#include<fstream>
#include<sstream>
#include<vector>
-#include<set>
-#include<pthread.h>
#include "boost/random.hpp"
using namespace std;
-typedef unsigned int seedType;
-typedef boost::mt19937 engine_type;
-typedef boost::gamma_distribution<> distribution_type;
-typedef boost::variate_generator<engine_type&, distribution_type> generator_type;
-typedef boost::uniform_01<engine_type> uniform_generator;
-
-struct Params {
- int no, nsamples;
- FILE *fo;
- boost::mt19937 *rng;
- double *pme_c, *pme_theta;
-};
-
struct Item {
int sid;
double conprb;
}
};
-int nThreads;
-
int model_type;
int m, M, N0, N1, nHits;
double totc;
-int BURNIN, NSAMPLES, GAP;
+int BURNIN, CHAINLEN, GAP;
char imdName[STRLEN], statName[STRLEN];
char thetaF[STRLEN], ofgF[STRLEN], groupF[STRLEN], refF[STRLEN], modelF[STRLEN];
char cvsF[STRLEN];
vector<double> theta, pme_theta, pme_c, eel;
-vector<int> s;
+vector<int> s, z;
vector<Item> hits;
vector<int> counts;
bool quiet;
-engine_type engine(time(NULL));
-Params *params;
-pthread_t *threads;
-pthread_attr_t attr;
-void *status;
-int rc;
+vector<double> arr;
+
+boost::mt19937 rng(time(NULL));
+boost::uniform_01<boost::mt19937> rg(rng);
void load_data(char* reference_name, char* statName, char* imdName) {
ifstream fin;
N1 = s.size() - 1;
nHits = hits.size();
- totc = N0 + N1 + (M + 1);
-
if (verbose) { printf("Loading Data is finished!\n"); }
}
-// assign threads
-void init() {
- int quotient, left;
- seedType seed;
- set<seedType> seedSet;
- set<seedType>::iterator iter;
- char outF[STRLEN];
-
- quotient = NSAMPLES / nThreads;
- left = NSAMPLES % nThreads;
-
- sprintf(cvsF, "%s.countvectors", imdName);
- seedSet.clear();
- params = new Params[nThreads];
- threads = new pthread_t[nThreads];
- for (int i = 0; i < nThreads; i++) {
- params[i].no = i;
-
- params[i].nsamples = quotient;
- if (i < left) params[i].nsamples++;
-
- if (i == 0) {
- params[i].fo = fopen(cvsF, "w");
- fprintf(params[i].fo, "%d %d\n", NSAMPLES, M + 1);
- }
- else {
- sprintf(outF, "%s%d", cvsF, i);
- params[i].fo = fopen(outF, "w");
- }
-
- do {
- seed = engine();
- iter = seedSet.find(seed);
- } while (iter != seedSet.end());
- params[i].rng = new engine_type(seed);
- seedSet.insert(seed);
-
- params[i].pme_c = new double[M + 1];
- memset(params[i].pme_c, 0, sizeof(double) * (M + 1));
- params[i].pme_theta = new double[M + 1];
- memset(params[i].pme_theta, 0, sizeof(double) * (M + 1));
- }
-
- /* set thread attribute to be joinable */
- pthread_attr_init(&attr);
- pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
-
-}
-
-void sampleTheta(engine_type& engine, vector<double>& theta) {
- distribution_type gm(1);
- generator_type gmg(engine, gm);
- double denom;
-
- theta.clear();
- theta.resize(M + 1);
- denom = 0.0;
- for (int i = 0; i <= M; i++) {
- theta[i] = gmg();
- denom += theta[i];
- }
- assert(denom > EPSILON);
- for (int i = 0; i <= M; i++) theta[i] /= denom;
-}
-
// arr should be cumulative!
// interval : [,)
// random number should be in [0, arr[len - 1])
// If by chance arr[len - 1] == 0.0, one possibility is to sample uniformly from 0...len-1
-int sample(uniform_generator& rg, vector<double>& arr, int len) {
+int sample(vector<double>& arr, int len) {
int l, r, mid;
double prb = rg() * arr[len - 1];
return l;
}
-void writeForSee(FILE* fo, vector<int>& counts) {
- for (int i = 1; i < M; i++) fprintf(fo, "%d ", counts[i]);
- fprintf(fo, "%d\n", counts[M]);
-}
-
-void writeCountVector(FILE* fo, vector<int>& counts) {
- for (int i = 0; i < M; i++) {
- fprintf(fo, "%d ", counts[i]);
- }
- fprintf(fo, "%d\n", counts[M]);
-}
-
-void* Gibbs(void* arg) {
+void init() {
int len, fr, to;
- int CHAINLEN;
- Params *params = (Params*)arg;
-
- vector<double> theta;
- vector<int> z, counts;
- vector<double> arr;
-
- uniform_generator rg(*params->rng);
-
- sampleTheta(*params->rng, theta);
-
- // generate initial state
arr.clear();
-
z.clear();
- z.resize(N1);
-
counts.clear();
+
+ z.resize(N1);
counts.resize(M + 1, 1); // 1 pseudo count
counts[0] += N0;
arr[j - fr] = theta[hits[j].sid] * hits[j].conprb;
if (j > fr) arr[j - fr] += arr[j - fr - 1]; // cumulative
}
- z[i] = hits[fr + sample(rg, arr, len)].sid;
+ z[i] = hits[fr + sample(arr, len)].sid;
++counts[z[i]];
}
- // Gibbs sampling
- char seeF[STRLEN];
- sprintf(seeF, "%s.see", statName);
- FILE *fsee = fopen(seeF, "w");
+ totc = N0 + N1 + (M + 1);
+
+ if (verbose) { printf("Initialization is finished!\n"); }
+}
+
+void writeCountVector(FILE* fo) {
+ for (int i = 0; i < M; i++) {
+ fprintf(fo, "%d ", counts[i]);
+ }
+ fprintf(fo, "%d\n", counts[M]);
+}
+
+void Gibbs(char* imdName) {
+ FILE *fo;
+ int fr, to, len;
- CHAINLEN = 1 + (params->nsamples - 1) * GAP;
- for (int ROUND = 1; ROUND <= BURNIN + CHAINLEN ; ROUND++) {
+ sprintf(cvsF, "%s.countvectors", imdName);
+ fo = fopen(cvsF, "w");
+ assert(CHAINLEN % GAP == 0);
+ fprintf(fo, "%d %d\n", CHAINLEN / GAP, M + 1);
+ //fprintf(fo, "%d %d\n", CHAINLEN, M + 1);
+
+ pme_c.clear(); pme_c.resize(M + 1, 0.0);
+ pme_theta.clear(); pme_theta.resize(M + 1, 0.0);
+ for (int ROUND = 1; ROUND <= BURNIN + CHAINLEN; ROUND++) {
for (int i = 0; i < N1; i++) {
--counts[z[i]];
arr[j - fr] = counts[hits[j].sid] * hits[j].conprb;
if (j > fr) arr[j - fr] += arr[j - fr - 1]; //cumulative
}
- z[i] = hits[fr + sample(rg, arr, len)].sid;
+ z[i] = hits[fr + sample(arr, len)].sid;
++counts[z[i]];
}
- writeForSee(fsee, counts);
-
if (ROUND > BURNIN) {
- if ((ROUND - BURNIN - 1) % GAP == 0) writeCountVector(params->fo, counts);
- for (int i = 0; i <= M; i++) {
- params->pme_c[i] += counts[i] - 1;
- params->pme_theta[i] += counts[i] / totc;
+ if ((ROUND - BURNIN - 1) % GAP == 0) writeCountVector(fo);
+ for (int i = 0; i <= M; i++) {
+ pme_c[i] += counts[i] - 1;
+ pme_theta[i] += counts[i] / totc;
}
}
- if (verbose & ROUND % 10 == 0) { printf("Thread %d, ROUND %d is finished!\n", params->no, ROUND); }
- }
- fclose(fsee);
-
- return NULL;
-}
-
-void release() {
- char inpF[STRLEN], command[STRLEN];
- string line;
-
- /* destroy attribute */
- pthread_attr_destroy(&attr);
- delete[] threads;
-
- pme_c.clear(); pme_c.resize(M + 1, 0.0);
- pme_theta.clear(); pme_theta.resize(M + 1, 0.0);
- for (int i = 0; i < nThreads; i++) {
- fclose(params[i].fo);
- delete params[i].rng;
- for (int j = 0; j <= M; j++) {
- pme_c[j] += params[i].pme_c[j];
- pme_theta[j] += params[i].pme_theta[j];
- }
- delete[] params[i].pme_c;
- delete[] params[i].pme_theta;
+ if (verbose) { printf("ROUND %d is finished!\n", ROUND); }
}
- delete[] params;
+ fclose(fo);
for (int i = 0; i <= M; i++) {
- pme_c[i] /= NSAMPLES;
- pme_theta[i] /= NSAMPLES;
+ pme_c[i] /= CHAINLEN;
+ pme_theta[i] /= CHAINLEN;
}
- // combine files
- FILE *fo = fopen(cvsF, "a");
- for (int i = 1; i < nThreads; i++) {
- sprintf(inpF, "%s%d", cvsF, i);
- ifstream fin(inpF);
- while (getline(fin, line)) {
- fprintf(fo, "%s\n", line.c_str());
- }
- fin.close();
- sprintf(command, "rm -f %s", inpF);
- int status = system(command);
- if (status != 0) { fprintf(stderr, "Fail to delete file %s!\n", inpF); exit(-1); }
- }
- fclose(fo);
+ if (verbose) { printf("Gibbs is finished!\n"); }
}
template<class ModelType>
int main(int argc, char* argv[]) {
if (argc < 7) {
- printf("Usage: rsem-run-gibbs reference_name sample_name sampleToken BURNIN NSAMPLES GAP [-p #Threads] [-q]\n");
+ printf("Usage: rsem-run-gibbs reference_name sample_name sampleToken BURNIN CHAINLEN GAP [-q]\n");
exit(-1);
}
BURNIN = atoi(argv[4]);
- NSAMPLES = atoi(argv[5]);
+ CHAINLEN = atoi(argv[5]);
GAP = atoi(argv[6]);
sprintf(imdName, "%s.temp/%s", argv[2], argv[3]);
sprintf(statName, "%s.stat/%s", argv[2], argv[3]);
load_data(argv[1], statName, imdName);
- nThreads = 1;
quiet = false;
- for (int i = 7; i < argc; i++) {
- if (!strcmp(argv[i], "-p")) nThreads = atoi(argv[i + 1]);
- if (!strcmp(argv[i], "-q")) quiet = true;
+ if (argc > 7 && !strcmp(argv[7], "-q")) {
+ quiet = true;
}
verbose = !quiet;
- if (nThreads > NSAMPLES) {
- nThreads = NSAMPLES;
- printf("Warning: Number of samples is less than number of threads! Change the number of threads to %d!\n", nThreads);
- }
-
- if (verbose) printf("Gibbs started!\n");
init();
- for (int i = 0; i < nThreads; i++) {
- rc = pthread_create(&threads[i], &attr, Gibbs, (void*)(¶ms[i]));
- if (rc != 0) { fprintf(stderr, "Cannot create thread %d! (numbered from 0)\n", i); }
- }
- for (int i = 0; i < nThreads; i++) {
- rc = pthread_join(threads[i], &status);
- if (rc != 0) { fprintf(stderr, "Cannot join thread %d! (numbered from 0)\n", i); }
- }
- release();
- if (verbose) printf("Gibbs finished!\n");
+ Gibbs(imdName);
sprintf(modelF, "%s.model", statName);
FILE *fi = fopen(modelF, "r");
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