1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942
|
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "libMems/dmSML/util.h"
#include "libMems/dmSML/timing.h"
#include "libMems/dmSML/asyncio.h"
#include "libMems/dmSML/buffer.h"
#include "libMems/dmSML/sorting.h"
#include "libMems/dmSML/sml.h"
#include "libMems/dmSML/dmsort.h"
// define this if you're using the ASCII sortgen data.
// don't define if you're using random data (dmsortgen)
//#define ASCII_KEYBYTES
// define this if using dmSML with sequences that have large
// stretches of NNNNN... such as an unfinished eukaryote
//#define NNNNN_KEYBYTES
// define this if you want to measure the overlapping
// of your sorting with I/O in the sorting phase --
// this makes the sort routine do nothing.
//#define NO_SORT_PERF_TEST
// define the following if you don't want to write
// data during the sort phase in order to get timings
//#define NO_WRITE_PERF_TEST
// define this to skip the binning phase in order to
// perform measurements on the sort phase. The bin
// files to use during sorting must already exist (duh!)
// #define NO_BINNING_PERF_TEST
// define this to test the performance of binning and
// restructuring without bin writing
//#define NO_BIN_WRITE_PERF_TEST
// define this to test the performance without restructuring
// each SML bin
//#define NO_RESTRUCTURE_PERF_TEST
/*
#define NELEMS(x) \
( sizeof((x)) / sizeof((x)[0]) )
#define MIN(x,y) ((x)<(y)?(x):(y))
#define MINRECS (1311)
#define MAXRECS (1311)
// this is somewhat less appealing than a config file,
// but speed is critical and parsing a config file at
// startup is just inconvenient. Besides, specifying
// what we care about is easy enough this way.
typedef struct device_s {
const char *devname;
const char *path;
iodevice_t dev;
} device_t;
*/
device_t *Devices;
int NumDevices;
// ugly hack
//#define BIN_SPECIAL (-10000)
int NSortBufs;
sort_buf_t *SortBufs;
// how the working set is allocated originally.
offset_t BufferSizeMin;
offset_t BufferSizeMax;
/*
// what we use to represent a bin.
typedef struct bin_s {
aFILE *file; // File we write/read on.
int dev; // This is an index into the Devices table.
offset_t nrecs; // Number of records written to bin.
buffer_list_t bufs; // Our list of buffers that holds our data.
} bin_t;
*/
// number specified by a cmdline param at runtime.
bin_t *Bins;
int NumBins;
int NumBinDevs; // number of binning devices
/*
typedef struct seqbuf_s {
aFILE *file; // Output file
int dev; // device table index for output file
offset_t bufpos; // position in current buffer
uint64 seq_pos; // position in sequence that is next to translate
buffer_list_t bufs; // list of buffers for data
} seqbuf_t;
*/
seqbuf_t Seqbuf;
aFILE *Data; // the data to sort
int DataDev; // the device the data file is on.
const char *OutFileName = "unset"; // the output file name.
aFILE *Output; // the output file (sorted data goes here)
int OutputDev; // the device the output goes on.
int BinToRead, BinToWrite, BinToSort;
working_set_t WS; // the Working Set we use to do our sorting.
offset_t NumRecs; // the total number of blocks to process
offset_t RecsProcessed; // number of blocks processed (put in bins to write out)
offset_t RecsRead; // number of records fully read in.
offset_t RecsUnread; // number of blocks on disk (not yet had 'read' called)
offset_t RecsCommitted; // number of records committed to be written.
offset_t RecsWritten; // number of records actually written on disk.
// timers
double RunningTime;
dmtimer_t *RunningTimer;
double BinningTime;
dmtimer_t *BinningTimer;
double SortingTime;
dmtimer_t *SortingTimer;
double QSortTime;
dmtimer_t *QSortTimer;
double ReadIdleTime;
dmtimer_t *ReadIdleTimer;
double SortIdleTime;
dmtimer_t *SortIdleTimer;
double WriteIdleTime;
dmtimer_t *WriteIdleTimer;
// buffer lists
buffer_list_t Free; // the free list
buffer_list_t ToProcess; // list read and to be processed
buffer_list_t Reading; // the list that's waiting on stuff to read.
buffer_list_t Restructure; // buffers that need post-read and pre-binning processing
static buffer_t * AllocateFree( void ) {
buffer_t * ret;
if( Free.nitems ) {
ret = PopHead( &Free );
} else {
printf( "error: called AllocateFree but free list is empty\n" );
return( NULL );
}
ret->device = NULL;
ret->file = NULL;
ret->last = ret->next = NULL;
ret->numrecs = 0;
ret->operation = OP_NONE;
return( ret );
}
static unsigned int divisor = 0;
static int ComputeBinNumber( const unsigned char key[10] ) {
int i;
unsigned int keyval = 0;
// how many bits can we use for the binning number?
// first time through, compute divisor
// assume even distribution
// strange constant is 256^3, because we're dealing
// with effectively a base 256 number here, and we can
// only handle 3 places without overflowing.
if( divisor == 0 ) {
divisor = (unsigned)16777216 / (unsigned)NumBins;
// need ceiling of this
divisor += (unsigned)16777216 % (unsigned)NumBins ? 1 : 0;
printf( "Divisor is: %u\n", divisor );
}
// now we compute the number represented by the first 3
// characters of the key, and divide it by divisor, the
// integral part gives the bin number.
for( i = 0; i < 3; i++ ) {
keyval <<= 8;
keyval += key[i];
}
// printf( "Key is %.2x %.2x %.2x \n", key[0],key[1], key[2] );
// printf( "Keyval is: %u\n", keyval );
// printf( "Bin is: %u\n", keyval / divisor );
return( keyval / divisor );
}
// just like ComputeBinNumber except we reserve one bin for zero keys.
static int ComputeNNNNNBinNumber( const unsigned char key[10] ) {
int i;
unsigned int keyval = 0;
if( divisor == 0 ) {
divisor = (unsigned)16777216 / ((unsigned)NumBins - 1);
// need ceiling of this
divisor += (unsigned)16777216 % ((unsigned)NumBins - 1) ? 1 : 0;
printf( "Divisor is: %u\n", divisor );
}
// now we compute the number represented by the first 3
// characters of the key, and divide it by divisor, the
// integral part gives the bin number.
for( i = 0; i < 3; i++ ) {
keyval <<= 8;
keyval += key[i];
}
// printf( "Key is %.2x %.2x %.2x \n", key[0],key[1], key[2] );
// printf( "Keyval is: %u\n", keyval );
// printf( "Bin is: %u\n", keyval / divisor );
if( keyval == 0 )
return 0;
return ( keyval / divisor ) + 1;
}
static int ComputeAsciiBinNumber( const unsigned char key[10] ) {
int i;
unsigned int keyval = 0;
// how many bits can we use for the binning number?
// first time through, compute divisor
if( divisor == 0 ) {
// strange constant is 95^4 -- the max possible value
// of the first five key characters + 1.
divisor = 81450625 / NumBins;
// need ceiling of this
divisor += 81450625 % NumBins ? 1 : 0;
}
// now we compute the number represented by the first 4
// characters of the key, and divide it by divisor, the
// integral part gives the bin number.
for( i = 0; i < 4; i++ ) {
keyval *= 95;
keyval += key[i] - ' ';
}
return( keyval / divisor );
}
static offset_t consumed_recs = 0;
static buffer_t *toprocess = NULL;
static void DoBinning( void ) {
//printf( "--------------- do binning -------------\n" );
while( 1 ) {
int bin = -1;
// if we don't already have a buffer to process, see if we
// can get one.
if( toprocess == NULL ) {
//printf( "toprocess == null -- no currently processing buffer\n" );
if( ToProcess.nitems ) {
//printf( "getting one off ToProcess list\n" );
toprocess = PopHead( &(ToProcess) );
consumed_recs = 0;
} else {
// we can't get anything to process
//printf( "nothing to process\n" );
return;
}
}
//printf( "processing records in current toprocess buffer\n" );
// try to process all the records in the toprocess buffer.
//printf( "for( ; consumed_recs (%d) < toprocess->numrecs (%d); ... ) {\n", consumed_recs, toprocess->numrecs );
for( ; consumed_recs < toprocess->numrecs; consumed_recs++, RecsProcessed++ ) {
buffer_t *headbuf;
record_t *rec = &(toprocess->recs[consumed_recs]);
// find what bin this next record belongs in.
#ifdef ASCII_KEYBYTES
bin = ComputeAsciiBinNumber( rec->key );
#else
#ifdef NNNNN_KEYBYTES
bin = ComputeNNNNNBinNumber( rec->key );
#else
bin = ComputeBinNumber( rec->key );
#endif
#endif
if( (bin >= NumBins) || (bin < 0) ) {
printf( "error: invalid bin from ComputeBinNumber: %d\n", bin );
}
//printf( "record bound for bin %d\n", bin );
// now, let's see what the situation is with that bin and its
// buffers. In particular, do we have a spot to put this record?
headbuf = Bins[bin].bufs.head;
// if we have a buffer, and the buffer is full or executing or
// if there's no buffer at all, let's try to get one
if( !headbuf ||
headbuf->numrecs == headbuf->totalrecs ||
headbuf->operation != OP_NONE ) {
//printf( "headbuf busy or full -- op: %d, numrecs: %d, totalrecs: %d\n",
//headbuf->operation, headbuf->numrecs, headbuf->totalrecs );
// first see if this is our 'special' buffer and if we can use it
if( headbuf->operation == BIN_SPECIAL ) {
//printf( "headbuf is only one left and finished so reclaiming for use\n" );
headbuf->numrecs = 0;
headbuf->operation = OP_NONE;
} else {
//printf( "trying to get buffer from free list\n" );
if( Free.nitems ) {
//printf( "got one from freelist\n" );
PushHead( &(Bins[bin].bufs), AllocateFree() );
headbuf = Bins[bin].bufs.head;
} else {
// printf( "no free buffers to use for bin -- binning BLOCKS!\n" );
return;
}
}
}
// now headbuf must exist, and it must be non-full so we can
// add our item.
headbuf->recs[headbuf->numrecs++] = *rec;
Bins[bin].nrecs++;
//printf( "added rec to bin\n" );
// if we made it full, write the thing
if( headbuf->numrecs >= headbuf->totalrecs ) {
//printf( "writing bin buffer because full\n" );
headbuf->file = Bins[bin].file;
headbuf->device = &(Devices[Bins[bin].dev].dev);
RecsCommitted += headbuf->numrecs;
#ifdef NO_BIN_WRITE_PERF_TEST
// just put it in the finished state
headbuf->operation = OP_FINISHED;
#else
WriteBuffer( headbuf, headbuf->numrecs, headbuf->device );
#endif
headbuf = NULL;
}
}
// if we hit the end of this buffer,
// put it back on the free list, and start the loop over
if( consumed_recs >= toprocess->numrecs ) {
//printf( "finished with this block\n" );
PushTail( &Free, toprocess );
toprocess = NULL;
}
//printf( "going back for more\n" );
}
}
void FinishBinning() {
int i;
buffer_t *b;
offset_t recs = 0;
// be sure to finish off the write operations.
for( i = 0; i < NumBins; i++ ) {
//printf( "bin: %d, nrecs: %d, operation: %d\n", i, Bins[i].nrecs, Bins[i].operation );
while( Bins[i].bufs.nitems ) {
// walk through the buffers, and if they haven't been executed,
// execute them.
b = PopHead( &(Bins[i].bufs) );
if( b->operation == OP_NONE && b->numrecs ) {
recs += b->numrecs;
b->file = Bins[i].file;
b->device = &(Devices[Bins[i].dev].dev);
#ifdef NO_BIN_WRITE_PERF_TEST
// just put it in the finished state
b->operation = OP_FINISHED;
#else
WriteBuffer( b, b->numrecs, b->device );
#endif
}
}
}
RecsCommitted += recs;
}
offset_t CalculateDataReadSize( buffer_t* b ){
// commented version is for traditional dmsort
// return MIN(b->totalrecs, RecsUnread) * sizeof( record_t );
return MIN(b->totalrecs + mask_length - 1, RecsUnread + mask_length - 1 );
}
static void DoReading( void ) {
buffer_t * b;
//printf( "do reading\n" );
if( RecsUnread && Free.nitems ) {
// allocate a buffer
b = AllocateFree();
// start reading into it.
b->file = Data;
ReadBuffer( b, MIN(b->totalrecs, RecsUnread), &(Devices[DataDev].dev) );
b->input_pos = NumRecs - RecsUnread;
// need to step back mask_length - 1 characters to get the complete sequence!!
// if( b->input_pos >= mask_length - 1 )
// b->input_pos -= mask_length - 1;
b->io_pos = b->input_pos;
// printf( "Reading offset %llu\n", b->io_pos );
b->io_size = CalculateDataReadSize( b );
// decrement recsunread appropriately
RecsUnread -= MIN(MIN(b->totalrecs,RecsUnread),RecsUnread);
// put the thing on the Reading list.
//printf( "new buffer on reading list\n" );
PushTail( &Reading, b );
}
}
static void HandleBinWriteCompletions( void ) {
int i;
buffer_t *b, *tmpnext;
//printf( "handle bin write completions\n" );
for( i = 0; i < NumBins; i++ ) {
b = Bins[i].bufs.head;
do {
if( !b ) {
break;
}
tmpnext = b->next;
if( b->operation == OP_FINISHED ) {
RecsWritten += b->numrecs;
if( Bins[i].bufs.nitems > 1 ) {
b->operation = OP_NONE;
PushHead( &Free, RemoveItem( &(Bins[i].bufs), b ) );
} else {
b->operation = BIN_SPECIAL;
}
}
b = tmpnext;
} while( b != Bins[i].bufs.head && Bins[i].bufs.nitems > 1 );
}
}
static void HandleSeqbufWriteCompletions( void ) {
buffer_t *b, *tmpnext;
//printf( "handle bin write completions\n" );
b = Seqbuf.bufs.head;
do {
if( !b ) {
break;
}
tmpnext = b->next;
if( b->operation == OP_FINISHED ) {
if( Seqbuf.bufs.nitems > 1 ) {
b->operation = OP_NONE;
PushHead( &Free, RemoveItem( &(Seqbuf.bufs), b ) );
}
}
b = tmpnext;
} while( b != Seqbuf.bufs.head && Seqbuf.bufs.nitems > 1 );
}
#define ALPHA_BITS 2
static void Translate32(uint32* dest, const char* src, const unsigned len){
uint8 start_bit = 0;
unsigned cur_word = 0;
uint32 word_mer = 0;
uint32 i = 0;
if( len == 0 )
return;
for(i=0; i < len; i++){
// uint32 tmp = DNA_TABLE[src[i]];
if(start_bit + ALPHA_BITS <= 32){
word_mer <<= ALPHA_BITS;
word_mer |= DNA_TABLE[src[i]];
dest[cur_word] = word_mer;
start_bit += ALPHA_BITS;
if(start_bit >= 32 && i < len - 1){
word_mer = 0;
start_bit %= 32;
cur_word++;
}
}else{
printf("Error, this should never happen with DNA sequence\n" );
/* uint8 over_bits = (start_bit + ALPHA_BITS) % 32;
uint32 tmp2 = tmp;
tmp2 <<= 32 - over_bits;
tmp >>= over_bits;
dest[cur_word] |= tmp;
cur_word++;
dest[cur_word] = 0;
dest[cur_word] |= tmp2;
start_bit = over_bits;
*/ }
}
if( start_bit != 0 ){
dest[cur_word] <<= 32 - start_bit;
}
}
void RestructureReadSMLBins( void ) {
char little_endian = 1;
mask_t bit;
mask_t mer, rc_mer;
record_t forward, reverse;
record_t begin[6]; // the first six records could potentially overwrite the sequence
int i;
offset_t seqI, extras, weight;
char* sequence;
sml_t *sml;
buffer_t *b, *tmpnext;
// variables for translation to 2-bit per base
buffer_t *headbuf;
int seq_bit;
int seq_word;
int word_remainder;
offset_t translate_length;
int config_value = 4554307;
// int seq_offset;
// go through and see if any have completed.
b = Restructure.head;
do {
if( !b ) {
break;
}
// is this the buffer we need to translate next?
if( b->input_pos != Seqbuf.seq_pos ){
b = b->next;
continue;
}
tmpnext = b->next;
sequence = (char *)b->recs;
sml = (sml_t*)b->recs;
// translate the sequence that was just read and write it out
headbuf = Seqbuf.bufs.head;
// if we have a buffer, and the buffer is full or executing or
// if there's no buffer at all, let's try to get one
if( !headbuf ||
headbuf->operation != OP_NONE ) {
//printf( "headbuf busy or full -- op: %d, numrecs: %d, totalrecs: %d\n",
//headbuf->operation, headbuf->numrecs, headbuf->totalrecs );
// first see if this is our 'special' buffer and if we can use it
if( headbuf->operation == OP_FINISHED ) {
//printf( "headbuf is only one left and finished so reclaiming for use\n" );
headbuf->numrecs = 0;
headbuf->operation = OP_NONE;
Seqbuf.bufpos = 0;
} else {
//printf( "trying to get buffer from free list\n" );
if( Free.nitems ) {
// printf( "got one from freelist\n" );
PushHead( &(Seqbuf.bufs), AllocateFree() );
headbuf = Seqbuf.bufs.head;
Seqbuf.bufpos = 0;
} else {
// printf( "no free buffers to use for Seqbuf -- restructuring BLOCKS!\n" );
return;
}
}
}
seq_bit = Seqbuf.bufpos * 2;
seq_word = seq_bit / 32;
word_remainder = seq_bit % 32;
if( word_remainder != 0 ){
seq_word++;
}
// int end_bit = 2 * (Seqbuf->bufpos + b->io_size - mask_length + 1);
// int end_remainder = end_bit % 32;
translate_length = b->io_size - mask_length + 1 - (word_remainder / 2);
if( b->io_size + b->input_pos >= NumRecs ){
// this is the last I/O, translate the whole thing
translate_length += mask_length - 1;
}
// translate_length -= end_remainder / 2;
// The number of bytes in headbuf->recs must ALWAYS be divisible by 4 when using
// Translate32, otherwise corruption will result
#ifndef NO_RESTRUCTURE_PERF_TEST
Translate32( (uint32*)(headbuf->recs) + seq_word, ((char*)b->recs) + (word_remainder / 2), translate_length );
#endif
// need to fill in beginning
if( word_remainder != 0 ){
int begin_mer = 0;
for( seqI = 0; seqI < word_remainder / 2; seqI++ ){
begin_mer <<= 2;
begin_mer |= DNA_TABLE[ sequence[ seqI ] ];
}
// ((uint32*)headbuf->recs)[ seq_word - 1 ] <<= 32 - word_remainder;
((uint32*)headbuf->recs)[ seq_word - 1 ] |= begin_mer;
}
Seqbuf.bufpos += translate_length + (word_remainder / 2);
Seqbuf.seq_pos += translate_length + (word_remainder / 2);
// if we made it full, write the thing
// each buf will consume headbuf->totalrecs / 4 bytes.
// there are headbuf->totalrecs * sizeof( record_t ) bytes available in the Seqbuf.
// thus we can fit 4 * sizeof( record_t ) bufs in each Seqbuf
if( Seqbuf.bufpos == headbuf->totalrecs * sizeof( record_t ) * 4 ||
b->io_size + b->input_pos >= NumRecs ) {
//printf( "writing bin buffer because full\n" );
headbuf->file = Seqbuf.file;
headbuf->device = &(Devices[Seqbuf.dev].dev);
WriteBuffer( headbuf, headbuf->totalrecs, headbuf->device );
headbuf->io_size = Seqbuf.bufpos / 4;
if( b->io_size + b->input_pos >= NumRecs ){
offset_t offI = 0;
offI = headbuf->io_size % 4;
if( offI != 0 )
headbuf->io_size += 4 - offI;
for( offI = 0; offI < 8; offI++ )
((char*)headbuf->recs)[ headbuf->io_size + offI ] = 0;
headbuf->io_size += 8;
}
headbuf = NULL;
}else if( Seqbuf.bufpos > headbuf->totalrecs * sizeof( record_t ) * 4 ){
printf( "Error. Over filled Seqbuf\n" );
}
// translate the sequence according to the current sequence mask
#ifndef NO_RESTRUCTURE_PERF_TEST
for( seqI = b->io_size - mask_length + 1; seqI > 0; seqI-- ){
bit = 1;
bit <<= mask_length - 1;
mer = 0;
weight = 0;
for( i = 0; i < mask_length; i++ ){
if( bit & seed_mask ){
mer <<= 2;
mer |= DNA_TABLE[ sequence[ seqI + i - 1 ] ];
}
bit >>= 1;
}
// copy the mer from the 64-bit integer based on the endian-ness of the system
// copy mer to forward key
mer <<= 64 - (2 * mask_weight);
// if( seqI + b->input_pos == config_value )
// __asm( nop );
if( little_endian ){
for( i = 0; i < MASK_T_BYTES; i++ )
forward.key[i] = ((char*)(&mer))[ sizeof( mer ) - i - 1 ];
}else{
for( i = 0; i < MASK_T_BYTES; i++ )
forward.key[i] = ((char*)(&mer))[ i ];
}
// reverse complement the mer
mer = ~mer;
for( i = 0; i < 64; i += 2 ){
rc_mer <<= 2;
rc_mer |= mer & 3;
mer >>= 2;
}
rc_mer <<= 64 - (2 * mask_weight);
// copy mer to reverse key
if( little_endian ){
for( i = 0; i < MASK_T_BYTES; i++ )
reverse.key[i] = ((char*)(&rc_mer))[ sizeof( mer ) - i - 1 ];
}else{
for( i = 0; i < MASK_T_BYTES; i++ )
reverse.key[i] = (((char*)(&rc_mer))[i]);
}
// put the lesser key in forward
if( COMPARE_KEYS( forward, reverse ) > 0)
forward = reverse;
// watch out for the last 6 records
if( seqI <= 6 ){
begin[ seqI - 1] = forward;
}else{
b->recs[ seqI - 1 ] = forward;
// set the position
sml[ seqI - 1 ].pos = b->input_pos + seqI - 1;
}
}
extras = b->io_size - mask_length + 1 < 6 ? b->io_size - mask_length + 1 : 6;
// fill in the first six records
for(; seqI < extras; seqI++ ){
b->recs[ seqI ] = begin[ seqI ];
// set the position
sml[ seqI ].pos = b->input_pos + seqI;
}
#else
if(1){ // define a new scope so the variables can be local
// simulate random data in each bin
int i;
unsigned int keyval = 0;
unsigned int tmpval = 0;
if( divisor == 0 ) {
divisor = (unsigned)16777216 / (unsigned)NumBins;
// need ceiling of this
divisor += (unsigned)16777216 % (unsigned)NumBins ? 1 : 0;
printf( "Divisor is: %u\n", divisor );
}
for( seqI = 0; seqI < b->numrecs; seqI++ ){
tmpval = keyval;
for( i = 3; i > 0; i-- ) {
b->recs[ seqI ].key[ i - 1 ] = (tmpval & 0xFF);
b->recs[ seqI ].key[ i - 1 ] = 0;
tmpval >>= 8;
}
keyval += divisor;
}
}
#endif
// b has been restructured, add it to the ToProcess list
PushTail( &ToProcess, RemoveItem( &Restructure, b ) );
b = tmpnext;
} while( b != Restructure.head && Restructure.nitems );
}
static void HandleReadingCompletions( void ) {
buffer_t *b, *tmpnext;
// just go through and see if any have completed.
b = Reading.head;
do {
if( !b ) {
break;
}
tmpnext = b->next;
if( b->operation == OP_FINISHED ) {
// migrate this to the toprocess list
b->operation = OP_NONE;
PushTail( &Restructure, RemoveItem( &Reading, b ) );
// bookkeeping
RecsRead += b->numrecs;
}
b = tmpnext;
} while( b != Reading.head && Reading.nitems );
}
void print_usage( const char* pname ){
printf( "Usage: %s <-m Working set size in MB> <-b buffer size> <-i input file> <-o output file> [-n number of records] <bin directory> <num bins> ... [bin directory] [num bins]\n", pname );
}
int InitdmSML( long working_mb, long buffer_size, const char* input_filename, const char* output_filename, const char* const* scratch_paths, uint64 seed ) {
int i, j;
offset_t desired_ws_size, actual_ws_size;
SMLHeader_t header;
struct {
const char * bin_dev;
int devnum;
int nbins;
} bins[8];
char *bin_name;
int scratchI = 0;
// initialize the timing stuff
InitTime();
// start the running timer now.
RunningTime = 0;
RunningTimer = StartTimer();
if( working_mb != 0 ){
desired_ws_size = working_mb;
desired_ws_size *= 1024 * 1024; // convert to bytes
}else{
// set desired working set size to half of physical memory...
#ifdef WIN32
{
/* MEMORYSTATUSEX ms;
memset( &ms, 0, sizeof( MEMORYSTATUSEX ) );
GlobalMemoryStatusEx( &ms );
desired_ws_size = ms.ullTotalPhys / 2;
*/
MEMORYSTATUS ms;
memset( &ms, 0, sizeof( MEMORYSTATUS ) );
GlobalMemoryStatus( &ms );
desired_ws_size = ms.dwTotalPhys / 2;
}
#else
{
// get it from /proc/meminfo
FILE *fp = fopen("/proc/meminfo", "r");
if ( fp )
{
long memTotal;
char buf[1024];
if ( fgets(buf, sizeof(buf), fp) )
{
sscanf(buf, "MemTotal: %ld kB", &memTotal);
fprintf( stderr, "%s", buf );
}
fclose(fp);
// allocate about 6/10 of physical memory
// leave the rest for buffer cache
desired_ws_size = memTotal * 512;
}
}
#endif
// never allocate more than 2GB
if( desired_ws_size / 1024 > 2048 * 1024 ){
desired_ws_size = 1024 * 1024;
desired_ws_size *= 2048;
}
// desired_ws_size /= sizeof( record_t ); // get working set size in records
}
if( buffer_size == 0 ){
buffer_size = 1;
while( desired_ws_size / (buffer_size*sizeof(record_t)) > 2048 ){
buffer_size *= 2;
}
}
BufferSizeMin = BufferSizeMax = buffer_size;
OutFileName = output_filename;
// find out how many scratch paths were given before the null terminator
for( ; ; scratchI++ ){
if( !scratch_paths || scratch_paths[ scratchI ] == NULL )
break;
}
NumBinDevs = scratchI;
NumDevices = 2 + NumBinDevs;
Devices = (device_t*)malloc( NumDevices * sizeof(device_t) );
DataDev = 0;
OutputDev = 1;
Devices[DataDev].devname = "Input device";
Devices[DataDev].path = input_filename;
Devices[DataDev].dev.buf = NULL;
Devices[OutputDev].devname = "Output device";
Devices[OutputDev].path = OutFileName;
Devices[OutputDev].dev.buf = NULL;
if( NumBinDevs == 0 ) {
return TOO_FEW_BINS;
} else if( NumBinDevs > 8 ) {
return TOO_MANY_BINS;
}
NumRecs = aStatFileSize( input_filename );
// calculate number of bins using nrecs and ws_size
NumBins = desired_ws_size / (200 * NumBinDevs);
NumBins = NumRecs / NumBins;
NumBins = NumBins < 5 * NumBinDevs ? 5 * NumBinDevs : NumBins; // don't allow fewer than 5 bins per dev
// round for equal number of bins per dev
if( NumBins % NumBinDevs != 0 )
NumBins = ( (NumBins / NumBinDevs) + 1 ) * NumBinDevs;
printf( "Creating %d bin files\n", NumBins );
for( i = 2; i < NumDevices; i++ ){
bin_name = (char*)malloc( 10 );
strcpy( bin_name, "bin dev__" );
bin_name[8] = 0x40 + i - 2;
Devices[i].devname = bin_name;
Devices[i].path = scratch_paths[ i - 2 ];
Devices[i].dev.buf = NULL;
bins[i - 2].bin_dev = bin_name;
bins[i - 2].nbins = NumBins / NumBinDevs; // allocate even an portion of bins per device
bins[i - 2].devnum = i;
}
// get buffer size.
if( BufferSizeMin == 0 ) {
BufferSizeMin = MINRECS;
BufferSizeMax = MAXRECS;
}
// open the input file
Data = aOpen( input_filename, A_READ );
if( Data == NULL ) {
printf( "couldn't open data file\n" );
return INPUT_NOT_OPENED;
}
// get working set size
if( desired_ws_size == 0 ) {
printf( "invalid working set size (%llu) -- must be at least 0\n", desired_ws_size );
return INVALID_WS_SIZE;
}
// init translation table
DNA_TABLE = CreateBasicDNATable();
// open the output file
Output = aOpen( OutFileName, A_WRITE );
if( !Output ) {
printf( "couldn't open output file!\n" );
return OUTPUT_NOT_OPENED;
}
header = InitSML( Output, NumRecs, seed );
seed_mask = header.seed;
mask_length = header.seed_length;
mask_weight = header.seed_weight;
if( NumRecs <= mask_length - 1 ){
printf( "Sequence must be at least %d characters in length\n", mask_length );
return SEQUENCE_TOO_SHORT;
}
NumRecs -= mask_length - 1;
printf( "NumRecs is: %llu \n", NumRecs );
// get the number of records we should process
RecsProcessed = 0;
RecsUnread = NumRecs;
if( NumRecs <= 0 ) {
return INVALID_NUMRECS;
printf( "invalid NumRecs: %llu\n", NumRecs );
}
// go ahead and create the working set.
actual_ws_size = MakeWorkingSet( &WS, desired_ws_size, BufferSizeMin, BufferSizeMax );
printf( "desired working set: %llu, actual working set: %llu\n",
desired_ws_size, actual_ws_size );
// initialize the Free list -- just put all the buffers on it.
for( i = 0; i < WS.nbufs; i++ ) {
PushHead( &Free, &(WS.bufs[i]) );
}
printf( "working set size : %llu\n", actual_ws_size );
printf( "total buffers : %d\n", WS.nbufs );
// FIXME: can any touching of the memory here help us?
// toprocess and reading list empty to start
ToProcess.nitems = Reading.nitems = 0;
ToProcess.head = Reading.head = NULL;
Restructure.nitems = 0;
Restructure.head = NULL;
// allocate Seqbuf
Seqbuf.file = Output;
Seqbuf.dev = OutputDev;
Seqbuf.bufpos = 0;
Seqbuf.seq_pos = 0;
if( Free.nitems ) {
PushHead( &(Seqbuf.bufs), AllocateFree() );
} else {
printf( "error: could not give a buffer to Seqbuf\n" );
return NO_FREE_BUFFERS;
}
// allocate the bins.
Bins = malloc( sizeof( *Bins ) * NumBins );
memset( Bins, 0, sizeof( *Bins ) * NumBins );
// allocate the bins in a round-robin fashion, so when we read
// things back for sorting, we're not swamping one device at a time --
// instead, things are spread out.
printf( "opening %d bins\n", NumBins );
j = -1;
for( i = 0; i < NumBins; i++ ) {
// find a bin on the next device.
while( 1 ) {
j = (j+1) % NumBinDevs;
if( bins[j].nbins ) {
// make this bin on that device, and
// round-robin switch to the next device.
const char *fname = Fmt("%sout%05d.binned",Devices[bins[j].devnum].path,i);
Bins[i].dev = bins[j].devnum;
Bins[i].fname = malloc( strlen( fname ) + 1 );
strcpy( Bins[i].fname, fname );
#ifndef NO_BINNING_PERF_TEST
Bins[i].file = aOpen( fname, A_WRITE );
//printf( "opened '%s' on device '%s'\n", fname, Devices[bins[j].devnum].devname );
if( Bins[i].file == NULL ) {
printf( "couldn't open output bin file '%s'\n", fname );
return BIN_NOT_OPENED;
}
#else
Bins[i].nrecs = aStatSize( fname );
if( Bins[i].nrecs == 0 ){
// just make sure the file exists
Bins[i].file = aOpen( fname, A_WRITE );
aClose( Bins[i].file );
Bins[i].file = NULL;
}
#endif // NO_BINNING_PERF_TEST
bins[j].nbins--;
break;
}
}
}
// now we allocate one buffer for each bin
// and each bin will hold onto at least one buffer
// so that we can guarantee no locking cases
for( i = 0; i < NumBins; i++ ) {
if( Free.nitems ) {
PushHead( &(Bins[i].bufs), AllocateFree() );
} else {
printf( "error: could not give one buffer to each bin\n" );
return NO_FREE_BUFFERS;
}
}
// all went well
return 0;
}
void DisplayStatusHeader( void ) {
printf( "time recs_read recs_processed recs_committed recs_written binning_rate free reading toprocess bins restructure\n" );
}
void DisplayStatus( void ) {
printf( "%f %llu %llu %llu %llu %f %d %d %d %d %d\n",
RunningTime, RecsRead, RecsProcessed, RecsCommitted, RecsWritten,
RecsProcessed/RunningTime, Free.nitems, Reading.nitems, ToProcess.nitems,
WS.nbufs - Free.nitems - Reading.nitems - ToProcess.nitems - Restructure.nitems, Restructure.nitems );
/*
int i;
printf( "-----------------------------------------------------------\n" );
printf( "Records Processed : %d/%d\n", RecsProcessed, NumRecs );
printf( "Records Committed : %d\n", RecsCommitted );
printf( "Records Written : %d\n", RecsWritten );
printf( "Records Read : %d\n", RecsRead );
printf( "Running Time : %f seconds\n", RunningTime );
printf( "Binning Rate : %f records/sec (%f bytes/sec)\n",
RecsProcessed / RunningTime, RecsProcessed * sizeof(record_t) / RunningTime );
printf( "Freelist entries : %d\n", Free.nitems );
printf( "Reading entries : %d\n", Reading.nitems );
printf( "ToProcess entries : %d\n", ToProcess.nitems );
printf( "Bin entries:\n" );
for( i = 0; i < NumBins; i++ ) {
printf( " %4d : %4d\n", i, Bins[i].bufs.nitems );
}
printf( "Device status:\n" );
for( i = 0; i < NumDevices; i++ ) {
printf( " %d : '%16s' : '%16s' : %s\n", i, Devices[i].devname,
Devices[i].path, Devices[i].dev.state == DEV_FREE ? "FREE" : "BUSY" );
}
*/
}
void UpdateIOState( void ) {
int i;
//printf( "update io state\n" );
// first update aio ops on the data file
aUpdateOperations( Data );
// next update aio ops on the bin files
for( i = 0; i < NumBins; i++ ) {
aUpdateOperations( Bins[i].file );
}
// update aio ops on the output file
aUpdateOperations( Output );
// next, let the working set adjust operation states and such
UpdateWSIOFinishedState( &WS );
// finally, let the devices start new operations if possible.
for( i = 0; i < NumDevices; i++ ) {
UpdateDeviceIOExecuteState( &WS, &(Devices[i].dev) );
}
}
void EnsureAllOperationsComplete( void ) {
int i;
int not_complete = 1;
dmtimer_t *wait;
wait = StartTimer();
while( not_complete ) {
UpdateIOState();
// see if we're done
not_complete = 0;
for( i = 0; i < WS.nbufs; i++ ) {
if( WS.bufs[i].device &&
WS.bufs[i].file &&
(WS.bufs[i].operation == OP_PENDING || WS.bufs[i].operation > OP_NONE) ) {
not_complete = 1;
break;
}
}
}
printf( "Ensure All Operations Complete: %d msec\n", ReadTimer( wait ) );
StopTimer( wait );
}
static double lasttime = 0;
void BinningPhase( void ) {
int i;
// for progress output
int iter;
int timeaccum;
// the main loop.
printf( "----------------- Starting -----------------\n" );
printf( "working set buffers : %d\n", WS.nbufs );
printf( "number of bins : %d\n", NumBins );
timeaccum = 0;
iter = 0;
DisplayStatusHeader();
while( RecsProcessed < NumRecs ) {
// print status every few seconds or so.
// not until timing gets fixed
//if( RunningTime - lasttime >= 5.0f ) {
if( (RunningTime - lasttime) >= 2.0f ) {
DisplayStatus();
lasttime = RunningTime;
}
// keep the async io running
// first update the operations on all our files.
UpdateIOState();
// Handle read and write completions
// (transition reads to ToProcess, writes to Free)
HandleReadingCompletions();
HandleSeqbufWriteCompletions();
RestructureReadSMLBins();
HandleBinWriteCompletions();
// do reading and binning
DoReading();
DoBinning();
// finish up the loop.
iter++;
RunningTime = (double)ReadTimer( RunningTimer ) / 1000.0;
}
printf( "total iters: %d\n", iter );
// now, we *must* take care to make sure all writes have completed
// We can't simply call aClose on a file. It's true that that will
// wait until all the currently scheduled operations on that file
// complete, but with the device method, we only allow one operation
// on any device at a time. Thus, we must ask the device managers
// to complete their own IO.
// FIXME: this could potentially be moved into the buffer stuff for
// a DeviceClose type of call, but then if there is lots of stuff
// pending, unless DeviceClose could know about more than one device
// at a time, we would get effectively synchronous IO here, so we
// have the ugly hack for now.
FinishBinning();
EnsureAllOperationsComplete();
// close the input file.
aClose( Data );
Data = NULL;
// Finally, close all the bin files
for( i = 0; i < NumBins; i++ ) {
aClose( Bins[i].file );
Bins[i].file = NULL;
}
printf( "Finally, RecsCommitted: %llu\n", RecsCommitted );
DisplayStatus();
}
void SortReading( void ) {
int i;
// if anything is in WAIT_READ, and we have crap to read yet,
// start reading it in.
for( i = 0; i < NSortBufs; i++ ) {
// quick out if we're done reading.
if( BinToRead >= NumBins ) {
return;
}
if( SortBufs[i].state == WAIT_READ ) {
// schedule a read here.
const char *fname = Fmt("%sout%05d.binned",Devices[Bins[BinToRead].dev].path,BinToRead);
aFILE *in = aOpen( fname, A_READ );
if( !in ) {
printf( "couldn't open '%s' to read!\n", fname );
}
if( Bins[BinToRead].nrecs > SortBufs[i].buf->totalrecs ) {
printf( "buffer not big enough to hold bin!\n" );
}
SortBufs[i].bin = BinToRead;
SortBufs[i].dev = &(Devices[Bins[BinToRead].dev].dev);
SortBufs[i].state = BUSY_READ;
SortBufs[i].buf->file = in;
ReadBuffer( SortBufs[i].buf, Bins[BinToRead].nrecs, SortBufs[i].dev );
printf( "scheduled read of bin %d\n", BinToRead );
BinToRead++;
return;
}
}
}
#ifdef USE_QSORT_ONLY
int comp_keys( record_t a, record_t b ){
int compval;
sml_t *mer_a, *mer_b;
mer_a = (sml_t*)&a;
mer_b = (sml_t*)&b;
/* if( ( mer_a->pos == 4554307 &&
mer_b->pos == 4407600 ) ||
( mer_a->pos == 4407600 &&
mer_b->pos == 4554307 ) )
__asm( nop );
*/ compval = COMPARE_KEYS( a, b );
return compval;
}
void QBrute( record_t a[], int lo, int hi ) {
if ((hi-lo) == 1) {
if( comp_keys( a[hi], a[lo] ) < 0 ) {
record_t T = a[lo];
a[lo] = a[hi];
a[hi] = T;
}
}
if ((hi-lo) == 2) {
int pmin = comp_keys( a[lo], a[lo+1] ) < 0 ? lo : lo+1;
pmin = comp_keys( a[pmin], a[lo+2] ) < 0 ? pmin : lo+2;
if (pmin != lo) {
record_t T = a[lo];
a[lo] = a[pmin];
a[pmin] = T;
}
QBrute(a, lo+1, hi);
}
if ((hi-lo) == 3) {
int pmin, pmax;
pmin = comp_keys( a[lo], a[lo+1] ) < 0 ? lo : lo+1;
pmin = comp_keys( a[pmin], a[lo+2] ) < 0 ? pmin : lo+2;
pmin = comp_keys( a[pmin], a[lo+3] ) < 0 ? pmin : lo+3;
if (pmin != lo) {
record_t T = a[lo];
a[lo] = a[pmin];
a[pmin] = T;
}
pmax = comp_keys( a[hi], a[hi-1] ) > 0 ? hi : hi-1;
pmax = comp_keys( a[pmax], a[hi-2] ) > 0 ? pmax : hi-2;
if (pmax != hi) {
record_t T = a[hi];
a[hi] = a[pmax];
a[pmax] = T;
}
QBrute(a, lo+1, hi-1);
}
}
void QSort( record_t a[], int lo0, int hi0 ) {
int lo = lo0;
int hi = hi0;
record_t pivot;
if ((hi-lo) <= 3) {
QBrute(a, lo, hi);
return;
}
// Pick a pivot and move it out of the way
pivot = a[(lo + hi) / 2];
a[(lo + hi) / 2] = a[hi];
a[hi] = pivot;
while( lo < hi ) {
// Search forward from a[lo] until an element is found that
// is greater than the pivot or lo >= hi
//while( a[lo] <= pivot && lo < hi ) {
while( (comp_keys( a[lo], pivot ) <= 0) && lo < hi ) {
lo++;
}
//
// Search backward from a[hi] until element is found that
// is less than the pivot, or hi <= lo
//
//while (pivot <= a[hi] && lo < hi ) {
while( (comp_keys( pivot, a[hi] ) <= 0) && lo < hi ) {
hi--;
}
//
// Swap elements a[lo] and a[hi]
//
if( lo < hi ) {
record_t T = a[lo];
a[lo] = a[hi];
a[hi] = T;
}
}
//
// Put the median in the "center" of the list
//
a[hi0] = a[hi];
a[hi] = pivot;
//
// Recursive calls, elements a[lo0] to a[lo-1] are less than or
// equal to pivot, elements a[hi+1] to a[hi0] are greater than
// pivot.
//
QSort( a, lo0, lo-1 );
QSort( a, hi+1, hi0 );
}
void RecSort( record_t a[], int nelems ) {
QSort( a, 0, nelems-1 );
}
int SortBuffer( buffer_t * buf ) {
RecSort( buf->recs, buf->numrecs );
return( 1 );
}
void SortSorting( void ) {
int i, finished;
int lowest = -1;
QSortTimer = StartTimer();
for( i = 0; i < NSortBufs; i++ ) {
if( SortBufs[i].state == SORTING ) {
if( lowest == -1 || SortBufs[i].bin < SortBufs[lowest].bin ) {
lowest = i;
}
}
}
if( lowest != -1 ) {
printf( "sorting bin %d\n", SortBufs[lowest].bin );
finished = SortBuffer( SortBufs[lowest].buf );
if( finished ) {
SortBufs[lowest].state = WRITE_RESTRUCTURE;
// SortBufs[lowest].state = WAIT_WRITE;
}
}
QSortTime += ReadTimer( QSortTimer ) / 1000.0;
StopTimer( QSortTimer );
}
#elif defined NO_SORT_PERF_TEST
void SortSorting( void ) {
int i;
QSortTimer = StartTimer();
for( i = 0; i < NSortBufs; i++ ) {
if( SortBufs[i].state == SORTING ) {
SortBufs[i].state = WAIT_WRITE;
}
}
QSortTime += ReadTimer( QSortTimer ) / 1000.0;
StopTimer( QSortTimer );
}
#else
sort_buf_t* CurrentSortBuf;
buffer_t* SortScratchBuffer;
void SortSorting( void ) {
int i;
QSortTimer = StartTimer();
// SortData -- sort everything in SORTING -- if it finishes, transition
// to WAIT_WRITE.
if( CurrentSortBuf == NULL ){
for( i = 0; i < NSortBufs; i++ ) {
// if this one is ready to sort, and it's the bin we're looking for...
if( SortBufs[i].state == SORTING && SortBufs[i].bin == BinToSort ) {
CurrentSortBuf = &SortBufs[i];
InitRadixSort( CurrentSortBuf, SortScratchBuffer );
printf( "scheduling sort of bin %d\n", BinToSort );
break;
}
}
}
// if there is something to sort right now then try to sort it.
if( CurrentSortBuf != NULL ){
if( CurrentSortBuf->state != WRITE_RESTRUCTURE ){
// automatically transitions to WAIT_WRITE when done.
RadixSort( CurrentSortBuf );
// prepare this bin for writing and setup to sort the next
if( CurrentSortBuf->state == WRITE_RESTRUCTURE ){
CurrentSortBuf = NULL;
BinToSort++;
}
}
}
QSortTime += ReadTimer( QSortTimer ) / 1000.0;
StopTimer( QSortTimer );
}
#endif
void RestructureSMLBinsForWrite( void ) {
int i;
offset_t j;
position_t* positions;
sml_t *sml;
for( i = 0; i < NSortBufs; i++ ) {
// if this one is ready to be restructured...
if( SortBufs[i].state == WRITE_RESTRUCTURE ) {
printf( "restructuring bin %d\n", SortBufs[i].bin );
positions = (position_t*)SortBufs[i].buf->recs;
sml = (sml_t*)SortBufs[i].buf->recs;
for( j = 0; j < Bins[SortBufs[i].bin].nrecs; j++ ){
positions[ j ] = sml[ j ].pos;
}
// set its state for writing
SortBufs[i].state = WAIT_WRITE;
}
}
}
// use this version if no pre-write modifications are required
/*
void RestructureSMLBinsForWrite( void ) {
int i;
for( i = 0; i < NSortBufs; i++ ) {
// if this one is ready to be restructured...
if( SortBufs[i].state == WRITE_RESTRUCTURE ) {
// set its state for writing
SortBufs[i].state = WAIT_WRITE;
}
}
}
*/
int CalculateSortWriteSize( int sortI ){
return Bins[SortBufs[sortI].bin].nrecs * sizeof( position_t );
}
void SortWriting( void ) {
int i;
for( i = 0; i < NSortBufs; i++ ) {
// if this one is ready to write, and it's the bin we're looking for...
if( SortBufs[i].state == WAIT_WRITE && SortBufs[i].bin == BinToWrite ) {
#ifdef NO_WRITE_PERF_TEST
// skip writing by setting the state to wait_read
SortBufs[i].state = WAIT_READ;
#else
printf( "scheduling write of bin %d\n", BinToWrite );
// write it out.
SortBufs[i].dev = &(Devices[OutputDev].dev);
SortBufs[i].state = BUSY_WRITE;
SortBufs[i].buf->file = Output;
WriteBuffer( SortBufs[i].buf, Bins[SortBufs[i].bin].nrecs, &(Devices[OutputDev].dev) );
SortBufs[i].buf->io_size = CalculateSortWriteSize( i );
#endif // NO_WRITE_PERF_TEST
BinToWrite++;
}
}
}
void SortHandleCompletions( void ) {
int i;
// transition states of those that finished.
for( i = 0; i < NSortBufs; i++ ) {
if( SortBufs[i].state == BUSY_READ || SortBufs[i].state == BUSY_WRITE ) {
if( SortBufs[i].buf->operation == OP_FINISHED ) {
//printf( "operation finished on buf %d\n", i );
SortBufs[i].buf->operation = OP_NONE;
SortBufs[i].state = SortBufs[i].state == BUSY_READ ? SORTING : WAIT_READ;
#ifdef NNNNN_KEYBYTES
// bin 0 doesn't need to be sorted
if( SortBufs[i].bin == 0 && SortBufs[i].state == SORTING )
SortBufs[i].state = WAIT_WRITE;
#endif
}
}
}
}
void SortUpdateIOState() {
int i;
//printf( "update io state\n" );
// first update aio ops on the data file
aUpdateOperations( Output );
// next update aio ops on the sortbuf files
for( i = 0; i < NSortBufs; i++ ) {
if( SortBufs[i].buf->file ) {
aUpdateOperations( SortBufs[i].buf->file );
}
}
// next, let the working set adjust operation states and such
UpdateWSIOFinishedState( &WS );
// finally, let the devices start new operations if possible.
for( i = 0; i < NumDevices; i++ ) {
UpdateDeviceIOExecuteState( &WS, &(Devices[i].dev) );
}
}
void SortingEnsureAllOperationsComplete() {
int i;
int not_complete = 1;
dmtimer_t *wait;
wait = StartTimer();
while( not_complete ) {
SortUpdateIOState();
// see if we're done
not_complete = 0;
for( i = 0; i < WS.nbufs; i++ ) {
if( WS.bufs[i].device &&
WS.bufs[i].file &&
(WS.bufs[i].operation == OP_PENDING || WS.bufs[i].operation > OP_NONE) ) {
not_complete = 1;
break;
}
}
}
// flush the output file to disk.
aFlush( Output );
printf( "Sort Ensure All Operations Complete: %d msec\n", ReadTimer( wait ) );
StopTimer( wait );
}
void SortingPhase( void ) {
// now reorganize the working set, and start up the sort procedure.
// we need to have the ability to read from N bin files at a time, where
// N is the number of bin devices.
// We read entire bin files at a time into each slot. We wait for the
// first one to finish, and then we sort it. We can start sorting the
// others too, as they finish. When the first sort is done, we write it
// out to the sorted output file, similarly we write everything out in
// order. When one is confirmed finished writing, we can start reading
// the next bin file from that device in.
int i;
offset_t recs_per_buffer;
offset_t biggest_bin = 0;
offset_t biggest_nrecs = 0;
NSortBufs = NumBinDevs;
for( i = 0; i < NumBins; i++ ) {
if( Bins[i].nrecs > biggest_nrecs ) {
biggest_nrecs = Bins[i].nrecs;
biggest_bin = i;
}
}
//recs_per_buffer = (WS.size / sizeof( record_t )) / NSortBufs;
recs_per_buffer = biggest_nrecs;
if( (WS.size / sizeof( record_t )) < (unsigned)recs_per_buffer ) {
printf( "working set holds %llu recs, but we need %llu\n",
(WS.size / sizeof( record_t )), recs_per_buffer );
}
NSortBufs = (WS.size / sizeof( record_t )) / recs_per_buffer;
printf( "NSortBufs = %d\n", NSortBufs );
// this goes from 0 to NumBins-1 as we read stuff.
BinToRead = 0;
BinToWrite = 0;
BinToSort = 0;
printf( "reorganizing working set: %llu recs per buffer, %d sort bufs\n", recs_per_buffer, NSortBufs );
ReorganizeWorkingSet( &WS, recs_per_buffer, recs_per_buffer );
#if !defined USE_QSORT_ONLY && !defined NO_SORT_PERF_TEST
// steal the last buffer for scratch space
NSortBufs--;
SortScratchBuffer = &(WS.bufs[NSortBufs]);
SortScratchBuffer->operation = SORTING_SCRATCH;
#endif
// nbufs should be same as NumBinDevs
printf( "reorganized working set has %d buffers of %llu bytes\n", WS.nbufs, recs_per_buffer * sizeof(record_t) );
SortBufs = malloc( sizeof( *SortBufs ) * NSortBufs );
memset( SortBufs, 0, sizeof( *SortBufs ) * NSortBufs );
// put everything in WAIT_READ;
for( i = 0; i < NSortBufs; i++ ) {
SortBufs[i].state = WAIT_READ;
SortBufs[i].buf = &(WS.bufs[i]);
SortBufs[i].dev = NULL;
}
#ifdef NNNNN_KEYBYTES
// process the first bin then restructure the working set again
while( BinToWrite < 1 ) {
SortReading();
SortSorting();
RestructureSMLBinsForWrite();
SortWriting();
SortUpdateIOState();
SortHandleCompletions();
}
SortingEnsureAllOperationsComplete();
for( i = 1; i < NumBins; i++ ) {
if( Bins[i].nrecs > biggest_nrecs ) {
biggest_nrecs = Bins[i].nrecs;
biggest_bin = i;
}
}
recs_per_buffer = biggest_nrecs;
if( (WS.size / sizeof( record_t )) < (unsigned)recs_per_buffer ) {
printf( "working set holds %llu recs, but we need %llu\n",
(WS.size / sizeof( record_t )), recs_per_buffer );
}
NSortBufs = (WS.size / sizeof( record_t )) / recs_per_buffer;
printf( "NSortBufs = %d\n", NSortBufs );
// this goes from 0 to NumBins-1 as we read stuff.
BinToRead = 1;
BinToWrite = 1;
BinToSort = 1;
printf( "reorganizing working set: %llu recs per buffer, %d sort bufs\n", recs_per_buffer, NSortBufs );
ReorganizeWorkingSet( &WS, recs_per_buffer, recs_per_buffer );
#if !defined USE_QSORT_ONLY && !defined NO_SORT_PERF_TEST
// steal the last buffer for scratch space
NSortBufs--;
SortScratchBuffer = &(WS.bufs[NSortBufs]);
SortScratchBuffer->operation = SORTING_SCRATCH;
#endif
// nbufs should be same as NumBinDevs
printf( "reorganized working set has %d buffers of %llu bytes\n", WS.nbufs, recs_per_buffer * sizeof(record_t) );
SortBufs = malloc( sizeof( *SortBufs ) * NSortBufs );
memset( SortBufs, 0, sizeof( *SortBufs ) * NSortBufs );
// put everything in WAIT_READ;
for( i = 0; i < NSortBufs; i++ ) {
SortBufs[i].state = WAIT_READ;
SortBufs[i].buf = &(WS.bufs[i]);
SortBufs[i].dev = NULL;
}
#endif
while( BinToWrite < NumBins ) {
// ReadFiles -- schedule reading operations if we can (are any buffers
// in WAIT_READ?)
//printf( "sortreading\n" );
SortReading();
// SortData -- sort everything in SORTING -- if it finishes, transition
// to WAIT_WRITE.
//printf( "sortsorting\n" );
SortSorting();
// Perform any necessary post-sort processing on the data to prepare it for
// writing out to the sorted file
RestructureSMLBinsForWrite();
// WriteFiles -- schedule writing operations for everything in WAIT_WRITE, if
// it is the next file we need to write (make sure to schedule in order).
//printf( "sortwriting\n" );
SortWriting();
// update io state
//printf( "sortupdateiostate\n" );
SortUpdateIOState();
// HandleCompletions -- if something finishes,
// if it was reading, transition to SORTING
// if it was writing, transition to WAIT_READ.
//printf( "sorthandlecompletions\n" );
SortHandleCompletions();
}
SortingEnsureAllOperationsComplete();
printf( "QSort took %f seconds\n", QSortTime );
}
int dmsort() {
// Do the first pass binning stuff
BinningTimer = StartTimer();
#ifndef NO_BINNING_PERF_TEST
BinningPhase();
BinningTime = ReadTimer( BinningTimer ) / 1000.0;
#endif // NO_BINNING_PERF_TEST
StopTimer( BinningTimer );
// Do the second pass sort
SortingTimer = StartTimer();
SortingPhase();
SortingTime = ReadTimer( SortingTimer ) / 1000.0;
StopTimer( SortingTimer );
RunningTime = ReadTimer( RunningTimer ) / 1000.0;
StopTimer( RunningTimer );
printf( "total time : %f sec\n", RunningTime );
printf( "binning time : %f sec (%f%%)\n", BinningTime, BinningTime/RunningTime * sizeof(record_t) );
printf( "sorting time : %f sec (%f%%)\n", SortingTime, SortingTime/RunningTime * sizeof(record_t) );
printf( "total rate : %f MB/sec\n", (((double)NumRecs)/10485.760)/RunningTime );
printf( "total bin rate : %f MB/sec\n", (((double)NumRecs)/10485.760)/BinningTime );
printf( "total sort rate : %f MB/sec\n", (((double)NumRecs)/10485.760)/SortingTime );
return 0;
}
int dmSML( const char* input_file, const char* output_file, const char* const* scratch_paths, uint64 seed ) {
long working_mb = 300;
long buffer_size = 1000;
int rval = 0;
int i = 0;
rval = InitdmSML( 0, 0, input_file, output_file, scratch_paths, seed );
if( rval != 0 )
return rval;
rval = dmsort();
// Hey slob! cleanup after yourself!
for( i = 0; i < NumBins; i++ ){
removeFile( Bins[ i ].fname, FALSE );
free( Bins[ i ].fname );
}
if( Bins )
free( Bins );
Bins = NULL;
NumBins = 0;
// for( i = 0; i < NumDevices; i++ )
// free( Devices[i].devname );
NumDevices = 0;
if( Devices )
free( Devices );
Devices = NULL;
if( SortBufs )
free( SortBufs );
SortBufs = NULL;
NSortBufs = 0;
BufferSizeMin = 0;
BufferSizeMax = 0;
memset( &Seqbuf, 0, sizeof( seqbuf_t ) );
DataDev = 0;
OutFileName = "unset";
// close the sorted file
aClose( Output );
Output = NULL;
OutputDev = 0;
BinToRead = 0;
BinToWrite = 0;
BinToSort = 0;
free( WS.bufs );
memset( &WS, 0, sizeof( working_set_t ) );
NumRecs = 0;
RecsProcessed = 0;
RecsRead = 0;
RecsUnread = 0;
RecsCommitted = 0;
RecsWritten = 0;
// timers
RunningTime = 0;
RunningTimer= NULL;
BinningTime = 0;
BinningTimer= NULL;
SortingTime = 0;
SortingTimer = NULL;
QSortTime = 0;
QSortTimer = NULL;
ReadIdleTime = 0;
ReadIdleTimer = NULL;
SortIdleTime = 0;
SortIdleTimer = NULL;
WriteIdleTime = 0;
WriteIdleTimer = NULL;
memset( &Free, 0, sizeof( buffer_list_t ) );
memset( &ToProcess, 0, sizeof( buffer_list_t ) );
memset( &Reading, 0, sizeof( buffer_list_t ) );
memset( &Restructure, 0, sizeof( buffer_list_t ) );
// static variables
divisor = 0;
consumed_recs = 0;
toprocess = NULL;
lasttime = 0;
// from asyncio.c
// OperationNumber = 0;
return rval;
}
|