jpayne@68: package kmer;
jpayne@68: 
jpayne@68: import java.util.Arrays;
jpayne@68: 
jpayne@68: import shared.Primes;
jpayne@68: import shared.Shared;
jpayne@68: import shared.Tools;
jpayne@68: import structures.IntList;
jpayne@68: 
jpayne@68: public class ScheduleMaker {
jpayne@68: 	
jpayne@68: 	public ScheduleMaker(int ways_, int bytesPerKmer_, boolean prealloc_, double memRatio_){
jpayne@68: 		this(ways_, bytesPerKmer_, prealloc_, memRatio_, 0, 0, 0, 0);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public ScheduleMaker(int ways_, int bytesPerKmer_, boolean prealloc_, double memRatio_, int initialSize_){
jpayne@68: 		this(ways_, bytesPerKmer_, prealloc_, memRatio_, initialSize_, 0, 0, 0);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public ScheduleMaker(int ways_, int bytesPerKmer_, boolean prealloc_, double memRatio_, int initialSize_, 
jpayne@68: 			int prepasses_, double prefilterFraction_, long filterMemoryOverride_){
jpayne@68: 		bytesPerKmer=bytesPerKmer_;
jpayne@68: 		prealloc=prealloc_;
jpayne@68: 		memRatio=(float)(memRatio_<=0 ? 1 : memRatio_);
jpayne@68: 		prepasses=prepasses_;
jpayne@68: 		prefilter=(prepasses>0);
jpayne@68: 		prefilterFraction=prefilter ? prefilterFraction_ : 0;
jpayne@68: 		assert(prefilter==prefilterFraction>0) : prefilter+", "+prefilterFraction_+", "+prefilterFraction;
jpayne@68: //		assert(false && prefilter==prefilterFraction>0) : prefilter+", "+prefilterFraction_+", "+prefilterFraction;
jpayne@68: 		if(prepasses<1){
jpayne@68: 			filterMemory0=filterMemory1=0;
jpayne@68: 		}else if(filterMemoryOverride>0){
jpayne@68: 			filterMemory0=filterMemory1=filterMemoryOverride;
jpayne@68: 		}else{
jpayne@68: 			double low=Tools.min(prefilterFraction, 1-prefilterFraction);
jpayne@68: 			double high=1-low;
jpayne@68: 			if(prepasses<0 || (prepasses&1)==1){//odd passes
jpayne@68: 				filterMemory0=(long)(usableMemory*low);
jpayne@68: 				filterMemory1=(long)(usableMemory*high);
jpayne@68: 			}else{//even passes
jpayne@68: 				filterMemory0=(long)(usableMemory*high);
jpayne@68: 				filterMemory1=(long)(usableMemory*low);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		tableMemory=(long)(usableMemory*.95-Tools.min(filterMemory0, filterMemory1));
jpayne@68: 		
jpayne@68: 		if(ways_<1){
jpayne@68: 			long maxKmers=(2*tableMemory)/bytesPerKmer;
jpayne@68: 			long minWays=Tools.min(10000, maxKmers/Integer.MAX_VALUE);
jpayne@68: 			ways_=(int)Tools.max(31, (int)(Tools.min(96, Shared.threads())*2.5), minWays);
jpayne@68: 			ways_=(int)Primes.primeAtLeast(ways_);
jpayne@68: 			assert(ways_>0);
jpayne@68: 			//		System.err.println("ways="+ways_);
jpayne@68: 		}
jpayne@68: 		ways=ways_;
jpayne@68: 
jpayne@68: 		final double maxSize0=(tableMemory*0.95*memRatio)/(bytesPerKmer*ways);
jpayne@68: 		assert(maxPrime>1 && maxSize0>2) : 
jpayne@68: 			"\nmaxPrime="+maxPrime+", maxSize0="+maxSize0+", tableMemory="+tableMemory+", usableMemory="+usableMemory+
jpayne@68: 			", \nprepasses="+prepasses+", filterMemory0="+filterMemory0+", filterMemory1="+filterMemory1+", prefilterFraction="+prefilterFraction+
jpayne@68: 			", \nmemRatio="+memRatio+", bytesPerKmer="+bytesPerKmer+", ways="+ways+
jpayne@68: 			", \ninitialSize="+initialSize_+", initialSizeDefault="+initialSizeDefault+", prealloc="+prealloc;
jpayne@68: 		
jpayne@68: 		lastSizeFraction=prealloc ? 1.0 : resizeMult/(1.0+resizeMult);
jpayne@68: 		maxSize=Primes.primeAtMost((int)Tools.min(maxPrime, maxSize0*lastSizeFraction));
jpayne@68: 		initialSize=(prealloc ? maxSize : Primes.primeAtMost(initialSize_>0 ? initialSize_ : initialSizeDefault));
jpayne@68: 		
jpayne@68: 		estimatedKmerCapacity=(long)(maxSize*HashArray.maxLoadFactorFinal*0.97*ways);
jpayne@68: 		
jpayne@68: //		System.err.println(Arrays.toString(makeSchedule()));
jpayne@68: 		
jpayne@68: //		System.err.println("ways="+ways+", maxSize="+maxSize+", estimatedKmerCapacity="+estimatedKmerCapacity+", "+Arrays.toString(makeSchedule()));
jpayne@68: //		
jpayne@68: //		assert(false) : 
jpayne@68: //			"\nmaxPrime="+maxPrime+", maxSize0="+maxSize0+", tableMemory="+tableMemory+", usableMemory="+usableMemory+
jpayne@68: //			", \nprepasses="+prepasses+", filterMemory0="+filterMemory0+", filterMemory1="+filterMemory1+", prefilterFraction="+prefilterFraction+
jpayne@68: //			", \nmemRatio="+memRatio+", bytesPerKmer="+bytesPerKmer+", ways="+ways+
jpayne@68: //			", \ninitialSize="+initialSize_+", initialSizeDefault="+initialSizeDefault+", prealloc="+prealloc+
jpayne@68: //			", \nmaxSize="+maxSize+", initialSize="+initialSize+", estimatedKmerCapacity="+estimatedKmerCapacity+
jpayne@68: //			", \n"+Arrays.toString(makeSchedule());
jpayne@68: //		assert(false) : Arrays.toString(makeSchedule());
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public int[] makeSchedule(){
jpayne@68: 		if(prealloc || maxSize<2L*initialSize){return new int[] {maxSize};}
jpayne@68: 		IntList list=new IntList(10);
jpayne@68: 		list.add(maxSize);
jpayne@68: 		for(double x=maxSize*invResizeMult; x>=initialSize; x=x*invResizeMult2){
jpayne@68: 			list.add((int)x);
jpayne@68: 		}
jpayne@68: 		if(list.size()>1 && list.lastElement()>=2*initialSize){
jpayne@68: 			list.add(initialSize);
jpayne@68: 		}
jpayne@68: 		list.reverse();
jpayne@68: //		if(list.lastElement()*2L<maxPrime){list.add(2*maxSize);}//This ensures that the program will crash rather than garbage-collecting for a long time
jpayne@68: 		int[] array=list.toArray();
jpayne@68: //		if(initialSize>2 && array.length>2 && array[0]>initialSize){array[0]=initialSize;}
jpayne@68: 		assert(Tools.isSorted(array)) : Arrays.toString(array);
jpayne@68: 		for(int i=0; i<array.length; i++){
jpayne@68: 			array[i]=array[i]==1 ? 1 : (int)Tools.min(maxPrime, Primes.primeAtLeast(array[i]));
jpayne@68: 		}
jpayne@68: 		return array;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: //	public static int[] makeScheduleStatic(int initialSize, int maxSize, boolean autoResize){
jpayne@68: //		if(!autoResize || initialSize>=maxSize){return null;}
jpayne@68: //		IntList list=new IntList(10);
jpayne@68: //		list.add((int)(maxSize*0.8));
jpayne@68: //		for(long x=maxSize; x>=initialSize; x=x/5){
jpayne@68: //			list.add((int)x);
jpayne@68: //		}
jpayne@68: //		if(list.size()>1 && list.lastElement()>=2*initialSize){
jpayne@68: //			list.add(initialSize);
jpayne@68: //		}
jpayne@68: //		list.reverse();
jpayne@68: //		int[] array=list.toArray();
jpayne@68: //		for(int i=0; i<array.length; i++){
jpayne@68: //			array[i]=array[i]==1 ? 1 : (int)Tools.min(maxPrime, Primes.primeAtLeast(array[i]));
jpayne@68: //		}
jpayne@68: //		return array;
jpayne@68: //	}
jpayne@68: 
jpayne@68: 	final double resizeMult=5.0;
jpayne@68: 	final double resizeMult2=3.0;
jpayne@68: 	final double invResizeMult=1/resizeMult;
jpayne@68: 	final double invResizeMult2=1/resizeMult2;
jpayne@68: 	final double lastSizeFraction;
jpayne@68: 	
jpayne@68: 	final long memory=Runtime.getRuntime().maxMemory();
jpayne@68: 	final double xmsRatio=Shared.xmsRatio();
jpayne@68: 	
jpayne@68: 	//TODO: Add term for JDK (Oracle/Open) and version.
jpayne@68: 	final long usableMemory=(long)Tools.max(((memory-96000000)*
jpayne@68: 			(xmsRatio>0.97 ? 0.82 : 0.72)), memory*0.45);
jpayne@68: 	
jpayne@68: 	final long filterMemoryOverride=0;
jpayne@68: 	
jpayne@68: 	final long filterMemory0, filterMemory1;
jpayne@68: 	final long tableMemory;
jpayne@68: 	final double prefilterFraction;
jpayne@68: 	final int prepasses;
jpayne@68: 	final boolean prefilter;
jpayne@68: 	final int bytesPerKmer;
jpayne@68: 	public final long estimatedKmerCapacity;
jpayne@68: 	
jpayne@68: 	public final int ways;
jpayne@68: 
jpayne@68: 	final int initialSize;
jpayne@68: 	final int maxSize;
jpayne@68: 	
jpayne@68: 	final boolean prealloc;
jpayne@68: 	final float memRatio;
jpayne@68: 
jpayne@68: 	static final int initialSizeDefault=128000;
jpayne@68: 	static final int maxPrime=(int)Primes.primeAtMost(Integer.MAX_VALUE-100-20);
jpayne@68: 	
jpayne@68: }