Mercurial > repos > rliterman > csp2

annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fun/DiskBench.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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jpayne@68 1 package fun;
jpayne@68 2
jpayne@68 3 import java.io.File;
jpayne@68 4 import java.io.IOException;
jpayne@68 5 import java.io.InputStream;
jpayne@68 6 import java.io.PrintStream;
jpayne@68 7 import java.util.ArrayList;
jpayne@68 8 import java.util.Arrays;
jpayne@68 9 import java.util.Locale;
jpayne@68 10 import java.util.Random;
jpayne@68 11
jpayne@68 12 import fileIO.ByteFile;
jpayne@68 13 import fileIO.ByteStreamWriter;
jpayne@68 14 import fileIO.FileFormat;
jpayne@68 15 import fileIO.QuickFile;
jpayne@68 16 import fileIO.ReadWrite;
jpayne@68 17 import fileIO.TextFile;
jpayne@68 18 import shared.Parse;
jpayne@68 19 import shared.Parser;
jpayne@68 20 import shared.PreParser;
jpayne@68 21 import shared.Shared;
jpayne@68 22 import shared.Timer;
jpayne@68 23 import shared.Tools;
jpayne@68 24 import stream.FastaReadInputStream;
jpayne@68 25 import structures.ByteBuilder;
jpayne@68 26
jpayne@68 27 /**
jpayne@68 28 * @author Brian Bushnell
jpayne@68 29 * @date December 6, 2017
jpayne@68 30 *
jpayne@68 31 */
jpayne@68 32 public class DiskBench {
jpayne@68 33
jpayne@68 34 public static void main(String[] args){
jpayne@68 35 //Start a timer immediately upon code entrance.
jpayne@68 36 Timer t=new Timer();
jpayne@68 37
jpayne@68 38 //Create an instance of this class
jpayne@68 39 DiskBench x=new DiskBench(args);
jpayne@68 40
jpayne@68 41 //Run the object
jpayne@68 42 x.process(t);
jpayne@68 43
jpayne@68 44 //Close the print stream if it was redirected
jpayne@68 45 Shared.closeStream(x.outstream);
jpayne@68 46 }
jpayne@68 47
jpayne@68 48 public DiskBench(String[] args){
jpayne@68 49
jpayne@68 50 {//Preparse block for help, config files, and outstream
jpayne@68 51 PreParser pp=new PreParser(args, getClass(), false);
jpayne@68 52 args=pp.args;
jpayne@68 53 outstream=pp.outstream;
jpayne@68 54 }
jpayne@68 55
jpayne@68 56 ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
jpayne@68 57 ReadWrite.MAX_ZIP_THREADS=Shared.threads();
jpayne@68 58
jpayne@68 59 Parser parser=new Parser();
jpayne@68 60 parser.overwrite=true;
jpayne@68 61 for(int i=0; i<args.length; i++){
jpayne@68 62 String arg=args[i];
jpayne@68 63 String[] split=arg.split("=");
jpayne@68 64 String a=split[0].toLowerCase();
jpayne@68 65 String b=split.length>1 ? split[1] : null;
jpayne@68 66
jpayne@68 67 if(a.equals("path")){
jpayne@68 68 path=b;
jpayne@68 69 if(path==null){path="";}
jpayne@68 70 else if(!path.endsWith("/")){path=path+"/";}
jpayne@68 71 }else if(a.equals("lines")){
jpayne@68 72 maxLines=Long.parseLong(b);
jpayne@68 73 if(maxLines<0){maxLines=Long.MAX_VALUE;}
jpayne@68 74 }else if(a.equals("data") || a.equals("size")){
jpayne@68 75 data=Parse.parseKMG(b);
jpayne@68 76 }else if(a.equals("passes")){
jpayne@68 77 passes=Integer.parseInt(b);
jpayne@68 78 }else if(a.equals("verbose")){
jpayne@68 79 verbose=Parse.parseBoolean(b);
jpayne@68 80 }else if(a.equals("gzip")){
jpayne@68 81 verbose=Parse.parseBoolean(b);
jpayne@68 82 }else if(a.equals("mode")){
jpayne@68 83 assert(b!=null) : "Bad parameter: "+arg;
jpayne@68 84 if(Tools.isDigit(b.charAt(0))){mode=Integer.parseInt(b);}
jpayne@68 85 else if("read".equalsIgnoreCase(b) || "r".equalsIgnoreCase(b)){mode=READ;}
jpayne@68 86 else if("write".equalsIgnoreCase(b) || "w".equalsIgnoreCase(b)){mode=WRITE;}
jpayne@68 87 else if("readwrite".equalsIgnoreCase(b) || "rw".equalsIgnoreCase(b)){mode=READWRITE;}
jpayne@68 88 else{assert(false) : "Bad mode: "+arg;}
jpayne@68 89 }else if(a.equals("read") || a.equals("r")){
jpayne@68 90 mode=READ;
jpayne@68 91 }else if(a.equals("write") || a.equals("w")){
jpayne@68 92 mode=WRITE;
jpayne@68 93 }else if(a.equals("readwrite") || a.equals("rw")){
jpayne@68 94 mode=READWRITE;
jpayne@68 95 }else if(a.equals("printtid")){
jpayne@68 96 printTid=Parse.parseBoolean(b);
jpayne@68 97 }else if(a.equals("processbis")){
jpayne@68 98 processBis=Parse.parseBoolean(b);
jpayne@68 99 }else if(a.equals("preread")){
jpayne@68 100 preRead=Parse.parseBoolean(b);
jpayne@68 101 }
jpayne@68 102
jpayne@68 103 else if(a.equals("method")){
jpayne@68 104 assert(b!=null) : "Bad parameter: "+arg;
jpayne@68 105 if(Tools.isDigit(b.charAt(0))){method=Integer.parseInt(b);}
jpayne@68 106 else if("BYTEFILE".equalsIgnoreCase(b) || "bf".equalsIgnoreCase(b)){method=BYTEFILE;}
jpayne@68 107 else if("TEXTFILE".equalsIgnoreCase(b) || "tf".equalsIgnoreCase(b)){method=TEXTFILE;}
jpayne@68 108 else if("QUICKFILE".equalsIgnoreCase(b) || "qf".equalsIgnoreCase(b)){method=QUICKFILE;}
jpayne@68 109 else if("BUFFEREDINPUTSTREAM".equalsIgnoreCase(b) || "bis".equalsIgnoreCase(b)){method=BUFFEREDINPUTSTREAM;}
jpayne@68 110 else if("FILEINPUTSTREAM".equalsIgnoreCase(b) || "fis".equalsIgnoreCase(b)){method=FILEINPUTSTREAM;}
jpayne@68 111 else if("BUFFEREDINPUTSTREAM2".equalsIgnoreCase(b) || "bis2".equalsIgnoreCase(b)){method=BUFFEREDINPUTSTREAM2;}
jpayne@68 112 else if("FILEINPUTSTREAM2".equalsIgnoreCase(b) || "fis2".equalsIgnoreCase(b)){method=FILEINPUTSTREAM2;}
jpayne@68 113 else{assert(false) : "Bad mode: "+arg;}
jpayne@68 114 }
jpayne@68 115 else if("BYTEFILE".equalsIgnoreCase(a) || "bf".equalsIgnoreCase(a)){method=BYTEFILE;}
jpayne@68 116 else if("TEXTFILE".equalsIgnoreCase(a) || "tf".equalsIgnoreCase(a)){method=TEXTFILE;}
jpayne@68 117 else if("QUICKFILE".equalsIgnoreCase(a) || "qf".equalsIgnoreCase(a)){method=QUICKFILE;}
jpayne@68 118 else if("BUFFEREDINPUTSTREAM".equalsIgnoreCase(a) || "bis".equalsIgnoreCase(a)){method=BUFFEREDINPUTSTREAM;}
jpayne@68 119 else if("FILEINPUTSTREAM".equalsIgnoreCase(a) || "fis".equalsIgnoreCase(a)){method=FILEINPUTSTREAM;}
jpayne@68 120 else if("BUFFEREDINPUTSTREAM2".equalsIgnoreCase(a) || "bis2".equalsIgnoreCase(a)){method=BUFFEREDINPUTSTREAM2;}
jpayne@68 121 else if("FILEINPUTSTREAM2".equalsIgnoreCase(a) || "fis2".equalsIgnoreCase(a)){method=FILEINPUTSTREAM2;}
jpayne@68 122 else if("buffer".equalsIgnoreCase(a) || "bufferlen".equalsIgnoreCase(a)){
jpayne@68 123 bufferlen=(int)Parse.parseKMGBinary(b);
jpayne@68 124 }
jpayne@68 125
jpayne@68 126 else if(parser.parse(arg, a, b)){
jpayne@68 127 //do nothing
jpayne@68 128 }else{
jpayne@68 129 outstream.println("Unknown parameter "+args[i]);
jpayne@68 130 assert(false) : "Unknown parameter "+args[i];
jpayne@68 131 // throw new RuntimeException("Unknown parameter "+args[i]);
jpayne@68 132 }
jpayne@68 133 }
jpayne@68 134
jpayne@68 135 {//Process parser fields
jpayne@68 136 overwrite=parser.overwrite;
jpayne@68 137 threads=Shared.threads();
jpayne@68 138 }
jpayne@68 139
jpayne@68 140 assert(FastaReadInputStream.settingsOK());
jpayne@68 141
jpayne@68 142 if(!ByteFile.FORCE_MODE_BF2){
jpayne@68 143 ByteFile.FORCE_MODE_BF2=false;
jpayne@68 144 ByteFile.FORCE_MODE_BF1=true;
jpayne@68 145 }
jpayne@68 146
jpayne@68 147 File pfile=new File(path);
jpayne@68 148 if(!pfile.exists()){pfile.mkdirs();}
jpayne@68 149 }
jpayne@68 150
jpayne@68 151 class WriteThread extends Thread{
jpayne@68 152
jpayne@68 153 public WriteThread(String fname_, long size_){
jpayne@68 154 fname=fname_;
jpayne@68 155 size=size_;
jpayne@68 156 }
jpayne@68 157
jpayne@68 158 @Override
jpayne@68 159 public void run(){
jpayne@68 160 t=new Timer();
jpayne@68 161 written=writeRandomData(fname, size, t, overwrite);
jpayne@68 162 }
jpayne@68 163
jpayne@68 164 String fname;
jpayne@68 165 long size;
jpayne@68 166 long written=0;
jpayne@68 167 Timer t;
jpayne@68 168
jpayne@68 169 }
jpayne@68 170
jpayne@68 171 public static long writeRandomData(final String fname, final long size, final Timer t, final boolean overwrite){
jpayne@68 172 if(t!=null){t.start();}
jpayne@68 173 long written=0;
jpayne@68 174 final Random randy=Shared.threadLocalRandom();
jpayne@68 175 FileFormat ffout=FileFormat.testOutput(fname, FileFormat.TEXT, null, true, overwrite, false, false);
jpayne@68 176 ByteStreamWriter bsw=new ByteStreamWriter(ffout);
jpayne@68 177 bsw.start();
jpayne@68 178 final ByteBuilder bb=new ByteBuilder(66000);
jpayne@68 179 final int shift=6;
jpayne@68 180 final int shiftsPerRand=32/shift;
jpayne@68 181 assert(shiftsPerRand>0);
jpayne@68 182 final long limit=size-20-shiftsPerRand*1000;
jpayne@68 183 while(written<limit){
jpayne@68 184 for(int i=0; i<1000; i+=shiftsPerRand){
jpayne@68 185 int x=randy.nextInt();
jpayne@68 186 for(int j=0; j<shiftsPerRand; j++){
jpayne@68 187 byte b=(byte)(33+x&63);
jpayne@68 188 bb.append(b);
jpayne@68 189 x>>=shift;
jpayne@68 190 }
jpayne@68 191 }
jpayne@68 192 // for(int i=0; i<1000; i+=shiftsPerRand){
jpayne@68 193 // long x=randy.nextLong();
jpayne@68 194 // for(int j=0; j<shiftsPerRand; j++){
jpayne@68 195 // byte b=(byte)(33+x&63);
jpayne@68 196 // bb.append(b);
jpayne@68 197 // x>>=shift;
jpayne@68 198 // }
jpayne@68 199 // }
jpayne@68 200 bb.nl();
jpayne@68 201 written+=bb.length;
jpayne@68 202 bsw.print(bb);
jpayne@68 203 bb.clear();
jpayne@68 204 }
jpayne@68 205 while(written<size-1){
jpayne@68 206 bb.append((byte)(33+(randy.nextInt()&63)));
jpayne@68 207 written++;
jpayne@68 208 }
jpayne@68 209 bb.nl();
jpayne@68 210 written+=bb.length;
jpayne@68 211 bsw.print(bb);
jpayne@68 212 bb.clear();
jpayne@68 213 bsw.poisonAndWait();
jpayne@68 214 File f=new File(fname);
jpayne@68 215 long diskSize=(f.length());
jpayne@68 216 if(t!=null){t.stop();}
jpayne@68 217 return diskSize;
jpayne@68 218 }
jpayne@68 219
jpayne@68 220 class ReadThread extends Thread{
jpayne@68 221
jpayne@68 222 public ReadThread(String fname_, int tid_){
jpayne@68 223 fname=fname_;
jpayne@68 224 tid=tid_;
jpayne@68 225 }
jpayne@68 226
jpayne@68 227 @Override
jpayne@68 228 public void run(){
jpayne@68 229 t=new Timer();
jpayne@68 230 FileFormat ffin=FileFormat.testInput(fname, FileFormat.TEXT, null, false, false, false);
jpayne@68 231
jpayne@68 232 if(method==BYTEFILE){
jpayne@68 233 runBf(ffin);
jpayne@68 234 }else if(method==QUICKFILE){
jpayne@68 235 runQf(ffin);
jpayne@68 236 }else if(method==TEXTFILE){
jpayne@68 237 runTf(ffin);
jpayne@68 238 }else if(method==BUFFEREDINPUTSTREAM){
jpayne@68 239 runBis(ffin, true);
jpayne@68 240 }else if(method==FILEINPUTSTREAM){
jpayne@68 241 runBis(ffin, false);
jpayne@68 242 }else if(method==BUFFEREDINPUTSTREAM2){
jpayne@68 243 runBis2(ffin, true);
jpayne@68 244 }else if(method==FILEINPUTSTREAM2){
jpayne@68 245 runBis2(ffin, false);
jpayne@68 246 }
jpayne@68 247 if(printTid){System.err.print(tid+",");}
jpayne@68 248 t.stop();
jpayne@68 249 }
jpayne@68 250
jpayne@68 251 private void runBf(FileFormat ffin){
jpayne@68 252 ByteFile bf=ByteFile.makeByteFile(ffin);
jpayne@68 253 for(byte[] line=bf.nextLine(); line!=null; line=bf.nextLine()){
jpayne@68 254 read+=line.length+1;
jpayne@68 255 }
jpayne@68 256 }
jpayne@68 257
jpayne@68 258 private void runQf(FileFormat ffin){
jpayne@68 259 QuickFile qf=new QuickFile(ffin);
jpayne@68 260 for(byte[] line=qf.nextLine(); line!=null; line=qf.nextLine()){
jpayne@68 261 read+=line.length+1;
jpayne@68 262 }
jpayne@68 263 }
jpayne@68 264
jpayne@68 265 private void runTf(FileFormat ffin){
jpayne@68 266 TextFile tf=new TextFile(ffin);
jpayne@68 267 for(String line=tf.nextLine(); line!=null; line=tf.nextLine()){
jpayne@68 268 read+=line.length()+1;
jpayne@68 269 }
jpayne@68 270 }
jpayne@68 271
jpayne@68 272 private void runBis(FileFormat ffin, boolean bufferedStream){
jpayne@68 273
jpayne@68 274 final byte[] buffer=new byte[bufferlen];
jpayne@68 275 InputStream is=ReadWrite.getInputStream(ffin.name(), bufferedStream, false);
jpayne@68 276
jpayne@68 277 for(int r=1; r>0; ){
jpayne@68 278 r=0;
jpayne@68 279 try {
jpayne@68 280 r=is.read(buffer);
jpayne@68 281 if(r>0){read+=r;}
jpayne@68 282
jpayne@68 283 if(processBis){
jpayne@68 284 int last=0;
jpayne@68 285 for(int i=1; i<r; i++){
jpayne@68 286 byte b=buffer[i];
jpayne@68 287 if(b=='\n'){
jpayne@68 288 cache=Arrays.copyOfRange(buffer, last, i);
jpayne@68 289 last=i+1;
jpayne@68 290 }
jpayne@68 291 }
jpayne@68 292 }
jpayne@68 293
jpayne@68 294 } catch (IOException e) {
jpayne@68 295 e.printStackTrace();
jpayne@68 296 }
jpayne@68 297 }
jpayne@68 298
jpayne@68 299 try {
jpayne@68 300 is.close();
jpayne@68 301 } catch (IOException e) {
jpayne@68 302 // TODO Auto-generated catch block
jpayne@68 303 e.printStackTrace();
jpayne@68 304 }
jpayne@68 305 }
jpayne@68 306
jpayne@68 307 private void runBis2(FileFormat ffin, boolean bufferedStream){
jpayne@68 308
jpayne@68 309 final byte[] buffer=new byte[bufferlen];
jpayne@68 310 InputStream is=ReadWrite.getInputStream(ffin.name(), bufferedStream, false);
jpayne@68 311
jpayne@68 312 list=new ArrayList<byte[]>(800);
jpayne@68 313 for(int r=1; r>0; ){
jpayne@68 314 r=0;
jpayne@68 315 try {
jpayne@68 316 r=is.read(buffer);
jpayne@68 317 if(r>0){read+=r;}
jpayne@68 318
jpayne@68 319 if(processBis){
jpayne@68 320 int last=0;
jpayne@68 321 for(int i=1; i<r; i++){
jpayne@68 322 byte b=buffer[i];
jpayne@68 323 if(b=='\n'){
jpayne@68 324 byte[] line=Arrays.copyOfRange(buffer, last, i);
jpayne@68 325 list.add(line);
jpayne@68 326 if(list.size()>=800){
jpayne@68 327 list=new ArrayList<byte[]>(800);
jpayne@68 328 }
jpayne@68 329 last=i+1;
jpayne@68 330 }
jpayne@68 331 }
jpayne@68 332 }
jpayne@68 333
jpayne@68 334 } catch (IOException e) {
jpayne@68 335 e.printStackTrace();
jpayne@68 336 }
jpayne@68 337 }
jpayne@68 338
jpayne@68 339 try {
jpayne@68 340 is.close();
jpayne@68 341 } catch (IOException e) {
jpayne@68 342 // TODO Auto-generated catch block
jpayne@68 343 e.printStackTrace();
jpayne@68 344 }
jpayne@68 345 }
jpayne@68 346
jpayne@68 347 byte[] cache;
jpayne@68 348 ArrayList<byte[]> list;
jpayne@68 349 String fname;
jpayne@68 350 long read=0;
jpayne@68 351 long lines=0;
jpayne@68 352 Timer t;
jpayne@68 353 final int tid;
jpayne@68 354
jpayne@68 355 }
jpayne@68 356
jpayne@68 357 String[] makeFnames(int pass){
jpayne@68 358 String[] fnames=new String[threads];
jpayne@68 359 Random randy=new Random();
jpayne@68 360 for(int i=0; i<threads; i++){
jpayne@68 361 fnames[i]=path+pass+"_"+i+"_"+(System.nanoTime()&0xFFFF)+"_"+randy.nextInt(4096);
jpayne@68 362 }
jpayne@68 363 return fnames;
jpayne@68 364 }
jpayne@68 365
jpayne@68 366 Timer readWrite(String[] fnamesW, String[] fnamesR){
jpayne@68 367 Timer t=new Timer();
jpayne@68 368
jpayne@68 369 WriteThread[] wta=new WriteThread[threads];
jpayne@68 370 long size=data/threads;
jpayne@68 371 for(int i=0; i<threads; i++){
jpayne@68 372 wta[i]=new WriteThread(fnamesW[i], size);
jpayne@68 373 }
jpayne@68 374 for(int i=0; i<threads; i++){
jpayne@68 375 wta[i].start();
jpayne@68 376 }
jpayne@68 377
jpayne@68 378 ReadThread[] rta=new ReadThread[threads];
jpayne@68 379 for(int i=0; i<threads; i++){
jpayne@68 380 rta[i]=new ReadThread(fnamesR[i], i);
jpayne@68 381 }
jpayne@68 382 for(int i=0; i<threads; i++){
jpayne@68 383 rta[i].start();
jpayne@68 384 }
jpayne@68 385
jpayne@68 386 for(int i=0; i<threads; i++){
jpayne@68 387 while(wta[i].getState()!=Thread.State.TERMINATED){
jpayne@68 388 try {
jpayne@68 389 wta[i].join();
jpayne@68 390 } catch (InterruptedException e) {
jpayne@68 391 // TODO Auto-generated catch block
jpayne@68 392 e.printStackTrace();
jpayne@68 393 }
jpayne@68 394 }
jpayne@68 395 }
jpayne@68 396
jpayne@68 397 for(int i=0; i<threads; i++){
jpayne@68 398 while(rta[i].getState()!=Thread.State.TERMINATED){
jpayne@68 399 try {
jpayne@68 400 rta[i].join();
jpayne@68 401 } catch (InterruptedException e) {
jpayne@68 402 // TODO Auto-generated catch block
jpayne@68 403 e.printStackTrace();
jpayne@68 404 }
jpayne@68 405 }
jpayne@68 406 }
jpayne@68 407
jpayne@68 408 t.stop();
jpayne@68 409 return t;
jpayne@68 410 }
jpayne@68 411
jpayne@68 412 Timer write(String[] fnames){
jpayne@68 413 Timer t=new Timer();
jpayne@68 414 WriteThread[] wta=new WriteThread[threads];
jpayne@68 415 long size=data/threads;
jpayne@68 416 for(int i=0; i<threads; i++){
jpayne@68 417 wta[i]=new WriteThread(fnames[i], size);
jpayne@68 418 }
jpayne@68 419 for(int i=0; i<threads; i++){
jpayne@68 420 wta[i].start();
jpayne@68 421 }
jpayne@68 422 for(int i=0; i<threads; i++){
jpayne@68 423 while(wta[i].getState()!=Thread.State.TERMINATED){
jpayne@68 424 try {
jpayne@68 425 wta[i].join();
jpayne@68 426 } catch (InterruptedException e) {
jpayne@68 427 // TODO Auto-generated catch block
jpayne@68 428 e.printStackTrace();
jpayne@68 429 }
jpayne@68 430 }
jpayne@68 431 }
jpayne@68 432 t.stop();
jpayne@68 433 return t;
jpayne@68 434 }
jpayne@68 435
jpayne@68 436 Timer read(String[] fnames){
jpayne@68 437
jpayne@68 438 Timer t=new Timer();
jpayne@68 439
jpayne@68 440 if(preRead){
jpayne@68 441 ReadThread rt=new ReadThread(fnames[0], 0);
jpayne@68 442 rt.start();
jpayne@68 443 while(rt.getState()!=Thread.State.TERMINATED){
jpayne@68 444 try {
jpayne@68 445 rt.join();
jpayne@68 446 } catch (InterruptedException e) {
jpayne@68 447 // TODO Auto-generated catch block
jpayne@68 448 e.printStackTrace();
jpayne@68 449 }
jpayne@68 450 }
jpayne@68 451 }
jpayne@68 452
jpayne@68 453 ReadThread[] rta=new ReadThread[threads];
jpayne@68 454 for(int i=0; i<threads; i++){
jpayne@68 455 rta[i]=new ReadThread(fnames[i], i);
jpayne@68 456 }
jpayne@68 457 for(int i=0; i<threads; i++){
jpayne@68 458 rta[i].start();
jpayne@68 459 }
jpayne@68 460 for(int i=0; i<threads; i++){
jpayne@68 461 while(rta[i].getState()!=Thread.State.TERMINATED){
jpayne@68 462 try {
jpayne@68 463 rta[i].join();
jpayne@68 464 } catch (InterruptedException e) {
jpayne@68 465 // TODO Auto-generated catch block
jpayne@68 466 e.printStackTrace();
jpayne@68 467 }
jpayne@68 468 }
jpayne@68 469 linesInternal+=(rta[i].list==null ? 0 : rta[i].list.size());
jpayne@68 470 }
jpayne@68 471 t.stop();
jpayne@68 472 return t;
jpayne@68 473 }
jpayne@68 474
jpayne@68 475 void delete(String[] fnames){
jpayne@68 476 for(String s : fnames){
jpayne@68 477 File f=new File(s);
jpayne@68 478 if(f.exists()){
jpayne@68 479 f.delete();
jpayne@68 480 }
jpayne@68 481 }
jpayne@68 482 }
jpayne@68 483
jpayne@68 484 void process(Timer t0){
jpayne@68 485
jpayne@68 486 t0.start();
jpayne@68 487 String[] fnamesW=makeFnames(0);
jpayne@68 488
jpayne@68 489 Timer t=write(fnamesW);
jpayne@68 490 String[] fnamesR=fnamesW;
jpayne@68 491 fnamesW=null;
jpayne@68 492
jpayne@68 493 final long initialWriteElapsed=t.elapsed;
jpayne@68 494
jpayne@68 495 System.err.println("Initial write: \t"+t.toString()+" \t"+String.format(Locale.ROOT, "%.3f MB/s", (1000.0*data)/t.elapsed));
jpayne@68 496
jpayne@68 497 for(int pass=0; pass<passes; pass++){
jpayne@68 498 if(mode==READWRITE){
jpayne@68 499 fnamesW=makeFnames(pass);
jpayne@68 500 t=readWrite(fnamesW, fnamesR);
jpayne@68 501 delete(fnamesR);
jpayne@68 502 fnamesR=fnamesW;
jpayne@68 503 fnamesW=null;
jpayne@68 504 }else if(mode==READ){
jpayne@68 505 t=read(fnamesR);
jpayne@68 506 }else{
jpayne@68 507 delete(fnamesR);
jpayne@68 508 fnamesW=makeFnames(pass);
jpayne@68 509 t=write(fnamesW);
jpayne@68 510 fnamesR=fnamesW;
jpayne@68 511 fnamesW=null;
jpayne@68 512 }
jpayne@68 513 System.err.println("Pass "+pass+": \t"+t.toString()+" \t"+String.format(Locale.ROOT, "%.3f MB/s", (1000.0*data)/t.elapsed));
jpayne@68 514 }
jpayne@68 515 delete(fnamesR);
jpayne@68 516
jpayne@68 517 t0.stop();
jpayne@68 518 System.err.println("Overall: \t"+t0.toString()+" \t"+String.format(Locale.ROOT, "%.3f MB/s", (1000.0*(data*passes))/(t0.elapsed-initialWriteElapsed)));
jpayne@68 519
jpayne@68 520 if(errorState){
jpayne@68 521 throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
jpayne@68 522 }
jpayne@68 523 }
jpayne@68 524
jpayne@68 525 /*--------------------------------------------------------------*/
jpayne@68 526
jpayne@68 527
jpayne@68 528 /*--------------------------------------------------------------*/
jpayne@68 529
jpayne@68 530 private String path="";
jpayne@68 531
jpayne@68 532 /*--------------------------------------------------------------*/
jpayne@68 533
jpayne@68 534 private int bufferlen=4096;
jpayne@68 535 private long data=8000000000L;
jpayne@68 536 private int passes=2;
jpayne@68 537
jpayne@68 538 public int linesInternal;
jpayne@68 539
jpayne@68 540 private int threads;
jpayne@68 541
jpayne@68 542 private long maxLines=Long.MAX_VALUE;
jpayne@68 543
jpayne@68 544 int mode=READWRITE;
jpayne@68 545 static final int READWRITE=1, READ=2, WRITE=3;
jpayne@68 546
jpayne@68 547 boolean printTid=false;
jpayne@68 548 boolean processBis=false;
jpayne@68 549 boolean preRead=false;
jpayne@68 550
jpayne@68 551 int method=BYTEFILE;
jpayne@68 552 static final int BYTEFILE=1;
jpayne@68 553 static final int TEXTFILE=2;
jpayne@68 554 static final int BUFFEREDINPUTSTREAM=3;
jpayne@68 555 static final int FILEINPUTSTREAM=4;
jpayne@68 556 static final int BUFFEREDINPUTSTREAM2=5;
jpayne@68 557 static final int FILEINPUTSTREAM2=6;
jpayne@68 558 static final int QUICKFILE=7;
jpayne@68 559
jpayne@68 560 /*--------------------------------------------------------------*/
jpayne@68 561
jpayne@68 562 /*--------------------------------------------------------------*/
jpayne@68 563
jpayne@68 564 private PrintStream outstream=System.err;
jpayne@68 565 public static boolean verbose=false;
jpayne@68 566 public boolean errorState=false;
jpayne@68 567 private boolean overwrite=true;
jpayne@68 568
jpayne@68 569 }