static void AdjustRegionH(struct region_h *rh, unsigned n)
{
for(;n;n--,rh++) {
AdjustBuffer(&rh->offset,1,sizeof(rh->offset));
AdjustBuffer(&rh->nline,1,sizeof(rh->nline));
AdjustBuffer(&rh->sw,4,sizeof(rh->sw.x));
}
}
static void AdjustLineH(struct line_h *lh, unsigned n)
{
for(;n;n--,lh++) {
AdjustBuffer(&lh->offset,1,sizeof(lh->offset));
AdjustBuffer(&lh->npair,1,sizeof(lh->npair));
AdjustBuffer(&lh->left,2,sizeof(lh->left));
AdjustBuffer(&lh->sw,4,sizeof(lh->sw.x));
}
}
status_t
LinkSender::FlushCompleted(size_t newBufferSize)
{
// we need to hide the incomplete message so that it's not flushed
int32 end = fCurrentEnd;
int32 start = fCurrentStart;
fCurrentEnd = fCurrentStart;
status_t status = Flush();
if (status < B_OK) {
fCurrentEnd = end;
return status;
}
char *oldBuffer = NULL;
status = AdjustBuffer(newBufferSize, &oldBuffer);
if (status != B_OK)
return status;
// move the incomplete message to the start of the buffer
fCurrentEnd = end - start;
if (oldBuffer != fBuffer) {
memcpy(fBuffer, oldBuffer + start, fCurrentEnd);
free(oldBuffer);
} else
memmove(fBuffer, fBuffer + start, fCurrentEnd);
return B_OK;
}
status_t
LinkSender::StartMessage(int32 code, size_t minSize)
{
// end previous message
if (EndMessage() < B_OK)
CancelMessage();
if (minSize > kMaxBufferSize - sizeof(message_header)) {
// we will handle this case in Attach, using an area
minSize = sizeof(area_id);
}
minSize += sizeof(message_header);
// Eventually flush buffer to make space for the new message.
// Note, we do not take the actual buffer size into account to not
// delay the time between buffer flushes too much.
if (fBufferSize > 0 && (minSize > SpaceLeft() || fCurrentStart >= kWatermark)) {
status_t status = Flush();
if (status < B_OK)
return status;
}
if (minSize > fBufferSize) {
if (AdjustBuffer(minSize) != B_OK)
return fCurrentStatus = B_NO_MEMORY;
}
message_header *header = (message_header *)(fBuffer + fCurrentStart);
header->size = 0;
// will be set later
header->code = code;
header->flags = 0;
STRACE(("info: LinkSender buffered header %ld (%lx) [%lu %lu %lu].\n",
code, code, header->size, header->code, header->flags));
fCurrentEnd += sizeof(message_header);
return B_OK;
}
// saves the read to the read archive
void CReadWriter::SaveRead(const Mosaik::Read& mr) {
// initialize
unsigned char readNameLen = (unsigned char)mr.Name.Length();
unsigned short numMate1Bases = (unsigned short)mr.Mate1.Bases.Length();
unsigned short numMate2Bases = (unsigned short)mr.Mate2.Bases.Length();
// return if both mates are empty
if((numMate1Bases == 0) && (numMate2Bases == 0)) return;
mNumBases += numMate1Bases + numMate2Bases;
bool isPairedEnd = false;
if(numMate2Bases > 0) isPairedEnd = true;
// calculate the entry size
unsigned short entrySize = 2 * numMate1Bases + readNameLen + SIZEOF_SHORT + 2;
if(isPairedEnd) entrySize += 2 * numMate2Bases + SIZEOF_SHORT;
if(mIsSOLiD) {
entrySize += SOLID_PREFIX_LENGTH;
if(isPairedEnd) entrySize += SOLID_PREFIX_LENGTH;
}
// check the memory buffer
if(mBufferPosition >= (mBufferLen - entrySize)) AdjustBuffer();
// ============================
// serialize data to our buffer
// ============================
// no need to leave space for entry size
unsigned int bufferOffset = mBufferPosition;
// store the read type
mBuffer[bufferOffset++] = (isPairedEnd ? 1 : 0);
// store the read name
mBuffer[bufferOffset++] = readNameLen;
memcpy(mBuffer + bufferOffset, mr.Name.CData(), readNameLen);
bufferOffset += readNameLen;
// ============
// store mate 1
// ============
// sanity check
if ( mr.Mate1.Bases.Length() != mr.Mate1.Qualities.Length() ) {
printf("ERROR: The lengths of bases(%u) and qualities(%u) of Read (%s) didn't match.\n", mr.Mate1.Bases.Length(), mr.Mate1.Qualities.Length(), mr.Name.CData());
exit(1);
}
// store the read length
memcpy(mBuffer + bufferOffset, (char*)&numMate1Bases, SIZEOF_SHORT);
bufferOffset += SIZEOF_SHORT;
// store the bases
memcpy(mBuffer + bufferOffset, mr.Mate1.Bases.CData(), numMate1Bases);
bufferOffset += numMate1Bases;
if(mIsSOLiD) {
memcpy(mBuffer + bufferOffset, mr.Mate1.SolidPrefixTransition, SOLID_PREFIX_LENGTH);
bufferOffset += SOLID_PREFIX_LENGTH;
}
// store the qualities
memcpy(mBuffer + bufferOffset, mr.Mate1.Qualities.CData(), numMate1Bases);
bufferOffset += numMate1Bases;
// ============
// store mate 2
// ============
if(isPairedEnd) {
// sanity check
if ( mr.Mate2.Bases.Length() != mr.Mate2.Qualities.Length() ) {
printf("ERROR: The lengths of bases(%u) and qualities(%u) of Read (%s) didn't match.\n", mr.Mate2.Bases.Length(), mr.Mate2.Qualities.Length(), mr.Name.CData());
exit(1);
}
// store the read length
memcpy(mBuffer + bufferOffset, (char*)&numMate2Bases, SIZEOF_SHORT);
bufferOffset += SIZEOF_SHORT;
// store the bases
memcpy(mBuffer + bufferOffset, mr.Mate2.Bases.CData(), numMate2Bases);
bufferOffset += numMate2Bases;
if(mIsSOLiD) {
memcpy(mBuffer + bufferOffset, mr.Mate2.SolidPrefixTransition, SOLID_PREFIX_LENGTH);
bufferOffset += SOLID_PREFIX_LENGTH;
}
// store the qualities
memcpy(mBuffer + bufferOffset, mr.Mate2.Qualities.CData(), numMate2Bases);
bufferOffset += numMate2Bases;
}
// check the buffer
if(bufferOffset >= mBufferLen) {
cout << endl << "ERROR: Buffer overrun detected when saving read. Used " << bufferOffset << " bytes, but allocated " << mBufferLen << " bytes." << endl;
exit(1);
}
// update the partition variables and buffer position
mPartitionMembers++;
mBufferPosition = bufferOffset;
// flush the buffer
if(mPartitionMembers >= mPartitionSize) WritePartition();
// increment the read counter
mNumReads++;
}
int main(int argc, char *argv[]) {
/* ******************** Step 0: Get Host Names and IDs ******************** */
MPI_Init(&argc, &argv); /* starts MPI */
par.t0 = 0;
Tstart(par.t0);
MPI_Comm_rank(MPI_COMM_WORLD, &par.id); /* get current process id */
MPI_Comm_size(MPI_COMM_WORLD, &par.np); /* get number of processes */
MPI_Get_processor_name(par.proc_name, &par.namelength);
Init(&par, &mat);
/* ******************** Step 0: Set some init values ******************** */
if (par.id == 0) {
if (argc == 4) {
par.foutdir = argv[3];
} else {
if (argc > 4 || argc < 2) {
fprintf(stderr,
"Wrong number of argument %d. ./matrix.ij ./vector.vec",argc);
exit(1);
} else
par.foutdir = NULL;
}
par.fmat = argv[1];
par.fvec = argv[2];
par.fout = NULL;
} else {
par.fmat = par.fvec = par.fout = par.foutdir = NULL;
};
if (par.id == 0) {
printf("PID %6d: Proc %2d of %d, %s\n", par.PID, par.id, par.np,
par.proc_name);
}
MPI_Barrier(MPI_COMM_WORLD);
/* ******************** Step 1: Distribute the data ******************** */
if (par.id == 0) {
Step1root(&par);
} else {
Step1other(&par);
}
AdjustBuffer(&par);
CreateCSR(&par, &mat); // here, all nodes have local mat and vec in CSR form
MPI_Barrier(MPI_COMM_WORLD);
Tstart(par.t1);
/* ******************** Step 2: Analyze non-zero entry******************** */
IndexCSC(&par, &mat);
/* ******************** Step 3: Analyze non-zero entry******************** */
DeterminNonlocalb(&par, &mat);
/* ******************** Step 4: Figure out which process needs which ******************** */
/* ******************** Step 5: Actual transfer the data ******************** */
if (par.id == 0)
printf("Starting transferring the vector b at ID=0\n");
Tstart(par.t2);
Tstart(par.t11);
TransferVector(&par, &mat);
Tstop(par.t11);
/* ******************** Step 6: Computing local product ******************** */
Tstart(par.t13);
if (par.id == 0)
printf("Starting computation at ID=0\n");
ComputeOutput(&par, &mat);
Tstop(par.t13);
Tstop(par.t2);
Tstop(par.t1);
/* ******************** Step 7: Gather Data ******************** */
GatherOutput(&par, &mat);
if (par.id == 0) {
WriteOutput(&par, &mat);
Tstop(par.t0);
printf("\n======================================================\n");
printf("Overall time t0 (sec):\t%.8lf\n", par.t0);
printf("Total time taken t1 (sec):$\t%.8lf\n", par.t1);
printf("Time taken (step5&6) t2 (sec):$\t%.8lf\n", par.t2);
printf("Time taken (fileio) t10 (sec):\t%.8lf\n", par.t10);
printf("Transfer needed vec t11 (sec):\t%.8lf\n", par.t11);
printf("Local computation t13 (sec):\t%.8lf\n", par.t13);
printf("Write output file t12 (sec):\t%.8lf\n", par.t12);
printf("======================================================\n");
}
FinalFreeMemory(&par, &mat);
MPI_Finalize();
return 0;
}
