-- Remove OpenMP as they did on the master branch. OpenMP as

    implemented won't work on Mac ARM64

NINJA/DistanceCalculator.hpp

@@ -20,8 +20,6 @@
 #include "sse2neon.h"
 #endif
 
-#include <omp.h> /* openmp */
-
 
 class DistanceCalculator{
 		const float bl45[21][21];

NINJA/DistanceReader.cpp

@@ -63,36 +63,26 @@ void DistanceReader::readDoubles(std::string **names, double** distances){
     unsigned int begin = 0, end = 0, numBegin = 0, numEnd = 0;
     int count = 0;
 
-    if (this->threads == 0){
-        omp_set_num_threads(omp_get_max_threads());
-    } else {
-        omp_set_num_threads(this->threads);
-    }
     if (this->distCalc != NULL) {//using distCalc on input alignment
     	this->clustersEqual = new int[this->K];
 
     	for (int i=0; i<this->K; i++)
     		this->clustersEqual[i] = -1;
 
-        //#pragma omp parallel for
     	for (int i=0; i<this->K; i++){
-	        //#pragma omp critical
     		if (this->clustersEqual[i] != -1){ //if this sequence is clustered, its distance to everyone else is maxed out
     			for (int j=i+1; j<this->K; j++)
     				distances[i][j-i-1] = this->distCalc->getMaxScore();
     			continue;
     		}
-		#pragma omp parallel for
     		for (int j=i+1; j<this->K; j++)
     		{
-		        //#pragma omp critical
         		if (this->clustersEqual[j] != -1){
         			distances[i][j-i-1] = this->distCalc->getMaxScore(); //seq j is already clustered to another one, therefore every sequence will have maximum score to it.
         			continue;
         		}
 			distances[i][j-i-1] = this->distCalc->calc(i,j);
 			if (distances[i][j-i-1] == 0 && (*this->distCalc->A[i]) == (*this->distCalc->A[j])){
-			  #pragma omp critical
 		   	  this->clustersEqual[j] = i; //because I do not check again for this->clustersEqual[j], this could cluster it to a sequence that is not the first one to show up. however, it should get the same result.
 			}
     		}
@@ -134,38 +124,28 @@ void DistanceReader::read(std::string **names, int** distances){ //possibly wron
     unsigned int begin = 0, end = 0, numBegin = 0, numEnd = 0;
     int count = 0;
 
-    if (this->threads == 0){
-        omp_set_num_threads(omp_get_max_threads());
-    } else {
-        omp_set_num_threads(this->threads);
-    }
     if (this->distCalc != NULL) {//using distCalc on input alignment
     	//int clustersEqual[this->K];
     	this->clustersEqual = new int[this->K];
 
     	for (int i=0; i<this->K; i++)
     		this->clustersEqual[i] = -1;
 
-		//#pragma omp parallel for
     	for (int i=0; i<this->K; i++){
-			//#pragma omp critical
     		if (this->clustersEqual[i] != -1){ //if this sequence is clustered, its distance to everyone else is maxed out
     			for (int j=i+1; j<this->K; j++)
     				distances[i][j-i-1] = this->distCalc->getMaxScore();
     			continue;
     		}
-			#pragma omp parallel for
     		for (int j=i+1; j<this->K; j++)
     		{
-				//#pragma omp critical
         		if (this->clustersEqual[j] != -1){
         			distances[i][j-i-1] = this->distCalc->getMaxScore(); //seq j is already clustered to another one, therefore every sequence will have maximum score to it.
         			continue;
         		}
 				//distances[i][j-i-1] = this->distCalc->testDifferenceCluster(i,j);
 				distances[i][j-i-1] = 100 * (int)(((100000000*this->distCalc->calc(i,j))+50)/100) ; // this gets the same rounding I have in the distance writer code
 				if (distances[i][j-i-1] == 0 && (*this->distCalc->A[i]) == (*this->distCalc->A[j])){
-					#pragma omp critical
 					this->clustersEqual[j] = i; //because I do not check again for this->clustersEqual[j], this could cluster it to a sequence that is not the first one to show up. however, it should get the same result.
 				}
     		}
@@ -213,12 +193,6 @@ void DistanceReader::readAndWrite(std::string **names, FILE* outFile){ //possibl
     for(int i = 0; i < this->K; ++i)
     	distances[i] = new double[this->K];
 
-    if (this->threads == 0){
-        omp_set_num_threads(omp_get_max_threads());
-    } else {
-        omp_set_num_threads(this->threads);
-    }
-    	#pragma omp parallel for
     	for (int i=0; i<this->K; i++){
     		for (int j=i+1; j<this->K; j++){
     			//distances[i][j-i-1] = this->distCalc->testDifferenceCluster(i,j);

NINJA/DistanceReader.hpp

@@ -4,8 +4,8 @@
  *  Created on: Feb 13, 2016
  *      Author: michel
  */
-#include "ExceptionHandler.hpp"
 #include "DistanceCalculator.hpp"
+#include "ExceptionHandler.hpp"
 
 #ifndef Included_DistanceReader_H
 #define Included_DistanceReader_H

NINJA/DistanceReaderExtMem.cpp

@@ -43,19 +43,15 @@ int DistanceReaderExtMem::read (std::string** names, float* R, FILE* diskD, floa
 
 	float* fBuff = new float[numColsToDisk];
 
-    omp_set_num_threads(omp_get_max_threads());
-
 	//TODO: implement threads here, more complicated that in the in memory function, but still feasible
 	if(this->distCalc != NULL){
     	while (row != K && buffPtr<buffSize) {
 
-    		//interleave columns in the
-			#pragma omp parallel for
+  		//interleave columns in the
 			for (int col=0; col<numColsToDisk; col++) {
 
 				float d = ((float)ceil((float)(10000000 * distCalc->calc(row, col))))/10000000;
 
-				#pragma omp atomic
 				R[row] += d;
 
 				fBuff[col] = d;
@@ -68,14 +64,12 @@ int DistanceReaderExtMem::read (std::string** names, float* R, FILE* diskD, floa
 				fwrite(fBuff,sizeof(float),numColsToDisk,diskD);
 
 			}
-			#pragma omp parallel for
 			for (int col=numColsToDisk; col<this->K; col++) {
 				#ifdef TEST_DIFF
 				float d = this->distCalc->testDifferenceCluster(row,col);
 				#endif
 				float d = ((float)ceil((float)(10000000 * distCalc->calc(row, col))))/10000000;
 
-				#pragma omp atomic
 				R[row] += d;
 
 				memD[row][col-numColsToDisk] = d;

NINJA/Makefile

@@ -34,7 +34,7 @@ SOURCES += TreeNode.cpp
 OBJECTS = $(SOURCES:.cpp=.o)
 
 #CXXFLAGS = -std=gnu++11 -Wall -mssse3 -fopenmp
-CXXFLAGS = -std=gnu++11 -Wall -fopenmp
+CXXFLAGS = -std=gnu++11 -Wall 
 ifeq ($(shell uname -m),x86_64)
 	CXXFLAGS += -mssse3
 endif