//Full Collision Detection Sweep
void sweep_and_prune(){
update_tokens();
sweep(xtokens);
sweep(ytokens);
prune();
}
int encode(int args[])
{
//freopen("hash.h", "r", stdin);
Hash *h = malloc(sizeof(Hash));
int size = 1 << (args[1]+1);
unsigned int time =1;
initialize(h, size, args[3], time);
int c=EMPTY, k, latestCode;
int bits=(args[3])?3:9;
printf("%d %d %d|", args[1], args[2], args[3]);
while((k = getchar()) != EOF)
if(findInHash(h, c , (char)k) != EMPTY)
c = findInHash(h, c , (char)k);
else
{
if(args[3] && findInHash(h, EMPTY, (char)k) == EMPTY) //Time to send escape sequence
{
if (c!=EMPTY)
{
putBits(bits, c);
h->shadowArray[c]->time=(++time);
}
putBits(bits, ESCAPE);
putBits(CHAR_BIT, k);
if(h->numElements < ( 1 << args[1]))
{
latestCode = insert(h, EMPTY, (char)k, 1);
if(latestCode>= (1<<(bits)))
{
putBits(bits, INCR);
bits++;
}
}
c = EMPTY;
}
else
{
putBits(bits, c);
h->shadowArray[c]->time=(++time);
if(h->numElements < ( 1 << args[1]))
{
latestCode = insert(h, c, (char)k, 1);
if(latestCode>= (1<<(bits)))
{
putBits(bits, INCR);
bits++;
}
}
c = findInHash(h, EMPTY, (char)k);
}
if(args[2] && h->numElements == ( 1 << args[1])-1)
{
putBits(bits, RESET);
putBits(bits, c);
prune(args, &h, time);
//bitchange
c=EMPTY;
}
}
if (c!=EMPTY)
putBits(bits, c);
flushBits();
//printHash(h);
freeHash (h);
return 0;
}
int decode()
{
int k;
Hash *h = malloc(sizeof(Hash));
Stack *kStack = NULL;
int oldC = EMPTY;
int newC, C;
char finalK;
//freopen("b.txt", "r", stdin);
int args[NUMARGS];
scanf("%d %d %d|", args+1, args+2, args+3);
int size = 1 << (args[1]+1);
unsigned int time =1;
initialize(h, size, args[3], time);
int bits = (args[3])?3:9;
while((newC = C = getBits(bits)) != EOF)
{
if(C==INCR)
{
bits++;
continue;
}
if(C == ESCAPE) //Time to add a new sequence
{
newC = C = getBits(CHAR_BIT);
if(h->numElements< ( 1 << (args[1])))
insert(h, EMPTY, (char)C, 1);
oldC = EMPTY;
putchar(C);
continue;
}
if(C == RESET)
{
Element *e = findArray(h, getBits(bits));
if (e && e->ch)
{
putchar(e->ch);
finalK=e->ch;
}
prune(args, &h, time);
//bitchange
oldC= EMPTY;
continue;
}
if(findArray(h, C)==EMPTY)
{
push(&kStack, finalK);
C = oldC;
}
else
{
Element *elem = findArray(h, C);
elem->time = time++;
}
Element *elem = findArray(h, C);
while (elem && elem->prefix!=EMPTY)
{
push(&kStack, elem->ch);
C = elem->prefix;
elem = findArray(h, C);
}
finalK = elem->ch;
putchar(finalK);
while(kStack)
{
k = pop(&kStack);
putchar(k);
}
if (oldC != EMPTY && h->numElements < ( 1 << (args[1])))
insert(h, oldC, finalK, 1);
oldC = newC;
}
//printArray(arr);
free(h);
return 0;
}
void SimpleSkeletonGrower::backward_grow()
{
if(_surface.is_loaded())
{
std::vector <osg::Vec3> backward_grow = _surface._relative_pts;
//1. Initialization: setup a grow_map for book-keeping the backward growing
//Key: rank of the <x,z> coords; Value: <low depth(y), high depth(y), isDone(1 or -1)>
//this is used in addition to the relative bound for growing a dense foilage
std::map <int, osg::Vec3> grow_map;
for(unsigned int i=0; i<_surface._surface_pts.size(); i++)
{
osg::Vec3 pt = _surface._surface_pts[i];
//only consider points that lay inside the boundary
if(!_pruner.is_inside_ortho(pt))
continue;
int rank = (pt.x()+1000)*2500 + (pt.z()+1000);
//check if exists, update its value
if(grow_map.find(rank) != grow_map.end())
{
osg::Vec3 paras = grow_map[rank];
osg::Vec3 new_paras = paras;
if(pt.y() < paras.x())
new_paras.x() = pt.y();
if(pt.y() > paras.y())
new_paras.y() = pt.y();
grow_map[rank] = new_paras;
}
//new cloud point
else
{
osg::Vec3 paras(pt.y(), pt.y(), -1);//new point has the same-depth and is un-done
grow_map[rank] = paras;
}
}
float inter_cons = 2.0f;
float neighbor_dist = pow(inter_cons*1.05, 0.5) * _close_threshold;
float neighbor_diag = neighbor_dist * 0.707f;
//2. Loop each node pt in grow_map, un-rank it, and pretend to be a point in the relative bound
for(std::map <int, osg::Vec3>::iterator it=grow_map.begin(); it!=grow_map.end(); it++)
{
//a. recover point, the y-coord is randomly picked between low and high
int rank = it->first;
//osg::Vec3 paras = it->second;
//int y = rand()%(int(paras.y()-paras.x())) + paras.x();
//osg::Vec3 pt(rank/2500-1000, y, rank%2500-1000);
osg::Vec3 pt(rank/2500-1000, rank%2500-1000, 0.0f);
backward_grow.push_back(pt);
//add more neighbor points
osg::Vec3 probe;
if(false)
{
probe = osg::Vec3(pt.x()+neighbor_dist, pt.y(), 0.0f);//right
if(!_pruner.is_inside_ortho(probe))
backward_grow.push_back(probe);
probe = osg::Vec3(pt.x()-neighbor_dist, pt.y(), 0.0f);//left
if(!_pruner.is_inside_ortho(probe))
backward_grow.push_back(probe);
probe = osg::Vec3(pt.x(), pt.y()+neighbor_dist, 0.0f);//top
if(!_pruner.is_inside_ortho(probe))
backward_grow.push_back(probe);
probe = osg::Vec3(pt.x(), pt.y()-neighbor_dist, 0.0f);//bottom
if(!_pruner.is_inside_ortho(probe))
backward_grow.push_back(probe);
}
probe = osg::Vec3(pt.x()+neighbor_diag, pt.y()+neighbor_diag, 0.0f);//top-right
if(!_pruner.is_inside_ortho(probe))
backward_grow.push_back(probe);
probe = osg::Vec3(pt.x()-neighbor_diag, pt.y()+neighbor_diag, 0.0f);//top-left
if(!_pruner.is_inside_ortho(probe))
backward_grow.push_back(probe);
probe = osg::Vec3(pt.x()+neighbor_diag, pt.y()-neighbor_diag, 0.0f);//bottom-right
if(!_pruner.is_inside_ortho(probe))
backward_grow.push_back(probe);
probe = osg::Vec3(pt.x()-neighbor_diag, pt.y()-neighbor_diag, 0.0f);//bottom-left
if(!_pruner.is_inside_ortho(probe))
backward_grow.push_back(probe);
}
//given the non-even retaive contour points, backward grow it to the nearest tree nodes
//each each node cannot grow more than twice, also the newly added retaive points are
//required to be mutually separated from previously added points, in addition to the old tree nodes
std::vector <LibraryElement> elements = _library._library_element;
std::vector <osg::Vec3> newly_added;
std::map <BDLSkeletonNode *, int> grown_cnt;
//put inside the loop becasue trees is updated, put outside for non-continuous effect
std::vector <BDLSkeletonNode *> trees = bfs();
BDLSkeletonNode *copied_root = BDLSkeletonNode::copy_tree(_root);
for(unsigned int j=0; j<backward_grow.size(); j++)
{
osg::Vec3 temp = backward_grow[j];
osg::Vec3 pt(temp.x(), 0.0f, temp.y());//add depth later
//b. find min projected distance from tree
float min_proj_dist = -1.0f;
for(unsigned int i=0; i<trees.size(); i++)
{
osg::Vec3 T = Transformer::toVec3(trees[i]);
float proj_dist = osg::Vec2(pt.x()-T.x(), pt.z()-T.z()).length2();
if(min_proj_dist == -1.0f || proj_dist < min_proj_dist)
min_proj_dist = proj_dist;
}
//c. find min projected distance from previously added points
float min_proj_dist2 = -1.0f;
for(unsigned int i=0; i<newly_added.size(); i++)
{
osg::Vec3 na = newly_added[i];
float proj_dist = osg::Vec2(pt.x()-na.x(), pt.z()-na.z()).length2();
if(min_proj_dist2 == -1.0f || proj_dist < min_proj_dist2)
min_proj_dist2 = proj_dist;
}
//c. if minimum projected distance from trees T is larger than _close_threshold, then backward grow it
float close_threshold2 = _close_threshold * _close_threshold;
if(min_proj_dist > close_threshold2 && (min_proj_dist2 > inter_cons*close_threshold2 || newly_added.empty()))
{
//find the closest node N in trees T to grow
BDLSkeletonNode *N = NULL;
float min_tree_dist = -1.0f;
for(unsigned int i=0; i<trees.size(); i++)
{
BDLSkeletonNode *tnode = trees[i];
//ensure N has _prev
if(!tnode->_prev)
continue;
//ensure N has no child
//if(tnode->_children.size() > 1)
// continue;
//check if N has been used more than twice first
if(grown_cnt.find(tnode) != grown_cnt.end() && grown_cnt[tnode] > 0)
continue;
float cur_dist = (pt - Transformer::toVec3(tnode)).length2();
if(min_tree_dist == -1.0f || cur_dist < min_tree_dist)
{
min_tree_dist = cur_dist;
N = tnode;
}
}
//fuel for backward grow is used up
if(!N)
return;
//add depth of pt = 'depth of N' +/- 'half length of N and N->_prev'
float par_len = BDLSkeletonNode::dist(N, N->_prev);
if(par_len > 1.0f)
pt.y() = N->_sy + rand()%int(par_len) - par_len/2.0f;
else
pt.y() = N->_sy + (rand()%3-1)*par_len/2.0f;
//update book-keeping
newly_added.push_back(pt);
if(grown_cnt.find(N) != grown_cnt.end())
grown_cnt[N]++;
else
grown_cnt[N] = 1;
//shorten the N-pt segment by 10% to prevent unwanted pruning
osg::Vec3 wrap = Transformer::toVec3(N);
osg::Vec3 dir = pt - wrap;
float desired_len = dir.length() * 0.95f;
dir.normalize();
pt = wrap + dir * desired_len;
//new tip node
BDLSkeletonNode *new_node = new BDLSkeletonNode(pt.x(), pt.y(), pt.z());
//use advanced approach to grow it as in laser data
if(true)
{
//before attaching, check if the divergent angle is too large
float div_ang = Transformer::divergent_angle(N->_prev, N, new_node);
if(div_ang > 30.0f)
{
//osg::Vec3 translateN = Transformer::toVec3(N->_prev) - wrap;
//float len = translateN.length();
//translateN.normalize();
//translateN = wrap + translateN * len * 0.5f;
//N->_sx = wrap.x();
//N->_sy = wrap.y();
//N->_sz = wrap.z();
//if(N->_prev->_prev)
//{
// N = N->_prev;
// div_ang = Transformer::divergent_angle(N->_prev, N, new_node);
//}
//search for the most similar divergent angle in the original tree
BDLSkeletonNode *a, *b;
if(Transformer::similar_angle_in_tree(copied_root, div_ang, a, b))
{
//printf("angle(%f) div(%f)\n", angle, Transformer::divergent_angle(a->_prev, a, b));
//construct an elemnt out of a and b
BDLSkeletonNode *support_tip = NULL;
BDLSkeletonNode *sub_tree = Transformer::extract_subtree(a->_prev, b, support_tip);
if(sub_tree && support_tip)
{
//should not add
//new_node->_prev = N;
//new_node->_prev_support = N;
//N->_children.push_back(new_node);
N->_prev_support = N->_prev;
LibraryElement element(sub_tree, SLink(sub_tree, sub_tree->_children[0]));
//rotation can't be random!
int min_tran_ang = -1;
float min_tran_ang_dist = -1.0f;
for(int ta=0; ta<360; ta+=12)
{
LibraryElement element_test = element;
Transformer::transform(N, ta, element_test);
std::vector <BDLSkeletonNode *> compare = Transformer::terminal_nodes(element_test._root);
for(unsigned int ter=0; ter<compare.size(); ter++)
{
float cur_dist = BDLSkeletonNode::dist(compare[ter], new_node);
if(min_tran_ang_dist == -1.0f || cur_dist < min_tran_ang_dist)
{
min_tran_ang_dist = cur_dist;
min_tran_ang = ta;
}
}
}
//printf("min_tran_ang_dist(%f)\n", min_tran_ang_dist);
std::vector <BDLSkeletonNode *> subtree = replace_branch(N, element, min_tran_ang);
prune(subtree);
//printf("%f %f %f\n", pt.x(), pt.y(), pt.z());
//pt = Transformer::toVec3(N);
//printf("%f %f %f\n", pt.x(), pt.y(), pt.z());
if(false || j==617)
{
Transformer::straight_up(element);
char buffer[100];
sprintf(buffer, "/tmp/log_sk/log_skeleton_%d", j);
BDLSkeletonNode::save_skeleton(element._root, buffer);
}
}
else
printf("SimplSkeletonGrower::backward_grow():extract_subtree: a(%p) b(%p) error\n", a, b);
delete new_node;
}
else
{
//if no suitable sub-tree can be found, just don't grow the node
//printf("%f %f %f\n", pt.x(), pt.y(), pt.z());
delete new_node;
}
}
else
{
//directly attach it to produce a straight branch
new_node->_prev = N;
N->_children.push_back(new_node);
//too far away, replace it
//if(desired_len > _close_threshold * 2.0f)
//{
// new_node->_prev_support = N;
// std::vector <BDLSkeletonNode *> subtree = replace_branch(new_node, elements[rand()%elements.size()], rand()%360);
// //prune(subtree); //prune leniently
//}
}
}
//visualize pt
//printf("%f %f %f\n", pt.x(), pt.y(), pt.z());
}
//d. continue for the next point
} //end for loop
BDLSkeletonNode::delete_this(copied_root);
}
}
static int ppr_mapper(orte_job_t *jdata)
{
int rc = ORTE_SUCCESS, j, n;
mca_base_component_t *c=&mca_rmaps_ppr_component.base_version;
orte_node_t *node;
orte_proc_t *proc;
orte_app_context_t *app;
orte_vpid_t total_procs, nprocs_mapped;
opal_hwloc_level_t start=OPAL_HWLOC_NODE_LEVEL;
hwloc_obj_t obj;
hwloc_obj_type_t lowest;
unsigned cache_level=0;
unsigned int nobjs, i;
bool pruning_reqd = false;
opal_hwloc_level_t level;
opal_list_t node_list;
opal_list_item_t *item;
orte_std_cntr_t num_slots;
orte_app_idx_t idx;
char **ppr_req, **ck;
size_t len;
bool initial_map=true;
/* only handle initial launch of loadbalanced
* or NPERxxx jobs - allow restarting of failed apps
*/
if (ORTE_FLAG_TEST(jdata, ORTE_JOB_FLAG_RESTART)) {
opal_output_verbose(5, orte_rmaps_base_framework.framework_output,
"mca:rmaps:ppr: job %s being restarted - ppr cannot map",
ORTE_JOBID_PRINT(jdata->jobid));
return ORTE_ERR_TAKE_NEXT_OPTION;
}
if (NULL != jdata->map->req_mapper &&
0 != strcasecmp(jdata->map->req_mapper, c->mca_component_name)) {
/* a mapper has been specified, and it isn't me */
opal_output_verbose(5, orte_rmaps_base_framework.framework_output,
"mca:rmaps:ppr: job %s not using ppr mapper",
ORTE_JOBID_PRINT(jdata->jobid));
return ORTE_ERR_TAKE_NEXT_OPTION;
}
if (NULL == jdata->map->ppr ||
ORTE_MAPPING_PPR != ORTE_GET_MAPPING_POLICY(jdata->map->mapping)) {
/* not for us */
opal_output_verbose(5, orte_rmaps_base_framework.framework_output,
"mca:rmaps:ppr: job %s not using ppr mapper PPR %s policy %s",
ORTE_JOBID_PRINT(jdata->jobid),
(NULL == jdata->map->ppr) ? "NULL" : jdata->map->ppr,
(ORTE_MAPPING_PPR == ORTE_GET_MAPPING_POLICY(jdata->map->mapping)) ? "PPRSET" : "PPR NOTSET");
return ORTE_ERR_TAKE_NEXT_OPTION;
}
opal_output_verbose(5, orte_rmaps_base_framework.framework_output,
"mca:rmaps:ppr: mapping job %s with ppr %s",
ORTE_JOBID_PRINT(jdata->jobid), jdata->map->ppr);
/* flag that I did the mapping */
if (NULL != jdata->map->last_mapper) {
free(jdata->map->last_mapper);
}
jdata->map->last_mapper = strdup(c->mca_component_name);
/* initialize */
memset(ppr, 0, OPAL_HWLOC_HWTHREAD_LEVEL * sizeof(opal_hwloc_level_t));
/* parse option */
n=0;
ppr_req = opal_argv_split(jdata->map->ppr, ',');
for (j=0; NULL != ppr_req[j]; j++) {
/* split on the colon */
ck = opal_argv_split(ppr_req[j], ':');
if (2 != opal_argv_count(ck)) {
/* must provide a specification */
orte_show_help("help-orte-rmaps-ppr.txt", "invalid-ppr", true, jdata->map->ppr);
opal_argv_free(ppr_req);
opal_argv_free(ck);
return ORTE_ERR_SILENT;
}
len = strlen(ck[1]);
if (0 == strncasecmp(ck[1], "node", len)) {
ppr[OPAL_HWLOC_NODE_LEVEL] = strtol(ck[0], NULL, 10);
ORTE_SET_MAPPING_POLICY(jdata->map->mapping, ORTE_MAPPING_BYNODE);
start = OPAL_HWLOC_NODE_LEVEL;
n++;
} else if (0 == strncasecmp(ck[1], "hwthread", len) ||
0 == strncasecmp(ck[1], "thread", len)) {
ppr[OPAL_HWLOC_HWTHREAD_LEVEL] = strtol(ck[0], NULL, 10);
start = OPAL_HWLOC_HWTHREAD_LEVEL;
ORTE_SET_MAPPING_POLICY(jdata->map->mapping, ORTE_MAPPING_BYHWTHREAD);
n++;
} else if (0 == strncasecmp(ck[1], "core", len)) {
ppr[OPAL_HWLOC_CORE_LEVEL] = strtol(ck[0], NULL, 10);
if (start < OPAL_HWLOC_CORE_LEVEL) {
start = OPAL_HWLOC_CORE_LEVEL;
ORTE_SET_MAPPING_POLICY(jdata->map->mapping, ORTE_MAPPING_BYCORE);
}
n++;
} else if (0 == strncasecmp(ck[1], "socket", len) ||
0 == strncasecmp(ck[1], "skt", len)) {
ppr[OPAL_HWLOC_SOCKET_LEVEL] = strtol(ck[0], NULL, 10);
if (start < OPAL_HWLOC_SOCKET_LEVEL) {
start = OPAL_HWLOC_SOCKET_LEVEL;
ORTE_SET_MAPPING_POLICY(jdata->map->mapping, ORTE_MAPPING_BYSOCKET);
}
n++;
} else if (0 == strncasecmp(ck[1], "l1cache", len)) {
ppr[OPAL_HWLOC_L1CACHE_LEVEL] = strtol(ck[0], NULL, 10);
if (start < OPAL_HWLOC_L1CACHE_LEVEL) {
start = OPAL_HWLOC_L1CACHE_LEVEL;
cache_level = 1;
ORTE_SET_MAPPING_POLICY(jdata->map->mapping, ORTE_MAPPING_BYL1CACHE);
}
n++;
} else if (0 == strncasecmp(ck[1], "l2cache", len)) {
ppr[OPAL_HWLOC_L2CACHE_LEVEL] = strtol(ck[0], NULL, 10);
if (start < OPAL_HWLOC_L2CACHE_LEVEL) {
start = OPAL_HWLOC_L2CACHE_LEVEL;
cache_level = 2;
ORTE_SET_MAPPING_POLICY(jdata->map->mapping, ORTE_MAPPING_BYL2CACHE);
}
n++;
} else if (0 == strncasecmp(ck[1], "l3cache", len)) {
ppr[OPAL_HWLOC_L3CACHE_LEVEL] = strtol(ck[0], NULL, 10);
if (start < OPAL_HWLOC_L3CACHE_LEVEL) {
start = OPAL_HWLOC_L3CACHE_LEVEL;
cache_level = 3;
ORTE_SET_MAPPING_POLICY(jdata->map->mapping, ORTE_MAPPING_BYL3CACHE);
}
n++;
} else if (0 == strncasecmp(ck[1], "numa", len)) {
ppr[OPAL_HWLOC_NUMA_LEVEL] = strtol(ck[0], NULL, 10);
if (start < OPAL_HWLOC_NUMA_LEVEL) {
start = OPAL_HWLOC_NUMA_LEVEL;
ORTE_SET_MAPPING_POLICY(jdata->map->mapping, ORTE_MAPPING_BYNUMA);
}
n++;
} else {
/* unknown spec */
orte_show_help("help-orte-rmaps-ppr.txt", "unrecognized-ppr-option", true, ck[1], jdata->map->ppr);
opal_argv_free(ppr_req);
opal_argv_free(ck);
return ORTE_ERR_SILENT;
}
opal_argv_free(ck);
}
opal_argv_free(ppr_req);
/* if nothing was given, that's an error */
if (0 == n) {
opal_output(0, "NOTHING GIVEN");
return ORTE_ERR_SILENT;
}
/* if more than one level was specified, then pruning will be reqd */
if (1 < n) {
pruning_reqd = true;
}
opal_output_verbose(5, orte_rmaps_base_framework.framework_output,
"mca:rmaps:ppr: job %s assigned policy %s",
ORTE_JOBID_PRINT(jdata->jobid),
orte_rmaps_base_print_mapping(jdata->map->mapping));
/* convenience */
level = start;
lowest = opal_hwloc_levels[start];
for (idx=0; idx < (orte_app_idx_t)jdata->apps->size; idx++) {
if (NULL == (app = (orte_app_context_t*)opal_pointer_array_get_item(jdata->apps, idx))) {
continue;
}
/* if the number of total procs was given, set that
* limit - otherwise, set to max so we simply fill
* all the nodes with the pattern
*/
if (0 < app->num_procs) {
total_procs = app->num_procs;
} else {
total_procs = ORTE_VPID_MAX;
}
/* get the available nodes */
OBJ_CONSTRUCT(&node_list, opal_list_t);
if(ORTE_SUCCESS != (rc = orte_rmaps_base_get_target_nodes(&node_list, &num_slots, app,
jdata->map->mapping, initial_map, false))) {
ORTE_ERROR_LOG(rc);
goto error;
}
/* flag that all subsequent requests should not reset the node->mapped flag */
initial_map = false;
/* if a bookmark exists from some prior mapping, set us to start there */
jdata->bookmark = orte_rmaps_base_get_starting_point(&node_list, jdata);
/* cycle across the nodes */
nprocs_mapped = 0;
for (item = opal_list_get_first(&node_list);
item != opal_list_get_end(&node_list);
item = opal_list_get_next(item)) {
node = (orte_node_t*)item;
/* bozo check */
if (NULL == node->topology || NULL == node->topology->topo) {
orte_show_help("help-orte-rmaps-ppr.txt", "ppr-topo-missing",
true, node->name);
rc = ORTE_ERR_SILENT;
goto error;
}
/* add the node to the map, if needed */
if (!ORTE_FLAG_TEST(node, ORTE_NODE_FLAG_MAPPED)) {
ORTE_FLAG_SET(node, ORTE_NODE_FLAG_MAPPED);
OBJ_RETAIN(node);
opal_pointer_array_add(jdata->map->nodes, node);
jdata->map->num_nodes++;
}
/* if we are mapping solely at the node level, just put
* that many procs on this node
*/
if (OPAL_HWLOC_NODE_LEVEL == start) {
obj = hwloc_get_root_obj(node->topology->topo);
for (j=0; j < ppr[start] && nprocs_mapped < total_procs; j++) {
if (NULL == (proc = orte_rmaps_base_setup_proc(jdata, node, idx))) {
rc = ORTE_ERR_OUT_OF_RESOURCE;
goto error;
}
nprocs_mapped++;
orte_set_attribute(&proc->attributes, ORTE_PROC_HWLOC_LOCALE, ORTE_ATTR_LOCAL, obj, OPAL_PTR);
}
} else {
/* get the number of lowest resources on this node */
nobjs = opal_hwloc_base_get_nbobjs_by_type(node->topology->topo,
lowest, cache_level,
OPAL_HWLOC_AVAILABLE);
/* map the specified number of procs to each such resource on this node,
* recording the locale of each proc so we know its cpuset
*/
for (i=0; i < nobjs; i++) {
obj = opal_hwloc_base_get_obj_by_type(node->topology->topo,
lowest, cache_level,
i, OPAL_HWLOC_AVAILABLE);
for (j=0; j < ppr[start] && nprocs_mapped < total_procs; j++) {
if (NULL == (proc = orte_rmaps_base_setup_proc(jdata, node, idx))) {
rc = ORTE_ERR_OUT_OF_RESOURCE;
goto error;
}
nprocs_mapped++;
orte_set_attribute(&proc->attributes, ORTE_PROC_HWLOC_LOCALE, ORTE_ATTR_LOCAL, obj, OPAL_PTR);
}
}
if (pruning_reqd) {
/* go up the ladder and prune the procs according to
* the specification, adjusting the count of procs on the
* node as we go
*/
level--;
prune(jdata->jobid, idx, node, &level, &nprocs_mapped);
}
}
if (!(ORTE_MAPPING_DEBUGGER & ORTE_GET_MAPPING_DIRECTIVE(jdata->map->mapping))) {
/* set the total slots used */
if ((int)node->num_procs <= node->slots) {
node->slots_inuse = (int)node->num_procs;
} else {
node->slots_inuse = node->slots;
}
/* if no-oversubscribe was specified, check to see if
* we have violated the total slot specification - regardless,
* if slots_max was given, we are not allowed to violate it!
*/
if ((node->slots < (int)node->num_procs) ||
(0 < node->slots_max && node->slots_max < (int)node->num_procs)) {
if (ORTE_MAPPING_NO_OVERSUBSCRIBE & ORTE_GET_MAPPING_DIRECTIVE(jdata->map->mapping)) {
orte_show_help("help-orte-rmaps-base.txt", "orte-rmaps-base:alloc-error",
true, node->num_procs, app->app);
ORTE_UPDATE_EXIT_STATUS(ORTE_ERROR_DEFAULT_EXIT_CODE);
rc = ORTE_ERR_SILENT;
goto error;
}
/* flag the node as oversubscribed so that sched-yield gets
* properly set
*/
ORTE_FLAG_SET(node, ORTE_NODE_FLAG_OVERSUBSCRIBED);
ORTE_FLAG_SET(jdata, ORTE_JOB_FLAG_OVERSUBSCRIBED);
/* check for permission */
if (ORTE_FLAG_TEST(node, ORTE_NODE_FLAG_SLOTS_GIVEN)) {
/* if we weren't given a directive either way, then we will error out
* as the #slots were specifically given, either by the host RM or
* via hostfile/dash-host */
if (!(ORTE_MAPPING_SUBSCRIBE_GIVEN & ORTE_GET_MAPPING_DIRECTIVE(jdata->map->mapping))) {
orte_show_help("help-orte-rmaps-base.txt", "orte-rmaps-base:alloc-error",
true, app->num_procs, app->app);
ORTE_UPDATE_EXIT_STATUS(ORTE_ERROR_DEFAULT_EXIT_CODE);
return ORTE_ERR_SILENT;
} else if (ORTE_MAPPING_NO_OVERSUBSCRIBE & ORTE_GET_MAPPING_DIRECTIVE(jdata->map->mapping)) {
/* if we were explicitly told not to oversubscribe, then don't */
orte_show_help("help-orte-rmaps-base.txt", "orte-rmaps-base:alloc-error",
true, app->num_procs, app->app);
ORTE_UPDATE_EXIT_STATUS(ORTE_ERROR_DEFAULT_EXIT_CODE);
return ORTE_ERR_SILENT;
}
}
}
}
/* if we haven't mapped all the procs, continue on to the
* next node
*/
if (total_procs == nprocs_mapped) {
break;
}
}
if (0 == app->num_procs) {
app->num_procs = nprocs_mapped;
}
if (ORTE_VPID_MAX != total_procs && nprocs_mapped < total_procs) {
/* couldn't map them all */
orte_show_help("help-orte-rmaps-ppr.txt", "ppr-too-many-procs",
true, app->app, app->num_procs, jdata->map->ppr);
rc = ORTE_ERR_SILENT;
goto error;
}
/* track the total number of processes we mapped - must update
* this AFTER we compute vpids so that computation is done
* correctly
*/
jdata->num_procs += app->num_procs;
while (NULL != (item = opal_list_remove_first(&node_list))) {
OBJ_RELEASE(item);
}
OBJ_DESTRUCT(&node_list);
}
return ORTE_SUCCESS;
error:
while (NULL != (item = opal_list_remove_first(&node_list))) {
OBJ_RELEASE(item);
}
OBJ_DESTRUCT(&node_list);
return rc;
}
// clear all rows of type "id" from the buffer.
void LogBuffer::clear(log_id_t id, uid_t uid) {
pthread_mutex_lock(&mLogElementsLock);
prune(id, ULONG_MAX, uid);
pthread_mutex_unlock(&mLogElementsLock);
}
float DspSegmentAlgorithm::frameSegmentation() {
time++;
//0时刻放入初值
if (time == 0) {
if((unsigned int)(m_pMemPool + *m_pMPidx)%sizeof(DSPStateTrace))
*m_pMPidx += sizeof(DSPStateTrace) - (unsigned int)(m_pMemPool + *m_pMPidx)%sizeof(DSPStateTrace);
DSPStateTrace* s0 = (DSPStateTrace* )(m_pMemPool + *m_pMPidx);
*m_pMPidx += sizeof(DSPStateTrace);
int cb[STATE_NUM_IN_WORD];
m_pDict->getWordCbId(ansList[0], NO_PREVIOUS_WORD, NO_NEXT_WORD, cb);
//种子放入第一字的I0状态
int cbidx0 = cb[INITIAL0];
float stateLh0 = m_pBC->getStateLh(cbidx0, time);
stateLh0;
s0->set(time, cbidx0, stateLh0, 0, NULL, -1);
(m_binSet + 1)->addStateTrace(s0);
//种子放入句首的sil
DSPStateTrace* s1 = (DSPStateTrace* )(m_pMemPool + *m_pMPidx);
*m_pMPidx += sizeof(DSPStateTrace);
int cbidx1 = NOISE_ID;
float stateLh1 = m_pBC->getStateLh(cbidx1, time);
s1->set(time, cbidx1, stateLh1, 0, NULL, -1);
m_binSet->addStateTrace(s1);
/*return 99;*/
//test
return 99;
}
//time != 0
for (int i = m_nBinsetLen - 1; i >= 0; i--) {
DSPStateTraceBin* b = m_binSet + i;
int cbidx = b->cbidx;
//在一句话的最后一字可能发生这样的情况，因为不存在下一字，无法协同发音，协同发音的状态ID的值为INVALID_STATE_ID
if (cbidx == -1)
continue;
float stateLh = m_pBC->getStateLh(cbidx, time);
/*if(stateLh < -50000000 || stateLh > 0)
return 88000 + cbidx;*/
//处理状态内跳转
for (int j = 0; j < b->contentSize; j++) {
DSPStateTrace* st = b->content[j];
/*if(st->lh < -5000000 || st->lh > 0)
return 101;*/
float newLh = st->lh + stateLh;
st->lh = newLh;
}
//状态剪枝
//b->prune(factory);
/*if(stateLh < -50000000 || stateLh > 0)
return 77000 + cbidx;*/
//处理状态间跳转
DSPStateTrace* previousBest = bestPreviousTrace(b);
if (previousBest == NULL)
continue;
/*if(stateLh < -50000000 || stateLh > 0)
return 66000 + cbidx;*/
if((unsigned int)(m_pMemPool + *m_pMPidx)%sizeof(DSPStateTrace))
*m_pMPidx += sizeof(DSPStateTrace) - (unsigned int)(m_pMemPool + *m_pMPidx)%sizeof(DSPStateTrace);
DSPStateTrace* copy = (DSPStateTrace* )(m_pMemPool + *m_pMPidx);
*m_pMPidx += sizeof(DSPStateTrace);
copy->set(previousBest->enterTime, previousBest->cbidx, previousBest->lh, 0, previousBest->prev, -1);
if (previousBest->prev != NULL)
previousBest->prev->refcnt++;
/*if(copy->lh < -50000000 || copy->lh > 0)
return 3303;
if(stateLh < -50000000 || stateLh > 0)
return 44000 + cbidx;*/
float newLh = stateLh + previousBest->lh;
DSPStateTrace* newTrace = (DSPStateTrace* )(m_pMemPool + *m_pMPidx);
*m_pMPidx += sizeof(DSPStateTrace);
newTrace->set(time, cbidx, newLh, 0, copy, -1);
copy->refcnt++;
b->addStateTrace(newTrace);
/*if(newTrace->lh < -50000000 || newTrace->lh > 0)
return cbidx;*/
//状态剪枝
prune(b);
/*if(test == 5)
return test;*/
}
return 99;
}
void ImageResource::clear()
{
prune();
clearImage();
setEncodedSize(0);
}
void PageCache::pruneToSizeNow(unsigned size, PruningReason pruningReason)
{
TemporaryChange<unsigned> change(m_maxSize, size);
prune(pruningReason);
}
void analyzeVideo(const std::string& folder, const Camera& calibrated_camera, float label_width)
{
// Start with a single hypotheses of the cube.
std::vector<ProbabalisticCube> cube_hypotheses;
cube_hypotheses.push_back(ProbabalisticCube());
for (int frame_i = 0;;)
{
printf("Frame %i\n", frame_i);
char buf[1024];
sprintf(buf, "%s/frame%05d.png", folder.c_str(), frame_i);
cv::Mat3b img = cv::imread(buf, cv::IMREAD_COLOR);
if (img.empty())
{
break;
}
const size_t num_hypotheses_before = cube_hypotheses.size();
printf("Num hypotheses before: %lu\n", num_hypotheses_before);
cube_hypotheses = predict(cube_hypotheses);
const size_t num_hypotheses_after = cube_hypotheses.size();
printf("Num hypotheses after: %lu\n", num_hypotheses_after);
printf("Brancing factor: %f\n", double(num_hypotheses_after) / num_hypotheses_before);
const size_t max_hypotheses = 216;
if (num_hypotheses_after > max_hypotheses)
{
const size_t pruned_num = num_hypotheses_after - max_hypotheses;
const double removed_percentage = pruned_num * 100.0 / num_hypotheses_after;
printf("Pruning to %lu hypotheses, removing %lu (%.1f%%) hypotheses.\n",
max_hypotheses, pruned_num, removed_percentage);
}
prune(cube_hypotheses, max_hypotheses);
printf("Most likely cubes:\n");
for (int i = 0; i < cube_hypotheses.size() && i < 5; ++i)
{
const ProbabalisticCube& cube = cube_hypotheses[i];
const std::string permutation = cube.cube_permutation.to_String();
const double likelihood_percent = exp(cube.log_likelihood) * 100.0;
printf("%d: %s %3.5f%%\n", i, permutation.c_str(), likelihood_percent);
}
std::vector<LabelContour> labels = findLabelContours(img, 12, true);
std::vector<std::vector<cv::Point2f>> detected_corners = findLabelCorners(labels);
std::vector<Camera> all_camera_candidates;
for (const auto& corners : detected_corners)
{
std::vector<Camera> cameras = predictCameraPosesForLabel(calibrated_camera, corners, label_width);
all_camera_candidates.insert(all_camera_candidates.end(), cameras.begin(), cameras.end());
}
std::vector<double> camera_scores;
camera_scores.reserve(all_camera_candidates.size());
{
cv::Mat1f accumulation(img.size(), 0.f);
for (const auto& cam : all_camera_candidates)
{
cv::Mat1f contribution(img.size(), 0.f);
std::vector<cv::Point2f> predicted_corners = projectCubeCorners(cam, label_width);
double score = scorePredictedCorners(predicted_corners, detected_corners);
camera_scores.push_back(score);
for (int i = 0; i < predicted_corners.size(); i += 4)
{
std::vector<cv::Point> corners = {
predicted_corners[i + 0],
predicted_corners[i + 1],
predicted_corners[i + 2],
predicted_corners[i + 3],
};
cv::polylines(contribution, corners, true, cv::Scalar(score * score));
}
accumulation += contribution;
}
double minval;
double maxval;
cv::minMaxLoc(accumulation, &minval, &maxval);
cv::imshow("accumulation", accumulation / maxval);
}
if (!camera_scores.empty())
{
std::vector<double> sorted_camera_scores = camera_scores;
std::sort(sorted_camera_scores.begin(), sorted_camera_scores.end());
std::reverse(sorted_camera_scores.begin(), sorted_camera_scores.end());
printf("Min score: %f max score: %f\n", sorted_camera_scores.back(), sorted_camera_scores.front());
for (int i = 0; i < sorted_camera_scores.size() && i < 5; ++i)
{
double score = sorted_camera_scores[i];
printf("#%d score: %f\n", i + 1, score);
}
}
if (!all_camera_candidates.empty())
{
const size_t index = std::distance(camera_scores.begin(),
std::max_element(camera_scores.begin(), camera_scores.end()));
printf("detected_corners size: %lu index: %lu\n", detected_corners.size(), index);
const Camera& cam = all_camera_candidates[index];
std::vector<cv::Point2f> predicted_corners = projectCubeCorners(cam, label_width);
cv::Mat3b canvas = img * 0.25f;
for (int i = 0; i < predicted_corners.size(); i += 4)
{
std::vector<cv::Point> corners = {
predicted_corners[i + 0],
predicted_corners[i + 1],
predicted_corners[i + 2],
predicted_corners[i + 3],
};
cv::polylines(canvas, corners, true, cv::Scalar(0, 0, 255));
}
{
std::vector<cv::Point> corners = {
detected_corners[index / 9][0],
detected_corners[index / 9][1],
detected_corners[index / 9][2],
detected_corners[index / 9][3],
};
cv::polylines(canvas, corners, true, cv::Scalar(255, 0, 255));
}
cv::imshow("predicted labels", canvas);
}
{
cv::Mat3b canvas = img * 0.25f;
drawLabels(canvas, labels, cv::Scalar(255, 255, 255));
for (const auto& corners : detected_corners)
{
cv::polylines(canvas, cast<cv::Point>(corners), true, cv::Scalar(0, 0, 255));
for (size_t i = 0; i < corners.size(); ++i)
{
char text[12];
sprintf(text, "%lu", i);
cv::putText(canvas, text, corners[i],
cv::FONT_HERSHEY_PLAIN, 1, cv::Scalar(0, 0, 255));
}
}
cv::imshow("detected labels", canvas);
}
if (int key = cv::waitKey(0) & 255)
{
if (key == 27)
{
break; // stop by pressing ESC
}
if (key == 32) // space
{
++frame_i;
}
if (key == 83) // right arrow
{
++frame_i;
}
if (key == 82) // up arrow
{
}
if (key == 81) // left arrow
{
--frame_i;
}
if (key == 84) // down arrow
{
}
if (key != 255)
{
printf("Key: %d\n", key);
fflush(stdout);
}
}
}
}
void quadtree::prune(uint32_t tolerance)
{
prune(root_, tolerance);
}
void SimpleSkeletonGrower::grow_potential(int no_branch)
{
//overview: maintain a volume to represent the potential energy at each step,
//then find the min_element_index and the min_rotate that require the minimum potential energy
if(!_surface.is_loaded() || !_root)
{
printf("SimpleSkeletonGrower::surface error\n");
return;
}
//find the dimensions of the volume
float v_height = -1.0f;
osg::Vec3 origin(0.0f, 0.0f, 0.0f);
for(unsigned int i=0; i<_surface._surface_pts.size(); i++)
{
float cur = (_surface._surface_pts[i] - origin).length2();
if(v_height == -1.0f || cur > v_height)
v_height = cur;
}
if(v_height == -1.0f)
{
printf("SimpleSkeletonGrower::grow_potential():v_height(-1.0f) error\n");
return;
}
//v_height = sqrt(v_height) * 1.5f; //old
v_height = sqrt(v_height) * 2.0f; //new
float v_step = v_height / 100.0f;
osg::Vec3 corner(-v_height/2.0f, -v_height/2.0f, 0.0f);
SimpleVolumeFloat space(v_height, v_height, v_height, v_step, v_step, v_step);
float energy_effect = v_step * 18;
//negative charges on initial skeleton
//bfs
std::queue <BDLSkeletonNode *> Queue;
Queue.push(_root);
while(!Queue.empty())
{
BDLSkeletonNode *front = Queue.front();
Queue.pop();
osg::Vec3 cur = Transformer::toVec3(front) - corner;
space.add_potential(cur.x(), cur.y(), cur.z(), -3, energy_effect);
for(unsigned int i=0; i<front->_children.size(); i++)
Queue.push(front->_children[i]);
}
//positive charges on volume surface
for(unsigned int i=0; i<_surface._surface_pts.size(); i++)
{
osg::Vec3 cur = _surface._surface_pts[i] - corner;
space.add_potential(cur.x(), cur.y(), cur.z(), 1, energy_effect*1.5f);
}
std::vector <LibraryElement> elements = _library._library_element;
for(int i=0; i<no_branch; i++)
{
//pick a tail first
//not by minimum generation, but by farest position from surface point
BDLSkeletonNode *tail = pick_branch(true);
if(!tail)
{
printf("SimpleSkeletonGrower::grow():converged at %d-th step.\n", i+1);
break;
}
//compute the node-->id dict
std::map <BDLSkeletonNode *, int> dict;
int id = 0;
//bfs on source
std::queue <BDLSkeletonNode *> Queue;
Queue.push(_root);
while(!Queue.empty())
{
BDLSkeletonNode *front = Queue.front();
Queue.pop();
dict[front] = id;
for(unsigned int j=0; j<front->_children.size(); j++)
Queue.push(front->_children[j]);
id++;
}
int tail_id = dict[tail];
//####trial starts####
int min_element_index = -1;
int min_rotate = -1;
float min_energy = -1.0f;
for(unsigned int e=0; e<elements.size(); e++)
for(int r=0; r<360; r+=30)
{
LibraryElement element_trial = elements[e];
if(false)
{
//copy the original(_root) tree and find the corresponding tail
BDLSkeletonNode *copy_root = BDLSkeletonNode::copy_tree(_root);
BDLSkeletonNode *copy_tail = NULL;
//bfs on target, Queue is now empty at this point
id = 0;
Queue.push(copy_root);
while(!Queue.empty())
{
BDLSkeletonNode *front = Queue.front();
Queue.pop();
if(id == tail_id)
copy_tail = front;
for(unsigned int j=0; j<front->_children.size(); j++)
Queue.push(front->_children[j]);
id++;
}
//branch replacement
std::vector <BDLSkeletonNode *> subtree_trial = replace_branch(copy_tail, element_trial, r);
std::vector <BDLSkeletonNode *> non_pruned_nodes = after_pruned(subtree_trial); //but logically
//prune(subtree_trial); //no need to do it actually
}
std::vector <BDLSkeletonNode *> subtree_trial = replace_branch_unchanged(tail, element_trial, r);
std::vector <BDLSkeletonNode *> non_pruned_nodes = after_pruned(subtree_trial); //but logically
//compute the potential energy
//float energy = non_pruned_nodes.empty() ? 23418715 : compute_potential_energy(subtree_trial, space);
float energy = compute_potential_energy(non_pruned_nodes, space);
if(energy == 23418715.0f) //to let it grow a little bit randomly even it's completely outside the segmentation
{
min_element_index = rand()%elements.size();
min_rotate = rand()%360;
min_energy = 0.0f;
}
else if(min_energy == -1.0f || energy > min_energy) //the max in value is the min potential energy for negative charge
{
min_element_index = e;
min_rotate = r;
min_energy = energy;
}
//delete the copied tree
//BDLSkeletonNode::delete_this(copy_root);
for(unsigned int j=0; j<subtree_trial.size(); j++)
delete subtree_trial[j];
}
//####trial ends####
//actual replacement
if(min_energy != -1.0f)
{
//printf("tail(%p) min_energy(%f) min_element_index(%d) min_rotate(%d)\n", tail, min_energy, min_element_index, min_rotate);
std::vector <BDLSkeletonNode *> subtree = replace_branch(tail, elements[min_element_index], min_rotate);
std::vector <BDLSkeletonNode *> update_nodes = after_pruned(subtree);
prune(subtree); //prune leniently
//update space
for(unsigned int j=0; j<update_nodes.size(); j++)
{
osg::Vec3 cur = Transformer::toVec3(update_nodes[j]) - corner;
space.add_potential(cur.x(), cur.y(), cur.z(), -3, energy_effect); //negative charge
}
}
//if(i > no_branch * 0.5f && i < no_branch * 0.75f)
if(i > no_branch * 0.75f)
{
if(!_approaching_done)
_close_threshold /= 2.0f;
_approaching_done = true;
}
else if(i >= no_branch * 0.90f)
_approaching_done = false;
}
//aftermath: should be shared for different grow methods
//prune strictly on entire tree
prune_strictly(_root);
if(true)
{
//printf("backward_grow()\n");
backward_grow();
prune_strictly(_root);
}
}
void SimpleSkeletonGrower::grow_exhaustive(int no_branch)
{
std::vector <LibraryElement> elements = _library._library_element;
for(int i=0; i<no_branch; i++)
{
//pick a tail first
BDLSkeletonNode *tail = pick_branch();
if(!tail)
{
printf("SimpleSkeletonGrower::grow():converged at %d-th step.\n", i+1);
break;
}
//compute the node-->id dict
std::map <BDLSkeletonNode *, int> dict;
int id = 0;
//bfs on source
std::queue <BDLSkeletonNode *> Queue;
Queue.push(_root);
while(!Queue.empty())
{
BDLSkeletonNode *front = Queue.front();
Queue.pop();
dict[front] = id;
for(unsigned int j=0; j<front->_children.size(); j++)
Queue.push(front->_children[j]);
id++;
}
int tail_id = dict[tail];
//####trial starts####
int min_element_index = -1;
int min_rotate = -1;
float min_energy = -1.0f;
for(unsigned int e=0; e<elements.size(); e++)
for(int r=0; r<360; r+=30)
{
LibraryElement element_trial = elements[e];
//copy the original(_root) tree and find the corresponding tail
BDLSkeletonNode *copy_root = BDLSkeletonNode::copy_tree(_root);
BDLSkeletonNode *copy_tail = NULL;
//bfs on target, Queue is now empty at this point
id = 0;
Queue.push(copy_root);
while(!Queue.empty())
{
BDLSkeletonNode *front = Queue.front();
Queue.pop();
if(id == tail_id)
copy_tail = front;
for(unsigned int j=0; j<front->_children.size(); j++)
Queue.push(front->_children[j]);
id++;
}
//branch replacement
std::vector <BDLSkeletonNode *> subtree_trial = replace_branch(copy_tail, element_trial, r);
prune(subtree_trial);
//find energy
float energy = compute_energy(copy_root);
if(energy >= 0.0f && (min_energy == -1.0f || energy < min_energy))
{
min_element_index = e;
min_rotate = r;
min_energy = energy;
}
//delete the copied tree
BDLSkeletonNode::delete_this(copy_root);
}
//####trial ends####
//actual replacement
if(min_energy != -1.0f)
{
std::vector <BDLSkeletonNode *> subtree = replace_branch(tail, elements[min_element_index], min_rotate);
prune(subtree);
}
}
}
void SimpleSkeletonGrower::prune(std::vector<BDLSkeletonNode *> roots)
{
for(unsigned int i=0; i<roots.size(); i++)
prune(roots[i]);
}
void hcct_enter(UINT32 routine_id, UINT16 call_site) {
++lss_enter_events;
lss_hcct_node_t *parent = stack[stack_idx];
lss_hcct_node_t *node;
// check if calling context is already in the tree
for (node = parent->first_child;
node != NULL;
node = node->next_sibling)
if (node->routine_id == routine_id &&
node->call_site == call_site) break;
// node was already in the tree
if (node != NULL) {
stack[++stack_idx] = node;
if (IsMonitored(node)) {
node->counter++;
return;
}
}
// add new child to parent
else {
pool_alloc(node_pool, free_list,
node, lss_hcct_node_t);
node->routine_id = routine_id;
node->call_site = call_site;
node->first_child = NULL;
node->next_sibling = parent->first_child;
node->parent = parent;
parent->first_child = node;
stack[++stack_idx] = node;
}
// Mark node as monitored
SetMonitored(node);
// if table is not full
if (!queue_full) {
#if KEEP_EPS
node->eps = 0;
#endif
node->counter = 1;
queue[num_queue_items++] = node;
queue_full = num_queue_items == epsilon;
return;
}
#if INLINE_UPD_MIN == 1
// version with swaps
#if 0
while (++min_idx < epsilon)
if (queue[min_idx]->counter == min) goto end;
UINT32 i;
min = queue[second_min_idx]->counter;
min_idx = epsilon-1;
swap_and_decr(second_min_idx, min_idx);
for (i = 0; i <= min_idx; ++i) {
if (queue[i]->counter > min) continue;
if (queue[i]->counter < min) {
second_min_idx = i;
min_idx = epsilon-1;
min = queue[i]->counter;
}
swap_and_decr(i, min_idx);
}
end:
#endif
#if UPDATE_MIN_SENTINEL == 1
// version with second_min + sentinel
while (queue[++min_idx]->counter > min);
if (min_idx < epsilon) goto end;
UINT32 i;
min = queue[second_min_idx]->counter;
for (min_idx = 0, i = 0; i < epsilon; ++i) {
if (queue[i]->counter < min) {
second_min_idx = min_idx;
min_idx = i;
min = queue[i]->counter;
}
}
queue[epsilon]->counter = min;
end:
// version with second_min
#else
while (++min_idx < epsilon)
if (queue[min_idx]->counter == min) goto end;
UINT32 i;
min = queue[second_min_idx]->counter;
for (min_idx = 0, i = 0; i < epsilon; ++i) {
if (queue[i]->counter < min) {
second_min_idx = min_idx;
min_idx = i;
min = queue[i]->counter;
}
}
end:
#endif
#else
// no explicit inlining: -O3 should do it anyway, though
update_min();
#endif
#if KEEP_EPS
node->eps=min;
#endif
node->counter = min + 1;
UnsetMonitored(queue[min_idx]);
if (queue[min_idx]->first_child==NULL)
prune(queue[min_idx]);
queue[min_idx]=node;
}
void PageCache::setMaxSize(unsigned maxSize)
{
m_maxSize = maxSize;
prune(PruningReason::None);
}
void c_elegans::update(){
if(has_gone){
has_gone=false;//prevent more than one update happening without call to rhs
if(!first_round){
if(next_comb(abl_neur, num_neur)){
holder->write_dat();
char ind_str[20];//won't ever have a 20 digit index
//handy buffer to overflow for those hacking this.
sprintf(ind_str, "%d", cur_ind);
err(std::string("Combinations exhausted in index ") + ind_str,
"c_elegans::update","rhs/c_elegans.cpp", FATAL_ERROR);
}
auto dat_inds =
std::shared_ptr<writer>(new writer(true));
dat_inds->add_data(data::create("Ablations", abl_neur.data(), abl_neur.size()), writer::OTHER);
holder->add_writer(dat_inds);
}
else{
first_round=false;
}
Matrix<double, Dynamic, Dynamic> ag_dense(num_neur, num_neur);
//insert code to zero it out later
auto ag_m = ag_full;
AEchem_trans = AEchem_trans_full;
auto fncval = [this](int i, int j, double val)->bool{
for(int kk = 0; kk < (int)this->abl_neur.size(); kk++){
if((int)this->abl_neur[kk] == i || (int)this->abl_neur[kk] == j){
return false;
}
}
return true;
};
AEchem_trans.prune(fncval);
ag_m.prune(fncval);
ag_dense = ag_m * Matrix<double, num_neur, num_neur, ColMajor>::Identity();
dmd(ag_dense);
auto sumvals = ag_dense.colwise().sum();
sparse_type temp(num_neur, num_neur);
//generate the sparse diagonal matrix to build the lapacian
std::vector<Triplet<double, int> > temp_tr;
for(int i = 0; i < (int)num_neur; i++){
temp_tr.push_back(Triplet<double, int>(i, i, sumvals[i]));
}
temp.setFromTriplets(temp_tr.begin(), temp_tr.end());
laplacian = temp - ag_m;
//initialize the Echem array
for(size_t i = 0; i < num_neur; i++){
if(GABAergic[i]){
Echem[i] = EchemInh;
}
else{
Echem[i] = EchemEx;
}
}
//Initialize the sig array
for(size_t i = 0; i < num_neur; i++){
sig[i] = 0.5;
}
eqS = sig * (ar/(ar*sig + ad));
//more initialization of temporary dense matrices
Matrix<double, Dynamic, Dynamic> ldense(num_neur,num_neur);
ldense = laplacian*Matrix<double, num_neur, num_neur>::Identity();
Matrix<double, Dynamic, Dynamic> aedense(num_neur, num_neur);
aedense= AEchem_trans*Matrix<double, num_neur, num_neur>::Identity();
Matrix<double, Dynamic, Dynamic> C(num_neur, num_neur);
//create the C matrix
C= memG*Matrix<double, num_neur, num_neur>::Identity() + gelec*ldense;
//initialize matrix to modify diagonal part of C
Matrix<double, num_neur, 1> tmp =(gchem * aedense * eqS.matrix());
for(size_t i = 0; i < num_neur; i++){
C(i, i) += tmp(i);
}
Matrix<double, num_neur, 1> Ivals;
Ivals.setZero();
double amp=2e4;
Ivals[276]=amp;
Ivals[278]=amp;
Matrix<double, num_neur, 1> b;
//create B vector
b= gchem*aedense*(eqS * Echem).matrix();
for(size_t i = 0; i < num_neur; i++){
b[i] += (memG*memV + Ivals[i]);
}
//calculate eqV
eqV.matrix() = C.inverse()*b;
vmean = eqV+(1.0/beta) * (1.0/sig - 1).log();
for(auto val : abl_neur){
eqV[val] = vmean [val] = eqS[val] = 0;
};
}
}
int main(int argc, char **argv)
{
clock_t begin, end;
double time_spent;
begin = clock();
int NUM_FINDCODE_CALLS = 0;
int NUM_HASHCELLS_VISITED = 0;
int c = 0; //char in (pref, char)
int prefix = EMPTY_CODE;
int index = EMPTY_CODE;
int MAXBITS = 15; //default
char DUMP_TO[PATH_MAX];
char INIT_FROM[PATH_MAX];
int PRUNE = -1;
Table *stringTable = initStringTable(MAXBITS);
//setting params from cmd line argv's STARTING FROM 2 BC ENCODE/DECODE
for (int i = 2; i < argc; ++i)
{
if (strcmp(argv[i], "-m") == 0) {
//ERROR CHECK FOR IF NEXT ARGV IS NOT INTEGER STRING???
MAXBITS = atoi(argv[i + 1]);
i++;
} else if (strcmp(argv[i], "-o") == 0) {
if(i + 1 == argc) {
fprintf(stderr, "usage: encode [-m MAXBITS | -o NAME | -i NAME | -p USED]* OR decode [-o NAME]*\n");
exit(EXIT_FAILURE);
//EDGE CASE: IF -O -O HI, THEN DO WE DUMP TO '-O' AND SIGNAL ERROR ON HI? OR DO WE DUMP TO -O, AND OVERRIDE WITH DUMPING TO 'HI'?
}
strncpy(DUMP_TO, argv[i + 1], strlen(argv[i + 1]));
i++;
} else if (strcmp(argv[i], "-i") == 0) {
if(i + 1 == argc) {
fprintf(stderr, "usage: encode [-m MAXBITS | -o NAME | -i NAME | -p USED]* OR decode [-o NAME]*\n");
exit(EXIT_FAILURE);
}
strncpy(INIT_FROM, argv[i + 1], strlen(argv[i + 1]));
i++;
} else if (strcmp(argv[i], "-p") == 0) {
if(i + 1 == argc) {
fprintf(stderr, "usage: encode [-m MAXBITS | -o NAME | -i NAME | -p USED]* OR decode [-o NAME]*\n");
exit(EXIT_FAILURE);
}
PRUNE = atoi(argv[i + 1]); //test if not an integer; what if prune is 0? w
i++;
if(PRUNE){}
} else {
fprintf(stderr, "usage: encode [-m MAXBITS | -o NAME | -i NAME | -p USED]* OR decode [-o NAME]*\n");
exit(EXIT_FAILURE);
}
}
fprintf(stderr, "argv[0]: %s\n", argv[0]);
if(strcmp(argv[1], "encode") == 0) {
//ENCODE
while((c = getchar()) != EOF) {
index = findCode(prefix, c, stringTable, &NUM_FINDCODE_CALLS, &NUM_HASHCELLS_VISITED);
if (index != -1) //(pref, char) found in stringTable
{
prefix = index;
(stringTable->table[prefix]->useCount)++;
continue;
} else { //not found in stringTable
putBits(stringTable->nBits, prefix);
insertToTable(prefix, c, &stringTable, PRUNE);
prefix = findCode(0, c, stringTable, &NUM_FINDCODE_CALLS, &NUM_HASHCELLS_VISITED); //start search again at finalChar of newly found sequence
(stringTable->table[prefix]->useCount)++;
}
}
putBits(stringTable->nBits, prefix);
flushBits();
// printTable(stringTable, "encode");
// fprintf(stderr, "\nNUM_FINDCODE_CALLS: %d\nNUM_HASHCELLS_VISITED: %d\nAVG_SEARCH_RATIO: %d\n", NUM_FINDCODE_CALLS, NUM_HASHCELLS_VISITED, NUM_HASHCELLS_VISITED / NUM_FINDCODE_CALLS);
} else if(strcmp(argv[1], "decode") == 0) {
//DECODE
char ENCODE_OR_DECODE[25] = "decode";
int oldIndex = 0, firstCharOfNewIndex = 0; //used to build stringTable, 1 step behind encode
int newIndex = 0;
int cascadingIndex = 0; //used to print a code string recursively
int kwkwk = 0; //used in kwkwk case
int prunedThisPass = 0;
int HIT_THE_LIMIT = 0;
while( (newIndex = cascadingIndex = getBits(stringTable->nBits)) != EOF) {
//nBits was incremented just before to accomodate increased nBits in ENCODE that hasn't been automatically detected in DECODE
//and we decrement it now bc it will be automatically incremented in INSERTTABLE
//but if == MAXBITS, then we did not artificially increment nBits last round
if(stringTable->last + 1 == stringTable->size && !HIT_THE_LIMIT ) {//2nd condition happens when table is already maxSize, in which case no more doubling or pruning happens
if(!prunedThisPass) //when pruning results in an at-limit table
stringTable->nBits--;
if(stringTable->size != 1<<stringTable->nBits){
fprintf(stderr, "size: %d, nBits: %d\n", stringTable->size, stringTable->nBits);
exit(EXIT_FAILURE);
} else {
}
}
if(newIndex > stringTable->last) //newIndex is an unknown code (kwkwk abnormal case)
{
kwkwk = 1;
if(newIndex < stringTable->size)
stringTable->table[newIndex]->useCount++; //useCount usually incremented in printRecursive function, which will not receive newIndex in this case
cascadingIndex = oldIndex;
}
printRecursive(&cascadingIndex, stringTable);
if (kwkwk == 1) {
printf("%c", firstCharOfNewIndex); //output should be oldCode, oldCode, firstCharOfOldCode
kwkwk = 0;
}
if(cascadingIndex >= stringTable->size) {
fprintf(stderr, "cascadingIndex: %d, size: %d\n", cascadingIndex, stringTable->size);
exit(EXIT_FAILURE);
}
firstCharOfNewIndex = stringTable->table[cascadingIndex]->c; //finalK = char(c)
if(oldIndex != 0 && !prunedThisPass) { //every time except first time, and after pruning, add new code to table
insertToTable(oldIndex, firstCharOfNewIndex, &stringTable, PRUNE);
}
prunedThisPass = 0;
oldIndex = newIndex;
if(stringTable->last + 1 >= stringTable->size) {
//decode is one step behind encode; deocde inserts new code every time it reads a code, starting from 2nd code
//encode adds a code at every code starting from 1st code. CURRENT CODE + firstChar of NEXT CODE was the last code
//encode tried to add to table and PRUNED or DOUBLE'd
//=>PRUNING or DOUBLING::
//if DOUBLING: next code will increment nBits
//if PRUNING: next code is encoded from a PRUNED table, not CURRENT table (and we don't insert next round)
if(stringTable->nBits != stringTable->MAXBITS) {
if(stringTable->nBits == 8){
exit(EXIT_FAILURE);
}
stringTable->nBits++;
} else { //next insert exceeds table size, and table size is MAXBITS size, so PRUNE
HIT_THE_LIMIT = 1;
if(PRUNE != -1) {
prune(&stringTable, PRUNE, ENCODE_OR_DECODE);
prunedThisPass = 1;
if (stringTable->last + 1 == stringTable->size)
{
fprintf(stderr, "HERE!!! last: %d, size: %d\n", stringTable->last, stringTable->size);
char temp[10] = "encode";
printTable(stringTable, temp);
}
if(stringTable->last + 1 != 1<<stringTable->MAXBITS)
HIT_THE_LIMIT = 0;
}
}
}
}
// printTable(stringTable, "decode");
}
moses(stringTable);
end = clock();
time_spent = (double)(end - begin) / CLOCKS_PER_SEC;
fprintf(stderr, "time_spent: %f\n", time_spent);
}
size_t TRILINOS_KLU_kernel /* final size of LU on output */
(
/* input, not modified */
Int n, /* A is n-by-n */
Int Ap [ ], /* size n+1, column pointers for A */
Int Ai [ ], /* size nz = Ap [n], row indices for A */
Entry Ax [ ], /* size nz, values of A */
Int Q [ ], /* size n, optional input permutation */
size_t lusize, /* initial size of LU on input */
/* output, not defined on input */
Int Pinv [ ], /* size n, inverse row permutation, where Pinv [i] = k if
* row i is the kth pivot row */
Int P [ ], /* size n, row permutation, where P [k] = i if row i is the
* kth pivot row. */
Unit **p_LU, /* LU array, size lusize on input */
Entry Udiag [ ], /* size n, diagonal of U */
Int Llen [ ], /* size n, column length of L */
Int Ulen [ ], /* size n, column length of U */
Int Lip [ ], /* size n, column pointers for L */
Int Uip [ ], /* size n, column pointers for U */
Int *lnz, /* size of L*/
Int *unz, /* size of U*/
/* workspace, not defined on input */
Entry X [ ], /* size n, undefined on input, zero on output */
/* workspace, not defined on input or output */
Int Stack [ ], /* size n */
Int Flag [ ], /* size n */
Int Ap_pos [ ], /* size n */
/* other workspace: */
Int Lpend [ ], /* size n workspace, for pruning only */
/* inputs, not modified on output */
Int k1, /* the block of A is from k1 to k2-1 */
Int PSinv [ ], /* inverse of P from symbolic factorization */
double Rs [ ], /* scale factors for A */
/* inputs, modified on output */
Int Offp [ ], /* off-diagonal matrix (modified by this routine) */
Int Offi [ ],
Entry Offx [ ],
/* --------------- */
TRILINOS_KLU_common *Common
)
{
Entry pivot ;
double abs_pivot, xsize, nunits, tol, memgrow ;
Entry *Ux ;
Int *Li, *Ui ;
Unit *LU ; /* LU factors (pattern and values) */
Int k, p, i, j, pivrow, kbar, diagrow, firstrow, lup, top, scale, len ;
size_t newlusize ;
#ifndef NDEBUG
Entry *Lx ;
#endif
ASSERT (Common != NULL) ;
scale = Common->scale ;
tol = Common->tol ;
memgrow = Common->memgrow ;
*lnz = 0 ;
*unz = 0 ;
/* ---------------------------------------------------------------------- */
/* get initial Li, Lx, Ui, and Ux */
/* ---------------------------------------------------------------------- */
PRINTF (("input: lusize %d \n", lusize)) ;
ASSERT (lusize > 0) ;
LU = *p_LU ;
/* ---------------------------------------------------------------------- */
/* initializations */
/* ---------------------------------------------------------------------- */
firstrow = 0 ;
lup = 0 ;
for (k = 0 ; k < n ; k++)
{
/* X [k] = 0 ; */
CLEAR (X [k]) ;
Flag [k] = EMPTY ;
Lpend [k] = EMPTY ; /* flag k as not pruned */
}
/* ---------------------------------------------------------------------- */
/* mark all rows as non-pivotal and determine initial diagonal mapping */
/* ---------------------------------------------------------------------- */
/* PSinv does the symmetric permutation, so don't do it here */
for (k = 0 ; k < n ; k++)
{
P [k] = k ;
Pinv [k] = FLIP (k) ; /* mark all rows as non-pivotal */
}
/* initialize the construction of the off-diagonal matrix */
Offp [0] = 0 ;
/* P [k] = row means that UNFLIP (Pinv [row]) = k, and visa versa.
* If row is pivotal, then Pinv [row] >= 0. A row is initially "flipped"
* (Pinv [k] < EMPTY), and then marked "unflipped" when it becomes
* pivotal. */
#ifndef NDEBUG
for (k = 0 ; k < n ; k++)
{
PRINTF (("Initial P [%d] = %d\n", k, P [k])) ;
}
#endif
/* ---------------------------------------------------------------------- */
/* factorize */
/* ---------------------------------------------------------------------- */
for (k = 0 ; k < n ; k++)
{
PRINTF (("\n\n==================================== k: %d\n", k)) ;
/* ------------------------------------------------------------------ */
/* determine if LU factors have grown too big */
/* ------------------------------------------------------------------ */
/* (n - k) entries for L and k entries for U */
nunits = DUNITS (Int, n - k) + DUNITS (Int, k) +
DUNITS (Entry, n - k) + DUNITS (Entry, k) ;
/* LU can grow by at most 'nunits' entries if the column is dense */
PRINTF (("lup %d lusize %g lup+nunits: %g\n", lup, (double) lusize,
lup+nunits));
xsize = ((double) lup) + nunits ;
if (xsize > (double) lusize)
{
/* check here how much to grow */
xsize = (memgrow * ((double) lusize) + 4*n + 1) ;
if (INT_OVERFLOW (xsize))
{
PRINTF (("Matrix is too large (Int overflow)\n")) ;
Common->status = TRILINOS_KLU_TOO_LARGE ;
return (lusize) ;
}
newlusize = memgrow * lusize + 2*n + 1 ;
/* Future work: retry mechanism in case of malloc failure */
LU = (Unit*) TRILINOS_KLU_realloc (newlusize, lusize, sizeof (Unit), LU, Common) ;
Common->nrealloc++ ;
*p_LU = LU ;
if (Common->status == TRILINOS_KLU_OUT_OF_MEMORY)
{
PRINTF (("Matrix is too large (LU)\n")) ;
return (lusize) ;
}
lusize = newlusize ;
PRINTF (("inc LU to %d done\n", lusize)) ;
}
/* ------------------------------------------------------------------ */
/* start the kth column of L and U */
/* ------------------------------------------------------------------ */
Lip [k] = lup ;
/* ------------------------------------------------------------------ */
/* compute the nonzero pattern of the kth column of L and U */
/* ------------------------------------------------------------------ */
#ifndef NDEBUG
for (i = 0 ; i < n ; i++)
{
ASSERT (Flag [i] < k) ;
/* ASSERT (X [i] == 0) ; */
ASSERT (IS_ZERO (X [i])) ;
}
#endif
top = lsolve_symbolic (n, k, Ap, Ai, Q, Pinv, Stack, Flag,
Lpend, Ap_pos, LU, lup, Llen, Lip, k1, PSinv) ;
#ifndef NDEBUG
PRINTF (("--- in U:\n")) ;
for (p = top ; p < n ; p++)
{
PRINTF (("pattern of X for U: %d : %d pivot row: %d\n",
p, Stack [p], Pinv [Stack [p]])) ;
ASSERT (Flag [Stack [p]] == k) ;
}
PRINTF (("--- in L:\n")) ;
Li = (Int *) (LU + Lip [k]);
for (p = 0 ; p < Llen [k] ; p++)
{
PRINTF (("pattern of X in L: %d : %d pivot row: %d\n",
p, Li [p], Pinv [Li [p]])) ;
ASSERT (Flag [Li [p]] == k) ;
}
p = 0 ;
for (i = 0 ; i < n ; i++)
{
ASSERT (Flag [i] <= k) ;
if (Flag [i] == k) p++ ;
}
#endif
/* ------------------------------------------------------------------ */
/* get the column of the matrix to factorize and scatter into X */
/* ------------------------------------------------------------------ */
construct_column (k, Ap, Ai, Ax, Q, X,
k1, PSinv, Rs, scale, Offp, Offi, Offx) ;
/* ------------------------------------------------------------------ */
/* compute the numerical values of the kth column (s = L \ A (:,k)) */
/* ------------------------------------------------------------------ */
lsolve_numeric (Pinv, LU, Stack, Lip, top, n, Llen, X) ;
#ifndef NDEBUG
for (p = top ; p < n ; p++)
{
PRINTF (("X for U %d : ", Stack [p])) ;
PRINT_ENTRY (X [Stack [p]]) ;
}
Li = (Int *) (LU + Lip [k]) ;
for (p = 0 ; p < Llen [k] ; p++)
{
PRINTF (("X for L %d : ", Li [p])) ;
PRINT_ENTRY (X [Li [p]]) ;
}
#endif
/* ------------------------------------------------------------------ */
/* partial pivoting with diagonal preference */
/* ------------------------------------------------------------------ */
/* determine what the "diagonal" is */
diagrow = P [k] ; /* might already be pivotal */
PRINTF (("k %d, diagrow = %d, UNFLIP (diagrow) = %d\n",
k, diagrow, UNFLIP (diagrow))) ;
/* find a pivot and scale the pivot column */
if (!lpivot (diagrow, &pivrow, &pivot, &abs_pivot, tol, X, LU, Lip,
Llen, k, n, Pinv, &firstrow, Common))
{
/* matrix is structurally or numerically singular */
Common->status = TRILINOS_KLU_SINGULAR ;
if (Common->numerical_rank == EMPTY)
{
Common->numerical_rank = k+k1 ;
Common->singular_col = Q [k+k1] ;
}
if (Common->halt_if_singular)
{
/* do not continue the factorization */
return (lusize) ;
}
}
/* we now have a valid pivot row, even if the column has NaN's or
* has no entries on or below the diagonal at all. */
PRINTF (("\nk %d : Pivot row %d : ", k, pivrow)) ;
PRINT_ENTRY (pivot) ;
ASSERT (pivrow >= 0 && pivrow < n) ;
ASSERT (Pinv [pivrow] < 0) ;
/* set the Uip pointer */
Uip [k] = Lip [k] + UNITS (Int, Llen [k]) + UNITS (Entry, Llen [k]) ;
/* move the lup pointer to the position where indices of U
* should be stored */
lup += UNITS (Int, Llen [k]) + UNITS (Entry, Llen [k]) ;
Ulen [k] = n - top ;
/* extract Stack [top..n-1] to Ui and the values to Ux and clear X */
GET_POINTER (LU, Uip, Ulen, Ui, Ux, k, len) ;
for (p = top, i = 0 ; p < n ; p++, i++)
{
j = Stack [p] ;
Ui [i] = Pinv [j] ;
Ux [i] = X [j] ;
CLEAR (X [j]) ;
}
/* position the lu index at the starting point for next column */
lup += UNITS (Int, Ulen [k]) + UNITS (Entry, Ulen [k]) ;
/* U(k,k) = pivot */
Udiag [k] = pivot ;
/* ------------------------------------------------------------------ */
/* log the pivot permutation */
/* ------------------------------------------------------------------ */
ASSERT (UNFLIP (Pinv [diagrow]) < n) ;
ASSERT (P [UNFLIP (Pinv [diagrow])] == diagrow) ;
if (pivrow != diagrow)
{
/* an off-diagonal pivot has been chosen */
Common->noffdiag++ ;
PRINTF ((">>>>>>>>>>>>>>>>> pivrow %d k %d off-diagonal\n",
pivrow, k)) ;
if (Pinv [diagrow] < 0)
{
/* the former diagonal row index, diagrow, has not yet been
* chosen as a pivot row. Log this diagrow as the "diagonal"
* entry in the column kbar for which the chosen pivot row,
* pivrow, was originally logged as the "diagonal" */
kbar = FLIP (Pinv [pivrow]) ;
P [kbar] = diagrow ;
Pinv [diagrow] = FLIP (kbar) ;
}
}
P [k] = pivrow ;
Pinv [pivrow] = k ;
#ifndef NDEBUG
for (i = 0 ; i < n ; i++) { ASSERT (IS_ZERO (X [i])) ;}
GET_POINTER (LU, Uip, Ulen, Ui, Ux, k, len) ;
for (p = 0 ; p < len ; p++)
{
PRINTF (("Column %d of U: %d : ", k, Ui [p])) ;
PRINT_ENTRY (Ux [p]) ;
}
GET_POINTER (LU, Lip, Llen, Li, Lx, k, len) ;
for (p = 0 ; p < len ; p++)
{
PRINTF (("Column %d of L: %d : ", k, Li [p])) ;
PRINT_ENTRY (Lx [p]) ;
}
#endif
/* ------------------------------------------------------------------ */
/* symmetric pruning */
/* ------------------------------------------------------------------ */
prune (Lpend, Pinv, k, pivrow, LU, Uip, Lip, Ulen, Llen) ;
*lnz += Llen [k] + 1 ; /* 1 added to lnz for diagonal */
*unz += Ulen [k] + 1 ; /* 1 added to unz for diagonal */
}
/* ---------------------------------------------------------------------- */
/* finalize column pointers for L and U, and put L in the pivotal order */
/* ---------------------------------------------------------------------- */
for (p = 0 ; p < n ; p++)
{
Li = (Int *) (LU + Lip [p]) ;
for (i = 0 ; i < Llen [p] ; i++)
{
Li [i] = Pinv [Li [i]] ;
}
}
#ifndef NDEBUG
for (i = 0 ; i < n ; i++)
{
PRINTF (("P [%d] = %d Pinv [%d] = %d\n", i, P [i], i, Pinv [i])) ;
}
for (i = 0 ; i < n ; i++)
{
ASSERT (Pinv [i] >= 0 && Pinv [i] < n) ;
ASSERT (P [i] >= 0 && P [i] < n) ;
ASSERT (P [Pinv [i]] == i) ;
ASSERT (IS_ZERO (X [i])) ;
}
#endif
/* ---------------------------------------------------------------------- */
/* shrink the LU factors to just the required size */
/* ---------------------------------------------------------------------- */
newlusize = lup ;
ASSERT ((size_t) newlusize <= lusize) ;
/* this cannot fail, since the block is descreasing in size */
LU = (Unit*) TRILINOS_KLU_realloc (newlusize, lusize, sizeof (Unit), LU, Common) ;
*p_LU = LU ;
return (newlusize) ;
}
/* recursively climb the topology, pruning procs beyond that allowed
* by the given ppr
*/
static void prune(orte_jobid_t jobid,
orte_app_idx_t app_idx,
orte_node_t *node,
opal_hwloc_level_t *level,
orte_vpid_t *nmapped)
{
hwloc_obj_t obj, top;
unsigned int i, nobjs;
hwloc_obj_type_t lvl;
unsigned cache_level = 0, k;
int nprocs;
hwloc_cpuset_t avail;
int n, limit, nmax, nunder, idx, idxmax = 0;
orte_proc_t *proc, *pptr, *procmax;
opal_hwloc_level_t ll;
char dang[64];
hwloc_obj_t locale;
opal_output_verbose(5, orte_rmaps_base_framework.framework_output,
"mca:rmaps:ppr: pruning level %d",
*level);
/* convenience */
ll = *level;
/* convenience */
lvl = opal_hwloc_levels[ll];
limit = ppr[ll];
if (0 == limit) {
/* no limit at this level, so move up if necessary */
if (0 == ll) {
/* done */
return;
}
--(*level);
prune(jobid, app_idx, node, level, nmapped);
return;
}
/* handle the darn cache thing again */
if (OPAL_HWLOC_L3CACHE_LEVEL == ll) {
cache_level = 3;
} else if (OPAL_HWLOC_L2CACHE_LEVEL == ll) {
cache_level = 2;
} else if (OPAL_HWLOC_L1CACHE_LEVEL == ll) {
cache_level = 1;
}
/* get the number of resources at this level on this node */
nobjs = opal_hwloc_base_get_nbobjs_by_type(node->topology->topo,
lvl, cache_level,
OPAL_HWLOC_AVAILABLE);
/* for each resource, compute the number of procs sitting
* underneath it and check against the limit
*/
for (i=0; i < nobjs; i++) {
obj = opal_hwloc_base_get_obj_by_type(node->topology->topo,
lvl, cache_level,
i, OPAL_HWLOC_AVAILABLE);
/* get the available cpuset */
avail = obj->cpuset;
/* look at the intersection of this object's cpuset and that
* of each proc in the job/app - if they intersect, then count this proc
* against the limit
*/
nprocs = 0;
for (n=0; n < node->procs->size; n++) {
if (NULL == (proc = (orte_proc_t*)opal_pointer_array_get_item(node->procs, n))) {
continue;
}
if (proc->name.jobid != jobid ||
proc->app_idx != app_idx) {
continue;
}
locale = NULL;
if (orte_get_attribute(&proc->attributes, ORTE_PROC_HWLOC_LOCALE, (void**)&locale, OPAL_PTR)) {
ORTE_ERROR_LOG(ORTE_ERR_NOT_FOUND);
return;
}
if (hwloc_bitmap_intersects(avail, locale->cpuset)) {
nprocs++;
}
}
opal_output_verbose(5, orte_rmaps_base_framework.framework_output,
"mca:rmaps:ppr: found %d procs limit %d",
nprocs, limit);
/* check against the limit */
while (limit < nprocs) {
/* need to remove procs - do this in a semi-intelligent
* manner to provide a little load balancing by cycling
* across the objects beneath this one, removing procs
* in a round-robin fashion until the limit is satisfied
*
* NOTE: I'm sure someone more knowledgeable with hwloc
* will come up with a more efficient way to do this, so
* consider this is a starting point
*/
/* find the first level that has more than
* one child beneath it - if all levels
* have only one child, then return this
* object
*/
top = find_split(node->topology->topo, obj);
hwloc_obj_type_snprintf(dang, 64, top, 1);
opal_output_verbose(5, orte_rmaps_base_framework.framework_output,
"mca:rmaps:ppr: SPLIT AT LEVEL %s", dang);
/* cycle across the children of this object */
nmax = 0;
procmax = NULL;
idx = 0;
/* find the child with the most procs underneath it */
for (k=0; k < top->arity && limit < nprocs; k++) {
/* get this object's available cpuset */
nunder = 0;
pptr = NULL;
for (n=0; n < node->procs->size; n++) {
if (NULL == (proc = (orte_proc_t*)opal_pointer_array_get_item(node->procs, n))) {
continue;
}
if (proc->name.jobid != jobid ||
proc->app_idx != app_idx) {
continue;
}
locale = NULL;
if (orte_get_attribute(&proc->attributes, ORTE_PROC_HWLOC_LOCALE, (void**)&locale, OPAL_PTR)) {
ORTE_ERROR_LOG(ORTE_ERR_NOT_FOUND);
return;
}
if (hwloc_bitmap_intersects(top->children[k]->cpuset, locale->cpuset)) {
nunder++;
if (NULL == pptr) {
/* save the location of the first proc under this object */
pptr = proc;
idx = n;
}
}
}
if (nmax < nunder) {
opal_output_verbose(5, orte_rmaps_base_framework.framework_output,
"mca:rmaps:ppr: PROCS UNDER CHILD %d %d MAX %d",
k, nunder, nmax);
nmax = nunder;
procmax = pptr;
idxmax = idx;
}
}
if (NULL == procmax) {
/* can't find anything to remove - error out */
goto error;
}
/* remove it */
opal_output_verbose(5, orte_rmaps_base_framework.framework_output,
"mca:rmaps:ppr: removing proc at posn %d",
idxmax);
opal_pointer_array_set_item(node->procs, idxmax, NULL);
node->num_procs--;
node->slots_inuse--;
if (node->slots_inuse < 0) {
node->slots_inuse = 0;
}
nprocs--;
*nmapped -= 1;
OBJ_RELEASE(procmax);
}
}
/* finished with this level - move up if necessary */
if (0 == ll) {
return;
}
--(*level);
prune(jobid, app_idx, node, level, nmapped);
return;
error:
opal_output(0, "INFINITE LOOP");
}
/*
* routine:
* main
*
* purpose:
* argument processing and primary dispatch
*
* returns:
* error codes per filesync.1 (ERR_* in filesync.h)
*
* notes:
* read filesync.1 in order to understand the argument processing
*
* most of the command line options just set some opt_ global
* variable that is later looked at by the code that actually
* implements the features. Only file names are really processed
* in this routine.
*/
int
main(int argc, char **argv)
{ int i;
int c;
errmask_t errs = ERR_OK;
int do_prune = 0;
char *srcname = 0;
char *dstname = 0;
struct base *bp;
/* keep the error messages simple */
argv[0] = "filesync";
/* gather together all of the options */
while ((c = getopt(argc, argv, "AaehmnqvyD:E:r:s:d:f:o:")) != EOF)
switch (c) {
case 'a': /* always scan for acls */
opt_acls = TRUE;
break;
case 'e': /* everything agrees */
opt_everything = TRUE;
break;
case 'h': /* halt on error */
opt_halt = TRUE;
break;
case 'm': /* preserve modtimes */
opt_mtime = TRUE;
break;
case 'n': /* notouch */
opt_notouch = TRUE;
break;
case 'q': /* quiet */
opt_quiet = TRUE;
break;
case 'v': /* verbose */
opt_verbose = TRUE;
break;
case 'y': /* yes */
opt_yes = TRUE;
break;
case 'D': /* debug options */
if (!isdigit(optarg[0])) {
dbg_usage();
exit(ERR_INVAL);
}
opt_debug |= strtol(optarg, (char **)NULL, 0);
break;
case 'E': /* error simulation */
if (dbg_set_error(optarg)) {
err_usage();
exit(ERR_INVAL);
}
opt_errors = TRUE;
break;
case 'f': /* force conflict resolution */
switch (optarg[0]) {
case 's':
opt_force = OPT_SRC;
break;
case 'd':
opt_force = OPT_DST;
break;
case 'o':
opt_force = OPT_OLD;
break;
case 'n':
opt_force = OPT_NEW;
break;
default:
fprintf(stderr,
gettext(ERR_badopt),
c, optarg);
errs |= ERR_INVAL;
break;
}
break;
case 'o': /* one way propagation */
switch (optarg[0]) {
case 's':
opt_oneway = OPT_SRC;
break;
case 'd':
opt_oneway = OPT_DST;
break;
default:
fprintf(stderr,
gettext(ERR_badopt),
c, optarg);
errs |= ERR_INVAL;
break;
}
break;
case 'r': /* restricted reconciliation */
if (num_restrs < MAX_RLIST)
rlist[ num_restrs++ ] = optarg;
else {
fprintf(stderr, gettext(ERR_tomany),
MAX_RLIST);
errs |= ERR_INVAL;
}
break;
case 's':
if ((srcname = qualify(optarg)) == 0)
errs |= ERR_MISSING;
break;
case 'd':
if ((dstname = qualify(optarg)) == 0)
errs |= ERR_MISSING;
break;
default:
case '?':
errs |= ERR_INVAL;
break;
}
if (opt_debug & DBG_MISC)
fprintf(stderr, "MISC: DBG=%s\n", showflags(dbgmap, opt_debug));
/* if we have file names, we need a source and destination */
if (optind < argc) {
if (srcname == 0) {
fprintf(stderr, gettext(ERR_nosrc));
errs |= ERR_INVAL;
}
if (dstname == 0) {
fprintf(stderr, gettext(ERR_nodst));
errs |= ERR_INVAL;
}
}
/* check for simple usage errors */
if (errs & ERR_INVAL) {
usage();
exit(errs);
}
/* locate our baseline and rules files */
if (c = findfiles())
exit(c);
/* figure out file creation defaults */
whoami();
/* read in our initial baseline */
if (!new_baseline && (c = read_baseline(file_base)))
errs |= c;
/* read in the rules file if we need or have rules */
if (optind >= argc && new_rules) {
fprintf(stderr, ERR_nonames);
errs |= ERR_INVAL;
} else if (!new_rules)
errs |= read_rules(file_rules);
/* if anything has failed with our setup, go no further */
if (errs) {
cleanup(errs);
exit(errs);
}
/*
* figure out whether or not we are willing to do a one-sided
* analysis (where we don't even look at the other side. This
* is an "I'm just curious what has changed" query, and we are
* only willing to do it if:
* we aren't actually going to do anything
* we have a baseline we can compare against
* otherwise, we are going to insist on being able to access
* both the source and destination.
*/
if (opt_notouch && !new_baseline)
opt_onesided = opt_oneway;
/*
* there are two interested usage scenarios:
* file names specified
* create new rules for the specified files
* evaulate and reconcile only the specified files
* no file names specified
* use already existing rules
* consider restricting them to specified subdirs/files
*/
if (optind < argc) {
/* figure out what base pair we're working on */
bp = add_base(srcname, dstname);
/* perverse default rules to avoid trouble */
if (new_rules) {
errs |= add_ignore(0, SUFX_RULES);
errs |= add_ignore(0, SUFX_BASE);
}
/* create include rules for each file/dir arg */
while (optind < argc)
errs |= add_include(bp, argv[ optind++ ]);
/*
* evaluate the specified base on each side,
* being careful to limit evaulation to new rules
*/
errs |= evaluate(bp, OPT_SRC, TRUE);
errs |= evaluate(bp, OPT_DST, TRUE);
} else {
/* note any possible evaluation restrictions */
for (i = 0; i < num_restrs; i++)
errs |= add_restr(rlist[i]);
/*
* we can only prune the baseline file if we have done
* a complete (unrestricted) analysis.
*/
if (i == 0)
do_prune = 1;
/* evaulate each base on each side */
for (bp = bases; bp; bp = bp->b_next) {
errs |= evaluate(bp, OPT_SRC, FALSE);
errs |= evaluate(bp, OPT_DST, FALSE);
}
}
/* if anything serious happened, skip reconciliation */
if (errs & ERR_FATAL) {
cleanup(errs);
exit(errs);
}
/* analyze and deal with the differenecs */
errs |= analyze();
/* see if there is any dead-wood in the baseline */
if (do_prune) {
c = prune();
if (c > 0 && opt_verbose)
fprintf(stdout, V_prunes, c);
}
/* print out a final summary */
summary();
/* update the rules and baseline files (if needed) */
(void) umask(my_umask);
errs |= write_baseline(file_base);
errs |= write_rules(file_rules);
if (opt_debug & DBG_MISC)
fprintf(stderr, "MISC: EXIT=%s\n", showflags(errmap, errs));
/* just returning ERR_RESOLVABLE upsets some people */
if (errs == ERR_RESOLVABLE && !opt_notouch)
errs = 0;
/* all done */
cleanup(0);
return (errs);
}
void SimpleSpeechRec::frameSegmentation() {
time++;
if (time == 0) {
timeZeroInit();
return;
}
SRecToken** newTokenBuffer = new SRecToken*[cbNum];
for (int i = 0; i < cbNum; i++) {
newTokenBuffer[i] = NULL;
}
int* cbTypeLookup = new int[cbNum];
for (int i = 0; i < cbNum; i++) {
cbTypeLookup[i] = dict->getCbType(i);
}
omp_set_dynamic(true);
#pragma omp parallel for
for (int i = 0; i < cbNum; i++) {
STokenBin* bin = binSet[i];
SRecToken* candToken = bin->getPreviousBest();
if (!candToken)
continue;
int cbType = (i == cbNum-1) ? DI_TAIL_NOISE: cbTypeLookup[i];
bool isCrossWord = isCrossWordCb(cbType);
SRecToken* candWord = NULL;
SRecToken* newToken = factory.getInstance();
//newToken->copyFrom(candToken);
if (isCrossWord) {
candWord = factory.getInstance();
candWord->copyFrom(candToken);
if (candToken->prev)
InterlockedIncrement(&candToken->prev->refcnt);
candWord->endTime = time;
} else {
candWord = candToken->prev;
newToken->CId = candToken->CId;
newToken->VId = candToken->VId;
newToken->wordId = candToken->wordId;
if (dict->triPhone) {
if (cbType == INITIAL1) {
newToken->CId = dict->getCVIdFromCbId(i);
} else if (cbType == FINAL0) {
newToken->VId = dict->getCVIdFromCbId(i);
newToken->wordId = dict->getWordIdFromCVLink(candToken->currentCbId, i);
}
}
else{
if (cbType == DI_INITIAL1) {
newToken->CId = dict->getCVIdFromCbId(i);
} else if (cbType == DI_FINAL0) {
newToken->VId = dict->getCVIdFromCbId(i);
newToken->wordId = dict->getWordIdFromCVLink(candToken->currentCbId, i);
}
}
}
//
newToken->currentCbId = i;
newToken->dur = 1;
double durLh = useSegmentModel ? bc->getDurLh(i, 1) : 0;
double stateLh = bc->getStateLh(i, time);
newToken->lh = candToken->lh + durLh + stateLh;
newToken->prev = candWord;
InterlockedIncrement(&candWord->refcnt);
newTokenBuffer[i] = newToken;
}
//状态驻留
for (int i = 0; i < cbNum; i++) {
STokenBin* bin = binSet.at(i);
int k =i;
if(m_bHeadNOise&&i == cbNum-1)
k= dict->noiseId;
double stateLh = bc->getStateLh(k, time);
for (auto j = bin->content.begin(); j != bin->content.end(); j++) {
SRecToken* t = *j;
t->dur += 1;
int dur = t->dur;
double deltaDurLh = useSegmentModel ? bc->getDurLhDelta(k, dur) : 0;
t->lh += deltaDurLh + stateLh;
}
}
//完成状态跳转
for (int i = 0; i < cbNum; i++) {
STokenBin* bin = binSet.at(i);
if (newTokenBuffer[i] != NULL)
bin->addToken(newTokenBuffer[i]);
prune(bin);
}
delete [] cbTypeLookup;
delete [] newTokenBuffer;
}