working on parallelizing unifrac.unweighted.

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 65b0a5090afb211b78c6abc9737f767af7176bff..ad012b542b82a99ad0ac40782688c325360268b0 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -275,7 +275,7 @@ int UnifracWeightedCommand::execute() {
 int UnifracWeightedCommand::createProcesses(Tree* t, Tree* randT, vector< vector<string> > namesOfGroupCombos, vector<double>& sums, vector< vector<double> >& scores) {
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-               int process = 0;
+               int process = 1;
                int num = 0;
                vector<int> processIDS;
                
@@ -295,52 +295,32 @@ int UnifracWeightedCommand::createProcesses(Tree* t, Tree* randT, vector< vector
                                
                                //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = outputDir + toString(getpid()) + ".results.temp";
+                               string tempFile = outputDir + toString(getpid()) + ".weightedcommand.results.temp";
                                m->openOutputFile(tempFile, out);
-                               out << results.size() << endl;
-                               for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) {  out << results[i] << '\t';  } out << endl;
+                               for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) {  out << scores[i][0] << '\t';  } out << endl;
                                out.close();
                                
                                exit(0);
                        }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
                }
                
+               driver(t, randT, namesOfGroupCombos, lines[0]->start, lines[0]->num, sums, scores);
+               
                //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);
                }
        
                //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]) + ".weightedcommand.results.temp";
                        m->openInputFile(s, in);
                        
-                       vector<double> r;
-                       
-                       //get quantiles
-                       while (!in.eof()) {
-                               int num;
-                               in >> num; 
-                               
-                               m->gobble(in);
-
-                               double w; 
-                               for (int j = 0; j < num; j++) {
-                                       in >> w;
-                                       r.push_back(w);
-                               }
-                               m->gobble(in);
-                       }
+                       for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) { in >> scores[i][0]; }
                        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();
@@ -358,7 +338,7 @@ int UnifracWeightedCommand::createProcesses(Tree* t, Tree* randT, vector< vector
 int UnifracWeightedCommand::driver(Tree* t, Tree* randT, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums, vector< vector<double> >& scores) { 
  try {
                int count = 0;
-               int total = start+num;
+               int total = num;
                int twentyPercent = (total * 0.20);
 
                for (int h = start; h < (start+num); h++) {
@@ -389,7 +369,7 @@ int UnifracWeightedCommand::driver(Tree* t, Tree* randT, vector< vector<string>
                        count++;
 
                        //report progress
-                       if((h) % twentyPercent == 0){   m->mothurOut("Random comparison percentage complete: " + toString(int((h / (float)total) * 100.0))); m->mothurOutEndLine();             }
+                       if((count) % twentyPercent == 0){       m->mothurOut("Random comparison percentage complete: " + toString(int((count / (float)total) * 100.0))); m->mothurOutEndLine();         }
                }
                
                m->mothurOut("Random comparison percentage complete: 100"); m->mothurOutEndLine();