//==============================================================================
double* PoissonData::getElemLoad(GlobalID elemID)
{
elem_->setElemID(elemID);
elem_->setElemLength(1.0/L_);
elem_->setTotalLength(1.0);
//now get a pointer to this element's connectivity array and
//calculate that connectivity (in place).
int size = 0;
GlobalID* elemConn = elem_->getElemConnPtr(size);
if (size == 0) messageAbort("loadElemLoads: bad conn ptr.");
calculateConnectivity(elemConn, size, elemID);
elem_->calculateCoords();
if (outputLevel_>1) {
double* x = elem_->getNodalX(size);
double* y = elem_->getNodalY(size);
FEI_COUT << localProc_ << ", elemID " << elemID << ", nodes: ";
for(int j=0; j<size; j++) {
FEI_COUT << elemConn[j] << " ";
FEI_COUT << "("<<x[j]<<","<<y[j]<<") ";
}
FEI_COUT << FEI_ENDL;
}
elem_->calculateLoad();
return( elem_->getElemLoad(size));
}
//==============================================================================
void PoissonData::calculateBCs() {
//
//This function figures out which nodes lie on the boundary. The ones that
//do are added to the BC set, along with appropriate alpha/beta/gamma values.
//
for(int i=0; i<numLocalElements_; i++) {
elem_->setElemID(elemIDs_[i]);
elem_->setElemLength(1.0/L_);
elem_->setTotalLength(1.0);
//now get a pointer to this element's connectivity array and
//calculate that connectivity (in place).
int size = 0;
GlobalID* nodeIDs = elem_->getElemConnPtr(size);
if (size == 0) messageAbort("loadElements: bad conn ptr.");
calculateConnectivity(nodeIDs, size, elemIDs_[i]);
elem_->calculateCoords();
double* xcoord = elem_->getNodalX(size);
double* ycoord = elem_->getNodalY(size);
//now loop over the nodes and see if any are on a boundary.
for(int j=0; j<size; j++) {
if ((std::abs(xcoord[j]) < 1.e-49) || (std::abs(xcoord[j] - 1.0) < 1.e-49) ||
(std::abs(ycoord[j]) < 1.e-49) || (std::abs(ycoord[j] - 1.0) < 1.e-49)) {
addBCNode(nodeIDs[j], xcoord[j], ycoord[j]);
}
}
}
}
//==============================================================================
void PoissonData::calculateDistribution() {
//
//Calculate which elements this processor owns. The element domain is a
//square, and we can assume that sqrt(numProcs_) divides evenly into
//L_. We're working with a (logically) 2D processor arrangement.
//Furthermore, the logical processor layout is such that processor 0 is at
//the bottom left corner of a 2D grid, and a side of the grid is of length
//sqrt(numProcs_). The element domain is numbered such that element 1 is at
//the bottom left corner of the square, and element numbers increase from
//left to right. i.e., element 1 is in position (1,1), element L is in
//position (1,L), element L+1 is in position (2,1).
//
//Use 1-based numbering for the elements and the x- and y- coordinates in
//the element grid, but use 0-based numbering for processor IDs and the
//coordinates in the processor grid.
//
numLocalElements_ = (L_*L_)/numProcs_;
elemIDs_ = new GlobalID[numLocalElements_];
if (!elemIDs_) messageAbort("ERROR allocating elemIDs_.");
elemIDsAllocated_ = true;
//0-based x-coordinate of this processor in the 2D processor grid.
procX_ = localProc_%int_sqrt(numProcs_);
//0-based maximum processor x-coordinate.
maxProcX_ = int_sqrt(numProcs_) - 1;
//0-based y-coordinate of this processor in the 2D processor grid.
procY_ = localProc_/int_sqrt(numProcs_);
//0-based maximum processor y-coordinate.
maxProcY_ = int_sqrt(numProcs_) - 1;
int sqrtElems = int_sqrt(numLocalElements_);
int sqrtProcs = int_sqrt(numProcs_);
//1-based first-element-on-this-processor
startElement_ = 1 + procY_*sqrtProcs*numLocalElements_ + procX_*sqrtElems;
if (outputLevel_>1) {
FEI_COUT << localProc_ << ", calcDist.: numLocalElements: "
<< numLocalElements_ << ", startElement: " << startElement_
<< FEI_ENDL;
FEI_COUT << localProc_ << ", procX: " << procX_ << ", procY_: " << procY_
<< ", maxProcX: " << maxProcX_ << ", maxProcY: " << maxProcY_
<< FEI_ENDL;
}
int offset = 0;
for(int i=0; i<sqrtElems; i++) {
for(int j=0; j<sqrtElems; j++) {
elemIDs_[offset] = (GlobalID)(startElement_ + i*L_ + j);
offset++;
}
}
}
//==============================================================================
void Poisson_Elem::calculateCoords() {
//
//This function calculates nodal x- and y-coordinates for this element.
//NOTE: element IDs are assumed to be 1-based.
//
if (!internalsAllocated_)
messageAbort("calculateCoords: internals not allocated.");
if (!elemLengthIsSet_)
messageAbort("calculateCoords: elemLength not set.");
if (!totalLengthIsSet_)
messageAbort("calculateCoords: totalLength not set.");
if (!ID_IsSet_)
messageAbort("calculateCoords: elemID not set.");
if (std::abs(elemLength_) < 1.e-49)
messageAbort("calculateCoords: elemLength == 0.");
int lowLeft = 0;
int lowRight = 1;
int upperRight = 2;
int upperLeft = 3;
int elemsPerSide = (int)std::ceil(totalLength_/elemLength_);
int elemX = (int)globalElemID_%elemsPerSide;
if (elemX==0) elemX = elemsPerSide;
int elemY = ((int)globalElemID_ - elemX)/elemsPerSide + 1;
//elemX and elemY are 1-based coordinates of this element in
//the global square of elements. The origin is position (1,1),
//which is at the bottom left of the square.
nodalX_[lowLeft] = (elemX-1)*elemLength_;
nodalX_[upperLeft] = nodalX_[lowLeft];
nodalX_[lowRight] = elemX*elemLength_;
nodalX_[upperRight] = nodalX_[lowRight];
nodalY_[lowLeft] = (elemY-1)*elemLength_;
nodalY_[lowRight] = nodalY_[lowLeft];
nodalY_[upperLeft] = elemY*elemLength_;
nodalY_[upperRight] = nodalY_[upperLeft];
}
//==============================================================================
void AztecDVBR_Matrix::setBindx(int nnzBlks, int* blkColInds) {
//
//This function simply allocates and fills the Amat_->bindx array.
//
Amat_->bindx = new int[nnzBlks];
for(int i=0; i<nnzBlks; i++) {
Amat_->bindx[i] = blkColInds[i];
if (blkColInds[i] < 0)
messageAbort("setBindx: negative block col index.");
}
}
//==============================================================================
PoissonData::PoissonData(int L,
int numProcs, int localProc, int outputLevel)
{
//
//PoissonData constructor.
//
//Arguments:
//
// L: global square size (number-of-elements along side)
// numProcs: number of processors participating in this FEI test.
// localProc: local processor number.
// outputLevel: affects the amount of screen output.
//
L_ = L;
startElement_ = 0;
numLocalElements_ = 0;
numProcs_ = numProcs;
localProc_ = localProc;
outputLevel_ = outputLevel;
check1();
elem_ = new Poisson_Elem();
int err = elem_->allocateInternals(1);
err += elem_->allocateLoad(1);
err += elem_->allocateStiffness(1);
if (err) messageAbort("Allocation error in element.");
fieldArraysAllocated_ = false;
elemIDsAllocated_ = false;
numFields_ = NULL;
fieldIDs_ = NULL;
elemIDs_ = NULL;
calculateDistribution();
numElemBlocks_ = 1;
elemBlockID_ = (GlobalID)0;
elemSetID_ = 0;
elemFormat_ = 0;
nodesPerElement_ = 4;
fieldsPerNode_ = 1;
initializeFieldStuff();
}
//==============================================================================
GlobalID* PoissonData::getElementConnectivity(GlobalID elemID)
{
//set the elemID on the internal Poisson_Elem instance.
elem_->setElemID(elemID);
elem_->setElemLength(1.0/L_);
elem_->setTotalLength(1.0);
//now get a pointer to the element's connectivity array and
//calculate that connectivity (in place).
int size = 0;
GlobalID* elemConn = elem_->getElemConnPtr(size);
if (size == 0) messageAbort("loadElements: bad conn ptr.");
calculateConnectivity(elemConn, size, elemID);
return(elemConn);
}
//==============================================================================
void PoissonData::check1() {
//
//Private function to be called from the constructor, simply makes sure that
//the constructor's input arguments were reasonable.
//
//If they aren't, a message is printed on standard err, and abort() is called.
//
if (L_ <= 0) messageAbort("bar length L <= 0.");
if (numProcs_ <= 0) messageAbort("numProcs <= 0.");
if (L_%int_sqrt(numProcs_))
messageAbort("L must be an integer multiple of sqrt(numProcs).");
if (localProc_ < 0) messageAbort("localProc < 0.");
if (localProc_ >= numProcs_) messageAbort("localProc >= numProcs.");
if (outputLevel_ < 0) messageAbort("outputLevel < 0.");
}
//==============================================================================
bool AztecDVBR_Matrix::readFromFile(const char *filename){
//
//readFromFile should be able to be called after the matrix is constructed,
//and before allocate has been called. i.e., example usage should include:
//
// AztecDVBR_Matrix A(map, update);
// A.readFromFile(fileName);
// A.matvec(b, c);
//
//i.e., readFromFile can take the place of the allocate and loadComplete
//calls.
//
FILE *infile = NULL;
MPI_Comm thisComm = amap_->getCommunicator();
MPI_Barrier(thisComm);
infile = fopen(filename, "r");
if (!infile) messageAbort("readFromFile: couldn't open file.");
int* num_nz_blocks = NULL;
int* blk_col_inds = NULL;
readAllocateInfo(infile, num_nz_blocks, blk_col_inds);
allocate(num_nz_blocks, blk_col_inds);
delete [] num_nz_blocks;
delete [] blk_col_inds;
fclose(infile);
infile = fopen(filename, "r");
readMatrixData(infile);
fclose(infile);
loadComplete();
return(true);
}
//==============================================================================
int AztecDVBR_Matrix::putBlockRow(int blkRow,
double* val,
int* blkColInds,
int numNzBlks) const {
if (!isAllocated()) return(1);
int index;
if (!inUpdate(blkRow, index)) {
fei::console_out() << "AztecDVBR_Matrix::putBlockRow: ERROR: blkRow "
<< blkRow << " not in local update list." << FEI_ENDL;
return(1);
}
//for each incoming block, we need to find its block column index
//in the bindx array, then go to that same position in the indx
//array to find out how many (point) entries are in that block.
//We can then use the indx entry to go to the val array and store
//the data.
int offset = 0;
for(int blk = 0; blk<numNzBlks; blk++) {
int indb = getBindxOffset(blkColInds[blk],
Amat_->bpntr[index], Amat_->bpntr[index+1]-1);
if (indb < 0) messageAbort("putBlockRow: blk col not found in row.");
int numEntries = Amat_->indx[indb+1] - Amat_->indx[indb];
int valOffset = Amat_->indx[indb];
//ok, now we're ready to store the stuff.
for(int i=0; i<numEntries; i++) {
Amat_->val[valOffset + i] = val[offset + i];
}
offset += numEntries;
}
return(0);
}
//==============================================================================
void AztecDVBR_Matrix::calcRpntr() {
//
//This function will use information from the Aztec_BlockMap 'amap_'
//to set the Amat_->rpntr array.
//
//rpntr[0..M] (where M = number-of-blocks)
//rpntr[0] = 0
//rpntr[k+1] - rpntr[k] = size of block k
//
const int* blkSizes = amap_->getBlockSizes();
Amat_->rpntr = new int[N_update_+1];
Amat_->rpntr[0] = 0;
for(int i=0; i<N_update_; i++) {
Amat_->rpntr[i+1] = Amat_->rpntr[i] + blkSizes[i];
if (blkSizes[i] < 0)
messageAbort("allocate: negative block size.");
}
}
//==============================================================================
void PoissonData::getBottomSharedNodes(int& numShared, GlobalID* sharedNodeIDs,
int* numProcsPerSharedNode,
int** sharingProcs) {
//
//This function decides whether any of the nodes along the bottom edge,
//including the left node but not the right node, are shared. It also
//decides which processors the nodes are shared with.
//
if (numProcs_ == 1) {
numShared = 0;
return;
}
if (procY_ == 0) {
//if this proc is on the bottom edge of the square...
if (procX_ > 0) {
//if this proc is not the bottom left proc...
numShared = 1;
int elemIndex = 0;
elem_->setElemID(elemIDs_[elemIndex]);
//now get a pointer to this element's connectivity array and
//calculate that connectivity (in place).
int size;
GlobalID* nodes = elem_->getElemConnPtr(size);
if (size == 0) messageAbort(": bad conn ptr.");
calculateConnectivity(nodes, size, elemIDs_[elemIndex]);
sharedNodeIDs[0] = nodes[0]; //elem's bottom left node is node 0
numProcsPerSharedNode[0] = 2;
sharingProcs[0][0] = localProc_;
sharingProcs[0][1] = localProc_ - 1;
return;
}
else {
//else this proc is the top right proc...
numShared = 0;
}
}
else {
//else this proc is not on the bottom edge of the square...
numShared = int_sqrt(numLocalElements_);
int lowerRightElemIndex = int_sqrt(numLocalElements_) - 1;
int sqrtElems = int_sqrt(numLocalElements_);
int shOffset = 0;
for(int i=0; i<sqrtElems; i++){
//stride across the bottom edge of the local elements, from
//right to left...
int size=0;
int elemIndex = lowerRightElemIndex-i;
elem_->setElemID(elemIDs_[elemIndex]);
//now get a pointer to this element's connectivity array and
//calculate that connectivity (in place).
GlobalID* nodes = elem_->getElemConnPtr(size);
if (size == 0) messageAbort(": bad conn ptr.");
calculateConnectivity(nodes, size, elemIDs_[elemIndex]);
//now put in the lower left node
sharedNodeIDs[shOffset] = nodes[0];
sharingProcs[shOffset][0] = localProc_ - int_sqrt(numProcs_);
sharingProcs[shOffset][1] = localProc_;
numProcsPerSharedNode[shOffset++] = 2;
}
if (procX_ > 0) {
//if this proc isn't on the left edge, the lower left node (the
//last one we put into the shared node list) is shared by 4 procs.
shOffset--;
numProcsPerSharedNode[shOffset] = 4;
sharingProcs[shOffset][2] = localProc_ - 1;
sharingProcs[shOffset][3] = sharingProcs[shOffset][0] - 1;
}
}
}
//==============================================================================
void AztecDVBR_Matrix::calcIndx(int nnzBlks) {
//
//This function allocates and fills the Amat_->indx array, which holds info
//on the number of entries in each nonzero block.
//
//indx[0..bpntr[M]], (where M = number of local block rows)
//indx[0] = 0
//indx[k+1]-indx[k] = number of entries in nonzero block k
//
Amat_->indx = new int[nnzBlks+1];
//we need to obtain block sizes for all local nonzero blocks. rpntr
//gives us the sizes for the blocks with column indices in the local
//update set, but we'll have to do some message passing to obtain the
//sizes of blocks with column indices in other procs' update sets.
int numProcs = amap_->getProcConfig()[AZ_N_procs];
if (numProcs > 1) {
//form a list of the column indices that are not local.
calcRemoteInds(remoteInds_, numRemoteBlocks_);
//now get sizes of blocks that correspond to remote rows.
remoteBlockSizes_ = new int[numRemoteBlocks_];
getRemoteBlkSizes(remoteBlockSizes_, remoteInds_, numRemoteBlocks_);
}
//now we're ready to set the block sizes in Amat_->indx.
int index;
Amat_->indx[0] = 0;
for(int i=0; i<amap_->getNumLocalBlocks(); i++) {
int rowBlkSize = Amat_->rpntr[i+1] - Amat_->rpntr[i];
int colStart = Amat_->bpntr[i];
int colEnd = Amat_->bpntr[i+1] - 1;
for(int j=colStart; j<=colEnd; j++) {
if (inUpdate(Amat_->bindx[j], index)) {
int colBlkSize = Amat_->rpntr[index+1] - Amat_->rpntr[index];
Amat_->indx[j+1] = Amat_->indx[j] + rowBlkSize*colBlkSize;
}
else { //it's a remoteIndex
if (numProcs == 1) {
char mesg[80];
sprintf(mesg,"calcIndx: blk col index %d not in update set.",
Amat_->bindx[j]);
messageAbort(mesg);
}
index = AZ_find_index(Amat_->bindx[j], remoteInds_,
numRemoteBlocks_);
if (index >= 0) {
Amat_->indx[j+1] = Amat_->indx[j] +
rowBlkSize*remoteBlockSizes_[index];
}
else { //if it wasn't in update or remoteInds, then panic!
messageAbort("calcIndx: block column index not found.");
}
}
} // end for j loop
nnzPerRow_[i] = Amat_->indx[colEnd+1] - Amat_->indx[colStart];
} // end for i loop
localNNZ_ = Amat_->indx[nnzBlks];
}
//==============================================================================
void AztecDVBR_Matrix::readAllocateInfo(FILE* infile,
int*& num_nz_blocks,
int*& blk_col_inds) {
//
//This function will read through infile and construct the lists
//num_nz_blocks (which is the number of nonzero blocks per row) and
//blk_col_inds (which is the block-column indices of those blocks).
//
//It is assumed that these two lists are empty when this function is
//called.
int i;
if (num_nz_blocks) delete [] num_nz_blocks;
if (blk_col_inds) delete [] blk_col_inds;
num_nz_blocks = new int[N_update_];
//we'll use a 2-D array for constructing the set of block column indices,
//because we need to keep them grouped by rows, and we aren't guaranteed
//that they'll be grouped by rows in the file.
int totalNumBlks = 0;
int** blkColInds = new int*[N_update_];
for(i=0; i<N_update_; i++) {
num_nz_blocks[i] = 0;
blkColInds[i] = NULL;
}
int blkRows, blkCols, rows, cols;
char line[256];
do {
fgets(line,256,infile);
} while(strchr(line,'%'));
sscanf(line,"%d %d %d %d",&blkRows, &blkCols, &rows, &cols);
if ((blkRows != blkCols) || (rows != cols))
messageAbort("readAllocateInfo: non-square matrix not allowed.");
int br, bc, pr, pc, index;
while (!feof(infile)) {
do {
fgets(line,256,infile);
} while(strchr(line,'%'));
if(feof(infile))break;
sscanf(line, "%d %d %d %d", &br, &bc, &pr, &pc);
if (inUpdate(br, index)) {
if ((bc < 0) || bc >= blkCols) {
char mesg[80];
sprintf(mesg,"readAllocateInfo: blkCols %d, 0-based col ind %d",
blkCols, bc);
fclose(infile);
messageAbort(mesg);
}
insertList(bc, blkColInds[index], num_nz_blocks[index]);
totalNumBlks++;
}
}
//so we've read the whole file, now flatten the 2-D list blkColInds
//into the required 1-D list blk_col_inds.
blk_col_inds = new int[totalNumBlks];
int offset = 0;
for(i=0; i<N_update_; i++) {
for(int j=0; j<num_nz_blocks[i]; j++) {
blk_col_inds[offset++] = blkColInds[i][j];
}
delete [] blkColInds[i];
}
delete [] blkColInds;
}
//==============================================================================
void AztecDVBR_Matrix::getRemoteBlkSizes(int* remoteBlkSizes,
int* remoteInds,
int len)
{
//
//remoteInds is a sorted list of indices that correspond to rows
//in remote processors' update lists. This function will spread the
//indices to all processors so that they can provide the blk sizes,
//then spread that information back to all processors.
//
#ifdef FEI_SER
return;
#else
int numProcs = amap_->getProcConfig()[AZ_N_procs];
int thisProc = amap_->getProcConfig()[AZ_node];
MPI_Comm comm = amap_->getCommunicator();
int* lengths = new int[numProcs];
lengths[0] = 0;
//gather up the lengths of the lists that each proc will be sending.
MPI_Allgather(&len, 1, MPI_INT, lengths, 1, MPI_INT, comm);
//now form a list of the offset at which each proc's contribution will
//be placed in the all-gathered list.
int* offsets = new int[numProcs];
offsets[0] = 0;
int totalLength = lengths[0];
for(int i=1; i<numProcs; i++) {
offsets[i] = offsets[i-1] + lengths[i-1];
totalLength += lengths[i];
}
//now we can allocate the list to recv into.
int* recvBuf = new int[totalLength];
//now we're ready to do the gather.
MPI_Allgatherv(remoteInds, len, MPI_INT, recvBuf, lengths, offsets,
MPI_INT, comm);
//now we'll run through the list and put block sizes into a list of
//the same length as the total recvBuf list.
int* blkSizes = new int[totalLength];
int index;
for(int j=0; j<totalLength; j++) {
if (inUpdate(recvBuf[j], index)) {
blkSizes[j] = Amat_->rpntr[index+1]-Amat_->rpntr[index];
}
else blkSizes[j] = 0;
}
//now we'll reduce this info back onto all processors. We'll use MPI_SUM.
//Since the sizes we did NOT supply hold a 0, and each spot in the list
//should only have a nonzero size from 1 processor, the result will be
//that each spot in the result list has the correct value.
int* recvSizes = new int[totalLength];
MPI_Allreduce(blkSizes, recvSizes, totalLength, MPI_INT, MPI_SUM, comm);
//and finally, we just need to run our section of the list of recv'd sizes,
//and transfer them into the remoteBlkSizes list.
int offset = offsets[thisProc];
for(int k=0; k<len; k++) {
remoteBlkSizes[k] = recvSizes[offset + k];
if (recvSizes[offset+k] <= 0)
messageAbort("getRemoteBlkSizes: recvd a size <= 0.");
}
delete [] lengths;
delete [] offsets;
delete [] recvBuf;
delete [] blkSizes;
delete [] recvSizes;
#endif
}