X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=bcc59675d3b545f68197a3f56911a769ebe249bb;hb=fefd5ee1517abd3bc38b469cb2dffc85a1571c7e;hp=6b0ef5a8b661efd635ad918965a4bd047e2aef52;hpb=60928795782d8f8648ec373d6a96b53032a77429;p=mothur.git

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 6b0ef5a..bcc5967 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -110,7 +110,7 @@ AlignCommand::AlignCommand(){
 //**********************************************************************************************************************
 AlignCommand::AlignCommand(string option)  {
 	try {
-		abort = false; calledHelp = false;  
+		abort = false; calledHelp = false;
 		ReferenceDB* rdb = ReferenceDB::getInstance();
 		
 		//allow user to run help
@@ -860,12 +860,14 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
 	try {
 		int num = 0;
 		processIDS.resize(0);
+        bool recalc = false;
+        
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 1;
 		
 		//loop through and create all the processes you want
 		while (process != processors) {
-			int pid = fork();
+			pid_t pid = fork();
 			
 			if (pid > 0) {
 				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
@@ -882,12 +884,48 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
 				
 				exit(0);
 			}else { 
-				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
-				for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
-				exit(0);
+				m->mothurOut("[ERROR]: unable to spawn the number of processes you requested, reducing number to " + toString(process) + "\n"); processors = process;
+                for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+                recalc = true;
+				break;
 			}
 		}
 		
+        if (recalc) {
+            for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
+            vector<unsigned long long> positions;
+			positions = m->divideFile(filename, processors);
+			for (int i = 0; i < (positions.size()-1); i++) {	lines.push_back(new linePair(positions[i], positions[(i+1)]));	}
+            
+            num = 0;
+            processIDS.resize(0);
+            process = 1;
+            
+            while (process != processors) {
+                pid_t pid = fork();
+                
+                if (pid > 0) {
+                    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){
+                    num = driver(lines[process], alignFileName + toString(m->mothurGetpid(process)) + ".temp", reportFileName + toString(m->mothurGetpid(process)) + ".temp", accnosFName + m->mothurGetpid(process) + ".temp", filename);
+                    
+                    //pass numSeqs to parent
+                    ofstream out;
+                    string tempFile = alignFileName + toString(m->mothurGetpid(process)) + ".num.temp";
+                    m->openOutputFile(tempFile, out);
+                    out << num << endl;
+                    out.close();
+                    
+                    exit(0);
+                }else {
+                    m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+                    for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+                    exit(0);
+                }
+            }
+        }
+        
 		//do my part
 		num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);