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HTML
247 lines
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HTML
<!-------- @HEADER
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!
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! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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!
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! Zoltan Toolkit for Load-balancing, Partitioning, Ordering and Coloring
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! Copyright 2012 Sandia Corporation
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!
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! Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
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! the U.S. Government retains certain rights in this software.
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!
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! Redistribution and use in source and binary forms, with or without
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! modification, are permitted provided that the following conditions are
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! met:
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!
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! 1. Redistributions of source code must retain the above copyright
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! notice, this list of conditions and the following disclaimer.
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!
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! 2. Redistributions in binary form must reproduce the above copyright
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! notice, this list of conditions and the following disclaimer in the
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! documentation and/or other materials provided with the distribution.
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!
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! 3. Neither the name of the Corporation nor the names of the
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! contributors may be used to endorse or promote products derived from
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! this software without specific prior written permission.
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!
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! THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
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! EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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! IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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! PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
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! CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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! EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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! PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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! PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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! LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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! NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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! SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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!
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! Questions? Contact Karen Devine kddevin@sandia.gov
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! Erik Boman egboman@sandia.gov
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!
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! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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!
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! @HEADER
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------->
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<HTML>
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<HEAD>
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<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
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<META NAME="GENERATOR" CONTENT="Mozilla/4.04 [en] (X11; U; SunOS 4.1.3_U1 sun4m) [Netscape]">
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<meta name="sandia.approval_type" content="formal">
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<meta name="sandia.approved" content="SAND2007-4748W">
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<meta name="author" content="Zoltan PI">
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<TITLE>Zoltan User's Guide: Migration Examples</TITLE>
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</HEAD>
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<BODY BGCOLOR="#FFFFFF">
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<div ALIGN=right><b><i><a href="ug.html">Zoltan User's Guide</a> | <a href="ug_examples_query.html">Next</a> | <a href="ug_examples_lb.html">Previous</a></i></b></div>
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<H2>
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<A NAME="Migration Example"></A>Migration Examples</H2>
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Data migration using Zoltan's migration tools can be accomplished
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in two different ways:
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<BLOCKQUOTE><A HREF="#Auto-migration example">auto-migration</A>, or
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<BR><A HREF="#User-guided Migration Example">user-guided migration</A>.</BLOCKQUOTE>
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The choice of migration method depends upon the complexity of the application's
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data. For some applications, only the objects used in balancing must be
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migrated; no auxiliary data structures must be moved. Particle simulations
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are examples of such applications; load balancing is based on the number
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of particles per processor, and only the particles and their data must
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be moved to establish the new decomposition. For such applications, Zoltan's
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auto-migration tools can be used. Other applications, such as finite element
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methods, perform load balancing on, say, the nodes of the finite element
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mesh, but nodes that are moved to new processors also need to have their
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connected elements moved to the new processors, and migrated elements may
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also need "ghost" nodes (i.e., copies of nodes assigned to other processors)
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to satisfy their connectivity requirements on the new processor. This complex
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data migration requires a more user-controlled approach to data migration
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than the auto-migration capabilities Zoltan can provide.
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<BR>
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<H2>
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<A NAME="Auto-migration example"></A>Auto-Migration Example</H2>
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In the <A HREF="#Auto-Migration Example Fig">figure</A> below, an example
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of the load-balancing calling sequence for a particle simulation using
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Zoltan's auto-migration tools is shown.
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The application
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requests auto-migration by turning on the <B>AUTO_MIGRATE</B> option
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through a call to <B><A HREF="ug_interface_init.html#Zoltan_Set_Param">Zoltan_Set_Param</A></B>
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and registers functions to pack and unpack a particle's data. During the
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call to <B><A HREF="ug_interface_lb.html#Zoltan_LB_Partition">Zoltan_LB_Partition</A></B>,
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Zoltan computes the new decomposition and, using calls
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to the packing and unpacking query functions, automatically migrates particles
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to their new processors. The application then frees the arrays returned
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by <B><A HREF="ug_interface_lb.html#Zoltan_LB_Partition">Zoltan_LB_Partition</A></B> and
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can continue computation without having to perform any additional operations
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for data migration.
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<BR>
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<BR>
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<CENTER><TABLE BORDER=2 COLS=1 WIDTH="90%" NOSAVE >
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<TR>
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<TD><A NAME="Auto-Migration Example Fig"></A>
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<TT>/* <I>Tell Zoltan to automatically migrate data for the application.</I>
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*/</TT>
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<BR><TT><A HREF="ug_interface_init.html#Zoltan_Set_Param">Zoltan_Set_Param</A>(zz, "AUTO_MIGRATE",
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"TRUE");</TT>
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<P><TT>/* <I>Register additional functions for packing and unpacking data</I>
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*/</TT>
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<BR><TT>/* <I>by migration tools. </I>*/</TT>
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<BR><TT><A HREF="ug_interface_init.html#Zoltan_Set_Fn">Zoltan_Set_Fn</A>(zz, <A HREF="ug_query_mig.html#ZOLTAN_OBJ_SIZE_FN">ZOLTAN_OBJ_SIZE_FN_TYPE</A>,</tt>
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<br><tt> (void (*)()) user_return_particle_data_size, NULL);</TT>
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<BR><TT><A HREF="ug_interface_init.html#Zoltan_Set_Fn">Zoltan_Set_Fn</A>(zz, <A HREF="ug_query_mig.html#ZOLTAN_PACK_OBJ_FN">ZOLTAN_PACK_OBJ_FN_TYPE</A>,</tt>
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<br><tt> (void (*)()) user_pack_particle_data, NULL);</TT>
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<BR><TT><A HREF="ug_interface_init.html#Zoltan_Set_Fn">Zoltan_Set_Fn</A>(zz, <A HREF="ug_query_mig.html#ZOLTAN_UNPACK_OBJ_FN">ZOLTAN_UNPACK_OBJ_FN_TYPE</A>,</tt>
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<br><tt> (void (*)()) user_unpack_particle_data, NULL);</TT>
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<BR><TT>...</TT>
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<BR><TT>/* <I>Perform computations</I> */</TT>
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<BR><TT>...</TT>
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<BR><TT>/* <I>Perform load balancing AND automatic data migration!</I>
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*/</TT>
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<BR><TT><A HREF="ug_interface_lb.html#Zoltan_LB_Partition">Zoltan_LB_Partition</A>(zz,&new,&num_gid_entries,&num_lid_entries,</tt>
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<br><tt> &num_imp,&imp_global_ids,&imp_local_ids,&imp_procs,&imp_to_part,</TT>
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<BR><TT> &num_exp,&exp_global_ids,&exp_local_ids,&exp_procs,&exp_to_part);</TT>
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<P><TT>/* <I>Free memory allocated for load-balancing results by Zoltan </I>
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*/</TT>
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<BR><TT><A HREF="ug_interface_lb.html#Zoltan_LB_Free_Part">Zoltan_LB_Free_Part</A>(&imp_global_ids, &imp_local_ids, &imp_procs, &imp_to_part);</TT>
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<BR><TT><A HREF="ug_interface_lb.html#Zoltan_LB_Free_Part">Zoltan_LB_Free_Part</A>(&exp_global_ids, &exp_local_ids, &exp_procs, &exp_to_part);</TT>
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<BR><TT>...</TT></TD>
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</TR>
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<CAPTION ALIGN=BOTTOM><I>Typical calling sequence for using the migration
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tools' auto-migration capability with the dynamic load-balancing tools.</I></CAPTION>
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</TABLE></CENTER>
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<H2>
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<A NAME="User-guided Migration Example"></A>User-Guided Migration Example</H2>
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In the following <A HREF="#User-guided Migration Example Fig">figure</A>,
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an example of user-guided migration using Zoltan's migration tools
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for a finite element application is shown. Several migration steps are
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needed to completely rebuild the application's data structures for the
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new decomposition. On each processor, newly imported nodes need copies
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of elements containing those nodes. Newly imported elements, then, need
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copies of "ghost" nodes, nodes that are in the element but are assigned
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to other processors. Each of these entities (nodes, elements, and ghost
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nodes) can be migrated in separate migration steps using the functions
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provided in the migration tools. First, the assignment of nodes to
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processors returned by <B><A HREF="ug_interface_lb.html#Zoltan_LB_Partition">Zoltan_LB_Partition</A></B>
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is established. Query functions that pack and unpack nodes are registered
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and <B><A HREF="ug_interface_mig.html#Zoltan_Migrate">Zoltan_Migrate</A></B>
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is called using the nodal decomposition returned from <B><A HREF="ug_interface_lb.html#Zoltan_LB_Partition">Zoltan_LB_Partition</A></B>.
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<B><A HREF="ug_interface_mig.html#Zoltan_Migrate">Zoltan_Migrate</A></B>
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packs the nodes to be exported, sends them to other processors, and unpacks
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nodes received by a processor. The packing routine <I>migrate_node_pack</I>
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includes with each node a list of the element IDs for elements containing
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that node. The unpacking routine <I>migrate_node_unpack</I> examines the
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list of element IDs and builds a list of requests for elements the processor
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needs but does not already store. At the end of the nodal migration, each
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processor has a list of element IDs for elements that it needs to support
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imported nodes but does not already store. Through a call to <B><A HREF="ug_interface_mig.html#Zoltan_Invert_Lists">Zoltan_Invert_Lists</A></B>,
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each processor computes the list of elements it has to send to other processors
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to satisfy their element requests. Packing and unpacking routines for elements
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are registered, and <B><A HREF="ug_interface_mig.html#Zoltan_Migrate">Zoltan_Migrate</A></B>
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is again used to move element data to new processors. Requests for ghost
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nodes can be built within the element packing and unpacking routines, and
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calls to <B><A HREF="ug_interface_mig.html#Zoltan_Invert_Lists">Zoltan_Invert_Lists</A></B>
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and <B><A HREF="ug_interface_mig.html#Zoltan_Migrate">Zoltan_Migrate</A></B>,
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with node packing and unpacking, satisfy requests for ghost nodes. In all
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three phases of migration, the migration tools handle communication;
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the application is responsible only for packing and unpacking data and
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for building the appropriate request lists.
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<BR>
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<BR>
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<CENTER><TABLE BORDER=2 COLS=1 WIDTH="90%" NOSAVE >
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<TR NOSAVE>
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<TD NOSAVE><A NAME="User-guided Migration Example Fig"></A><TT>/* <I>Assume
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Zoltan returns a decomposition of the</I> */</TT>
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<BR><TT>/* <I>nodes of a finite element mesh.</I> */</TT>
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<BR><TT><A HREF="ug_interface_lb.html#Zoltan_LB_Partition">Zoltan_LB_Partition</A>(zz,&new,&num_gid_entries,&num_lid_entries,</tt>
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<br><tt> &num_imp,&imp_global_ids,&imp_local_ids,&imp_procs,&imp_to_part,</TT>
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<BR><TT> &num_exp,&exp_global_ids,&exp_local_ids,&exp_procs,&exp_to_part);</TT>
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<P><TT>/* <I>Migrate the nodes as directed by the results of Zoltan_LB_Partition.</I>
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*/</TT>
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<BR><TT>/* <I>While unpacking nodes, build list of requests for elements
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needed</I> */</TT>
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<BR><TT>/* <I>to support the imported nodes.</I>*/</TT>
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<BR><TT><A HREF="ug_interface_init.html#Zoltan_Set_Fn">Zoltan_Set_Fn</A>(zz, <A HREF="ug_query_mig.html#ZOLTAN_OBJ_SIZE_FN">ZOLTAN_OBJ_SIZE_FN_TYPE</A>,</tt>
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<br><tt> (void (*)()) migrate_node_size, NULL);</TT>
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<BR><TT><A HREF="ug_interface_init.html#Zoltan_Set_Fn">Zoltan_Set_Fn</A>(zz, <A HREF="ug_query_mig.html#ZOLTAN_PACK_OBJ_FN">ZOLTAN_PACK_OBJ_FN_TYPE</A>,</tt>
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<br><tt> (void (*)()) migrate_pack_node, NULL);</TT>
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<BR><TT><A HREF="ug_interface_init.html#Zoltan_Set_Fn">Zoltan_Set_Fn</A>(zz, <A HREF="ug_query_mig.html#ZOLTAN_UNPACK_OBJ_FN">ZOLTAN_UNPACK_OBJ_FN_TYPE</A>,</tt>
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<br><tt> (void (*)()) migrate_unpack_node, NULL);</TT>
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<BR><TT><A HREF="ug_interface_mig.html#Zoltan_Migrate">Zoltan_Migrate</A>(zz,num_import,imp_global_ids,imp_local_ids,imp_procs,imp_to_part,</TT>
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<BR><TT> num_export,exp_global_ids,exp_local_ids,exp_procs,exp_to_part);</TT>
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<P><TT>/* <I>Prepare for migration of requested elements.</I> */</TT>
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<BR><TT><A HREF="ug_interface_init.html#Zoltan_Set_Fn">Zoltan_Set_Fn</A>(zz, <A HREF="ug_query_mig.html#ZOLTAN_PACK_OBJ_FN">ZOLTAN_PACK_OBJ_FN_TYPE</A>,</tt>
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<br><tt> (void (*)()) migrate_pack_element, NULL);</TT>
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<BR><TT><A HREF="ug_interface_init.html#Zoltan_Set_Fn">Zoltan_Set_Fn</A>(zz, <A HREF="ug_query_mig.html#ZOLTAN_UNPACK_OBJ_FN">ZOLTAN_UNPACK_OBJ_FN_TYPE</A>,</tt>
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<br><tt> (void (*)()) migrate_unpack_element, NULL);</TT>
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<BR><TT><A HREF="ug_interface_init.html#Zoltan_Set_Fn">Zoltan_Set_Fn</A>(zz, <A HREF="ug_query_mig.html#ZOLTAN_OBJ_SIZE_FN">ZOLTAN_OBJ_SIZE_FN_TYPE</A>,</tt>
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<br><tt> (void (*)()) migrate_element_size, NULL);</TT>
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<P><TT>/* <I>From the request lists, a processor knows which elements it
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needs</I> */</TT>
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<BR><TT>/* <I>to support the imported nodes; it must compute which elements
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to</I> */</TT>
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<BR><TT>/* <I>send to other processors. </I>*/</TT>
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<BR><TT><A HREF="ug_interface_mig.html#Zoltan_Invert_Lists">Zoltan_Invert_Lists</A>(zz,
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Num_Elt_Requests, Elt_Requests_Global_IDs, </TT>
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<BR><TT> Elt_Requests_Local_IDs,
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Elt_Requests_Procs, Elt_Requests_to_Part,</TT>
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<BR><TT> &num_tmp_exp,
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&tmp_exp_global_ids, </TT>
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<BR><TT> &tmp_exp_local_ids,
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&tmp_exp_procs, &tmp_exp_to_part); </TT>
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<P><TT>/* <I>Processor now knows which elements to send to other processors.</I>
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*/</TT>
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<BR><TT>/* <I>Send the requested elements. While unpacking elements, build
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</I>*/</TT>
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<BR><TT>/* <I>request lists for "ghost" nodes needed by the imported elements.</I>
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*/</TT>
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<BR><TT><A HREF="ug_interface_mig.html#Zoltan_Migrate">Zoltan_Migrate</A>(zz,
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Num_Elt_Requests, Elt_Requests_Global_IDs, </TT>
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<BR><TT> Elt_Requests_Local_IDs, Elt_Requests_Procs, Elt_Request_to_Part,</TT>
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<BR><TT> num_tmp_exp_objs, tmp_exp_global_ids, </TT>
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<BR><TT> tmp_exp_local_ids, tmp_exp_procs, tmp_exp_to_part);</TT>
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<P><TT>/* <I>Repeat process for "ghost" nodes.</I> */</TT>
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<BR><TT>...</TT></TD>
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</TR>
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<CAPTION ALIGN=BOTTOM><I>Typical calling sequence for user-guided use of
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the migration tools in Zoltan</I>.</CAPTION>
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</TABLE></CENTER>
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<BR>
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<HR WIDTH="100%">[<A HREF="ug.html">Table of Contents</A> |
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<A HREF="ug_examples_query.html">Next: Query-Function Examples</A>
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| <A HREF="ug_examples_lb.html">Previous: Load-Balancing Example</A> | <a href="https://www.sandia.gov/general/privacy-security/index.html">Privacy and Security</a>]
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