working on parallelizing unifrac.unweighted.

[mothur.git] / weighted.cpp

diff --git a/weighted.cpp b/weighted.cpp
index d068369cca57d73c260e56e522b51fc5eef97fea..c9ad81295aaacb3bd4ae7eb8f7e8ca7c1cef9b80 100644 (file)
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -74,7 +74,7 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
 EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector<double>& sums) {
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-               int process = 0;
+               int process = 1;
                int num = 0;
                vector<int> processIDS;
                
@@ -88,7 +88,8 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
                                processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
                                process++;
                        }else if (pid == 0){
-                               results = driver(t, namesOfGroupCombos, lines[process]->start, lines[process]->num, sums);
+                               EstOutput Myresults;
+                               Myresults = driver(t, namesOfGroupCombos, lines[process]->start, lines[process]->num, sums);
                                
                                if (m->control_pressed) { exit(0); }
                                
@@ -96,18 +97,20 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
                                
                                //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = outputDir + toString(getpid()) + ".results.temp";
+                               string tempFile = outputDir + toString(getpid()) + ".weighted.results.temp";
                                m->openOutputFile(tempFile, out);
-                               out << results.size() << endl;
-                               for (int i = 0; i < results.size(); i++) {  out << results[i] << '\t';  } out << endl;
+                               out << Myresults.size() << endl;
+                               for (int i = 0; i < Myresults.size(); i++) {  out << Myresults[i] << '\t';  } out << endl;
                                out.close();
                                
                                exit(0);
                        }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
                }
+       
+               results = driver(t, namesOfGroupCombos, lines[0]->start, lines[0]->num, sums);
                
                //force parent to wait until all the processes are done
-               for (int i=0;i<processors;i++) { 
+               for (int i=0;i<(processors-1);i++) { 
                        int temp = processIDS[i];
                        wait(&temp);
                }
@@ -115,37 +118,27 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
                if (m->control_pressed) { return results; }
                
                //get data created by processes
-               for (int i=0;i<processors;i++) { 
+               for (int i=0;i<(processors-1);i++) { 
                        ifstream in;
-                       string s = outputDir + toString(processIDS[i]) + ".results.temp";
+                       string s = outputDir + toString(processIDS[i]) + ".weighted.results.temp";
                        m->openInputFile(s, in);
                        
-                       vector<double> r;
-                       
                        //get quantiles
                        while (!in.eof()) {
                                int num;
-                               in >> num; 
+                               in >> num; m->gobble(in);
                                
                                if (m->control_pressed) { break; }
-                               
-                               m->gobble(in);
 
                                double w; 
                                for (int j = 0; j < num; j++) {
                                        in >> w;
-                                       r.push_back(w);
+                                       results.push_back(w);
                                }
                                m->gobble(in);
                        }
                        in.close();
                        remove(s.c_str());
-       
-                       //save quan in quantiles
-                       for (int j = 0; j < r.size(); j++) {
-                               //put all values of r into results
-                               results.push_back(r[j]);   
-                       }
                }
                
                m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
@@ -167,7 +160,7 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
                vector<double> D;
                
                int count = 0;
-               int total = start+num;
+               int total = num;
                int twentyPercent = (total * 0.20);
 
                for (int h = start; h < (start+num); h++) {
@@ -203,7 +196,7 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
                        count++;
                        
                        //report progress
-                       if((h) % twentyPercent == 0){   m->mothurOut("Percentage complete: " + toString(int((h / (float)total) * 100.0))); m->mothurOutEndLine();               }
+                       if((count) % twentyPercent == 0){       m->mothurOut("Percentage complete: " + toString(int((count / (float)total) * 100.0))); m->mothurOutEndLine();           }
                }
                
                m->mothurOut("Percentage complete: 100"); m->mothurOutEndLine();