Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/kmer/ScheduleMaker.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 package kmer;
2
3 import java.util.Arrays;
4
5 import shared.Primes;
6 import shared.Shared;
7 import shared.Tools;
8 import structures.IntList;
9
10 public class ScheduleMaker {
11
12 public ScheduleMaker(int ways_, int bytesPerKmer_, boolean prealloc_, double memRatio_){
13 this(ways_, bytesPerKmer_, prealloc_, memRatio_, 0, 0, 0, 0);
14 }
15
16 public ScheduleMaker(int ways_, int bytesPerKmer_, boolean prealloc_, double memRatio_, int initialSize_){
17 this(ways_, bytesPerKmer_, prealloc_, memRatio_, initialSize_, 0, 0, 0);
18 }
19
20 public ScheduleMaker(int ways_, int bytesPerKmer_, boolean prealloc_, double memRatio_, int initialSize_,
21 int prepasses_, double prefilterFraction_, long filterMemoryOverride_){
22 bytesPerKmer=bytesPerKmer_;
23 prealloc=prealloc_;
24 memRatio=(float)(memRatio_<=0 ? 1 : memRatio_);
25 prepasses=prepasses_;
26 prefilter=(prepasses>0);
27 prefilterFraction=prefilter ? prefilterFraction_ : 0;
28 assert(prefilter==prefilterFraction>0) : prefilter+", "+prefilterFraction_+", "+prefilterFraction;
29 // assert(false && prefilter==prefilterFraction>0) : prefilter+", "+prefilterFraction_+", "+prefilterFraction;
30 if(prepasses<1){
31 filterMemory0=filterMemory1=0;
32 }else if(filterMemoryOverride>0){
33 filterMemory0=filterMemory1=filterMemoryOverride;
34 }else{
35 double low=Tools.min(prefilterFraction, 1-prefilterFraction);
36 double high=1-low;
37 if(prepasses<0 || (prepasses&1)==1){//odd passes
38 filterMemory0=(long)(usableMemory*low);
39 filterMemory1=(long)(usableMemory*high);
40 }else{//even passes
41 filterMemory0=(long)(usableMemory*high);
42 filterMemory1=(long)(usableMemory*low);
43 }
44 }
45 tableMemory=(long)(usableMemory*.95-Tools.min(filterMemory0, filterMemory1));
46
47 if(ways_<1){
48 long maxKmers=(2*tableMemory)/bytesPerKmer;
49 long minWays=Tools.min(10000, maxKmers/Integer.MAX_VALUE);
50 ways_=(int)Tools.max(31, (int)(Tools.min(96, Shared.threads())*2.5), minWays);
51 ways_=(int)Primes.primeAtLeast(ways_);
52 assert(ways_>0);
53 // System.err.println("ways="+ways_);
54 }
55 ways=ways_;
56
57 final double maxSize0=(tableMemory*0.95*memRatio)/(bytesPerKmer*ways);
58 assert(maxPrime>1 && maxSize0>2) :
59 "\nmaxPrime="+maxPrime+", maxSize0="+maxSize0+", tableMemory="+tableMemory+", usableMemory="+usableMemory+
60 ", \nprepasses="+prepasses+", filterMemory0="+filterMemory0+", filterMemory1="+filterMemory1+", prefilterFraction="+prefilterFraction+
61 ", \nmemRatio="+memRatio+", bytesPerKmer="+bytesPerKmer+", ways="+ways+
62 ", \ninitialSize="+initialSize_+", initialSizeDefault="+initialSizeDefault+", prealloc="+prealloc;
63
64 lastSizeFraction=prealloc ? 1.0 : resizeMult/(1.0+resizeMult);
65 maxSize=Primes.primeAtMost((int)Tools.min(maxPrime, maxSize0*lastSizeFraction));
66 initialSize=(prealloc ? maxSize : Primes.primeAtMost(initialSize_>0 ? initialSize_ : initialSizeDefault));
67
68 estimatedKmerCapacity=(long)(maxSize*HashArray.maxLoadFactorFinal*0.97*ways);
69
70 // System.err.println(Arrays.toString(makeSchedule()));
71
72 // System.err.println("ways="+ways+", maxSize="+maxSize+", estimatedKmerCapacity="+estimatedKmerCapacity+", "+Arrays.toString(makeSchedule()));
73 //
74 // assert(false) :
75 // "\nmaxPrime="+maxPrime+", maxSize0="+maxSize0+", tableMemory="+tableMemory+", usableMemory="+usableMemory+
76 // ", \nprepasses="+prepasses+", filterMemory0="+filterMemory0+", filterMemory1="+filterMemory1+", prefilterFraction="+prefilterFraction+
77 // ", \nmemRatio="+memRatio+", bytesPerKmer="+bytesPerKmer+", ways="+ways+
78 // ", \ninitialSize="+initialSize_+", initialSizeDefault="+initialSizeDefault+", prealloc="+prealloc+
79 // ", \nmaxSize="+maxSize+", initialSize="+initialSize+", estimatedKmerCapacity="+estimatedKmerCapacity+
80 // ", \n"+Arrays.toString(makeSchedule());
81 // assert(false) : Arrays.toString(makeSchedule());
82 }
83
84 public int[] makeSchedule(){
85 if(prealloc || maxSize<2L*initialSize){return new int[] {maxSize};}
86 IntList list=new IntList(10);
87 list.add(maxSize);
88 for(double x=maxSize*invResizeMult; x>=initialSize; x=x*invResizeMult2){
89 list.add((int)x);
90 }
91 if(list.size()>1 && list.lastElement()>=2*initialSize){
92 list.add(initialSize);
93 }
94 list.reverse();
95 // if(list.lastElement()*2L<maxPrime){list.add(2*maxSize);}//This ensures that the program will crash rather than garbage-collecting for a long time
96 int[] array=list.toArray();
97 // if(initialSize>2 && array.length>2 && array[0]>initialSize){array[0]=initialSize;}
98 assert(Tools.isSorted(array)) : Arrays.toString(array);
99 for(int i=0; i<array.length; i++){
100 array[i]=array[i]==1 ? 1 : (int)Tools.min(maxPrime, Primes.primeAtLeast(array[i]));
101 }
102 return array;
103 }
104
105 // public static int[] makeScheduleStatic(int initialSize, int maxSize, boolean autoResize){
106 // if(!autoResize || initialSize>=maxSize){return null;}
107 // IntList list=new IntList(10);
108 // list.add((int)(maxSize*0.8));
109 // for(long x=maxSize; x>=initialSize; x=x/5){
110 // list.add((int)x);
111 // }
112 // if(list.size()>1 && list.lastElement()>=2*initialSize){
113 // list.add(initialSize);
114 // }
115 // list.reverse();
116 // int[] array=list.toArray();
117 // for(int i=0; i<array.length; i++){
118 // array[i]=array[i]==1 ? 1 : (int)Tools.min(maxPrime, Primes.primeAtLeast(array[i]));
119 // }
120 // return array;
121 // }
122
123 final double resizeMult=5.0;
124 final double resizeMult2=3.0;
125 final double invResizeMult=1/resizeMult;
126 final double invResizeMult2=1/resizeMult2;
127 final double lastSizeFraction;
128
129 final long memory=Runtime.getRuntime().maxMemory();
130 final double xmsRatio=Shared.xmsRatio();
131
132 //TODO: Add term for JDK (Oracle/Open) and version.
133 final long usableMemory=(long)Tools.max(((memory-96000000)*
134 (xmsRatio>0.97 ? 0.82 : 0.72)), memory*0.45);
135
136 final long filterMemoryOverride=0;
137
138 final long filterMemory0, filterMemory1;
139 final long tableMemory;
140 final double prefilterFraction;
141 final int prepasses;
142 final boolean prefilter;
143 final int bytesPerKmer;
144 public final long estimatedKmerCapacity;
145
146 public final int ways;
147
148 final int initialSize;
149 final int maxSize;
150
151 final boolean prealloc;
152 final float memRatio;
153
154 static final int initialSizeDefault=128000;
155 static final int maxPrime=(int)Primes.primeAtMost(Integer.MAX_VALUE-100-20);
156
157 }