diff --git a/rtk/IO.cpp b/rtk/IO.cpp
index b33afbd..4765688 100644
--- a/rtk/IO.cpp
+++ b/rtk/IO.cpp
@@ -483,7 +483,8 @@ cerr<<"fini";
 
 void smplVec::shuffle_singl() {
 	//auto engine = std::default_random_engine{};
-	auto engine = std::mt19937_64{};
+	std::random_device rd;
+	auto engine = std::mt19937_64{rd()};
 	std::shuffle(std::begin(arr), std::end(arr), engine);	
 }
 
diff --git a/rtk/Rare.cpp b/rtk/Rare.cpp
index 94028ac..c342804 100644
--- a/rtk/Rare.cpp
+++ b/rtk/Rare.cpp
@@ -1,29 +1,33 @@
 #include "Rare.h"
 
-const char* rar_ver="0.91";
+const char* rar_ver="0.92";
 
 
 rareStruct* calcDivRar(int i, Matrix* Mo, DivEsts* div, long rareDep,
 	vector<vector<uint>>* abundInRow, vector<vector<uint>>* occuencesInRow,
 	string outF, int repeats, int writeFiles){
-	smplVec* cur = Mo->getSampleVec(i);
-	string curS = Mo->getSampleName(i);
-	div->SampleName = curS;
+	
+	smplVec* cur        = Mo->getSampleVec(i);
+	string curS         = Mo->getSampleName(i);
+	div->SampleName     = curS;
 	std::vector<vector<uint>> cnts;
 	vector<rare_map> cntsMap;
 	string cntsName;
 	string skippedNames;
 	bool wrAtAll(writeFiles > 0);
+	
 	cur->rarefy(rareDep, outF, repeats,
 					div, cntsMap, cntsName, skippedNames, abundInRow, occuencesInRow,
 					writeFiles, false, wrAtAll);
-	//delete cur;
-	//return div;
-	rareStruct* tmpRS 			= new rareStruct();// 	= {*div, retCnts};
-	tmpRS->div 							= div;
-	tmpRS->cnts 						= cntsMap;
-	tmpRS->cntsName 				= cntsName;
-	tmpRS->skippedNames			= skippedNames;
+					
+    // put everything in our nice return container
+	rareStruct* tmpRS       = new rareStruct();
+	tmpRS->div              = div;
+	tmpRS->cnts             = cntsMap;
+	tmpRS->cntsName         = cntsName;
+	tmpRS->skippedNames     = skippedNames;
+	tmpRS->i                = i;
+	
 	delete cur;
 	return tmpRS;
 }
@@ -44,12 +48,13 @@ rareStruct* calcDivRarVec(int i, vector<string> fileNames, DivEsts* div, long ra
 					div, cntsMap, cntsName, skippedNames, abundInRow, occuencesInRow,
 					writeFiles, false, wrAtAll);
 
-	rareStruct* tmpRS 			= new rareStruct();// 	= {*div, retCnts};
-	tmpRS->div 							= div;
-	tmpRS->cnts 						= cntsMap;
-	tmpRS->cntsName 				= cntsName;
-	tmpRS->skippedNames			= skippedNames;
-	tmpRS->IDs 							= cur->getRowNames();
+	rareStruct* tmpRS       = new rareStruct();// 	= {*div, retCnts};
+	tmpRS->div              = div;
+	tmpRS->cnts             = cntsMap;
+	tmpRS->cntsName         = cntsName;
+	tmpRS->skippedNames     = skippedNames;
+	tmpRS->IDs              = cur->getRowNames();
+	tmpRS->i                = i;
 
 	delete cur;
 
@@ -230,7 +235,7 @@ void options::print_rare_details(){
 
 
 
-void rareExtremLowMem(string inF, string outF, int writeFiles, string arg4, int repeats, int numThr = 1, bool storeBinary = false){
+void rareExtremLowMem(options * opts, string inF, string outF, int writeFiles, string arg4, int repeats, int numThr = 1, bool storeBinary = false){
 	// this mode takes the file, reads it in memory
 	// prints the columns to their own files
 	// then it loads those files again and
@@ -266,85 +271,105 @@ void rareExtremLowMem(string inF, string outF, int writeFiles, string arg4, int
 	vector< vector< rare_map > > MaRare (NoOfMatrices);
 	std::vector<string> cntsNames;
 	vector < vector < string > > tmpMatFiles (NoOfMatrices );
-	int done = 0; // number of samples processed for multithreading
-	uint i = 0;
-	std::future<rareStruct*> *tt = new std::future<rareStruct*>[numThr - 1];
-
-
-	//rarefection code
-	vector<DivEsts*> divvs(fileNames.size(),NULL);
-	while(i < fileNames.size()){
-
-		// allow multithreading
-		int thirds = (int) floor((fileNames.size()-3)/3);
-		if(i < 3 || i % thirds == 0  ){
-			cout << "At Sample " << i+1 << " of " << fileNames.size() << " Samples" << std::endl  ;
-			if(i > 3 && i % thirds == 0 ){
-					cout << "..." << std::endl ;
-			}
-		}else if( i == 3){
-			cout << "..." << std::endl ;
-		}
-
-		uint toWhere = done + numThr - 1;
-		if ((uint)((uint)fileNames.size() - 2 ) < toWhere){
-			toWhere = fileNames.size() - 2;
-		}
-		// launch samples in threads
-		for (; i < toWhere; i++){
-			DivEsts * div 	= new DivEsts();
-			div->SampleName = SampleNames[i];
-			tt[i - done] = async(std::launch::async, calcDivRarVec, i, fileNames,  div, rareDep, &abundInRow, &occuencesInRow, outF, repeats, writeFiles);
-		}
-		// launch one in the mainthread
-		DivEsts * div 	= new DivEsts();
-		div->SampleName = SampleNames[i];
-		rareStruct* tmpRS;
-		tmpRS = calcDivRarVec(i, fileNames,  div, rareDep, &abundInRow, &occuencesInRow, outF, repeats, writeFiles);
-		i++;
-
-
-		// process created data, first threads, then main thread
-		i = done;
-		for (; i < toWhere; i++){
-			rareStruct* tmpRSas;
-			tmpRSas 		= tt[i-done].get();
-			divvs[i] 		= tmpRSas->div;
-			string curS 	= SampleNames[i];
-			//divvs[i-done]->print2file(outF + curS + "_alpha_div.tsv");
-
-			// add the matrices to the container
-			if(NoOfMatrices > 0){
-				if(storeBinary == true){
-					binaryStoreSample(tmpMatFiles, tmpRSas, rowNames,outF, cntsNames, true);
-				}else{
-					memoryStoreSample(tmpRSas, MaRare, cntsNames, true);
-				}
-			}
-
-			delete tmpRSas;
+    vector<DivEsts*> divvs(fileNames.size(),NULL);
+	vector < job > slots(opts->threads);
+	size_t smpls = Mo->smplNum();
+	// now start a async in each slot
+    uint i          = 0; 
+	bool breakpoint(true);
+		while (breakpoint) {
+		    
+    	    // check for any finished jobs
+    	    for( uint j = 0; j < slots.size(); j++ ){
+                if( i >= smpls){
+					breakpoint = false;
+                    // break in case we have more slots than work
+                    break;
+                }
+                
+                // open new slots
+    	        if( slots[j].inUse == false){
+   	            
+    	            slots[j].inUse = true;
+    	            // launch an async task
+    	            DivEsts * div   = new DivEsts();
+    	            div->SampleName = SampleNames[i];
+    	            slots[j].fut    = async(std::launch::async, calcDivRarVec, i, fileNames, div, rareDep, &abundInRow, &occuencesInRow, outF, opts->repeats, opts->write);
+                        	      
+    	            // send user some feedback
+    	            int thirds = 1;
+    	            if(smpls > 4){
+        	            thirds = (int) floor((smpls-3)/3);
+        	        }
+    	            
+		            if(i < 3 || i % thirds == 0  ){
+			            cout << "At Sample " << i+1 << " of " << smpls << " Samples" << std::endl;
+			            if(i > 3 && i % thirds == 0 ){
+					            cout << "..." << std::endl ;
+			            }
+		            }else if( i == 3){
+			            cout << "..." << std::endl ;
+		            }
+    	            
+    	            i++;
+    	            
+    	        }else if(slots[j].fut.wait_for(std::chrono::milliseconds(20)) == std::future_status::ready){
+    	            
+    	            // move the information
+    	            rareStruct* tmpRS;
+				    tmpRS               = slots[j].fut.get();
+				    divvs[tmpRS->i]     = tmpRS->div;
+		            string curS 	    = SampleNames[tmpRS->i];
+        		    cout << curS << std::endl;
+				    // add the matrices to the container
+				    if (NoOfMatrices > 0) {
+					    if (opts->writeSwap) {
+						    binaryStoreSample(tmpMatFiles, tmpRS, rowNames, outF, cntsNames, true);
+					    }
+					    else {
+						    memoryStoreSample(tmpRS, MaRare, cntsNames, true);
+					    }
+				    }
+
+				    delete tmpRS;
+    	            // free slot
+    	            slots[j].inUse = false;
+    	        }
+    	    }
+    	 
+		
 		}
 
-		// main thread divv push back
-		divvs[i] 			= tmpRS->div;
-		string curS 	= SampleNames[i];
-		//divvs[i]->print2file(outF + curS + "_alpha_div.tsv");
-
-
-		// add the matrices to the container
-		if(NoOfMatrices > 0){
-			if(storeBinary == true){
-				binaryStoreSample(tmpMatFiles, tmpRS, rowNames,outF, cntsNames, true);
-			}else{
-				memoryStoreSample(tmpRS, MaRare, cntsNames, true);
-			}
+		// wait for the threads to finish up.
+		for(uint j = 0; j < slots.size(); j++){
+		    if(slots[j].inUse == false ){
+		        // only copy if there is work to be done
+		        continue;
+		    }
+    		slots[j].fut.wait();
+		    // move the information
+            rareStruct* tmpRS;
+		    tmpRS               = slots[j].fut.get();
+		    divvs[tmpRS->i]     = tmpRS->div;
+		    string curS 	    = SampleNames[tmpRS->i];
+
+		    // add the matrices to the container
+		    if (NoOfMatrices > 0) {
+			    if (opts->writeSwap) {
+				    binaryStoreSample(tmpMatFiles, tmpRS, rowNames, outF, cntsNames, true);
+			    }
+			    else {
+				    memoryStoreSample(tmpRS, MaRare, cntsNames, true);
+			    }
+		    }
+
+		    delete tmpRS;
+            // free slot
+            slots[j].inUse = false;
 		}
-
-		delete tmpRS;
-		i++;
-		done = i;
-	}
-
+		
+		
+		
 	// print the div estimates out into a file
 	printDivMat(outF , divvs, true);
 	for (size_t i = 0; i < divvs.size(); i++){
@@ -589,7 +614,7 @@ int main(int argc, char* argv[])
 	}
 	else if (mode == "swap") {
 		vector < vector < string > > tmpMatFiles(opts->write);
-		rareExtremLowMem(inF, outF, opts->write, arg4, opts->repeats, numThr, opts->writeSwap);
+		rareExtremLowMem(opts, inF, outF, opts->write, arg4, opts->repeats, numThr, opts->writeSwap);
 		printf("Time taken: %.2fs\n", (double)(clock() - tStart) / CLOCKS_PER_SEC);
 		std::exit(0);
 	}
@@ -626,69 +651,106 @@ int main(int argc, char* argv[])
 		//object to keep matrices
 		vector < vector < string > > tmpMatFiles(opts->write);
 		//cerr << "TH";
-		std::future<rareStruct*> *tt = new std::future<rareStruct*>[numThr - 1];
-		uint i = 0; uint done = 0;
-		while (i < Mo->smplNum()) {
-			int thirds = (int)floor((Mo->smplNum() - 3) / 3);
-			if (i < 3 || i % thirds == 0) {
-				cout << "At Sample " << i + 1 << " of " << Mo->smplNum() << " Samples" << std::endl;
-				if (i > 3 && i % thirds == 0) {
-					cout << "..." << std::endl;
-				}
-			}
-			else if (i == 3) {
-				cout << "..." << std::endl;
-			}
-			uint toWhere = done + numThr - 1; if ((uint)((uint)Mo->smplNum() - 2) < toWhere) { toWhere = Mo->smplNum() - 2; }
-			for (; i < toWhere; i++) {
-				DivEsts * div = new DivEsts();
-				tt[i - done] = async(std::launch::async, calcDivRar, i, Mo, div, rareDep, &abundInRow, &occuencesInRow, outF, opts->repeats, opts->write);
-			}
-			//use main thread to calc one sample as well
-			DivEsts * div = new DivEsts();
-			rareStruct* tmpRS;
-			tmpRS = calcDivRar(i, Mo, div, rareDep, &abundInRow, &occuencesInRow, outF, opts->repeats, opts->write);
-
-
-			i++;
-			i = done;
-			for (; i < toWhere; i++) {
-				rareStruct* tmpRS;
-				tmpRS = tt[i - done].get();
-				divvs[i] = tmpRS->div;
-				string curS = Mo->getSampleName(i);
-				//divvs[i-done]->print2file(outF + curS + "_alpha_div.tsv");
-
-				// add the matrices to the container
-				if (NoOfMatrices > 0) {
-					if (opts->writeSwap) {
-						binaryStoreSample(tmpMatFiles, tmpRS, rowNames, outF, cntsNames, false);
-					}
-					else {
-						memoryStoreSample(tmpRS, MaRare, cntsNames, false);
-					}
-				}
+        // vector keeping all the slots
+		vector < job > slots(opts->threads);
+		
+		// now start a async in each slot
+		uint i          = 0; 
+
+
+		size_t smpls = Mo->smplNum();
+		bool breakpoint(true);
+		while (breakpoint) {
+		    
+
+    	    // check for any finished jobs
+    	    for( uint j = 0; j < slots.size(); j++ ){
+                if( i >= smpls){
+					breakpoint = false;
+                    // break in case we have more slots than work
+                    break;
+                }
+                
+                // open new slots
+    	        if( slots[j].inUse == false){
+   	            
+    	            slots[j].inUse = true;
+    	            // launch an async task
+    	            DivEsts * div   = new DivEsts();
+    	            slots[j].fut    = async(std::launch::async, calcDivRar, i, Mo, div, rareDep, &abundInRow, &occuencesInRow, outF, opts->repeats, opts->write);
+    	            
+    	            // send user some feedback
+    	            int thirds = 1;
+    	            if(smpls > 4){
+        	            thirds = (int) floor((smpls-3)/3);
+        	        }
+		            if(i < 3 || i % thirds == 0  ){
+			            cout << "At Sample " << i+1 << " of " << smpls << " Samples" << std::endl  ;
+			            if(i > 3 && i % thirds == 0 ){
+					            cout << "..." << std::endl ;
+			            }
+		            }else if( i == 3){
+			            cout << "..." << std::endl ;
+		            }
+                	            
+    	            i++;
+    	            
+    	        }else if(slots[j].fut.wait_for(std::chrono::milliseconds(20)) == std::future_status::ready){
+    	            
+    	            // move the information
+    	            rareStruct* tmpRS;
+				    tmpRS               = slots[j].fut.get();
+				    divvs[tmpRS->i]     = tmpRS->div;
+				    string curS         = Mo->getSampleName(tmpRS->i);
+
+				    // add the matrices to the container
+				    if (NoOfMatrices > 0) {
+					    if (opts->writeSwap) {
+						    binaryStoreSample(tmpMatFiles, tmpRS, rowNames, outF, cntsNames, false);
+					    }
+					    else {
+						    memoryStoreSample(tmpRS, MaRare, cntsNames, false);
+					    }
+				    }
+
+				    delete tmpRS;
+    	            // free slot
+    	            slots[j].inUse = false;
+    	        }
+    	    }
+    	 
+		
+		}
 
-				delete tmpRS;
-			}
-			// main thread divv push back
-			divvs[i] = tmpRS->div;
-			string curS = Mo->getSampleName(i);
-			//divvs[i]->print2file(outF + curS + "_alpha_div.tsv");
-
-			// add the matrices to the container
-			if (NoOfMatrices > 0) {
-				if (opts->writeSwap) {
-					binaryStoreSample(tmpMatFiles, tmpRS, rowNames, outF, cntsNames, false);
-				}
-				else {
-					memoryStoreSample(tmpRS, MaRare, cntsNames, false);
-				}
-			}
-			delete tmpRS;
-			i++;
-			done = i;
+		// wait for the threads to finish up.
+		for(uint j = 0; j < slots.size(); j++){
+		    if(slots[j].inUse == false ){
+		        // only copy if there is work to be done
+		        continue;
+		    }
+    		slots[j].fut.wait();
+		    // move the information
+            rareStruct* tmpRS;
+		    tmpRS               = slots[j].fut.get();
+		    divvs[tmpRS->i]     = tmpRS->div;
+		    string curS         = Mo->getSampleName(tmpRS->i);
+
+		    // add the matrices to the container
+		    if (NoOfMatrices > 0) {
+			    if (opts->writeSwap) {
+				    binaryStoreSample(tmpMatFiles, tmpRS, rowNames, outF, cntsNames, false);
+			    }
+			    else {
+				    memoryStoreSample(tmpRS, MaRare, cntsNames, false);
+			    }
+		    }
+
+		    delete tmpRS;
+            // free slot
+            slots[j].inUse = false;
 		}
+
+		// output matrix
 		printDivMat(outF, divvs, true);
 		for (size_t i = 0; i < divvs.size(); i++) {
 			delete divvs[i];
@@ -717,7 +779,7 @@ int main(int argc, char* argv[])
 		computeCE(ACE, occuencesInRow);
 		writeGlobalDiv(ICE, ACE, chao2, outF + "_gDiv.tsv");
 
-		printf("Time taken: %.2fs\n", (double)(clock() - tStart) / CLOCKS_PER_SEC);
+		printf("CPU time taken: %.2fs\n", (double)(clock() - tStart) / CLOCKS_PER_SEC);
 		//cout << "Finished\n";
 		std::exit(0);
 	}
diff --git a/rtk/Rare.h b/rtk/Rare.h
index 2283274..5a261b5 100644
--- a/rtk/Rare.h
+++ b/rtk/Rare.h
@@ -3,12 +3,19 @@
 #include "options.h"
 
 struct rareStruct{
+	int i;
 	DivEsts* div;
 	string cntsName;
 	//std::vector<vector<uint>> cnts;
 	vector<rare_map> cnts;
 	string skippedNames;
 	vector<string> IDs;
+	
+};
+
+struct job {
+  std::future <rareStruct*> fut;
+  bool inUse = false;
 };
 
 void binaryStoreSample(vector< vector< string > > & tmpMatFiles, rareStruct* tmpRS,