finley/src/Mesh_prepare.c


/* $Id$ */

/*******************************************************
 *
 *           Copyright 2003-2007 by ACceSS MNRF
 *       Copyright 2007 by University of Queensland
 *
 *                http://esscc.uq.edu.au
 *        Primary Business: Queensland, Australia
 *  Licensed under the Open Software License version 3.0
 *     http://www.opensource.org/licenses/osl-3.0.php
 *
 *******************************************************/

/**************************************************************/

/*   Finley: Mesh: prepares the mesh for further calculations  */

/**************************************************************/

#include "Mesh.h"

/**************************************************************/

void Finley_Mesh_prepare(Finley_Mesh* in, bool_t optimize) {
     dim_t newGlobalNumDOFs=0, numReducedNodes=0,i;
     index_t* distribution=NULL, *maskReducedNodes=NULL, *indexReducedNodes=NULL, *node_distribution=NULL;
     if (in==NULL) return;
     if (in->Nodes == NULL) return;

     /* first step is to distribute the elements according to a global distribution of DOF */

     distribution=TMPMEMALLOC(in->MPIInfo->size+1,index_t);
     node_distribution=TMPMEMALLOC(in->MPIInfo->size+1,index_t);
     if (! (Finley_checkPtr(distribution) || Finley_checkPtr(node_distribution))) {
        /* first we create dense labeling for the DOFs */
        newGlobalNumDOFs=Finley_NodeFile_createDenseDOFLabeling(in->Nodes);

        /* create a distribution of the global DOFs and determine
           the MPI_rank controling the DOFs on this processor      */
        Paso_MPIInfo_setDistribution(in->MPIInfo,0,newGlobalNumDOFs-1,distribution);

        /* now the mesh is re-distributed according to the mpiRankOfDOF vector */
        /* this will redistribute the Nodes and Elements including overlap and will create an element coloring 
           but will not create any mappings (see later in this function)                                   */
        if (Finley_noError()) Finley_Mesh_distributeByRankOfDOF(in,distribution);
     }

     /* at this stage we are able to start an optimization of the DOF distribution using ParaMetis */
     /* on return distribution is altered and new DOF ids have been assigned */
     if (Finley_noError() && optimize && in->MPIInfo->size>1) {

         Finley_Mesh_optimizeDOFDistribution(in,distribution);

         if (Finley_noError()) Finley_Mesh_distributeByRankOfDOF(in,distribution); 

     }
     /* now a local labeling of the DOF is introduced */
     if (Finley_noError() && optimize) {
       Finley_Mesh_optimizeDOFLabeling(in,distribution); 
     }
     /* rearrange elements with the attempt to bring elements closer to memory locations of the nodes (distributed shared memory!): */
     if (Finley_noError()) Finley_Mesh_optimizeElementOrdering(in);


     /* create the global indices */
     if (Finley_noError()) {
        maskReducedNodes=TMPMEMALLOC(in->Nodes->numNodes,index_t);
        indexReducedNodes=TMPMEMALLOC(in->Nodes->numNodes,index_t);
        if (! ( Finley_checkPtr(maskReducedNodes) ||  Finley_checkPtr(indexReducedNodes) ) ) {

          #pragma omp parallel for private(i) schedule(static)
          for (i=0;i<in->Nodes->numNodes;++i) maskReducedNodes[i]=-1;

          Finley_Mesh_markNodes(maskReducedNodes,0,in,1);
   
          numReducedNodes=Finley_Util_packMask(in->Nodes->numNodes,maskReducedNodes,indexReducedNodes);

          Finley_NodeFile_createDenseNodeLabeling(in->Nodes, node_distribution, distribution); 

          Finley_NodeFile_createDenseReducedDOFLabeling(in->Nodes,maskReducedNodes); 
          Finley_NodeFile_createDenseReducedNodeLabeling(in->Nodes,maskReducedNodes);
          /* create the missing mappings */
          if (Finley_noError()) Finley_Mesh_createNodeFileMappings(in,numReducedNodes,indexReducedNodes,distribution, node_distribution);
        }

        TMPMEMFREE(maskReducedNodes);
        TMPMEMFREE(indexReducedNodes);
     }

     TMPMEMFREE(distribution);
     TMPMEMFREE(node_distribution);

     Finley_Mesh_setTagsInUse(in);

     return;
}

/*                                                      */
/*  tries to reduce the coloring for all element files: */
/*                                                      */
void Finley_Mesh_createColoring(Finley_Mesh* in, index_t *node_localDOF_map) {
  if (Finley_noError()) Finley_ElementFile_createColoring(in->Elements,in->Nodes->numNodes,node_localDOF_map);
  if (Finley_noError()) Finley_ElementFile_createColoring(in->FaceElements,in->Nodes->numNodes,node_localDOF_map);
  if (Finley_noError()) Finley_ElementFile_createColoring(in->Points,in->Nodes->numNodes,node_localDOF_map);
  if (Finley_noError()) Finley_ElementFile_createColoring(in->ContactElements,in->Nodes->numNodes,node_localDOF_map);
}
/*                                                                    */
/*  redistribute elements to minimize communication during assemblage */
/*                                                                    */
void Finley_Mesh_optimizeElementOrdering(Finley_Mesh* in) {
  if (Finley_noError()) Finley_ElementFile_optimizeOrdering(&(in->Elements));
  if (Finley_noError()) Finley_ElementFile_optimizeOrdering(&(in->FaceElements));
  if (Finley_noError()) Finley_ElementFile_optimizeOrdering(&(in->Points));
  if (Finley_noError()) Finley_ElementFile_optimizeOrdering(&(in->ContactElements));
}

/*                                                                    */
/*  redistribute elements to minimize communication during assemblage */
void Finley_Mesh_setTagsInUse(Finley_Mesh* in)
{
    if (Finley_noError()) Finley_NodeFile_setTagsInUse(in->Nodes);
    if (Finley_noError()) Finley_ElementFile_setTagsInUse(in->Elements);
    if (Finley_noError()) Finley_ElementFile_setTagsInUse(in->FaceElements);
    if (Finley_noError()) Finley_ElementFile_setTagsInUse(in->Points);
    if (Finley_noError()) Finley_ElementFile_setTagsInUse(in->ContactElements);
}
1
2	/* $Id$ */
3
4	/*******************************************************
5	*
6	* Copyright 2003-2007 by ACceSS MNRF
7	* Copyright 2007 by University of Queensland
8	*
9	* http://esscc.uq.edu.au
10	* Primary Business: Queensland, Australia
11	* Licensed under the Open Software License version 3.0
12	* http://www.opensource.org/licenses/osl-3.0.php
13	*
14	*******************************************************/
15
16	/**************************************************************/
17
18	/* Finley: Mesh: prepares the mesh for further calculations */
19
20	/**************************************************************/
21
22	#include "Mesh.h"
23
24	/**************************************************************/
25
26	void Finley_Mesh_prepare(Finley_Mesh* in, bool_t optimize) {
27	dim_t newGlobalNumDOFs=0, numReducedNodes=0,i;
28	index_t* distribution=NULL, maskReducedNodes=NULL, indexReducedNodes=NULL, *node_distribution=NULL;
29	if (in==NULL) return;
30	if (in->Nodes == NULL) return;
31
32	/* first step is to distribute the elements according to a global distribution of DOF */
33
34	distribution=TMPMEMALLOC(in->MPIInfo->size+1,index_t);
35	node_distribution=TMPMEMALLOC(in->MPIInfo->size+1,index_t);
36	if (! (Finley_checkPtr(distribution) \|\| Finley_checkPtr(node_distribution))) {
37	/* first we create dense labeling for the DOFs */
38	newGlobalNumDOFs=Finley_NodeFile_createDenseDOFLabeling(in->Nodes);
39
40	/* create a distribution of the global DOFs and determine
41	the MPI_rank controling the DOFs on this processor */
42	Paso_MPIInfo_setDistribution(in->MPIInfo,0,newGlobalNumDOFs-1,distribution);
43
44	/* now the mesh is re-distributed according to the mpiRankOfDOF vector */
45	/* this will redistribute the Nodes and Elements including overlap and will create an element coloring
46	but will not create any mappings (see later in this function) */
47	if (Finley_noError()) Finley_Mesh_distributeByRankOfDOF(in,distribution);
48	}
49
50	/* at this stage we are able to start an optimization of the DOF distribution using ParaMetis */
51	/* on return distribution is altered and new DOF ids have been assigned */
52	if (Finley_noError() && optimize && in->MPIInfo->size>1) {
53
54	Finley_Mesh_optimizeDOFDistribution(in,distribution);
55
56	if (Finley_noError()) Finley_Mesh_distributeByRankOfDOF(in,distribution);
57
58	}
59	/* now a local labeling of the DOF is introduced */
60	if (Finley_noError() && optimize) {
61	Finley_Mesh_optimizeDOFLabeling(in,distribution);
62	}
63	/* rearrange elements with the attempt to bring elements closer to memory locations of the nodes (distributed shared memory!): */
64	if (Finley_noError()) Finley_Mesh_optimizeElementOrdering(in);
65
66
67	/* create the global indices */
68	if (Finley_noError()) {
69	maskReducedNodes=TMPMEMALLOC(in->Nodes->numNodes,index_t);
70	indexReducedNodes=TMPMEMALLOC(in->Nodes->numNodes,index_t);
71	if (! ( Finley_checkPtr(maskReducedNodes) \|\| Finley_checkPtr(indexReducedNodes) ) ) {
72
73	#pragma omp parallel for private(i) schedule(static)
74	for (i=0;i<in->Nodes->numNodes;++i) maskReducedNodes[i]=-1;
75
76	Finley_Mesh_markNodes(maskReducedNodes,0,in,1);
77
78	numReducedNodes=Finley_Util_packMask(in->Nodes->numNodes,maskReducedNodes,indexReducedNodes);
79
80	Finley_NodeFile_createDenseNodeLabeling(in->Nodes, node_distribution, distribution);
81
82	Finley_NodeFile_createDenseReducedDOFLabeling(in->Nodes,maskReducedNodes);
83	Finley_NodeFile_createDenseReducedNodeLabeling(in->Nodes,maskReducedNodes);
84	/* create the missing mappings */
85	if (Finley_noError()) Finley_Mesh_createNodeFileMappings(in,numReducedNodes,indexReducedNodes,distribution, node_distribution);
86	}
87
88	TMPMEMFREE(maskReducedNodes);
89	TMPMEMFREE(indexReducedNodes);
90	}
91
92	TMPMEMFREE(distribution);
93	TMPMEMFREE(node_distribution);
94
95	Finley_Mesh_setTagsInUse(in);
96
97	return;
98	}
99
100	/* */
101	/* tries to reduce the coloring for all element files: */
102	/* */
103	void Finley_Mesh_createColoring(Finley_Mesh* in, index_t *node_localDOF_map) {
104	if (Finley_noError()) Finley_ElementFile_createColoring(in->Elements,in->Nodes->numNodes,node_localDOF_map);
105	if (Finley_noError()) Finley_ElementFile_createColoring(in->FaceElements,in->Nodes->numNodes,node_localDOF_map);
106	if (Finley_noError()) Finley_ElementFile_createColoring(in->Points,in->Nodes->numNodes,node_localDOF_map);
107	if (Finley_noError()) Finley_ElementFile_createColoring(in->ContactElements,in->Nodes->numNodes,node_localDOF_map);
108	}
109	/* */
110	/* redistribute elements to minimize communication during assemblage */
111	/* */
112	void Finley_Mesh_optimizeElementOrdering(Finley_Mesh* in) {
113	if (Finley_noError()) Finley_ElementFile_optimizeOrdering(&(in->Elements));
114	if (Finley_noError()) Finley_ElementFile_optimizeOrdering(&(in->FaceElements));
115	if (Finley_noError()) Finley_ElementFile_optimizeOrdering(&(in->Points));
116	if (Finley_noError()) Finley_ElementFile_optimizeOrdering(&(in->ContactElements));
117	}
118
119	/* */
120	/* redistribute elements to minimize communication during assemblage */
121	void Finley_Mesh_setTagsInUse(Finley_Mesh* in)
122	{
123	if (Finley_noError()) Finley_NodeFile_setTagsInUse(in->Nodes);
124	if (Finley_noError()) Finley_ElementFile_setTagsInUse(in->Elements);
125	if (Finley_noError()) Finley_ElementFile_setTagsInUse(in->FaceElements);
126	if (Finley_noError()) Finley_ElementFile_setTagsInUse(in->Points);
127	if (Finley_noError()) Finley_ElementFile_setTagsInUse(in->ContactElements);
128	}
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