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thirdParty/Zoltan/docs/ug_html/ug_alg_parmetis.html
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<!-------- @HEADER
|
||||
!
|
||||
! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
!
|
||||
! Zoltan Toolkit for Load-balancing, Partitioning, Ordering and Coloring
|
||||
! Copyright 2012 Sandia Corporation
|
||||
!
|
||||
! Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
|
||||
! the U.S. Government retains certain rights in this software.
|
||||
!
|
||||
! Redistribution and use in source and binary forms, with or without
|
||||
! modification, are permitted provided that the following conditions are
|
||||
! met:
|
||||
!
|
||||
! 1. Redistributions of source code must retain the above copyright
|
||||
! notice, this list of conditions and the following disclaimer.
|
||||
!
|
||||
! 2. Redistributions in binary form must reproduce the above copyright
|
||||
! notice, this list of conditions and the following disclaimer in the
|
||||
! documentation and/or other materials provided with the distribution.
|
||||
!
|
||||
! 3. Neither the name of the Corporation nor the names of the
|
||||
! contributors may be used to endorse or promote products derived from
|
||||
! this software without specific prior written permission.
|
||||
!
|
||||
! THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
|
||||
! EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
||||
! IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
|
||||
! PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
|
||||
! CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
|
||||
! EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
|
||||
! PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
|
||||
! PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
|
||||
! LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
|
||||
! NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
|
||||
! SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
!
|
||||
! Questions? Contact Karen Devine kddevin@sandia.gov
|
||||
! Erik Boman egboman@sandia.gov
|
||||
!
|
||||
! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
!
|
||||
! @HEADER
|
||||
------->
|
||||
<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
|
||||
<html>
|
||||
<head>
|
||||
<meta http-equiv="Content-Type"
|
||||
content="text/html; charset=iso-8859-1">
|
||||
<meta name="GENERATOR"
|
||||
content="Mozilla/4.76 [en] (X11; U; Linux 2.4.2-2smp i686) [Netscape]">
|
||||
<meta name="sandia.approval_type" content="formal">
|
||||
<meta name="sandia.approved" content="SAND2007-4748W">
|
||||
<meta name="author" content="Zoltan PI">
|
||||
|
||||
<title>Zoltan User's Guide: ParMETIS Interface</title>
|
||||
</head>
|
||||
<body bgcolor="#ffffff">
|
||||
<div align="right"><b><i><a href="ug.html">Zoltan User's Guide</a>
|
||||
| <a href="ug_alg_ptscotch.html">Next</a> | <a
|
||||
href="ug_graph_vs_hg.html">Previous</a></i></b></div>
|
||||
<h2>
|
||||
<a name="ParMETIS"></a>ParMETIS - Parallel Graph Partitioning</h2>
|
||||
<a href="https://www-users.cs.umn.edu/%7Ekarypis/metis/parmetis/">ParMETIS</a>
|
||||
is a parallel library for graph partitioning (for static load
|
||||
balancing)
|
||||
and repartitioning (for dynamic load balancing) developed at the
|
||||
University
|
||||
of Minnesota by Karypis, Schloegel and Kumar [<a
|
||||
href="ug_refs.html#parmetis">Karypis
|
||||
and Kumar</a>]. Note that ParMetis must be obtained separately and has a different license than Zoltan (see page 31 of <a
|
||||
href="https://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/manual.pdf">
|
||||
this manual</a>). ParMETIS is strictly speaking not a method but
|
||||
rather a collection of methods. In the Zoltan context, ParMETIS is a
|
||||
method
|
||||
with many sub-methods. Zoltan provides an interface to all the ParMETIS
|
||||
(sub-)methods. The user selects which ParMETIS method to use
|
||||
through
|
||||
the parameter PARMETIS_METHOD. Most of the ParMETIS methods are based
|
||||
on
|
||||
either multilevel Kernighan-Lin partitioning or a diffusion algorithm.
|
||||
The names of the ParMETIS methods used by Zoltan are identical to those
|
||||
in the ParMETIS library. For further information about the various <a
|
||||
href="https://www-users.cs.umn.edu/%7Ekarypis/metis/parmetis/">ParMETIS</a>
|
||||
methods and parameters, please consult the <a
|
||||
href="https://www-users.cs.umn.edu/%7Ekarypis/metis/parmetis/">ParMETIS</a>
|
||||
User's Guide.
|
||||
<p>Graph partitioning is a useful abstraction for load balancing. The
|
||||
main
|
||||
idea is to represent the computational application as a weighted graph.
|
||||
The nodes or vertices in the graph correspond to objects in
|
||||
Zoltan.
|
||||
Each object may have a weight that normally represents the amount of
|
||||
computation.
|
||||
The edges or arcs in the graph usually correspond to communication
|
||||
costs.
|
||||
In graph partitioning, the problem is to find a partition of the
|
||||
graph
|
||||
(that is, each vertex is assigned to one out of <i>k</i>
|
||||
possible
|
||||
sets called parts) that minimizes the cut size (weight) subject to
|
||||
the parts having approximately equal size (weight). In
|
||||
repartitioning,
|
||||
it is assumed that a partition already exists. The problem is to
|
||||
find
|
||||
a good partition that is also "similar" in some sense to the
|
||||
existing
|
||||
partition. This keeps the migration cost low. All the problems
|
||||
described
|
||||
above are NP-hard so no efficient exact algorithm is known, but
|
||||
heuristics work well in practice.<br>
|
||||
</p>
|
||||
<p>We give only a brief summary of the various ParMETIS methods here;
|
||||
for
|
||||
more details see the <a
|
||||
href="https://www-users.cs.umn.edu/%7Ekarypis/metis/parmetis/">ParMETIS</a>
|
||||
documentation. The methods fall into three categories:
|
||||
</p>
|
||||
<ol>
|
||||
<li>
|
||||
Part* - Perform graph partitioning without consideration of the initial
|
||||
distribution. (LB_APPROACH=partition)<br>
|
||||
</li>
|
||||
<li>
|
||||
AdaptiveRepart - Incremental
|
||||
algorithms with small migration cost. (LB_APPROACH=repartition)</li>
|
||||
<li>
|
||||
Refine* - Refines a given partition (balance). Can be applied
|
||||
multiple times to reduce the communication cost (cut weight) if
|
||||
desired. (LB_APPROACH=refine)</li>
|
||||
</ol>
|
||||
As a rule of thumb, use one of the Part* methods if you have a poor
|
||||
initial
|
||||
balance and you are willing to spend some time doing migration. One
|
||||
such
|
||||
case is static load balancing; that is, you need to balance only once.
|
||||
Use AdaptiveRepart or the Repart* methods when you have a reasonably
|
||||
good
|
||||
load balance that you wish to update incrementally. These methods are
|
||||
well
|
||||
suited for dynamic load balancing (for example, adaptive
|
||||
mesh
|
||||
refinement). A reasonable strategy is to call PartKway once to obtain a
|
||||
good initial balance and later update this balance using
|
||||
AdaptiveRepart.
|
||||
|
||||
<p>
|
||||
Zoltan supports the multiconstraint partitioning
|
||||
feature of ParMETIS through multiple object weights (see <i><a
|
||||
href="ug_param.html#General_Parameters">OBJ_WEIGHT_DIM</a></i>).
|
||||
</p>
|
||||
<p>The graph given to Zoltan/ParMETIS must be symmetric. Any self edges
|
||||
(loops) will be ignored. Multiple edges between a pair of vertices is
|
||||
not allowed. All weights must be non-negative. The graph does not have to
|
||||
be connected.
|
||||
</p>
|
||||
<p>Zoltan is currently compatible with ParMETIS version 3.1 and 4.0.x.
|
||||
The ParMETIS source code can be obtained from
|
||||
the <a href="https://glaros.dtc.umn.edu/gkhome/views/metis/parmetis">
|
||||
ParMETIS home page</a>. ParMETIS has a separate license:
|
||||
<i>'PARMETIS can be freely used for educational and research purposes by non-profit institutions and US government agencies only. Other organizations are allowed to
|
||||
use PARMETIS only for evaluation purposes, and any further uses will require prior approval from <a href="https://www.license.umn.edu/Products/ParMETIS---Mesh-Graph-Partitioning-Algorithm__Z09041.aspx">the technology transfer office at the University of Minnesota</a>'
|
||||
</i> <br>
|
||||
If you do not wish to install ParMETIS, it
|
||||
is possible to compile Zoltan without any references to ParMETIS;
|
||||
(when you 'make' Zoltan, comment out the PARMETIS_LIBPATH variable in
|
||||
the
|
||||
configuration file <i><a href="ug_usage.html#Building%20the%20Library">Utilities/Config/Config.<platform></a></i>).
|
||||
</p>
|
||||
<br>
|
||||
|
||||
<table nosave="" width="100%">
|
||||
<tbody>
|
||||
<tr>
|
||||
<td valign="top"><b>Value of LB_METHOD:</b></td>
|
||||
<td><b>GRAPH</b></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td valign="top"><b>Value of GRAPH_PACKAGE:</b></td>
|
||||
<td><b>Parmetis</b></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><b>Parameters:</b></td>
|
||||
<td><br>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td valign="top"><i> LB_APPROACH<br>
|
||||
</i></td>
|
||||
<td>The load balancing approach:. <br>
|
||||
<i>PARTITION</i> - partition from scratch, not taking
|
||||
the current data distribution into account<br>
|
||||
<i>REPARTITION</i> - partition but try to stay close to the
|
||||
current partition/distribution
|
||||
<br>
|
||||
<i>REFINE</i> - refine the current partition/distribution;
|
||||
assumes only small changes
|
||||
</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td valign="top"><i> PARMETIS_METHOD</i></td>
|
||||
<td>The specific ParMETIS method to be used (see below).
|
||||
Note: See also <a href="ug_alg.html#LB_APPROACH">LB_APPROACH</a>,
|
||||
which is a simpler way to specify the overall load balance approach.
|
||||
Only use <i>PARMETIS_METHOD</i> if you really need a specific
|
||||
implementation.<br>
|
||||
<i>PartKway</i> - multilevel Kernighan-Lin partitioning
|
||||
<br>
|
||||
<i>PartGeom</i> - space filling curves (coordinate based)
|
||||
<br>
|
||||
<i>PartGeomKway</i> - hybrid method based on PartKway and
|
||||
PartGeom
|
||||
(needs both graph data and coordinates)
|
||||
<br>
|
||||
<i>AdaptiveRepart - </i>adaptive repartitioning (only in
|
||||
ParMETIS 3.0
|
||||
and higher)
|
||||
<br>
|
||||
<i>RefineKway</i> - refine the current partition (balance)</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td>The method names are case insensitive.</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td valign="top"> <i>PARMETIS_OUTPUT_LEVEL</i></td>
|
||||
<td>Amount of output the load-balancing algorithm should
|
||||
produce.
|
||||
<br>
|
||||
0 = no output, 1 = print timing info. Turning on more bits displays
|
||||
more information (for example, 3=1+2, 5=1+4, 7=1+2+4).</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td> <i>PARMETIS_COARSE_ALG</i></td>
|
||||
<td>Coarse algorithm for PartKway. 1 = serial, 2 = parallel.
|
||||
(ParMETIS
|
||||
2 only)</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td> <i>PARMETIS_SEED</i></td>
|
||||
<td>Random seed for ParMETIS.</td>
|
||||
</tr>
|
||||
<tr nosave="" valign="top">
|
||||
<td> <i>PARMETIS_ITR</i></td>
|
||||
<td nosave="">Ratio of interprocessor communication time to
|
||||
redistribution
|
||||
time. A high value will emphasize reducing the edge cut, while a small
|
||||
value will try to keep the change in the new partition (distribution)
|
||||
small.
|
||||
This parameter is used only by AdaptiveRepart. A value of between 100
|
||||
and
|
||||
1000 is good for most problems.</td>
|
||||
</tr>
|
||||
<tr nosave="" valign="top">
|
||||
<td> <i>CHECK_GRAPH</i></td>
|
||||
<td nosave="">Level of error checking for graph input: 0 = no
|
||||
checking, 1
|
||||
= on-processor checking, 2 = full checking. (CHECK_GRAPH==2 is very
|
||||
slow
|
||||
and should be used only during debugging).</td>
|
||||
</tr>
|
||||
<tr nosave="" valign="top">
|
||||
<td> <i>SCATTER_GRAPH</i></td>
|
||||
<td nosave="">Scatter graph data by distributing contiguous
|
||||
chunks of objects
|
||||
(vertices) of roughly equal size to each processor before calling the
|
||||
partitioner.
|
||||
0 = don't scatter;
|
||||
1 = scatter only if all objects are on a single processor;
|
||||
2 = scatter if at least one processor owns no objects;
|
||||
3 = always scatter. </td>
|
||||
</tr>
|
||||
<tr nosave="" valign="top">
|
||||
<td> <i>GRAPH_SYMMETRIZE</i></td>
|
||||
<td nosave="">How to symmetrize the graph:
|
||||
NONE = graph is symmetric and no symmetrization is needed <br/>
|
||||
TRANSPOSE = if M is adjacency matrix of the input graph, output will be the graph representation of M+M<sup>T</sup> <br/>
|
||||
BIPARTITE = graph is symmetrized in a bipartite way : [[ 0 M ][M<sup>t</sup> 0]]
|
||||
</td>
|
||||
</tr>
|
||||
|
||||
<tr nosave="" valign="top">
|
||||
<td> <i>GRAPH_SYM_WEIGHT</i></td>
|
||||
<td nosave="">How edge weights are handled during symmetrization:
|
||||
ADD = weights of each arc are added <br/>
|
||||
MAX = only the heaviest arc weight is kept <br/>
|
||||
<p>See more informations about graph build options on this <a href="ug_graph_build.html">page</a></p>
|
||||
|
||||
<!-- ERROR = fail if complementary arcs don't have the same weight. -->
|
||||
</td>
|
||||
</tr>
|
||||
|
||||
<!-- <tr nosave="" valign="top"> -->
|
||||
<!-- <td> <i>GRAPH_BIPARTITE_TYPE</i></td> -->
|
||||
<!-- <td nosave=""> In the case of a bipartite symmetrization, -->
|
||||
<!-- NONE = graph is symmetric and no symmetrization is needed <br/> -->
|
||||
<!-- TRANSPOSE = if M is adjacency matrix of the input graph, output will be the graph representation of M+M<sup>T</sup> <br/> -->
|
||||
<!-- BIPARTITE = graph is symmetrized in a bipartite way : [[ 0 M ][M<sup>t</sup> 0]] -->
|
||||
<!-- </td> -->
|
||||
<!-- </tr> -->
|
||||
|
||||
<tr>
|
||||
<td valign="top"><b>Default values:</b></td>
|
||||
<td><br>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td><i>LB_APPROACH</i> = Repartition</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td><i>PARMETIS_METHOD</i> = AdaptiveRepart</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td><i>PARMETIS_OUTPUT_LEVEL</i> = 0</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td><i>PARMETIS_COARSE_ALG </i>= 2</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td><i>PARMETIS_SEED </i>= 15</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td><i>PARMETIS_ITR </i>= 100</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td><i>USE_OBJ_SIZE </i>= 1</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td><i>CHECK_GRAPH</i> = 1</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td><i>SCATTER_GRAPH </i>= 1</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td><i>GRAPH_SYMMETRIZE </i>= NONE</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td><i>GRAPH_SYM_WEIGHT </i>= ADD</td>
|
||||
</tr>
|
||||
|
||||
|
||||
<tr>
|
||||
<td valign="top"><b>Required Query Functions:</b></td>
|
||||
<td><br>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>For all submethods:</td>
|
||||
<td><b><a href="ug_query_lb.html#ZOLTAN_NUM_OBJ_FN">ZOLTAN_NUM_OBJ_FN</a></b></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td><b><a href="ug_query_lb.html#ZOLTAN_OBJ_LIST_FN">ZOLTAN_OBJ_LIST_FN</a></b>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>Only PartGeom & PartGeomKway:</td>
|
||||
<td><b><a href="ug_query_lb.html#ZOLTAN_NUM_GEOM_FN">ZOLTAN_NUM_GEOM_FN</a></b></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td>
|
||||
<b><a href="ug_query_lb.html#ZOLTAN_GEOM_MULTI_FN">ZOLTAN_GEOM_MULTI_FN</a></b>
|
||||
or <b><a href="ug_query_lb.html#ZOLTAN_GEOM_FN">ZOLTAN_GEOM_FN</a></b>
|
||||
</td>
|
||||
</tr>
|
||||
<tr nosave="" valign="top">
|
||||
<td>All but PartGeom:</td>
|
||||
<td nosave="">
|
||||
<b><a href="ug_query_lb.html#ZOLTAN_NUM_EDGES_MULTI_FN">ZOLTAN_NUM_EDGES_MULTI_FN</a></b>
|
||||
or
|
||||
<b><a href="ug_query_lb.html#ZOLTAN_NUM_EDGES_FN">ZOLTAN_NUM_EDGES_FN</a></b>
|
||||
<br>
|
||||
<b><a href="ug_query_lb.html#ZOLTAN_EDGE_LIST_MULTI_FN">ZOLTAN_EDGE_LIST_MULTI_FN</a></b>
|
||||
or
|
||||
<b><a href="ug_query_lb.html#ZOLTAN_EDGE_LIST_FN">ZOLTAN_EDGE_LIST_FN</a></b>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td valign="top"><b>Optional Query Functions:</b></td>
|
||||
<td><br>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td>
|
||||
<b><a href="ug_query_mig.html#ZOLTAN_OBJ_SIZE_MULTI_FN">ZOLTAN_OBJ_SIZE_MULTI_FN</a></b>
|
||||
or
|
||||
<b><a href="ug_query_mig.html#ZOLTAN_OBJ_SIZE_FN">ZOLTAN_OBJ_SIZE_FN</a></b> for <i>PARMETIS_METHOD</i>=<i>AdaptiveRepart</i>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td><br>
|
||||
</td>
|
||||
<td>
|
||||
<b><a href="ug_query_lb.html#ZOLTAN_PART_MULTI_FN">ZOLTAN_PART_MULTI_FN</a></b>
|
||||
or
|
||||
<b><a href="ug_query_lb.html#ZOLTAN_PART_FN">ZOLTAN_PART_FN</a></b> for part remapping in ParMETIS.
|
||||
</td>
|
||||
</tr>
|
||||
|
||||
</tbody>
|
||||
</table>
|
||||
</p>
|
||||
<hr width="100%">[<a href="ug.html">Table of Contents</a> | <a
|
||||
href="ug_alg_ptscotch.html">Next:
|
||||
PT-Scotch</a> | <a href="ug_graph_vs_hg.html">Previous:
|
||||
Graph vs. Hypergraph Partitioning</a> | <a href="https://www.sandia.gov/general/privacy-security/index.html">Privacy and Security</a>]
|
||||
</body>
|
||||
</html>
|
||||
Reference in New Issue
Block a user