fixed cluster.split bug

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index f09aa997a506076b99584228c2b2272a6530a6fc..70c0a7806c2902b73f20601ff1fda5b330aa8c10 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -29,6 +29,7 @@ vector<string> DistanceCommand::getValidParameters(){
 //**********************************************************************************************************************
 DistanceCommand::DistanceCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["phylip"] = tempOutNames;
@@ -422,6 +423,21 @@ int DistanceCommand::execute(){
                        else { driver(0, numSeqs, outputFile, "square");  }
                }else{ //you have multiple processors
                        
+                       unsigned long int numDists = 0;
+                       
+                       if (output == "square") {
+                                numDists = numSeqs * numSeqs;
+                       }else {
+                               for(int i=0;i<numSeqs;i++){
+                                       for(int j=0;j<i;j++){
+                                               numDists++;
+                                               if (numDists > processors) { break; }
+                                       }
+                               }
+                       }
+                       
+                       if (numDists < processors) { processors = numDists; }
+                       
                        for (int i = 0; i < processors; i++) {
                                lines.push_back(new linePair());
                                if (output != "square") {
@@ -431,19 +447,10 @@ int DistanceCommand::execute(){
                                        lines[i]->start = int ((float(i)/float(processors)) * numSeqs);
                                        lines[i]->end = int ((float(i+1)/float(processors)) * numSeqs);
                                }
+                               //cout << i << '\t' << lines[i]->start << '\t' << lines[i]->end << endl;
                        }
 
                        createProcesses(outputFile); 
-               
-                       map<int, int>::iterator it = processIDS.begin();
-                       rename((outputFile + toString(it->second) + ".temp").c_str(), outputFile.c_str());
-                       it++;
-                       
-                       //append and remove temp files
-                       for (; it != processIDS.end(); it++) {
-                               m->appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
-                               remove((outputFile + toString(it->second) + ".temp").c_str());
-                       }
                }
        #else
                //ifstream inFASTA;
@@ -525,7 +532,7 @@ int DistanceCommand::execute(){
 void DistanceCommand::createProcesses(string filename) {
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-               int process = 0;
+               int process = 1;
                processIDS.clear();
                
                //loop through and create all the processes you want
@@ -533,20 +540,36 @@ void DistanceCommand::createProcesses(string filename) {
                        int pid = fork();
                        
                        if (pid > 0) {
-                               processIDS[lines[process]->end] = pid;  //create map from line number to pid so you can append files in correct order later
+                               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){
                                if (output != "square") {  driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff); }
                                else { driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", "square"); }
                                exit(0);
-                       }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+                       }else { 
+                               m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine(); 
+                               perror(" : ");
+                               for (int i=0;i<processIDS.size();i++) {  int temp = processIDS[i]; kill (temp, SIGINT); }
+                               exit(0);
+                       }
                }
-       
+               
+               //parent does its part
+               if (output != "square") {  driver(lines[0]->start, lines[0]->end, filename, cutoff); }
+               else { driver(lines[0]->start, lines[0]->end, filename, "square"); }
+               
+               
                //force parent to wait until all the processes are done
-               for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) { 
-                       int temp = it->second;
+               for (int i=0;i<processIDS.size();i++) { 
+                       int temp = processIDS[i];
                        wait(&temp);
                }
+               
+               //append and remove temp files
+               for (int i=0;i<processIDS.size();i++) { 
+                       m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
+                       remove((filename + toString(processIDS[i]) + ".temp").c_str());
+               }
 #endif
        }
        catch(exception& e) {