/* =============================================================================
* TMlist_insert
* -- Return TRUE on success, else FALSE
* =============================================================================
*/
bool_t
TMlist_insert (TM_ARGDECL list_t* listPtr, void* dataPtr)
{
list_node_t* prevPtr;
list_node_t* nodePtr;
list_node_t* currPtr;
prevPtr = TMfindPrevious(TM_ARG listPtr, dataPtr);
currPtr = (list_node_t*)TM_SHARED_READ_P(prevPtr->nextPtr);
#ifdef LIST_NO_DUPLICATES
if ((currPtr != NULL) &&
listPtr->comparator->compare_tm(TM_ARG TM_SHARED_READ_P(currPtr->dataPtr), dataPtr) == 0) {
return FALSE;
}
#endif
nodePtr = TMallocNode(TM_ARG dataPtr);
if (nodePtr == NULL) {
return FALSE;
}
TM_SHARED_WRITE_P(nodePtr->nextPtr, currPtr);
TM_SHARED_WRITE_P(prevPtr->nextPtr, nodePtr);
TM_SHARED_WRITE_L(listPtr->size, (TM_SHARED_READ_L(listPtr->size) + 1));
return TRUE;
}
TM_SAFE
bool_t
TMheap_insert ( heap_t* heapPtr, void* dataPtr)
{
long size = (long)TM_SHARED_READ(heapPtr->size);
long capacity = (long)TM_SHARED_READ(heapPtr->capacity);
if ((size + 1) >= capacity) {
long newCapacity = capacity * 2;
void** newElements = (void**)TM_MALLOC(newCapacity * sizeof(void*));
if (newElements == NULL) {
return FALSE;
}
TM_SHARED_WRITE(heapPtr->capacity, newCapacity);
long i;
void** elements = (void **)TM_SHARED_READ_P(heapPtr->elements);
for (i = 0; i <= size; i++) {
newElements[i] = (void*)TM_SHARED_READ_P(elements[i]);
}
free(heapPtr->elements);
TM_SHARED_WRITE_P(heapPtr->elements, newElements);
}
size++;
TM_SHARED_WRITE(heapPtr->size, size);
void** elements = (void**)TM_SHARED_READ_P(heapPtr->elements);
TM_SHARED_WRITE_P(elements[size], dataPtr);
siftUp(heapPtr, size);
return TRUE;
}
/* =============================================================================
* TMheap_insert
* -- Returns false on failure
* =============================================================================
*/
bool
TMheap_insert (TM_ARGDECL heap_t* heapPtr, void* dataPtr)
{
long size = (long)TM_SHARED_READ_L(heapPtr->size);
long capacity = (long)TM_SHARED_READ_L(heapPtr->capacity);
if ((size + 1) >= capacity) {
long newCapacity = capacity * 2;
void** newElements = (void**)TM_MALLOC(newCapacity * sizeof(void*));
if (newElements == NULL) {
return false;
}
TM_SHARED_WRITE_L(heapPtr->capacity, newCapacity);
long i;
void** elements = TM_SHARED_READ_P(heapPtr->elements);
for (i = 0; i <= size; i++) {
newElements[i] = (void*)TM_SHARED_READ_P(elements[i]);
}
TM_FREE(elements);
TM_SHARED_WRITE_P(heapPtr->elements, newElements);
}
size++;
TM_SHARED_WRITE_L(heapPtr->size, size);
void** elements = (void**)TM_SHARED_READ_P(heapPtr->elements);
TM_SHARED_WRITE_P(elements[size], dataPtr);
TMsiftUp(TM_ARG heapPtr, size);
return true;
}
/* =============================================================================
* TMheapify
* =============================================================================
*/
TM_SAFE
void
TMheapify ( heap_t* heapPtr, long startIndex)
{
void** elements = (void**)TM_SHARED_READ_P(heapPtr->elements);
//long (*compare)(const void*, const void*) TM_IFUNC_DECL = heapPtr->compare;
long (*compare)(const void*, const void*) TM_SAFE = heapPtr->compare;
long size = (long)TM_SHARED_READ(heapPtr->size);
long index = startIndex;
while (1) {
long leftIndex = LEFT_CHILD(index);
long rightIndex = RIGHT_CHILD(index);
long maxIndex = -1;
if (leftIndex <= size)
{
long ret;
void *e1, *e2;
e1 = (void*)TM_SHARED_READ_P(elements[leftIndex]);
e2 = (void*)TM_SHARED_READ_P(elements[index]);
TM_IFUNC_CALL2(ret, compare, e1, e2);
if (ret > 0)
maxIndex = leftIndex;
else
maxIndex = index;
} else {
maxIndex = index;
}
if (rightIndex <= size)
{
long ret;
void *e1, *e2;
e1 = (void*)TM_SHARED_READ_P(elements[rightIndex]);
e2 = (void*)TM_SHARED_READ_P(elements[maxIndex]);
TM_IFUNC_CALL2(ret, compare, e1, e2);
if (ret > 0)
maxIndex = rightIndex;
}
if (maxIndex == index) {
break;
} else {
void* tmpPtr = (void*)TM_SHARED_READ_P(elements[index]);
TM_SHARED_WRITE_P(elements[index],
(void*)TM_SHARED_READ_P(elements[maxIndex]));
TM_SHARED_WRITE_P(elements[maxIndex], tmpPtr);
index = maxIndex;
}
}
}
/* =============================================================================
* TMqueue_push
* =============================================================================
*/
bool_t
TMqueue_push (TM_ARGDECL queue_t* queuePtr, void* dataPtr)
{
long pop = (long)TM_SHARED_READ(queuePtr->pop);
long push = (long)TM_SHARED_READ(queuePtr->push);
long capacity = (long)TM_SHARED_READ(queuePtr->capacity);
assert(pop != push);
/* Need to resize */
long newPush = (push + 1) % capacity;
if (newPush == pop) {
long newCapacity = capacity * QUEUE_GROWTH_FACTOR;
void** newElements = (void**)TM_MALLOC(newCapacity * sizeof(void*));
if (newElements == NULL) {
return FALSE;
}
long dst = 0;
void** elements = (void**)TM_SHARED_READ_P(queuePtr->elements);
if (pop < push) {
long src;
for (src = (pop + 1); src < push; src++, dst++) {
newElements[dst] = (void*)TM_SHARED_READ_P(elements[src]);
}
} else {
long src;
for (src = (pop + 1); src < capacity; src++, dst++) {
newElements[dst] = (void*)TM_SHARED_READ_P(elements[src]);
}
for (src = 0; src < push; src++, dst++) {
newElements[dst] = (void*)TM_SHARED_READ_P(elements[src]);
}
}
TM_FREE(elements);
TM_SHARED_WRITE_P(queuePtr->elements, newElements);
TM_SHARED_WRITE(queuePtr->pop, newCapacity - 1);
TM_SHARED_WRITE(queuePtr->capacity, newCapacity);
push = dst;
newPush = push + 1; /* no need modulo */
}
void** elements = (void**)TM_SHARED_READ_P(queuePtr->elements);
TM_SHARED_WRITE_P(elements[push], dataPtr);
TM_SHARED_WRITE(queuePtr->push, newPush);
return TRUE;
}
/* =============================================================================
* TMheapify
* =============================================================================
*/
static void
TMheapify (TM_ARGDECL heap_t* heapPtr, long startIndex)
{
void** elements = (void**)TM_SHARED_READ_P(heapPtr->elements);
long (*compare)(TM_ARGDECL const void*, const void*) = heapPtr->compare->compare_tm;
long size = (long)TM_SHARED_READ_L(heapPtr->size);
long index = startIndex;
while (1) {
long leftIndex = LEFT_CHILD(index);
long rightIndex = RIGHT_CHILD(index);
long maxIndex = -1;
if ((leftIndex <= size) &&
(compare(TM_ARG
(void*)TM_SHARED_READ_P(elements[leftIndex]),
(void*)TM_SHARED_READ_P(elements[index])) > 0))
{
maxIndex = leftIndex;
} else {
maxIndex = index;
}
if ((rightIndex <= size) &&
(compare(TM_ARG
(void*)TM_SHARED_READ_P(elements[rightIndex]),
(void*)TM_SHARED_READ_P(elements[maxIndex])) > 0))
{
maxIndex = rightIndex;
}
if (maxIndex == index) {
break;
} else {
void* tmpPtr = (void*)TM_SHARED_READ_P(elements[index]);
TM_SHARED_WRITE_P(elements[index],
(void*)TM_SHARED_READ_P(elements[maxIndex]));
TM_SHARED_WRITE_P(elements[maxIndex], tmpPtr);
index = maxIndex;
}
}
}
/* =============================================================================
* TMsiftUp
* =============================================================================
*/
static void
TMsiftUp (TM_ARGDECL heap_t* heapPtr, long startIndex)
{
void** elements = (void**)TM_SHARED_READ_P(heapPtr->elements);
long (*compare)(TM_ARGDECL const void*, const void*) = heapPtr->compare->compare_tm;
long index = startIndex;
while ((index > 1)) {
long parentIndex = PARENT(index);
void* parentPtr = (void*)TM_SHARED_READ_P(elements[parentIndex]);
void* thisPtr = (void*)TM_SHARED_READ_P(elements[index]);
if (compare(TM_ARG parentPtr, thisPtr) >= 0) {
break;
}
void* tmpPtr = parentPtr;
TM_SHARED_WRITE_P(elements[parentIndex], thisPtr);
TM_SHARED_WRITE_P(elements[index], tmpPtr);
index = parentIndex;
}
}
/* =============================================================================
* TMlist_remove
* -- Returns TRUE if successful, else FALSE
* =============================================================================
*/
bool_t
TMlist_remove (TM_ARGDECL list_t* listPtr, void* dataPtr)
{
list_node_t* prevPtr;
list_node_t* nodePtr;
prevPtr = TMfindPrevious(TM_ARG listPtr, dataPtr);
nodePtr = (list_node_t*)TM_SHARED_READ_P(prevPtr->nextPtr);
if ((nodePtr != NULL) &&
(listPtr->compare(nodePtr->dataPtr, dataPtr) == 0))
{
TM_SHARED_WRITE_P(prevPtr->nextPtr, TM_SHARED_READ_P(nodePtr->nextPtr));
TM_SHARED_WRITE_P(nodePtr->nextPtr, (struct list_node*)NULL);
TMfreeNode(TM_ARG nodePtr);
TM_SHARED_WRITE(listPtr->size, (TM_SHARED_READ(listPtr->size) - 1));
assert(listPtr->size >= 0);
return TRUE;
}
return FALSE;
}
/* =============================================================================
* TMheap_remove
* -- Returns NULL if empty
* =============================================================================
*/
void*
TMheap_remove (TM_ARGDECL heap_t* heapPtr)
{
long size = (long)TM_SHARED_READ_L(heapPtr->size);
if (size < 1) {
return NULL;
}
void** elements = (void**)TM_SHARED_READ_P(heapPtr->elements);
void* dataPtr = (void*)TM_SHARED_READ_P(elements[1]);
TM_SHARED_WRITE_P(elements[1], TM_SHARED_READ_P(elements[size]));
TM_SHARED_WRITE_L(heapPtr->size, (size - 1));
TMheapify(TM_ARG heapPtr, 1);
return dataPtr;
}
/* =============================================================================
* sequencer_run
* =============================================================================
*/
void
sequencer_run (void* argPtr)
{
TM_THREAD_ENTER();
long threadId = thread_getId();
sequencer_t* sequencerPtr = (sequencer_t*)argPtr;
hashtable_t* uniqueSegmentsPtr;
endInfoEntry_t* endInfoEntries;
table_t** startHashToConstructEntryTables;
constructEntry_t* constructEntries;
table_t* hashToConstructEntryTable;
uniqueSegmentsPtr = sequencerPtr->uniqueSegmentsPtr;
endInfoEntries = sequencerPtr->endInfoEntries;
startHashToConstructEntryTables = sequencerPtr->startHashToConstructEntryTables;
constructEntries = sequencerPtr->constructEntries;
hashToConstructEntryTable = sequencerPtr->hashToConstructEntryTable;
segments_t* segmentsPtr = sequencerPtr->segmentsPtr;
assert(segmentsPtr);
vector_t* segmentsContentsPtr = segmentsPtr->contentsPtr;
long numSegment = vector_getSize(segmentsContentsPtr);
long segmentLength = segmentsPtr->length;
long i;
long j;
long i_start;
long i_stop;
long numUniqueSegment;
long substringLength;
long entryIndex;
/*
* Step 1: Remove duplicate segments
*/
// #if defined(HTM) || defined(STM)
long numThread = thread_getNumThread();
{
/* Choose disjoint segments [i_start,i_stop) for each thread */
long partitionSize = (numSegment + numThread/2) / numThread; /* with rounding */
i_start = threadId * partitionSize;
if (threadId == (numThread - 1)) {
i_stop = numSegment;
} else {
i_stop = i_start + partitionSize;
}
}
// #else /* !(HTM || STM) */
// i_start = 0;
// i_stop = numSegment;
// #endif /* !(HTM || STM) */
for (i = i_start; i < i_stop; i+=CHUNK_STEP1) {
TM_BEGIN();
{
long ii;
long ii_stop = MIN(i_stop, (i+CHUNK_STEP1));
for (ii = i; ii < ii_stop; ii++) {
void* segment = vector_at(segmentsContentsPtr, ii);
TMHASHTABLE_INSERT(uniqueSegmentsPtr,
segment,
segment);
} /* ii */
}
TM_END();
}
thread_barrier_wait();
/*
* Step 2a: Iterate over unique segments and compute hashes.
*
* For the gene "atcg", the hashes for the end would be:
*
* "t", "tc", and "tcg"
*
* And for the gene "tcgg", the hashes for the start would be:
*
* "t", "tc", and "tcg"
*
* The names are "end" and "start" because if a matching pair is found,
* they are the substring of the end part of the pair and the start
* part of the pair respectively. In the above example, "tcg" is the
* matching substring so:
*
* (end) (start)
* a[tcg] + [tcg]g = a[tcg]g (overlap = "tcg")
*/
/* uniqueSegmentsPtr is constant now */
numUniqueSegment = hashtable_getSize(uniqueSegmentsPtr);
entryIndex = 0;
// #if defined(HTM) || defined(STM)
{
/* Choose disjoint segments [i_start,i_stop) for each thread */
long num = uniqueSegmentsPtr->numBucket;
long partitionSize = (num + numThread/2) / numThread; /* with rounding */
i_start = threadId * partitionSize;
if (threadId == (numThread - 1)) {
i_stop = num;
} else {
i_stop = i_start + partitionSize;
}
}
{
/* Approximate disjoint segments of element allocation in constructEntries */
long partitionSize = (numUniqueSegment + numThread/2) / numThread; /* with rounding */
entryIndex = threadId * partitionSize;
}
// #else /* !(HTM || STM) */
// i_start = 0;
// i_stop = uniqueSegmentsPtr->numBucket;
// entryIndex = 0;
//#endif /* !(HTM || STM) */
for (i = i_start; i < i_stop; i++) {
list_t* chainPtr = uniqueSegmentsPtr->buckets[i];
list_iter_t it;
list_iter_reset(&it, chainPtr);
while (list_iter_hasNext(&it, chainPtr)) {
char* segment =
(char*)((pair_t*)list_iter_next(&it, chainPtr))->firstPtr;
constructEntry_t* constructEntryPtr;
long j;
ulong_t startHash;
bool_t status;
/* Find an empty constructEntries entry */
TM_BEGIN();
while (((void*)TM_SHARED_READ_P(constructEntries[entryIndex].segment)) != NULL) {
entryIndex = (entryIndex + 1) % numUniqueSegment; /* look for empty */
}
constructEntryPtr = &constructEntries[entryIndex];
TM_SHARED_WRITE_P(constructEntryPtr->segment, segment);
TM_END();
entryIndex = (entryIndex + 1) % numUniqueSegment;
/*
* Save hashes (sdbm algorithm) of segment substrings
*
* endHashes will be computed for shorter substrings after matches
* have been made (in the next phase of the code). This will reduce
* the number of substrings for which hashes need to be computed.
*
* Since we can compute startHashes incrementally, we go ahead
* and compute all of them here.
*/
/* constructEntryPtr is local now */
constructEntryPtr->endHash = (ulong_t)hashString(&segment[1]);
startHash = 0;
for (j = 1; j < segmentLength; j++) {
startHash = (ulong_t)segment[j-1] +
(startHash << 6) + (startHash << 16) - startHash;
TM_BEGIN();
status = TMTABLE_INSERT(startHashToConstructEntryTables[j],
(ulong_t)startHash,
(void*)constructEntryPtr );
TM_END();
assert(status);
}
/*
* For looking up construct entries quickly
*/
startHash = (ulong_t)segment[j-1] +
(startHash << 6) + (startHash << 16) - startHash;
TM_BEGIN();
status = TMTABLE_INSERT(hashToConstructEntryTable,
(ulong_t)startHash,
(void*)constructEntryPtr);
TM_END();
assert(status);
}
}
thread_barrier_wait();
/*
* Step 2b: Match ends to starts by using hash-based string comparison.
*/
for (substringLength = segmentLength-1; substringLength > 0; substringLength--) {
table_t* startHashToConstructEntryTablePtr =
startHashToConstructEntryTables[substringLength];
list_t** buckets = startHashToConstructEntryTablePtr->buckets;
long numBucket = startHashToConstructEntryTablePtr->numBucket;
long index_start;
long index_stop;
// #if defined(HTM) || defined(STM)
{
/* Choose disjoint segments [index_start,index_stop) for each thread */
long partitionSize = (numUniqueSegment + numThread/2) / numThread; /* with rounding */
index_start = threadId * partitionSize;
if (threadId == (numThread - 1)) {
index_stop = numUniqueSegment;
} else {
index_stop = index_start + partitionSize;
}
}
// #else /* !(HTM || STM) */
// index_start = 0;
// index_stop = numUniqueSegment;
//#endif /* !(HTM || STM) */
/* Iterating over disjoint itervals in the range [0, numUniqueSegment) */
for (entryIndex = index_start;
entryIndex < index_stop;
entryIndex += endInfoEntries[entryIndex].jumpToNext)
{
if (!endInfoEntries[entryIndex].isEnd) {
continue;
}
/* ConstructEntries[entryIndex] is local data */
constructEntry_t* endConstructEntryPtr =
&constructEntries[entryIndex];
char* endSegment = endConstructEntryPtr->segment;
ulong_t endHash = endConstructEntryPtr->endHash;
list_t* chainPtr = buckets[endHash % numBucket]; /* buckets: constant data */
list_iter_t it;
list_iter_reset(&it, chainPtr);
/* Linked list at chainPtr is constant */
while (list_iter_hasNext(&it, chainPtr)) {
constructEntry_t* startConstructEntryPtr =
(constructEntry_t*)list_iter_next(&it, chainPtr);
char* startSegment = startConstructEntryPtr->segment;
long newLength = 0;
/* endConstructEntryPtr is local except for properties startPtr/endPtr/length */
TM_BEGIN();
/* Check if matches */
if (TM_SHARED_READ(startConstructEntryPtr->isStart) &&
(TM_SHARED_READ_P(endConstructEntryPtr->startPtr) != startConstructEntryPtr) &&
(strncmp(startSegment,
&endSegment[segmentLength - substringLength],
substringLength) == 0))
{
TM_SHARED_WRITE(startConstructEntryPtr->isStart, FALSE);
constructEntry_t* startConstructEntry_endPtr;
constructEntry_t* endConstructEntry_startPtr;
/* Update endInfo (appended something so no longer end) */
TM_LOCAL_WRITE(endInfoEntries[entryIndex].isEnd, FALSE);
/* Update segment chain construct info */
startConstructEntry_endPtr =
(constructEntry_t*)TM_SHARED_READ_P(startConstructEntryPtr->endPtr);
endConstructEntry_startPtr =
(constructEntry_t*)TM_SHARED_READ_P(endConstructEntryPtr->startPtr);
assert(startConstructEntry_endPtr);
assert(endConstructEntry_startPtr);
TM_SHARED_WRITE_P(startConstructEntry_endPtr->startPtr,
endConstructEntry_startPtr);
TM_LOCAL_WRITE_P(endConstructEntryPtr->nextPtr,
startConstructEntryPtr);
TM_SHARED_WRITE_P(endConstructEntry_startPtr->endPtr,
startConstructEntry_endPtr);
TM_SHARED_WRITE(endConstructEntryPtr->overlap, substringLength);
newLength = (long)TM_SHARED_READ(endConstructEntry_startPtr->length) +
(long)TM_SHARED_READ(startConstructEntryPtr->length) -
substringLength;
TM_SHARED_WRITE(endConstructEntry_startPtr->length, newLength);
} /* if (matched) */
TM_END();
if (!endInfoEntries[entryIndex].isEnd) { /* if there was a match */
break;
}
} /* iterate over chain */
} /* for (endIndex < numUniqueSegment) */
thread_barrier_wait();
/*
* Step 2c: Update jump values and hashes
*
* endHash entries of all remaining ends are updated to the next
* substringLength. Additionally jumpToNext entries are updated such
* that they allow to skip non-end entries. Currently this is sequential
* because parallelization did not perform better.
. */
if (threadId == 0) {
if (substringLength > 1) {
long index = segmentLength - substringLength + 1;
/* initialization if j and i: with i being the next end after j=0 */
for (i = 1; !endInfoEntries[i].isEnd; i+=endInfoEntries[i].jumpToNext) {
/* find first non-null */
}
/* entry 0 is handled seperately from the loop below */
endInfoEntries[0].jumpToNext = i;
if (endInfoEntries[0].isEnd) {
constructEntry_t* constructEntryPtr = &constructEntries[0];
char* segment = constructEntryPtr->segment;
constructEntryPtr->endHash = (ulong_t)hashString(&segment[index]);
}
/* Continue scanning (do not reset i) */
for (j = 0; i < numUniqueSegment; i+=endInfoEntries[i].jumpToNext) {
if (endInfoEntries[i].isEnd) {
constructEntry_t* constructEntryPtr = &constructEntries[i];
char* segment = constructEntryPtr->segment;
constructEntryPtr->endHash = (ulong_t)hashString(&segment[index]);
endInfoEntries[j].jumpToNext = MAX(1, (i - j));
j = i;
}
}
endInfoEntries[j].jumpToNext = i - j;
}
}
thread_barrier_wait();
} /* for (substringLength > 0) */
thread_barrier_wait();
/*
* Step 3: Build sequence string
*/
if (threadId == 0) {
long totalLength = 0;
for (i = 0; i < numUniqueSegment; i++) {
constructEntry_t* constructEntryPtr = &constructEntries[i];
if (constructEntryPtr->isStart) {
totalLength += constructEntryPtr->length;
}
}
sequencerPtr->sequence = (char*)P_MALLOC((totalLength+1) * sizeof(char));
char* sequence = sequencerPtr->sequence;
assert(sequence);
char* copyPtr = sequence;
long sequenceLength = 0;
for (i = 0; i < numUniqueSegment; i++) {
constructEntry_t* constructEntryPtr = &constructEntries[i];
/* If there are several start segments, we append in arbitrary order */
if (constructEntryPtr->isStart) {
long newSequenceLength = sequenceLength + constructEntryPtr->length;
assert( newSequenceLength <= totalLength );
copyPtr = sequence + sequenceLength;
sequenceLength = newSequenceLength;
do {
long numChar = segmentLength - constructEntryPtr->overlap;
if ((copyPtr + numChar) > (sequence + newSequenceLength)) {
TM_PRINT0("ERROR: sequence length != actual length\n");
break;
}
memcpy(copyPtr,
constructEntryPtr->segment,
(numChar * sizeof(char)));
copyPtr += numChar;
} while ((constructEntryPtr = constructEntryPtr->nextPtr) != NULL);
assert(copyPtr <= (sequence + sequenceLength));
}
}
assert(sequence != NULL);
sequence[sequenceLength] = '\0';
}
TM_THREAD_EXIT();
}
/* =============================================================================
* computeGraph
* =============================================================================
*/
void
computeGraph (void* argPtr)
{
TM_THREAD_ENTER();
graph* GPtr = ((computeGraph_arg_t*)argPtr)->GPtr;
graphSDG* SDGdataPtr = ((computeGraph_arg_t*)argPtr)->SDGdataPtr;
long myId = thread_getId();
long numThread = thread_getNumThread();
ULONGINT_T j;
ULONGINT_T maxNumVertices = 0;
ULONGINT_T numEdgesPlaced = SDGdataPtr->numEdgesPlaced;
/*
* First determine the number of vertices by scanning the tuple
* startVertex list
*/
long i;
long i_start;
long i_stop;
createPartition(0, numEdgesPlaced, myId, numThread, &i_start, &i_stop);
for (i = i_start; i < i_stop; i++) {
if (SDGdataPtr->startVertex[i] > maxNumVertices) {
maxNumVertices = SDGdataPtr->startVertex[i];
}
}
TM_BEGIN();
long tmp_maxNumVertices = (long)TM_SHARED_READ_L(global_maxNumVertices);
long new_maxNumVertices = MAX(tmp_maxNumVertices, maxNumVertices) + 1;
TM_SHARED_WRITE_L(global_maxNumVertices, new_maxNumVertices);
TM_END();
thread_barrier_wait();
maxNumVertices = global_maxNumVertices;
if (myId == 0) {
GPtr->numVertices = maxNumVertices;
GPtr->numEdges = numEdgesPlaced;
GPtr->intWeight = SDGdataPtr->intWeight;
GPtr->strWeight = SDGdataPtr->strWeight;
for (i = 0; i < numEdgesPlaced; i++) {
if (GPtr->intWeight[numEdgesPlaced-i-1] < 0) {
GPtr->numStrEdges = -(GPtr->intWeight[numEdgesPlaced-i-1]) + 1;
GPtr->numIntEdges = numEdgesPlaced - GPtr->numStrEdges;
break;
}
}
GPtr->outDegree =
(LONGINT_T*)P_MALLOC((GPtr->numVertices) * sizeof(LONGINT_T));
assert(GPtr->outDegree);
GPtr->outVertexIndex =
(ULONGINT_T*)P_MALLOC((GPtr->numVertices) * sizeof(ULONGINT_T));
assert(GPtr->outVertexIndex);
}
thread_barrier_wait();
createPartition(0, GPtr->numVertices, myId, numThread, &i_start, &i_stop);
for (i = i_start; i < i_stop; i++) {
GPtr->outDegree[i] = 0;
GPtr->outVertexIndex[i] = 0;
}
ULONGINT_T outVertexListSize = 0;
thread_barrier_wait();
ULONGINT_T i0 = -1UL;
for (i = i_start; i < i_stop; i++) {
ULONGINT_T k = i;
if ((outVertexListSize == 0) && (k != 0)) {
while (i0 == -1UL) {
for (j = 0; j < numEdgesPlaced; j++) {
if (k == SDGdataPtr->startVertex[j]) {
i0 = j;
break;
}
}
k--;
}
}
if ((outVertexListSize == 0) && (k == 0)) {
i0 = 0;
}
for (j = i0; j < numEdgesPlaced; j++) {
if (i == GPtr->numVertices-1) {
break;
}
if ((i != SDGdataPtr->startVertex[j])) {
if ((j > 0) && (i == SDGdataPtr->startVertex[j-1])) {
if (j-i0 >= 1) {
outVertexListSize++;
GPtr->outDegree[i]++;
ULONGINT_T t;
for (t = i0+1; t < j; t++) {
if (SDGdataPtr->endVertex[t] !=
SDGdataPtr->endVertex[t-1])
{
outVertexListSize++;
GPtr->outDegree[i] = GPtr->outDegree[i]+1;
}
}
}
}
i0 = j;
break;
}
}
if (i == GPtr->numVertices-1) {
if (numEdgesPlaced-i0 >= 0) {
outVertexListSize++;
GPtr->outDegree[i]++;
ULONGINT_T t;
for (t = i0+1; t < numEdgesPlaced; t++) {
if (SDGdataPtr->endVertex[t] != SDGdataPtr->endVertex[t-1]) {
outVertexListSize++;
GPtr->outDegree[i]++;
}
}
}
}
} /* for i */
thread_barrier_wait();
prefix_sums(GPtr->outVertexIndex, GPtr->outDegree, GPtr->numVertices);
thread_barrier_wait();
TM_BEGIN();
TM_SHARED_WRITE_L(
global_outVertexListSize,
((long)TM_SHARED_READ_L(global_outVertexListSize) + outVertexListSize)
);
TM_END();
thread_barrier_wait();
outVertexListSize = global_outVertexListSize;
if (myId == 0) {
GPtr->numDirectedEdges = outVertexListSize;
GPtr->outVertexList =
(ULONGINT_T*)P_MALLOC(outVertexListSize * sizeof(ULONGINT_T));
assert(GPtr->outVertexList);
GPtr->paralEdgeIndex =
(ULONGINT_T*)P_MALLOC(outVertexListSize * sizeof(ULONGINT_T));
assert(GPtr->paralEdgeIndex);
GPtr->outVertexList[0] = SDGdataPtr->endVertex[0];
}
thread_barrier_wait();
/*
* Evaluate outVertexList
*/
i0 = -1UL;
for (i = i_start; i < i_stop; i++) {
ULONGINT_T k = i;
while ((i0 == -1UL) && (k != 0)) {
for (j = 0; j < numEdgesPlaced; j++) {
if (k == SDGdataPtr->startVertex[j]) {
i0 = j;
break;
}
}
k--;
}
if ((i0 == -1) && (k == 0)) {
i0 = 0;
}
for (j = i0; j < numEdgesPlaced; j++) {
if (i == GPtr->numVertices-1) {
break;
}
if (i != SDGdataPtr->startVertex[j]) {
if ((j > 0) && (i == SDGdataPtr->startVertex[j-1])) {
if (j-i0 >= 1) {
long ii = GPtr->outVertexIndex[i];
ULONGINT_T r = 0;
GPtr->paralEdgeIndex[ii] = i0;
GPtr->outVertexList[ii] = SDGdataPtr->endVertex[i0];
r++;
ULONGINT_T t;
for (t = i0+1; t < j; t++) {
if (SDGdataPtr->endVertex[t] !=
SDGdataPtr->endVertex[t-1])
{
GPtr->paralEdgeIndex[ii+r] = t;
GPtr->outVertexList[ii+r] = SDGdataPtr->endVertex[t];
r++;
}
}
}
}
i0 = j;
break;
}
} /* for j */
if (i == GPtr->numVertices-1) {
ULONGINT_T r = 0;
if (numEdgesPlaced-i0 >= 0) {
long ii = GPtr->outVertexIndex[i];
GPtr->paralEdgeIndex[ii+r] = i0;
GPtr->outVertexList[ii+r] = SDGdataPtr->endVertex[i0];
r++;
ULONGINT_T t;
for (t = i0+1; t < numEdgesPlaced; t++) {
if (SDGdataPtr->endVertex[t] != SDGdataPtr->endVertex[t-1]) {
GPtr->paralEdgeIndex[ii+r] = t;
GPtr->outVertexList[ii+r] = SDGdataPtr->endVertex[t];
r++;
}
}
}
}
} /* for i */
thread_barrier_wait();
if (myId == 0) {
P_FREE(SDGdataPtr->startVertex);
P_FREE(SDGdataPtr->endVertex);
GPtr->inDegree =
(LONGINT_T*)P_MALLOC(GPtr->numVertices * sizeof(LONGINT_T));
assert(GPtr->inDegree);
GPtr->inVertexIndex =
(ULONGINT_T*)P_MALLOC(GPtr->numVertices * sizeof(ULONGINT_T));
assert(GPtr->inVertexIndex);
}
thread_barrier_wait();
for (i = i_start; i < i_stop; i++) {
GPtr->inDegree[i] = 0;
GPtr->inVertexIndex[i] = 0;
}
/* A temp. array to store the inplied edges */
ULONGINT_T* impliedEdgeList;
if (myId == 0) {
impliedEdgeList = (ULONGINT_T*)P_MALLOC(GPtr->numVertices
* MAX_CLUSTER_SIZE
* sizeof(ULONGINT_T));
global_impliedEdgeList = impliedEdgeList;
}
thread_barrier_wait();
impliedEdgeList = global_impliedEdgeList;
createPartition(0,
(GPtr->numVertices * MAX_CLUSTER_SIZE),
myId,
numThread,
&i_start,
&i_stop);
for (i = i_start; i < i_stop; i++) {
impliedEdgeList[i] = 0;
}
/*
* An auxiliary array to store implied edges, in case we overshoot
* MAX_CLUSTER_SIZE
*/
ULONGINT_T** auxArr;
if (myId == 0) {
auxArr = (ULONGINT_T**)P_MALLOC(GPtr->numVertices * sizeof(ULONGINT_T*));
assert(auxArr);
global_auxArr = auxArr;
}
thread_barrier_wait();
auxArr = global_auxArr;
createPartition(0, GPtr->numVertices, myId, numThread, &i_start, &i_stop);
for (i = i_start; i < i_stop; i++) {
/* Inspect adjacency list of vertex i */
for (j = GPtr->outVertexIndex[i];
j < (GPtr->outVertexIndex[i] + GPtr->outDegree[i]);
j++)
{
ULONGINT_T v = GPtr->outVertexList[j];
ULONGINT_T k;
for (k = GPtr->outVertexIndex[v];
k < (GPtr->outVertexIndex[v] + GPtr->outDegree[v]);
k++)
{
if (GPtr->outVertexList[k] == i) {
break;
}
}
if (k == GPtr->outVertexIndex[v]+GPtr->outDegree[v]) {
TM_BEGIN();
/* Add i to the impliedEdgeList of v */
long inDegree = (long)TM_SHARED_READ_L(GPtr->inDegree[v]);
TM_SHARED_WRITE_L(GPtr->inDegree[v], (inDegree + 1));
if (inDegree < MAX_CLUSTER_SIZE) {
TM_SHARED_WRITE_L(impliedEdgeList[v*MAX_CLUSTER_SIZE+inDegree],
i);
} else {
/* Use auxiliary array to store the implied edge */
/* Create an array if it's not present already */
ULONGINT_T* a = NULL;
if ((inDegree % MAX_CLUSTER_SIZE) == 0) {
a = (ULONGINT_T*)TM_MALLOC(MAX_CLUSTER_SIZE
* sizeof(ULONGINT_T));
assert(a);
TM_SHARED_WRITE_P(auxArr[v], a);
} else {
a = auxArr[v];
}
TM_SHARED_WRITE_L(a[inDegree % MAX_CLUSTER_SIZE], i);
}
TM_END();
}
}
} /* for i */
thread_barrier_wait();
prefix_sums(GPtr->inVertexIndex, GPtr->inDegree, GPtr->numVertices);
if (myId == 0) {
GPtr->numUndirectedEdges = GPtr->inVertexIndex[GPtr->numVertices-1]
+ GPtr->inDegree[GPtr->numVertices-1];
GPtr->inVertexList =
(ULONGINT_T *)P_MALLOC(GPtr->numUndirectedEdges * sizeof(ULONGINT_T));
}
thread_barrier_wait();
/*
* Create the inVertex List
*/
for (i = i_start; i < i_stop; i++) {
for (j = GPtr->inVertexIndex[i];
j < (GPtr->inVertexIndex[i] + GPtr->inDegree[i]);
j++)
{
if ((j - GPtr->inVertexIndex[i]) < MAX_CLUSTER_SIZE) {
GPtr->inVertexList[j] =
impliedEdgeList[i*MAX_CLUSTER_SIZE+j-GPtr->inVertexIndex[i]];
} else {
GPtr->inVertexList[j] =
auxArr[i][(j-GPtr->inVertexIndex[i]) % MAX_CLUSTER_SIZE];
}
}
}
thread_barrier_wait();
if (myId == 0) {
P_FREE(impliedEdgeList);
}
for (i = i_start; i < i_stop; i++) {
if (GPtr->inDegree[i] > MAX_CLUSTER_SIZE) {
P_FREE(auxArr[i]);
}
}
thread_barrier_wait();
if (myId == 0) {
P_FREE(auxArr);
}
TM_THREAD_EXIT();
}
