pcluster
build_simsub_cluster(pclustergeometry cf, uint size, uint * idx, uint clf)
{
pcluster t;
uint leaves;
pcluster s;
assert(size > 0);
leaves = 0;
if (size > clf) {
s = build_help_cluster(cf, idx, size, clf, 0, &leaves);
t = new_cluster(size, idx, leaves, cf->dim);
leaves = 0;
leaves_into_sons(cf, clf, s, t, &leaves);
update_bbox_cluster(t);
}
else {
t = new_cluster(size, idx, 0, cf->dim);
update_support_bbox_cluster(cf, t);
}
update_cluster(t);
return t;
}
void
coarsen_cluster(pcluster t, uint minsize)
{
bool a = false;
uint i;
for (i = 0; i < t->sons; i++) {
if (t->son[i]->size < minsize) {
a = true;
break;
}
}
if (a) {
for (i = 0; i < t->sons; i++)
del_cluster(t->son[i]);
t->sons = 0;
freemem(t->son);
t->son = NULL;
}
else
for (i = 0; i < t->sons; i++)
coarsen_cluster(t->son[i], minsize);
update_cluster(t);
}
void
balance_cluster(pcluster t, uint depth)
{
uint i;
if ((t->son) && (depth > 0))
for (i = 0; i < t->sons; i++)
balance_cluster(t->son[i], depth - 1);
else if ((t->son) && (depth == 0))
cut_cluster(t, depth);
else if ((!t->son) && (depth > 0))
extend_cluster(t, depth);
update_cluster(t);
}
void
cut_cluster(pcluster t, uint depth)
{
uint i;
if ((t->son) && (depth > 0))
for (i = 0; i < t->sons; i++)
cut_cluster(t->son[i], depth - 1);
else if ((t->son) && (depth == 0)) {
for (i = 0; i < t->sons; i++)
del_cluster(t->son[i]);
t->sons = 0;
freemem(t->son);
t->son = NULL;
}
update_cluster(t);
}
void
extend_cluster(pcluster t, uint depth)
{
uint i;
if ((t->son) && (depth > 0))
for (i = 0; i < t->sons; i++)
extend_cluster(t->son[i], depth - 1);
else if ((!t->son) && (depth > 0)) {
t->sons = 1;
t->son = (pcluster *) allocmem(sizeof(pcluster));
t->son[0] = new_cluster(t->size, t->idx, 0, t->dim);
for (i = 0; i < t->dim; i++) {
t->son[0]->bmin[i] = t->bmin[i];
t->son[0]->bmax[i] = t->bmax[i];
}
extend_cluster(t->son[0], depth - 1);
}
update_cluster(t);
}
int setup_configfs(void)
{
int rv;
clear_configfs();
rv = add_configfs_base();
if (rv < 0)
return rv;
/* add configfs entries for existing nodes */
update_cluster();
/* the kernel has its own defaults for these values which we
don't want to change unless these have been set; -1 means
they have not been set on command line or config file */
if (cfgk_debug != -1)
set_configfs_debug(cfgk_debug);
if (cfgk_timewarn != -1)
set_configfs_timewarn(cfgk_timewarn);
if (cfgk_protocol == PROTO_DETECT) {
rv = detect_protocol();
if (rv == PROTO_TCP || rv == PROTO_SCTP)
cfgk_protocol = rv;
}
if (cfgk_protocol == PROTO_TCP || cfgk_protocol == PROTO_SCTP)
set_configfs_protocol(cfgk_protocol);
if (cfgk_protocol == PROTO_SCTP)
set_proc_rmem();
return 0;
}
int set_configfs_members(char *name, int new_count, int *new_members,
int renew_count, int *renew_members)
{
char path[PATH_MAX];
char buf[32];
int i, w, fd, rv, id, old_count, *old_members;
int do_renew;
/*
* create lockspace dir if it doesn't exist yet
*/
memset(path, 0, PATH_MAX);
snprintf(path, PATH_MAX, "%s/%s", SPACES_DIR, name);
if (!path_exists(path)) {
if (create_path(path))
return -1;
}
/*
* remove/add lockspace members
*/
rv = update_dir_members(name);
if (rv)
return rv;
old_members = dir_members;
old_count = dir_members_count;
for (i = 0; i < old_count; i++) {
id = old_members[i];
if (id_exists(id, new_count, new_members))
continue;
memset(path, 0, PATH_MAX);
snprintf(path, PATH_MAX, "%s/%s/nodes/%d",
SPACES_DIR, name, id);
log_debug("set_members rmdir \"%s\"", path);
rv = rmdir(path);
if (rv) {
log_error("%s: rmdir failed: %d", path, errno);
goto out;
}
}
/*
* remove lockspace dir after we've removed all the nodes
* (when we're shutting down and adding no new nodes)
*/
if (!new_count) {
memset(path, 0, PATH_MAX);
snprintf(path, PATH_MAX, "%s/%s", SPACES_DIR, name);
log_debug("set_members lockspace rmdir \"%s\"", path);
rv = rmdir(path);
if (rv)
log_error("%s: rmdir failed: %d", path, errno);
}
for (i = 0; i < new_count; i++) {
id = new_members[i];
do_renew = 0;
if (id_exists(id, renew_count, renew_members))
do_renew = 1;
else if (id_exists(id, old_count, old_members))
continue;
if (!is_cluster_member(id))
update_cluster();
/*
* create node's dir
*/
memset(path, 0, PATH_MAX);
snprintf(path, PATH_MAX, "%s/%s/nodes/%d",
SPACES_DIR, name, id);
if (do_renew) {
log_debug("set_members renew rmdir \"%s\"", path);
rv = rmdir(path);
if (rv) {
log_error("%s: renew rmdir failed: %d",
path, errno);
/* don't quit here, there's a case where
* this can happen, where a node identified
* for renewal was not really added
* previously */
}
}
log_debug("set_members mkdir \"%s\"", path);
rv = create_path(path);
if (rv)
goto out;
/*
* set node's nodeid
*/
memset(path, 0, PATH_MAX);
snprintf(path, PATH_MAX, "%s/%s/nodes/%d/nodeid",
SPACES_DIR, name, id);
rv = fd = open(path, O_WRONLY);
if (rv < 0) {
log_error("%s: open failed: %d", path, errno);
goto out;
}
memset(buf, 0, 32);
snprintf(buf, 32, "%d", id);
rv = do_write(fd, buf, strlen(buf));
if (rv < 0) {
log_error("%s: write failed: %d, %s", path, errno, buf);
close(fd);
goto out;
}
close(fd);
/*
* set node's weight
*/
w = get_weight(id, name);
memset(path, 0, PATH_MAX);
snprintf(path, PATH_MAX, "%s/%s/nodes/%d/weight",
SPACES_DIR, name, id);
rv = fd = open(path, O_WRONLY);
if (rv < 0) {
log_error("%s: open failed: %d", path, errno);
goto out;
}
memset(buf, 0, 32);
snprintf(buf, 32, "%d", w);
rv = do_write(fd, buf, strlen(buf));
if (rv < 0) {
log_error("%s: write failed: %d, %s", path, errno, buf);
close(fd);
goto out;
}
close(fd);
}
rv = 0;
out:
return rv;
}
pcluster
build_adaptive_cluster(pclustergeometry cf, uint size, uint * idx, uint clf)
{
pcluster t;
uint direction;
uint size0, size1;
uint i, j;
real a, m;
assert(size > 0);
if (size > clf) {
update_point_bbox_clustergeometry(cf, size, idx);
/* compute the direction of partition */
direction = 0;
a = cf->hmax[0] - cf->hmin[0];
for (j = 1; j < cf->dim; j++) {
m = cf->hmax[j] - cf->hmin[j];
if (a < m) {
a = m;
direction = j;
}
}
/* build sons */
if (a > 0.0) {
m = (cf->hmax[direction] + cf->hmin[direction]) / 2.0;
size0 = 0;
size1 = 0;
for (i = 0; i < size; i++) {
if (cf->x[idx[i]][direction] < m) {
j = idx[i];
idx[i] = idx[size0];
idx[size0] = j;
size0++;
}
else {
size1++;
}
}
/* build sons */
if (size0 > 0) {
if (size1 > 0) {
/* both sons are not empty */
t = new_cluster(size, idx, 2, cf->dim);
t->son[0] = build_adaptive_cluster(cf, size0, idx, clf);
t->son[1] = build_adaptive_cluster(cf, size1, idx + size0, clf);
update_bbox_cluster(t);
}
else {
/* only the first son is not empty */
assert(size0 == size);
t = new_cluster(size, idx, 0, cf->dim);
update_bbox_cluster(t);
}
}
else {
/* only the second son is not empty */
assert(size1 > 0);
assert(size1 == size);
t = new_cluster(size, idx, 0, cf->dim);
update_bbox_cluster(t);
}
}
else {
assert(a == 0.0);
t = new_cluster(size, idx, 0, cf->dim);
update_support_bbox_cluster(cf, t);
}
}
else {
t = new_cluster(size, idx, 0, cf->dim);
update_support_bbox_cluster(cf, t);
}
update_cluster(t);
return t;
}
pcluster
build_pca_cluster(pclustergeometry cf, uint size, uint * idx, uint clf)
{
const uint dim = cf->dim;
pamatrix C, Q;
pavector v;
prealavector lambda;
real *x, *y;
real w;
uint i, j, k, size0, size1;
pcluster t;
assert(size > 0);
size0 = 0;
size1 = 0;
if (size > clf) {
x = allocreal(dim);
y = allocreal(dim);
/* determine weight of current cluster */
w = 0.0;
for (i = 0; i < size; ++i) {
w += cf->w[idx[i]];
}
w = 1.0 / w;
for (j = 0; j < dim; ++j) {
x[j] = 0.0;
}
/* determine center of mass */
for (i = 0; i < size; ++i) {
for (j = 0; j < dim; ++j) {
x[j] += cf->w[idx[i]] * cf->x[idx[i]][j];
}
}
for (j = 0; j < dim; ++j) {
x[j] *= w;
}
C = new_zero_amatrix(dim, dim);
Q = new_zero_amatrix(dim, dim);
lambda = new_realavector(dim);
/* setup covariance matrix */
for (i = 0; i < size; ++i) {
for (j = 0; j < dim; ++j) {
y[j] = cf->x[idx[i]][j] - x[j];
}
for (j = 0; j < dim; ++j) {
for (k = 0; k < dim; ++k) {
C->a[j + k * C->ld] += cf->w[idx[i]] * y[j] * y[k];
}
}
}
/* get eigenvalues and eigenvectors of covariance matrix */
eig_amatrix(C, lambda, Q);
/* get eigenvector from largest eigenvalue */
v = new_avector(0);
init_column_avector(v, Q, dim - 1);
/* separate cluster with v as separation-plane */
for (i = 0; i < size; ++i) {
/* x_i - X */
for (j = 0; j < dim; ++j) {
y[j] = cf->x[idx[i]][j] - x[j];
}
/* <y,v> */
w = 0.0;
for (j = 0; j < dim; ++j) {
w += y[j] * v->v[j];
}
if (w >= 0.0) {
j = idx[i];
idx[i] = idx[size0];
idx[size0] = j;
size0++;
}
else {
size1++;
}
}
assert(size0 + size1 == size);
del_amatrix(Q);
del_amatrix(C);
del_realavector(lambda);
del_avector(v);
freemem(x);
freemem(y);
/* recursion */
if (size0 > 0) {
if (size1 > 0) {
t = new_cluster(size, idx, 2, cf->dim);
t->son[0] = build_pca_cluster(cf, size0, idx, clf);
t->son[1] = build_pca_cluster(cf, size1, idx + size0, clf);
update_bbox_cluster(t);
}
else {
t = new_cluster(size, idx, 1, cf->dim);
t->son[0] = build_pca_cluster(cf, size0, idx, clf);
update_bbox_cluster(t);
}
}
else {
assert(size1 > 0);
t = new_cluster(size, idx, 1, cf->dim);
t->son[0] = build_pca_cluster(cf, size1, idx, clf);
update_bbox_cluster(t);
}
}
else {
t = new_cluster(size, idx, 0, cf->dim);
update_support_bbox_cluster(cf, t);
}
update_cluster(t);
return t;
}
pcluster
build_regular_cluster(pclustergeometry cf, uint size, uint * idx,
uint clf, uint direction)
{
pcluster t;
uint newd;
uint size0, size1;
uint i, j;
real a, b, m;
assert(size > 0);
if (size > clf) {
size0 = 0;
size1 = 0;
update_point_bbox_clustergeometry(cf, size, idx);
if (direction < cf->dim - 1) {
newd = direction + 1;
}
else {
newd = 0;
}
m = cf->hmax[direction] - cf->hmin[direction];
if (m > 0.0) {
m = (cf->hmax[direction] + cf->hmin[direction]) / 2.0;
for (i = 0; i < size; i++) {
if (cf->x[idx[i]][direction] < m) {
j = idx[i];
idx[i] = idx[size0];
idx[size0] = j;
size0++;
}
else {
size1++;
}
}
/* build sons */
if (size0 > 0) {
if (size1 > 0) {
/* both sons are not empty */
t = new_cluster(size, idx, 2, cf->dim);
a = cf->hmin[direction];
b = cf->hmax[direction];
cf->hmax[direction] = m;
t->son[0] = build_regular_cluster(cf, size0, idx, clf, newd);
cf->hmax[direction] = b;
cf->hmin[direction] = m;
t->son[1] =
build_regular_cluster(cf, size1, idx + size0, clf, newd);
cf->hmin[direction] = a;
update_bbox_cluster(t);
}
else {
/* only the first son is not empty */
t = new_cluster(size, idx, 1, cf->dim);
b = cf->hmax[direction];
cf->hmax[direction] = m;
t->son[0] = build_regular_cluster(cf, size, idx, clf, newd);
cf->hmax[direction] = b;
update_bbox_cluster(t);
}
}
else {
/* only the second son is not empty */
assert(size1 > 0);
t = new_cluster(size, idx, 1, cf->dim);
a = cf->hmin[direction];
cf->hmin[direction] = m;
t->son[0] = build_regular_cluster(cf, size, idx, clf, newd);
cf->hmin[direction] = a;
update_bbox_cluster(t);
}
}
else {
assert(m == 0.0);
t = new_cluster(size, idx, 1, cf->dim);
t->son[0] = build_regular_cluster(cf, size, idx, clf, newd);
update_bbox_cluster(t);
}
}
else {
t = new_cluster(size, idx, 0, cf->dim);
update_support_bbox_cluster(cf, t);
}
update_cluster(t);
return t;
}
static pcluster
read_cdf_part(int nc_file, size_t clusters, size_t coeffs,
int nc_sons, int nc_size, int nc_coeff,
uint * idx, int dim, size_t * clusteridx, size_t * coeffidx)
{
pcluster t, t1;
uint *idx1;
uint size;
uint sons;
uint i;
size_t start, count;
ptrdiff_t stride;
int val, result;
/* Get number of sons */
start = *clusteridx;
count = 1;
stride = 1;
result = nc_get_vars(nc_file, nc_sons, &start, &count, &stride, &val);
assert(result == NC_NOERR);
sons = val;
/* Get size of cluster */
result = nc_get_vars(nc_file, nc_size, &start, &count, &stride, &val);
assert(result == NC_NOERR);
size = val;
/* Create new cluster */
t = new_cluster(size, idx, sons, dim);
/* Increase cluster index */
(*clusteridx)++;
/* Handle sons */
if (sons > 0) {
idx1 = idx;
for (i = 0; i < sons; i++) {
t1 = read_cdf_part(nc_file, clusters, coeffs,
nc_sons, nc_size, nc_coeff,
idx1, dim, clusteridx, coeffidx);
t->son[i] = t1;
idx1 += t1->size;
}
assert(idx1 == idx + size);
}
/* Get bounding box */
start = (*coeffidx);
count = dim;
result = nc_get_vars(nc_file, nc_coeff, &start, &count, &stride, t->bmin);
start += dim;
result = nc_get_vars(nc_file, nc_coeff, &start, &count, &stride, t->bmax);
start += dim;
(*coeffidx) = start;
/* Finish initialization */
update_cluster(t);
return t;
}
/*--------------- Clustering by K-Mean Method ----------------------*/
bool k_Mean(int cluster_no, Double2D obs, int* obs_c, int dim, int pattern_no)
{
int s,t;
int check;
int flag,no=0,n;
double dist,dmin;
bool success=true;
if(cluster_no > pattern_no){
obs_c[pattern_no] = random_no(cluster_no);
}
else{
Cluster *cl = new Cluster[cluster_no];
for(int i=0;i<cluster_no;i++){
cl[i].vec = AllocDouble_1D(dim);
cl[i].acc = AllocDouble_1D(dim);
}
for(int i=0; i<cluster_no; i++){
cl[i].c = i;
n = random_no(pattern_no);
for(int j=0; j< dim; j++) cl[i].vec[j] = obs[j][n];
}
flag = 0;
check = 0;
while(!flag && check<CHECK){
check++;
for(int i=0; i<cluster_no; i++){
cl[i].patterns = 0;
for(int k=0; k< dim; k++) cl[i].acc[k]= 0.0;
}
for(n=0; n < pattern_no; n++){
dmin=0.0;
for(s=0; s<cluster_no; s++){
for(t=0, dist=0.0; t < dim; t++)
dist +=
(obs[t][n]-cl[s].vec[t])*(obs[t][n]-cl[s].vec[t]);
if(!s || (dist < dmin)){
dmin = dist;
no = s;
}
}
obs_c[n] = cl[no].c;
for(int k=0; k<dim; k++) cl[no].acc[k] += obs[k][n];
cl[no].patterns++;
}
flag = update_cluster(cl,cluster_no,dim);
}
for(int i=0;i<cluster_no;i++){
FreeDouble_1D(cl[i].vec);
FreeDouble_1D(cl[i].acc);
}
for(s=0; s<cluster_no; s++){
//printf("%d %d %f\n",s,cl[s].patterns,cl[s].vec[0]);
if (cl[s].patterns==0)
success=false;
}
delete [] cl;
}
return success;
}
