void CS(int lb[], int ub[], int maxI, int nnest, int dim, Nest *Nests, double (*fobj)(int, double x[], int)){
srand(time(0));
unsigned long germe[6] = { rand(), rand(), rand(), rand(), rand(), rand() };
RngStream_SetPackageSeed (germe);
RngStream g1 = RngStream_CreateStream ("Laplace");
double pa = 0.25;
Nest new_Nest[nnest], best;
init(nnest,dim,lb,ub,Nests,g1);
memcpy(new_Nest, Nests, sizeof(new_Nest));
get_best_nest(nnest,dim, &best, new_Nest, Nests,fobj);
double fxmin = best.fx;
int t;
for (t = 0; t < 1; t++){
get_cuckoos(nnest,lb, ub, dim, &best, new_Nest, Nests,g1);
get_best_nest(nnest,dim, &best, new_Nest, Nests, fobj);
empty_nests(nnest,dim, lb, ub, new_Nest, Nests,pa,g1);
get_best_nest(nnest,dim, &best, new_Nest, Nests, fobj);
if(best.fx < fxmin){
fxmin = best.fx;
}
stRank(Nests, nnest, dim, g1);
}
show_nest(nnest,dim, Nests, new_Nest, &best, fxmin);
}
/**
* Bittorrent example launcher
*/
int main(int argc, char *argv[])
{
xbt_dynar_t host_list;
msg_host_t host;
unsigned i;
MSG_init(&argc, argv);
/* Check the arguments */
if (argc < 3) {
printf("Usage: %s platform_file deployment_file \n", argv[0]);
return -1;
}
const char *platform_file = argv[1];
const char *deployment_file = argv[2];
MSG_create_environment(platform_file);
host_list = MSG_hosts_as_dynar();
xbt_dynar_foreach(host_list, i, host) {
char descr[512];
RngStream stream;
snprintf(descr, sizeof descr, "RngSream<%s>", MSG_host_get_name(host));
stream = RngStream_CreateStream(descr);
MSG_host_set_data(host, stream);
}
int main(int argc, char const *argv[]){
srand(time(0));
unsigned long germe[6] = { rand(), rand(), rand(), rand(), rand(), rand() };
RngStream_SetPackageSeed (germe);
RngStream g1 = RngStream_CreateStream ("Laplace");
double (*fObj)(int, int, double[]);
printf("Funcion 1\n");
fObj=function;
GWO(lb, ub, fObj, g1);
showPack();
printf("Funcion 6\n");
fObj=function6;
GWO(lb, ub, fObj, g1);
showPack();
printf("Funcion 7\n");
fObj=function7;
GWO(-1.28, 1.28, fObj, g1);
showPack();
printf("Funcion 8\n");
fObj = function8;
GWO(-500, 500, fObj, g1);
showPack();
RngStream_DeleteStream (&g1);
return 0;
}
JNIEXPORT void JNICALL Java_org_simgrid_msg_RngStream_create(JNIEnv *env, jobject jrngstream, jstring jname) {
const char *name = env->GetStringUTFChars(jname, 0);
RngStream rngstream = RngStream_CreateStream(name);
//Bind the RngStream object
env->SetLongField(jrngstream, jrngstream_bind, (intptr_t)rngstream);
env->ReleaseStringUTFChars(jname, name);
}
TEST_F(ArsGammaTest, GenerateSample) {
double gamma_args[] = {2.0, 2.0};
RngStream rng = RngStream_CreateStream("");
double samp;
samp = gamma_sampler.sample(rng, gamma_args);
EXPECT_GT(samp, 0.0);
EXPECT_GT(gamma_sampler.x0, 0.0);
EXPECT_GT(gamma_sampler.x1, gamma_sampler.x0);
EXPECT_EQ(gamma_sampler.hull.num_hull_segments, 2);
EXPECT_EQ(gamma_sampler.hull.upper_hull_max, -INFINITY);
}
int main (int argc, char const *argv[])
{
srand(time(0));
for (int i = 0; i < 30; ++i){
unsigned long germe[6] = { rand(), rand(), rand(), rand(), rand(), rand() };
RngStream_SetPackageSeed (germe);
g1 = RngStream_CreateStream ("Laplace");
GWO();
showPack();
RngStream_DeleteStream (&g1);
}
return 0;
}
TEST_F(ArsGammaTest, GammaMomentTest) {
double gamma_args[] = {2.0, 2.0};
RngStream rng = RngStream_CreateStream("");
double samp, mean = 0.0;
int n = 1, nsamp = 100000;
while(n <= nsamp) {
samp = gamma_sampler.sample(rng, gamma_args);
mean = mean * (n - 1.0) / n + samp / n;
n++;
}
double true_mean = gamma_args[0] / gamma_args[1];
double true_se = sqrt(true_mean / gamma_args[1] / nsamp);
EXPECT_GT(mean, true_mean - 2.6 * true_se);
EXPECT_LT(mean, true_mean + 2.6 * true_se);
}
TEST_F(ArsWeibullTest, WeibullMomentTest) {
double weibull_args[] = {2.0, 2.0};
double k = 2.0;
double ell = 2.0;
RngStream rng = RngStream_CreateStream("");
double samp, mean = 0.0;
int n = 1, nsamp = 100000;
while(n <= nsamp) {
samp = weibull_sampler.sample(rng, weibull_args);
ASSERT_GT(samp, 0.0);
mean = mean * (n - 1.0) / n + samp / n;
n++;
}
double true_mean = ell * exp(lgamma(1.0 + 1.0 / k));
double true_se = sqrt((ell * ell * exp(lgamma(1.0 + 2.0 / k)) - true_mean * true_mean) / nsamp);
EXPECT_GT(mean, true_mean - 2.6 * true_se);
EXPECT_LT(mean, true_mean + 2.6 * true_se);
}
/** Bittorrent example launcher */
int main(int argc, char* argv[])
{
msg_host_t host;
unsigned i;
MSG_init(&argc, argv);
/* Check the arguments */
xbt_assert(argc > 2, "Usage: %s platform_file deployment_file", argv[0]);
MSG_create_environment(argv[1]);
xbt_dynar_t host_list = MSG_hosts_as_dynar();
xbt_dynar_foreach (host_list, i, host) {
char descr[512];
snprintf(descr, sizeof descr, "RngSream<%s>", MSG_host_get_name(host));
RngStream stream = RngStream_CreateStream(descr);
MSG_host_set_data(host, stream);
}
SEXP R_RngStreams_Init (SEXP R_obj, SEXP R_name)
/*----------------------------------------------------------------------*/
/* Create and initialize Stream generator object. */
/* */
/* parameters: */
/* obj ... (S4 class) ... rstream object */
/* R_name ... (string) ... name of the Stream */
/* */
/* return: */
/* pointer to Stream object */
/*----------------------------------------------------------------------*/
{
SEXP R_newstream;
RngStream newstream; /* Notice: RngStream is a pointer to a structure */
const char *name;
/* check argument */
if (!R_name || TYPEOF(R_name) != STRSXP)
error("bad string\n");
/* get pointer to argument string */
name = CHAR(STRING_ELT(R_name,0));
/* create Stream generator object */
newstream = RngStream_CreateStream(name);
/* this must not be a NULL pointer */
if (newstream == NULL)
error("cannot create Stream object\n");
/* make R external pointer and store pointer to Stream generator */
PROTECT(R_newstream = R_MakeExternalPtr(newstream, RngStreams_tag(), R_obj));
UNPROTECT(1);
/* register destructor as C finalizer */
R_RegisterCFinalizer(R_newstream, R_RngStreams_free);
/* return pointer to R */
return R_newstream;
} /* end of R_RngStreams_init() */
primal_t *primal_create (instance_t *inst)
{
primal_t *primal = (primal_t*) malloc(sizeof(primal_t));
primal->inst = instance_copy(inst);
primal->state = primal_state_undef;
primal->guiding_x = (int*) calloc(inst->n, sizeof(int));
primal->improving_partial_x = (int*) calloc(inst->n, sizeof(int));
primal->best_x = (int*) calloc(inst->n, sizeof(int));
primal->best_z = INFINITY;
primal->sol = solution_alloc(inst);
primal->tabu = (double*) calloc(inst->n, sizeof(double));
primal->n_moves = 0;
primal->n_moves_at_last_improvement = 0;
primal->rng = RngStream_CreateStream("");
return primal;
}
SEXP r_create_stream (SEXP sexp_name)
{
RngStream newstream;
SEXP sexp_newstream;
int i;
const char *name = CHAR(STRING_ELT(sexp_name,0));
newstream = RngStream_CreateStream(name);
PROTECT(sexp_newstream = allocVector(REALSXP, 20));
for (i = 0; i < 6; ++i) {
REAL(sexp_newstream)[i] = (double) newstream->Cg[i];
REAL(sexp_newstream)[i+6] = (double) newstream->Bg[i];
REAL(sexp_newstream)[i+12] = (double) newstream->Ig[i];
}
REAL(sexp_newstream)[18] = (int) newstream->Anti;
REAL(sexp_newstream)[19] = (int) newstream->IncPrec;
UNPROTECT(1);
RngStream_DeleteStream(&newstream);
return(sexp_newstream);
}
void pepbayes_v3(double *Y, double *hyper_param, int *pstart,
int *pnum, int *n_position, int *n_peptide, int *n_indiv, int *nP,
int *cen_ind, int *cen_pep, int *cen_num, int *cen_pos,
int *n_iter, int *n_sweep, int *n_burn,
double *OutProbs, int *write)
{
R_CStackLimit = (uintptr_t)-1;
// miscellaneous useful quantities
int p, i, j, k = 0, c, d;
int pep, pos, th_id;
int *pos_ind_by_pep;
double *ProbSum;
int total_iterations = *n_burn+(*n_sweep)*(*n_iter);
int percent_complete = 10;
adpt zeta_adpt;
adpt m_adpt;
zeta_adpt.total_count = 0;
zeta_adpt.count = 0;
zeta_adpt.tune = 2.5;
m_adpt.total_count = 0;
m_adpt.count = 0;
m_adpt.tune = 5.0;
RngStream rng[*nP];
//statically allocated struct for Adaptive Rejection Sampling
ARS_workspace workspace;
// missing data variables
double *Exprs; // censor-completed expressions
int *Gamma; // cluster membership indicator
double *W; // t-distribution weights
double dof = 4.0; // t-distribution degrees of freedom
double *D; // imputed censored tails
// component membership probability parameters
double *Omega_logit; // membership probabilities, on logit scale
int *Omega_ind; // indicator for whether omega_{cp} > 0
double *A, *B, *U; // prior parameters for omega probabilities
double lambda_a, lambda_b; //hyperparameters for A, B
double a_0, b_0; // hyperparameters for U
double **xA, **xB; // vectors required for ARS
// location-related parameters
double *Mu; // peptide specific means
double kappa = 10.0; // prior mean precision
double *Alpha_pep; // peptide effects
double m = 2.0, zeta = 1.0; // prior mean and variance of peptide effects
double m_0, v_0; // hyperparameters for m
// variance parameters
double *Sig2; // peptide response variance
double alpha = 10.0; // prior parameter
double beta = 10.0; // prior parameter
double alpha_0, beta_0; // rates on alpha, beta (hyperparameters)
double *xAlpha; // vector needed for ARS
// file pointers
FILE *AFILE, *BFILE, *PFILE, *VARFILE, *Sig2FILE, *MUFILE, *DFILE, *OFILE;
FILE *ALPHAFILE;
// retreive and initialize hyperparameter values
a_0 = hyper_param[0];
b_0 = hyper_param[1];
lambda_a = hyper_param[2];
lambda_b = hyper_param[3];
alpha_0 = hyper_param[4];
beta_0 = hyper_param[5];
m_0 = hyper_param[6];
v_0 = hyper_param[7];
// begin memory allocation
Gamma = (int*) R_alloc(*n_peptide*(*n_indiv), sizeof(int));
Exprs = (double*) R_alloc(*n_peptide*(*n_indiv), sizeof(double));
W = (double *) R_alloc(*n_peptide*(*n_indiv), sizeof(double));
double *RB = (double *) R_alloc(*n_peptide*(*n_indiv), sizeof(double));
// xA and xB hold starting values for ARS of a_p, b_p, and alpha.
xA = (double**) R_alloc(*n_position, sizeof(double*));
xB = (double**) R_alloc(*n_position, sizeof(double*));
xAlpha = (double*) R_alloc(NMAX, sizeof(double));
// initial values for hull quantiles.
xAlpha[0] = 1.0;
xAlpha[1] = 2.0;
Omega_ind = (int*) R_alloc(*n_peptide, sizeof(int));
Omega_logit = (double*) R_alloc(*n_peptide, sizeof(double));
pos_ind_by_pep = (int*) R_alloc(*n_peptide, sizeof(int));
ProbSum = (double*) R_alloc(*n_peptide*(*n_indiv), sizeof(double));
for(p = 0; p < *n_position; p++)
{
xA[p] = (double*) R_alloc(NMAX, sizeof(double));
xB[p] = (double*) R_alloc(NMAX, sizeof(double));
for(c = 0; c < pnum[p]; c++)
{
pos_ind_by_pep[pstart[p] + c] = k;
}
k++;
}
Alpha_pep = (double*) R_alloc(*n_peptide, sizeof(double));
Sig2 = (double*) R_alloc(*n_peptide, sizeof(double));
A = (double*) R_alloc(*n_position, sizeof(double));
B = (double*) R_alloc(*n_position, sizeof(double));
U = (double*) R_alloc(*n_position, sizeof(double));
Mu = (double*) R_alloc(*n_peptide, sizeof(double));
double* likworkspace = (double *) R_alloc((*n_peptide)*(*n_indiv), sizeof(double));
// check whether our data is censored at all,
// if so prepare for augmentation.
if(*cen_num > 0)
{
D = (double*) R_alloc(*cen_num, sizeof(double));
for(i = 0; i < *cen_num; i++)
{
D[i] = 0.0;
}
}
if(*write == 1)
{
AFILE = fopen("afile.txt", "w");
BFILE = fopen("bfile.txt", "w");
PFILE = fopen("pfile.txt", "w");
OFILE = fopen("ofile.txt", "w");
ALPHAFILE = fopen("alphafile.txt", "w");
VARFILE = fopen("varfile.txt", "w");
Sig2FILE = fopen("sig2file.txt", "w");
MUFILE = fopen("mufile.txt", "w");
if(*cen_num > 0)
{
DFILE = fopen("dfile.txt", "w");
}
}
for(i = 0; i < *nP; i++)
{
rng[i] = RngStream_CreateStream("");
}
GetRNGstate();
initialize_chain(ProbSum, Exprs, Y, W, Omega_ind, Omega_logit, Alpha_pep,
Gamma, Sig2, Mu, A, B, U,
n_position, pstart, pnum, n_peptide, n_indiv,
xA, xB, RB);
PutRNGstate();
Rprintf("parameters initialized \n");
for(i = 1; i <= total_iterations; i++)
{
R_CheckUserInterrupt();
update_dof_integrated(&dof, Exprs, W, Alpha_pep, Gamma,
Sig2, Mu, likworkspace, *n_indiv, *n_peptide, rng[0]);
#pragma omp parallel private(th_id, workspace, pos) num_threads(*nP)
{
th_id = omp_get_thread_num();
#pragma omp for
for(pep = 0; pep < *n_peptide; pep++)
{
pos = pos_ind_by_pep[pep];
update_peptide(Exprs, Mu + pep, Alpha_pep + pep,
W, Omega_ind + pep, Omega_logit + pep, Gamma,
Sig2 + pep, alpha, beta,
U[pos], A[pos], B[pos],
m, zeta, dof, kappa, *n_indiv, *n_peptide, pep, rng[th_id], RB);
}
#pragma omp for
for(p = 0; p < *n_position; p++)
{
update_position_p(Omega_ind, Omega_logit,
A + p, B + p, U + p,
a_0, b_0, lambda_a, lambda_b,
p, *n_indiv, pnum, pstart, rng[th_id],
xA[p], xB[p], &workspace);
}
// update gammas, alphas, omegas
if((i > *n_burn) && ((i - *n_burn) % (*n_sweep) == 0 ))
{
#pragma omp for
for(d = 0; d < (*n_indiv)*(*n_peptide); d++)
{
ProbSum[d] += RB[d];
}
}
}
update_global_params(&m, &zeta, &alpha, &beta, &kappa,
Mu, Sig2, Alpha_pep, Omega_ind,
m_0, v_0, alpha_0, beta_0,
*n_indiv, *n_peptide, rng[0], &m_adpt, &zeta_adpt,
&workspace, xAlpha, *nP);
if(i % TEST_INT_LENGTH == 0)
{
update_tuning(&m_adpt, i, *n_burn);
update_tuning(&zeta_adpt, i, *n_burn);
}
// check whether we need to update complete data
if((*cen_num > 0) & (i > *n_burn/2))
{
update_censoring(W, D, *cen_num, cen_ind, cen_pep, Y, Exprs,
Gamma, Alpha_pep, Mu, *n_indiv, Sig2, rng[0]);
}
if((i > *n_burn) && ((i - *n_burn) % (*n_sweep) == 0 ) && *write == 1)
{
store_mcmc_output(Alpha_pep, Mu, A, B, U, Sig2, D, Omega_logit,
Omega_ind, kappa, alpha, beta, m, zeta,
dof, *n_peptide, *n_indiv, *n_position, cen_num,
AFILE, BFILE, PFILE, VARFILE, Sig2FILE, MUFILE, DFILE,
OFILE, ALPHAFILE);
}
if( 100*((double) i)/total_iterations >= percent_complete)
{
Rprintf("MCMC %d percent complete\n", percent_complete);
percent_complete += 10;
}
}
// finalize marginal PPA
for(d = 0; d < (*n_indiv)*(*n_peptide); d++)
{
OutProbs[d] = ProbSum[d]/(*n_iter);
}
Rprintf("M acceptance rate: %.3lf, Zeta acceptance rate: %.3lf\n", (double)(m_adpt.total_count)/(*n_iter*(*n_sweep)),
(double)(zeta_adpt.total_count)/(*n_iter*(*n_sweep)));
Rprintf("closing files\n");
if(*write == 1)
{
fclose(AFILE);
fclose(BFILE);
fclose(PFILE);
fclose(OFILE);
fclose(VARFILE);
fclose(ALPHAFILE);
fclose(Sig2FILE);
fclose(MUFILE);
if(*cen_num > 0)
{
fclose(DFILE);
}
}
return;
}
VALUE rng_initialize(VALUE self) {
RngStream stream = RngStream_CreateStream(NULL);
VALUE stream_ptr = Data_Wrap_Struct(rb_cObject, 0, rng_free, (void*) stream);
rb_iv_set(self, "@stream_prt", stream_ptr);
return self;
}
RNG_lecuyer(int seed1, int seed2) {
_stream = RngStream_CreateStream("RNG_lecuyer");
set_seed(seed1, seed2);
}
