scotchDecomp, ptscotchDecomp: Updated documentation
Patch contributed by Bruno Santos Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=2032
This commit is contained in:
Henry Weller
parent
04dcee7680
commit
1a5ba9c4ff
@ -12,6 +12,10 @@
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list-style-type: square;
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}
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.contents ol {
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margin-left: 20px;
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}
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/* colour and underline to match OpenFOAM style */
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div.title
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{
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@ -21,95 +21,6 @@ License
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You should have received a copy of the GNU General Public License
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along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
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From scotch forum:
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By: Francois PELLEGRINI RE: Graph mapping 'strategy' string [ reply ]
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2008-08-22 10:09 Strategy handling in Scotch is a bit tricky. In order
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not to be confused, you must have a clear view of how they are built.
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Here are some rules:
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1- Strategies are made up of "methods" which are combined by means of
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"operators".
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2- A method is of the form "m{param=value,param=value,...}", where "m"
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is a single character (this is your first error: "f" is a method name,
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not a parameter name).
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3- There exist different sort of strategies : bipartitioning strategies,
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mapping strategies, ordering strategies, which cannot be mixed. For
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instance, you cannot build a bipartitioning strategy and feed it to a
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mapping method (this is your second error).
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To use the "mapCompute" routine, you must create a mapping strategy, not
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a bipartitioning one, and so use stratGraphMap() and not
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stratGraphBipart(). Your mapping strategy should however be based on the
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"recursive bipartitioning" method ("b"). For instance, a simple (and
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hence not very efficient) mapping strategy can be :
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"b{sep=f}"
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which computes mappings with the recursive bipartitioning method "b",
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this latter using the Fiduccia-Mattheyses method "f" to compute its
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separators.
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If you want an exact partition (see your previous post), try
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"b{sep=fx}".
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However, these strategies are not the most efficient, as they do not
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make use of the multi-level framework.
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To use the multi-level framework, try for instance:
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"b{sep=m{vert=100,low=h,asc=f}x}"
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The current default mapping strategy in Scotch can be seen by using the
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"-vs" option of program gmap. It is, to date:
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b
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{
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job=t,
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map=t,
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poli=S,
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sep=
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(
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m
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{
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asc=b
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{
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bnd=d{pass=40,dif=1,rem=1}f{move=80,pass=-1,bal=0.005},
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org=f{move=80,pass=-1,bal=0.005},
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width=3
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},
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low=h{pass=10}f{move=80,pass=-1,bal=0.0005},
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type=h,
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vert=80,
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rat=0.8
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}
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| m
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{
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asc=b
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{
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bnd=d{pass=40,dif=1,rem=1}f{move=80,pass=-1,bal=0.005},
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org=f{move=80,pass=-1,bal=0.005},
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width=3
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},
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low=h{pass=10}f{move=80,pass=-1,bal=0.0005},
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type=h,
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vert=80,
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rat=0.8
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}
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)
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}
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Note: writeGraph=true : writes out .dgr files for debugging. Run with e.g.
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mpirun -np 4 dgpart 2 'region0_%r.dgr'
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- %r gets replaced by current processor rank
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- decompose into 2 domains
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\*---------------------------------------------------------------------------*/
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#include "ptscotchDecomp.H"
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@ -25,7 +25,24 @@ Class
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Foam::ptscotchDecomp
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Description
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PTScotch domain decomposition
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PTScotch domain decomposition.
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For the main details about how to define the strategies, see scotchDecomp.
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Nonetheless, when decomposing in parallel, using <tt>writeGraph=true</tt>
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will write out \c .dgr files for debugging. For example, use these files
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with \c dgpart as follows:
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\verbatim
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mpirun -np 4 dgpart 2 'region0_%r.dgr'
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\endverbatim
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where:
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\li \c %r gets replaced by current processor rank
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\li it will decompose into 2 domains
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SeeAlso
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Foam::scotchDecomp
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SourceFiles
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ptscotchDecomp.C
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@ -21,102 +21,6 @@ License
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You should have received a copy of the GNU General Public License
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along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
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From scotch forum:
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By: Francois PELLEGRINI RE: Graph mapping 'strategy' string [ reply ]
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2008-08-22 10:09 Strategy handling in Scotch is a bit tricky. In order
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not to be confused, you must have a clear view of how they are built.
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Here are some rules:
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1- Strategies are made up of "methods" which are combined by means of
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"operators".
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2- A method is of the form "m{param=value,param=value,...}", where "m"
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is a single character (this is your first error: "f" is a method name,
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not a parameter name).
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3- There exist different sort of strategies : bipartitioning strategies,
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mapping strategies, ordering strategies, which cannot be mixed. For
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instance, you cannot build a bipartitioning strategy and feed it to a
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mapping method (this is your second error).
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To use the "mapCompute" routine, you must create a mapping strategy, not
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a bipartitioning one, and so use stratGraphMap() and not
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stratGraphBipart(). Your mapping strategy should however be based on the
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"recursive bipartitioning" method ("b"). For instance, a simple (and
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hence not very efficient) mapping strategy can be :
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"b{sep=f}"
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which computes mappings with the recursive bipartitioning method "b",
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this latter using the Fiduccia-Mattheyses method "f" to compute its
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separators.
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If you want an exact partition (see your previous post), try
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"b{sep=fx}".
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However, these strategies are not the most efficient, as they do not
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make use of the multi-level framework.
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To use the multi-level framework, try for instance:
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"b{sep=m{vert=100,low=h,asc=f}x}"
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The current default mapping strategy in Scotch can be seen by using the
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"-vs" option of program gmap. It is, to date:
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r
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{
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job=t,
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map=t,
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poli=S,
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sep=
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(
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m
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{
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asc=b
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{
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bnd=
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(
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d{pass=40,dif=1,rem=1}
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|
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)
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f{move=80,pass=-1,bal=0.002491},
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org=f{move=80,pass=-1,bal=0.002491},
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width=3
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},
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low=h{pass=10}
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f{move=80,pass=-1,bal=0.002491},
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type=h,
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vert=80,
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rat=0.8
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}
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| m
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{
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asc=b
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{
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bnd=
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(
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d{pass=40,dif=1,rem=1}
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|
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)
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f{move=80,pass=-1,bal=0.002491},
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org=f{move=80,pass=-1,bal=0.002491},
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width=3
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},
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low=h{pass=10}
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f{move=80,pass=-1,bal=0.002491},
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type=h,
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vert=80,
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rat=0.8
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}
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)
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}
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Note: instead of gmap run gpart \<nProcs\> -vs \<grfFile\>
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where \<grfFile\> can be obtained by running with 'writeGraph=true'
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\*---------------------------------------------------------------------------*/
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#include "scotchDecomp.H"
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@ -2,7 +2,7 @@
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========= |
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\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
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\\ / O peration |
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\\ / A nd | Copyright (C) 2011-2015 OpenFOAM Foundation
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\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
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\\/ M anipulation |
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-------------------------------------------------------------------------------
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License
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@ -27,9 +27,184 @@ Class
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Description
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Scotch domain decomposition.
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When run in parallel will collect the whole graph on to the master,
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decompose and send back. Run ptscotchDecomp for proper distributed
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decompose and send back. Use ptscotchDecomp for proper distributed
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decomposition.
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Quoting from the Scotch forum, on the 2008-08-22 10:09, Francois
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PELLEGRINI posted the following details:
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\verbatim
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RE: Graph mapping 'strategy' string
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Strategy handling in Scotch is a bit tricky. In order
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not to be confused, you must have a clear view of how they are built.
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Here are some rules:
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1- Strategies are made up of "methods" which are combined by means of
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"operators".
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2- A method is of the form "m{param=value,param=value,...}", where "m"
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is a single character (this is your first error: "f" is a method name,
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not a parameter name).
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3- There exist different sort of strategies : bipartitioning strategies,
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mapping strategies, ordering strategies, which cannot be mixed. For
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instance, you cannot build a bipartitioning strategy and feed it to a
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mapping method (this is your second error).
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To use the "mapCompute" routine, you must create a mapping strategy, not
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a bipartitioning one, and so use stratGraphMap() and not
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stratGraphBipart(). Your mapping strategy should however be based on the
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"recursive bipartitioning" method ("b"). For instance, a simple (and
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hence not very efficient) mapping strategy can be :
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"b{sep=f}"
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which computes mappings with the recursive bipartitioning method "b",
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this latter using the Fiduccia-Mattheyses method "f" to compute its
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separators.
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If you want an exact partition (see your previous post), try
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"b{sep=fx}".
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However, these strategies are not the most efficient, as they do not
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make use of the multi-level framework.
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To use the multi-level framework, try for instance:
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"b{sep=m{vert=100,low=h,asc=f}x}"
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The current default mapping strategy in Scotch can be seen by using the
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"-vs" option of program gmap. It is, to date:
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r
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{
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job=t,
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map=t,
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poli=S,
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sep=
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(
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m
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{
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asc=b
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{
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bnd=
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(
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d{pass=40,dif=1,rem=1}
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|
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)
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f{move=80,pass=-1,bal=0.002491},
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org=f{move=80,pass=-1,bal=0.002491},
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width=3
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},
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low=h{pass=10}
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f{move=80,pass=-1,bal=0.002491},
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type=h,
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vert=80,
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rat=0.8
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}
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| m
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{
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asc=b
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{
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bnd=
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(
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d{pass=40,dif=1,rem=1}
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)
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f{move=80,pass=-1,bal=0.002491},
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org=f{move=80,pass=-1,bal=0.002491},
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width=3
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},
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low=h{pass=10}
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f{move=80,pass=-1,bal=0.002491},
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type=h,
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vert=80,
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rat=0.8
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}
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)
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}
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\endverbatim
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Given that this information was written in 2008, this example strategy will
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unlikely work as-is with the more recent Scotch versions. Therefore, the
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steps for getting the current default strategy from within Scotch, is to do
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the following steps:
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<ol>
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<li> Edit the file <tt>system/decomposeParDict</tt> and use the following
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settings:
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\verbatim
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method scotch;
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scotchCoeffs
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{
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writeGraph true;
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}
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\endverbatim
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</li>
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<li> Run \c decomposePar. For example, it will write a file named
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<tt>region0.grf</tt>.
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</li>
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<li> Now, instead of using \c gmap, run \c gpart with the following
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command structure to get the default strategy:
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\verbatim
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gpart \<nProcs\> -vs \<grfFile\>
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\endverbatim
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where:
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<ul>
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<li> \<grfFile\> is the file that was obtained with the option
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<tt>writeGraph=true</tt>, namely <tt>region0.grf</tt>.
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</li>
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<li> \<nProcs\> is the \c numberOfSubdomains defined in the dictionary
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file.
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</li>
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</ul>
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</li>
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<li> At the end of the execution will be shown a long string, similar to
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the following example (complete line was cropped at <tt>[...]</tt>):
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\verbatim
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S Strat=m{asc=b{width=3,bnd=d{pass=40,dif=1,rem=0}[...],type=h}
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\endverbatim
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</li>
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<li> Edit the file <tt>system/decomposeParDict</tt> once again and add
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the \c strategy entry as exemplified:
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\verbatim
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method scotch;
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scotchCoeffs
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{
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//writeGraph true;
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strategy "m{asc=b{width=3,bnd=d{pass=40,dif=1,rem=0}[...],type=h}";
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}
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\endverbatim
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</li>
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<li> Finally, run \c decomposePar once again, to at least test if it
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works as intended.
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</li>
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</ol>
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Note
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\c gpart can be found in the current search path by adding the respective
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\c bin folder from the Scotch installation, namely by running the following
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commands:
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\verbatim
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source $(foamEtcFile config.sh/scotch)
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export PATH=$PATH:$SCOTCH_ARCH_PATH/bin
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\endverbatim
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SourceFiles
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scotchDecomp.C
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Reference in New Issue
Block a user