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starrygl-DynamicHistory
Commit 27d6712a by Wenjie Huang
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add METIS to git submodule

parent f9c80767
Showing with 61 additions and 24 deletions
.gitignore
...@@ -171,5 +171,3 @@ cython_debug/ ...@@ -171,5 +171,3 @@ cython_debug/
/dataset /dataset
/test_* /test_*
/*.ipynb /*.ipynb
/third_party
!/third_party/ldg_partition
.gitmodules
[submodule "third_party/ldg_partition"] [submodule "third_party/ldg_partition"]
path = third_party/ldg_partition path = third_party/ldg_partition
url = https://gitee.com/onlynagesha/graph-partition-v4 url = https://gitee.com/onlynagesha/graph-partition-v4
[submodule "third_party/METIS"]
path = third_party/METIS
url = https://github.com/KarypisLab/METIS
branch = v5.1.1-DistDGL-v0.5
CMakeLists.txt
...@@ -5,7 +5,7 @@ project(starrygl VERSION 0.1) ...@@ -5,7 +5,7 @@ project(starrygl VERSION 0.1)
option(WITH_PYTHON "Link to Python when building" ON) option(WITH_PYTHON "Link to Python when building" ON)
option(WITH_CUDA "Link to CUDA when building" ON) option(WITH_CUDA "Link to CUDA when building" ON)
option(WITH_METIS "Link to METIS 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_MTMETIS "Link to multi-threaded METIS when building" OFF)
option(WITH_LDG "Link to (multi-threaded optionally) LDG when building" ON) option(WITH_LDG "Link to (multi-threaded optionally) LDG when building" ON)
set(CMAKE_CXX_STANDARD 17) set(CMAKE_CXX_STANDARD 17)
...@@ -43,22 +43,53 @@ if(WITH_CUDA) ...@@ -43,22 +43,53 @@ if(WITH_CUDA)
endif() endif()
if(WITH_METIS) if(WITH_METIS)
add_definitions(-DWITH_METIS) # add_definitions(-DWITH_METIS)
set(GKLIB_DIR "${CMAKE_SOURCE_DIR}/third_party/GKlib") # set(GKLIB_DIR "${CMAKE_SOURCE_DIR}/third_party/GKlib")
set(METIS_DIR "${CMAKE_SOURCE_DIR}/third_party/METIS") # set(METIS_DIR "${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")
set(GKLIB_INCLUDE_DIRS "${GKLIB_DIR}/include") # include_directories(${METIS_INCLUDE_DIRS})
file(GLOB_RECURSE GKLIB_LIBRARIES "${GKLIB_DIR}/lib/lib*.a")
set(METIS_INCLUDE_DIRS "${METIS_DIR}/include") # add_library(metis_partition SHARED "csrc/partition/metis.cpp")
file(GLOB_RECURSE METIS_LIBRARIES "${METIS_DIR}/lib/lib*.a") # target_link_libraries(metis_partition PRIVATE ${TORCH_LIBRARIES})
# target_link_libraries(metis_partition PRIVATE ${GKLIB_LIBRARIES})
# target_link_libraries(metis_partition PRIVATE ${METIS_LIBRARIES})
include_directories(${METIS_INCLUDE_DIRS}) add_definitions(-DWITH_METIS)
set(METIS_DIR "${CMAKE_SOURCE_DIR}/third_party/mts/METIS")
set(METIS_GKLIB_DIR "${METIS_DIR}/GKlib")
file(GLOB METIS_SRCS "${METIS_DIR}/libmetis/*.c")
file(GLOB METIS_GKLIB_SRCS "${METIS_GKLIB_DIR}/*.c")
if (MSVC)
file(GLOB METIS_GKLIB_WIN32_SRCS "${METIS_GKLIB_DIR}/win32/*.c")
set(METIS_GKLIB_SRCS ${METIS_GKLIB_SRCS} ${METIS_GKLIB_WIN32_SRCS})
endif()
add_library(metis_partition SHARED
"csrc/partition/metis.cpp"
${METIS_SRCS} ${METIS_GKLIB_SRCS}
)
target_include_directories(metis_partition PRIVATE "${METIS_DIR}/include")
target_include_directories(metis_partition PRIVATE "${METIS_GKLIB_DIR}")
if (MSVC)
target_include_directories(metis_partition PRIVATE "${METIS_GKLIB_DIR}/win32")
endif()
target_compile_definitions(metis_partition PRIVATE -DIDXTYPEWIDTH=64)
target_compile_definitions(metis_partition PRIVATE -DREALTYPEWIDTH=32)
target_compile_options(metis_partition PRIVATE -O3)
add_library(metis_partition SHARED "csrc/partition/metis.cpp")
target_link_libraries(metis_partition PRIVATE ${TORCH_LIBRARIES}) target_link_libraries(metis_partition PRIVATE ${TORCH_LIBRARIES})
target_link_libraries(metis_partition PRIVATE ${GKLIB_LIBRARIES}) if (UNIX)
target_link_libraries(metis_partition PRIVATE ${METIS_LIBRARIES}) target_link_libraries(metis_partition PRIVATE m)
endif()
endif() endif()
if(WITH_MTMETIS) if(WITH_MTMETIS)
......
cora.py
from torch_geometric.datasets import Planetoid from torch_geometric.datasets import Planetoid
from torch_geometric.utils import add_remaining_self_loops, to_undirected from torch_geometric.utils import add_remaining_self_loops, to_undirected, remove_self_loops
import os.path as osp import os.path as osp
import sys import sys
...@@ -13,7 +13,8 @@ if __name__ == "__main__": ...@@ -13,7 +13,8 @@ if __name__ == "__main__":
data = Planetoid("/mnt/nfs/hwj/pyg_datasets/Planetoid/Cora", "Cora")[0] data = Planetoid("/mnt/nfs/hwj/pyg_datasets/Planetoid/Cora", "Cora")[0]
if data.is_directed(): if data.is_directed():
data.edge_index, _ = to_undirected(data.edge_index) data.edge_index, _ = to_undirected(data.edge_index)
data.edge_index, _ = add_remaining_self_loops(data.edge_index) # data.edge_index, _ = add_remaining_self_loops(data.edge_index)
data.edge_index, _ = remove_self_loops(data.edge_index)
print(f"num_nodes: {data.num_nodes}") print(f"num_nodes: {data.num_nodes}")
print(f"num_edges: {data.num_edges}") print(f"num_edges: {data.num_edges}")
...@@ -22,11 +23,12 @@ if __name__ == "__main__": ...@@ -22,11 +23,12 @@ if __name__ == "__main__":
data = GraphData.from_pyg_data(data) data = GraphData.from_pyg_data(data)
num_parts_list = [1, 2, 3, 5, 7, 9, 11] num_parts_list = [1, 2, 3, 5, 7, 9, 11]
algos = ["metis", 'mt-metis', "random"] # algos = ["metis", 'mt-metis', "random"]
algos = ["metis", "random"]
root = osp.splitext(osp.abspath(__file__))[0] root = osp.splitext(osp.abspath(__file__))[0]
print(f"root: {root}") print(f"root: {root}")
for num_parts in num_parts_list: for num_parts in num_parts_list:
for algo in algos: for algo in algos:
print(f"======== {num_parts} + {algo} ========") print(f"======== {num_parts} + {algo} ========")
data.save_partition(root, num_parts, algo) data.save_partition(root, num_parts, algorithm=algo)
csrc/partition/metis.cpp
#include <torch/all.h> #include <torch/all.h>
#include <metis.h> #include <metis.h>
#include <mtmetis.h>
#include "utils.h" #include "utils.h"
......
csrc/partition/mtmetis.cpp
#include <torch/all.h> #include <torch/all.h>
#include <metis.h>
#include <mtmetis.h> #include <mtmetis.h>
#include "utils.h" #include "utils.h"
......
starrygl/data/graph.py
...@@ -202,15 +202,18 @@ class GraphData: ...@@ -202,15 +202,18 @@ class GraphData:
logging.info(f"running partition aglorithm: {algorithm}") logging.info(f"running partition aglorithm: {algorithm}")
partition_kwargs = partition_kwargs or {} partition_kwargs = partition_kwargs or {}
not_self_loop = (edge_index[0] != edge_index[1])
if node_weight is not None: if node_weight is not None:
node_weight = self.node()[node_weight] node_weight = self.node()[node_weight]
if edge_weight is not None: if edge_weight is not None:
edge_weight = self.edge()[edge_weight] edge_weight = self.edge()[edge_weight]
edge_weight = edge_weight[not_self_loop]
if algorithm == "metis": if algorithm == "metis":
node_parts = metis_partition( node_parts = metis_partition(
edge_index, edge_index[:,not_self_loop],
num_nodes, num_parts, num_nodes, num_parts,
node_weight=node_weight, node_weight=node_weight,
edge_weight=edge_weight, edge_weight=edge_weight,
...@@ -218,7 +221,7 @@ class GraphData: ...@@ -218,7 +221,7 @@ class GraphData:
) )
elif algorithm == "mt-metis": elif algorithm == "mt-metis":
node_parts = mt_metis_partition( node_parts = mt_metis_partition(
edge_index, edge_index[:,not_self_loop],
num_nodes, num_parts, num_nodes, num_parts,
node_weight=node_weight, node_weight=node_weight,
edge_weight=edge_weight, edge_weight=edge_weight,
...@@ -226,7 +229,7 @@ class GraphData: ...@@ -226,7 +229,7 @@ class GraphData:
) )
elif algorithm == "random": elif algorithm == "random":
node_parts = random_partition( node_parts = random_partition(
edge_index, edge_index[:,not_self_loop],
num_nodes, num_parts, num_nodes, num_parts,
**partition_kwargs, **partition_kwargs,
) )
......
METIS @ f5ae915a
Subproject commit f5ae915a84d3bbf1508b529af90292dd7085b9ec
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