Metis

安装

官方文档
方法一：Metis从安装到使用全教程(Linux): 这个里面有使用介绍，但是安装后，可以按照教程例子测试了。如果需要在程序中调用，好像不好使，可能是需要配置环境变量啥的。

方法二：ubuntu安装metis: 简单暴力，好用，适合需要在代码中调用的需求。

sudo apt-get install libmetis-dev

安装完，仍然需要做如下配置：
include/metis.h 中修改以下代码，做到与自己计算机位数匹配(32bit or 64 bit).
不知道位置的可以按如下查询：

whereis metis # 查找命令
metis: /usr/include/metis.h
sudo vim /usr/include/metis.h

//if your system is 64 bit.
#define IDXTYPEWIDTH 64 //if your system is 32 bit
#define IDXTYPEWIDTH 32

示例

图划分软件Metis的使用
数据集

7 11 001
5 1 3 2 2 1
1 1 3 2 4 1
5 3 4 2 2 2 1 2
2 1 3 2 6 2 7 5
1 1 3 3 6 2
5 2 4 2 7 6
6 6 4 5

注意上面的提供的代码是邻接表格式的，第一行表示顶点和表的边的数量(7,11)，后面每行表示行号对应的顶点的邻居点及边权，例如，第二行表示第一个顶点的三条边: 1->(5,1),1->(3,2), 1->(2,1)。
然而Metis接收的数据格式是CSR，相关介绍见:稀疏矩阵存储格式总结+存储效率对比:COO,CSR,DIA,ELL,HYB. 下面的示例代码中完成了格式的转换。

代码：

#include <metis.h>
#include <vector>
#include <iostream>
#include <fstream>
#include <string>
#include <sstream>using namespace std;vector<idx_t> func(vector<idx_t> &xadj, vector<idx_t> &adjncy, vector<idx_t> &adjwgt, decltype(METIS_PartGraphKway) *METIS_PartGraphFunc) {idx_t nVertices = xadj.size() - 1; // 节点数idx_t nEdges = adjncy.size() / 2;  // 边数idx_t nWeights = 1;                // 节点权重维数idx_t nParts = 2;                  // 子图个数≥2idx_t objval;                      // 目标函数值vector<idx_t> part(nVertices, 0);  // 划分结果int ret = METIS_PartGraphFunc(&nVertices, &nWeights, xadj.data(), adjncy.data(),NULL, NULL, adjwgt.data(), &nParts, NULL,NULL, NULL, &objval, part.data());if (ret != rstatus_et::METIS_OK) { cout << "METIS_ERROR" << endl; }cout << "METIS_OK" << endl;cout << "objval: " << objval << endl;for (unsigned part_i = 0; part_i < part.size(); part_i++) {cout << part_i + 1 << " " << part[part_i] << endl;}return part;
}int main() {ifstream ingraph("graph.txt");int vexnum, edgenum;string line;getline(ingraph, line);istringstream tmp(line);tmp >> vexnum >> edgenum;vector<idx_t> xadj(0);vector<idx_t> adjncy(0); // 压缩图表示vector<idx_t> adjwgt(0); // 节点权重idx_t a, w;for (int i = 0; i < vexnum; i++) {xadj.push_back(adjncy.size()); // 对应csr的: row offsets, csr格式见：https://www.cnblogs.com/xbinworld/p/4273506.htmlgetline(ingraph, line);istringstream tmp(line);while (tmp >> a >> w) {adjncy.push_back(a - 1); // 节点id从0开始 // column indicesadjwgt.push_back(w);     // values}}xadj.push_back(adjncy.size());ingraph.close();vector<idx_t> part = func(xadj, adjncy, adjwgt, METIS_PartGraphRecursive);//vector<idx_t> part = func(xadj, adjncy, adjwgt, METIS_PartGraphKway);ofstream outpartition("partition.txt");for (int i = 0; i < part.size(); i++) { outpartition << i + 1 << " " << part[i] << endl; }outpartition.close();return 0;
}

运行命令：

g++ test2.cc -lmetis
./a.out

运行结果：

METIS_OK
objval: 5
1 1
2 1
3 1
4 0
5 1
6 0
7 0

Parmetis

安装

官网
官方PDF!!!
方案一：
Installing and using the ParMetis library
c++ - ParMETIS:对 `ParMETIS_V3_PartMeshKway’的 undefined reference
方案二：

sudo apt-get install libparmetis-dev  # 安装
mpic++ test_parmetis.cc -lparmetis # 运行案例

pymetis

摘抄自
PyMetis is a Python wrapper for the Metis graph partititioning software by George Karypis, Vipin Kumar and others. It includes version 5.1.0 of Metis and wraps it using the Pybind11 wrapper generator library. So far, it only wraps the most basic graph partitioning functionality (which is enough for my current use), but extending it in case you need more should be quite straightforward. Using PyMetis to partition your meshes is really easy–essentially all you need to pass into PyMetis is an adjacency list for the graph and the number of parts you would like.

例子

import numpy as np
import pymetis
adjacency_list = [np.array([4, 2, 1]),np.array([0, 2, 3]),np.array([4, 3, 1, 0]),np.array([1, 2, 5, 6]),np.array([0, 2, 5]),np.array([4, 3, 6]),np.array([5, 3])]
n_cuts, membership = pymetis.part_graph(2, adjacency=adjacency_list)
# n_cuts = 3
# membership = [1, 1, 1, 0, 1, 0, 0]nodes_part_0 = np.argwhere(np.array(membership) == 0).ravel() # [3, 5, 6]
nodes_part_1 = np.argwhere(np.array(membership) == 1).ravel() # [0, 1, 2, 4]

part_graph

def part_graph(nparts, adjacency=None, xadj=None, adjncy=None,vweights=None, eweights=None, recursive=None):"""Return a partition (cutcount, part_vert) into nparts for an input graph.The input graph is given in either a Pythonic way as the `adjacency' parameteror in the direct C-like way that Metis likes as `xadj' and `adjncy'. Itis an error to specify both graph inputs.The Pythonic graph specifier `adjacency' is required to have the followingproperties:- len(adjacency) needs to return the number of vertices- adjacency[i] needs to be an iterable of vertices adjacent to vertex i.Both directions of an undirected graph edge are required to be stored.If you would like to use *eweights* (edge weights), you need to use thexadj/adjncy way of specifying graph connectivity. This works as follows:The adjacency structure of the graph is stored as follows: Theadjacency list of vertex *i* is stored in array *adjncy* starting atindex ``xadj[i]`` and ending at (but not including) index ``xadj[i +1]``. That is, for each vertex i, its adjacency list is stored inconsecutive locations in the array *adjncy*, and the array *xadj* isused to point to where it begins and where it ends.The weights of the edges (if any) are stored in an additional arraycalled *eweights*. This array contains *2m* elements (where *m* is thenumber of edges, taking into account the undirected nature of thegraph), and the weight of edge ``adjncy[j]`` is stored at location``adjwgt[j]``. The edge-weights must be integers greater than zero. Ifall the edges of the graph have the same weight (i.e., the graph isunweighted), then the adjwgt can be set to ``None``.(quoted with slight adaptations from the Metis docs)"""xadj, adjncy = _prepare_graph(adjacency, xadj, adjncy)if recursive is None:if nparts > 8:recursive = Falseelse:recursive = Truefrom pymetis._internal import part_graphif nparts == 1:# metis has a bug in this case--it disregards the index basereturn 0, [0] * (len(xadj)-1)return part_graph(nparts, xadj, adjncy, vweights, eweights, recursive)

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Linux 环境下metis与parmetis安装与使用

文章目录

Metis

安装

示例

相关接口函数

Parmetis

安装

pymetis

例子

part_graph

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