_libraries(${PROJECT_NAME} PRIVATE mtmetis_partition)
+endif()
+
+if (WITH_LDG)
+    message(STATUS "Current project '${PROJECT_NAME}' uses LDG graph partitioning algorithm.")
+    target_link_libraries(${PROJECT_NAME} PRIVATE ldg_partition)
+endif()
+
+# add libsampler.so
+set(SAMLPER_NAME "${PROJECT_NAME}_sampler")
+set(BOOST_INCLUDE_DIRS "${CMAKE_SOURCE_DIR}/third_party/boost_1_83_0")
+include_directories(${BOOST_INCLUDE_DIRS})
+file(GLOB_RECURSE SAMPLER_SRCS "csrc/sampler/*.cpp")
+add_library(${SAMLPER_NAME} SHARED ${SAMPLER_SRCS})
+target_include_directories(${SAMLPER_NAME} PRIVATE "csrc/sampler/include")
+
+target_compile_options(${SAMLPER_NAME} PRIVATE -O3)
+target_link_libraries(${SAMLPER_NAME} PRIVATE ${TORCH_LIBRARIES})
+target_compile_definitions(${SAMLPER_NAME} PRIVATE -DTORCH_EXTENSION_NAME=lib${SAMLPER_NAME})
+
+
+
+if(WITH_PYTHON)
+    find_library(TORCH_PYTHON_LIBRARY torch_python PATHS "${TORCH_INSTALL_PREFIX}/lib")
+    target_link_libraries(${SAMLPER_NAME} PRIVATE ${TORCH_PYTHON_LIBRARY})
+endif()

GDELT4.out

+ERROR:root:cannot import name 'libstarrygl' from 'starrygl.lib' (unknown location)
+ERROR:root:unable to import libstarrygl.so, some features may not be available.
+ERROR:root:cannot import name 'libstarrygl_sampler' from 'starrygl.lib' (unknown location)
+ERROR:root:unable to import libstarrygl_sampler.so, some features may not be available.
+libibverbs: Warning: couldn't load driver 'libsiw-rdmav34.so': libsiw-rdmav34.so: cannot open shared object file: No such file or directory
+libibverbs: Warning: couldn't load driver 'libbnxt_re-rdmav34.so': libbnxt_re-rdmav34.so: cannot open shared object file: No such file or directory
+libibverbs: Warning: couldn't load driver 'libhns-rdmav34.so': libhns-rdmav34.so: cannot open shared object file: No such file or directory
+libibverbs: Warning: couldn't load driver 'libqedr-rdmav34.so': libqedr-rdmav34.so: cannot open shared object file: No such file or directory
+libibverbs: Warning: couldn't load driver 'libmthca-rdmav34.so': libmthca-rdmav34.so: cannot open shared object file: No such file or directory
+libibverbs: Warning: couldn't load driver 'libcxgb4-rdmav34.so': libcxgb4-rdmav34.so: cannot open shared object file: No such file or directory
+libibverbs: Warning: couldn't load driver 'libhfi1verbs-rdmav34.so': libhfi1verbs-rdmav34.so: cannot open shared object file: No such file or directory
+libibverbs: Warning: couldn't load driver 'libmlx4-rdmav34.so': libmlx4-rdmav34.so: cannot open shared object file: No such file or directory
+libibverbs: Warning: couldn't load driver 'libefa-rdmav34.so': libefa-rdmav34.so: cannot open shared object file: No such file or directory
+libibverbs: Warning: couldn't load driver 'libipathverbs-rdmav34.so': libipathverbs-rdmav34.so: cannot open shared object file: No such file or directory
+libibverbs: Warning: couldn't load driver 'libocrdma-rdmav34.so': libocrdma-rdmav34.so: cannot open shared object file: No such file or directory
+libibverbs: Warning: couldn't load driver 'libvmw_pvrdma-rdmav34.so': libvmw_pvrdma-rdmav34.so: cannot open shared object file: No such file or directory
+libibverbs: Warning: couldn't load driver 'librxe-rdmav34.so': librxe-rdmav34.so: cannot open shared object file: No such file or directory
+get_neighbors consume: 14.4084ususe cuda on 0
+33336461 7121936 9088019
+torch.Size([2, 33336461]) 33336461
+torch.Size([2, 9088019]) 9088019
+torch.Size([2, 7121936]) 7121936
+tensor([33336], device='cuda:0')
+Epoch 0:
+torch.Size([2, 1000]) 1000
+Traceback (most recent call last):
+  File "train_tgnn.py", line 290, in <module>
+    main()
+  File "train_tgnn.py", line 215, in main
+    for roots,mfgs,metadata,sample_time in trainloader:
+  File "/home/zlj/starrygl/starrygl/sample/data_loader.py", line 146, in __next__
+    batch_data = graph_sample(self.graph,
+  File "/home/zlj/starrygl/starrygl/sample/batch_data.py", line 141, in graph_sample
+    return to_block(graph,data,out,mailbox,device)
+  File "/home/zlj/starrygl/starrygl/sample/batch_data.py", line 81, in to_block
+    ind_dict = graph.edge_attr.all_to_all_ind2ptr(dist_eid,group = group)
+  File "/home/zlj/starrygl/starrygl/distributed/utils.py", line 195, in all_to_all_ind2ptr
+    send_ptr = torch.ops.torch_sparse.ind2ptr(dist_index.part, self.num_parts())
+TypeError: 'int' object is not callable

config/DyRep.yml

+sampling:
+  - layer: 1
+    neighbor: 
+      - 10
+    strategy: 'recent'
+    prop_time: False
+    history: 1
+    duration: 0
+    num_thread: 32
+memory: 
+  - type: 'node'
+    dim_time: 100
+    deliver_to: 'self'
+    mail_combine: 'last'
+    memory_update: 'gru'
+    mailbox_size: 1
+    combine_node_feature: True
+    dim_out: 100
+gnn:
+  - arch: 'transformer_attention'
+    use_src_emb: True
+    use_dst_emb: True
+    layer: 1
+    att_head: 2
+    dim_time: 100
+    dim_out: 100
+train:
+  - epoch: 50
+    batch_size: 100
+    # reorder: 16
+    lr: 0.0001
+    dropout: 0.1
+    att_dropout: 0.2
+    all_on_gpu: True
\ No newline at end of file

config/TGN.yml

@@ -18,13 +18,15 @@ memory:
     dim_out: 100
 gnn:
   - arch: 'transformer_attention'
+    use_src_emb: False
+    use_dst_emb: False
     layer: 1
     att_head: 2
     dim_time: 100
     dim_out: 100
 train:
-  - epoch: 5
-    #batch_size: 100
+  - epoch: 20
+    batch_size: 200
     # reorder: 16
     lr: 0.0001
     dropout: 0.2

config/TIGE.yml

+sampling:
+  - layer: 1
+    neighbor: 
+      - 10
+    strategy: 'recent'
+    prop_time: False
+    history: 1
+    duration: 0
+    num_thread: 32
+memory: 
+  - type: 'node'
+    dim_time: 100
+    deliver_to: 'self'
+    mail_combine: 'last'
+    memory_update: 'gru'
+    mailbox_size: 1
+    combine_node_feature: True
+    dim_out: 100
+gnn:
+  - arch: 'transformer_attention'
+    use_src_emb: True
+    use_dst_emb: True
+    layer: 1
+    att_head: 2
+    dim_time: 100
+    dim_out: 100
+train:
+  - epoch: 20
+    batch_size: 200
+    # reorder: 16
+    lr: 0.0001
+    dropout: 0.2
+    att_dropout: 0.2
+    all_on_gpu: True
\ No newline at end of file

csrc/export.cpp

@@ -5,6 +5,7 @@
 
 PYBIND11_MODULE(TORCH_EXTENSION_NAME, m) {
     #ifdef WITH_CUDA
+    #ifdef WITH_CUDA
     m.def("uvm_storage_new", &uvm_storage_new, "return storage of unified virtual memory");
     m.def("uvm_storage_to_cuda", &uvm_storage_to_cuda, "share uvm storage with another cuda device");
     m.def("uvm_storage_to_cpu", &uvm_storage_to_cpu, "share uvm storage with cpu");

data_maker.py

@@ -114,11 +114,15 @@ edge_weight_dict = {}
 edge_weight_dict['edata'] = 2*neg_nums
 edge_weight_dict['sample_data'] = 1*neg_nums
 edge_weight_dict['neg_data'] = 1
-partition_save('./dataset/here/'+data_name, data, 1, 'metis_for_tgnn',
-               edge_weight_dict=edge_weight_dict)
-partition_save('./dataset/here/'+data_name, data, 2, 'metis_for_tgnn',
-               edge_weight_dict=edge_weight_dict)
-partition_save('./dataset/here/'+data_name, data, 4, 'metis_for_tgnn',
+#partition_save('./dataset/here/'+data_name, data, 1, 'metis_for_tgnn',
+#               edge_weight_dict=edge_weight_dict)
+#partition_save('./dataset/here/'+data_name, data, 2, 'metis_for_tgnn',
+#               edge_weight_dict=edge_weight_dict)
+#partition_save('./dataset/here/'+data_name, data, 4, 'metis_for_tgnn',
+#               edge_weight_dict=edge_weight_dict)
+#partition_save('./dataset/here/'+data_name, data, 8, 'metis_for_tgnn',
+#               edge_weight_dict=edge_weight_dict)
+partition_save('./dataset/here/'+data_name, data, 16, 'metis_for_tgnn',
                edge_weight_dict=edge_weight_dict)
 #
 # partition_save('./dataset/here/'+data_name, data, 4, 'metis_for_tgnn',

docs/source/advanced/data_proc.rst

+Advanced Data Preprocessing
+===========================
+
+.. note::
+    详细介绍一下StarryGL几种数据管理类，例如GraphData，的使用细节，内部索引结构的设计和底层操作。
\ No newline at end of file

docs/source/advanced/index.rst

@@ -4,4 +4,4 @@ Advanced Concepts
 .. toctree::
     sampling_parallel/index
     partition_parallel/index
-    timeline_parallel/index
\ No newline at end of file
+    timeline_parallel/index

docs/source/advanced/pp_training.rst

+Distributed Partition Parallel
+==============================
+
+.. note::
+    分布式分区并行训练部分
\ No newline at end of file

docs/source/advanced/tp_training.rst

+Distributed Timeline Parallel
+=============================
+
+.. note::
+    分布式时序并行
\ No newline at end of file

docs/source/advanced/ts_sampling.rst

+Distributed Temporal Sampling
+=============================
+
+.. note::
+    基于分布式时序图采样的训练模式
\ No newline at end of file

docs/source/api/python/index.rst

@@ -7,4 +7,4 @@ Package References
     memory
     data_loader
     graph_core
-    cache
\ No newline at end of file
+    cache

requirements.txt

@@ -13,4 +13,4 @@ torch_spline_conv==1.2.2+pt21cu118
 
 ogb
 tqdm
-networkx
\ No newline at end of file
+networkx