How to debug for this top result

Hi,
The following is the result of top command got by running my multi-threaded program that uses mysql. Here %wa is much greater than %us. I ran jconsole but could not find any thread lock or any other irregularities. I use a blocking queue which is accessed by some 200 threads. I think that may cause this much. But i don't know the exact way of tracing the source of the problem. I hear profiling, etc. But don't know which part of my code causes this. how to find it.
I use intel dual core with 1GB RAM. Default JVM size.
top - 11:49:50 up 1:21, 5 users, load average: 12.74, 6.11, 2.89
Tasks: 177 total, 2 running, 174 sleeping, 0 stopped, 1 zombie
Cpu(s): 10.0%us, 17.0%sy, 8.4%ni, 7.1%id, 56.9%wa, 0.0%hi, 0.5%si, 0.0%st
Mem: 1025372k total, 1011940k used, 13432k free, 4976k buffers
Swap: 2096440k total, 55672k used, 2040768k free, 272444k cached
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
5258 raja 20 0 277m 37m 10m S 41.0 3.8 4:09.34 java
2568 nobody 20 0 28728 17m 3284 S 2.6 1.7 0:02.97 mysqld
4008 mysql 20 0 137m 19m 4264 S 1.3 2.0 0:04.30 mysqld
5935 root 39 19 5072 1420 1008 S 1.0 0.1 0:01.14 makewhatis
2603 root 20 0 339m 59m 10m S 0.7 5.9 2:58.37 Xorg
6 root RT -5 0 0 0 S 0.3 0.0 0:01.42 migration/1
673 root 15 -5 0 0 0 D 0.3 0.0 0:00.79 kjournald
1773 root 15 -5 0 0 0 R 0.3 0.0 0:07.55 kondemand/0
1954 dbus 20 0 3080 1336 764 S 0.3 0.1 0:02.84 dbus-daemon
2177 root 20 0 6780 1884 1572 S 0.3 0.2 0:01.53 NetworkManager
3370 raja 20 0 130m 18m 12m S 0.3 1.8 0:13.69 gnome-terminal
5257 raja 20 0 212m 19m 10m S 0.3 2.0 0:01.25 rmiregistry
5582 raja 20 0 74224 17m 8924 S 0.3 1.8 0:30.47 npviewer.bin
5631 raja 20 0 2556 1104 840 R 0.3 0.1 0:04.05 top
1 root 20 0 2008 704 500 S 0.0 0.1 0:00.98 init
2 root 15 -5 0 0 0 S 0.0 0.0 0:00.00 kthreadd
3 root RT -5 0 0 0 S 0.0 0.0 0:01.46 migration/0
Thanks.

When I have seen this behaviour, it is because you are writing data faster than the computer can keep up. You appear to be very low on free memeory which will make this problem worse. On my systems, this appears to be a problem if the "free" memory is less than 20% of your total memory.
What happens is that every process which runs occasionally, now blocks waiting for disk and appears in the load average.
I suggest you look at your vmstat to see what your disk activity looks like.

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    How do I interpret this validation result?
    13366 [Element <7>] [Rings 3, 4][Edge <0> in ring <3>][Edge <0> in ring <4>]
    --ORA-13366: invalid combination of interior exterior rings
    --Cause: In an Oracle Spatial geometry, interior and exterior rings are not used consistently.
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    here is the result...
    SQL> select c.geom.sdo_elem_info from de_lec c where c.lec_gcode = '9417';
    SDO_ELEM_INFO_ARRAY(1, 1003, 1, 69097, 2003, 1, 70747, 2003, 1, 74383, 1003, 1, 122715, 2003, 1, 124
    , 1003, 1, 233915, 2003, 1, 235071, 2003, 1, 236407, 2003, 1, 236469, 1003, 1, 252279, 1003, 1, 2652
    1003, 1, 290105, 1003, 1, 301625, 2003, 1, 302471, 1003, 1, 309783, 1003, 1, 320973, 1003, 1, 33194
    1003, 1, 354945, 1003, 1, 374059, 1003, 1, 378163, 1003, 1, 392505, 1003, 1, 394375, 1003, 1, 398463
    003, 1, 416955, 1003, 1, 419939, 1003, 1, 422193, 1003, 1, 423811, 1003, 1, 425763, 1003, 1, 428065,
    03, 1, 433357, 1003, 1, 436003, 1003, 1, 441597, 1003, 1, 442599, 1003, 1, 450817, 1003, 1, 453779,
    3, 1, 459279, 1003, 1, 460957, 1003, 1, 463733, 1003, 1, 472079, 1003, 1, 473515, 1003, 1, 475225, 1
    , 1, 477279, 1003, 1, 478213, 1003, 1, 480013, 1003, 1, 482317, 1003, 1, 484677, 1003, 1, 485797, 10
    1, 487885, 1003, 1, 489137, 1003, 1, 490473, 1003, 1, 494967, 1003, 1, 495533, 1003, 1, 496545, 100
    1, 502053, 1003, 1, 502731, 1003, 1, 507419, 1003, 1, 509385, 1003, 1, 510463, 1003, 1, 511541, 1003
    , 513055, 1003, 1, 515103, 1003, 1, 515485, 1003, 1, 516215, 1003, 1, 518501, 1003, 1, 518893, 1003,
    521707, 1003, 1, 522173, 1003, 1, 523241, 1003, 1, 523753, 1003, 1, 524655, 1003, 1, 525181, 1003,
    526689, 1003, 1, 527041, 1003, 1, 527631, 1003, 1, 528079, 1003, 1, 529339, 1003, 1, 529505, 1003, 1
    30239, 1003, 1, 530351, 1003, 1, 531627, 1003, 1, 531835, 1003, 1, 532029, 1003, 1, 532363, 1003, 1,
    3919, 1003, 1, 534317, 1003, 1, 534755, 1003, 1, 535307, 1003, 1, 535545, 1003, 1, 536431, 1003, 1,
    117, 1003, 1, 537379, 1003, 1, 537871, 1003, 1, 538127, 1003, 1, 538459, 1003, 1, 539661, 1003, 1, 5
    89, 1003, 1, 540359, 1003, 1, 540585, 1003, 1, 540713, 1003, 1, 541065, 1003, 1, 541391, 1003, 1, 54
    1, 1003, 1, 543035, 1003, 1, 545329, 1003, 1, 545743, 1003, 1, 546109, 1003, 1, 546209, 1003, 1, 546
    , 1003, 1, 546945, 1003, 1, 546991, 1003, 1, 547333, 1003, 1, 547969, 1003, 1, 548239, 1003, 1, 5483
    1003, 1, 549721, 1003, 1, 550091, 1003, 1, 550203, 1003, 1, 550417, 1003, 1, 550511, 1003, 1, 55062
    1003, 1, 550915, 1003, 1, 551459, 1003, 1, 551701, 1003, 1, 551889, 1003, 1, 552763, 1003, 1, 552957
    003, 1, 555273, 1003, 1, 555331, 1003, 1, 555489, 1003, 1, 556235, 1003, 1, 556551, 1003, 1, 556699,
    03, 1, 557223, 1003, 1, 558425, 1003, 1, 558735, 1003, 1, 558825, 1003, 1, 559043, 1003, 1, 559237,
    3, 1, 559513, 1003, 1, 559679, 1003, 1, 559829, 1003, 1, 559977, 1003, 1, 560099, 1003, 1, 560877, 1
    , 1, 561599, 1003, 1, 561667, 1003, 1, 562085, 1003, 1, 562361, 1003, 1, 563011, 1003, 1, 564005, 10
    1, 564445, 1003, 1, 564587, 1003, 1, 564659, 1003, 1, 564775, 1003, 1, 564959, 1003, 1, 565105, 100
    1, 565535, 1003, 1, 565591, 1003, 1, 565679, 1003, 1, 565881, 1003, 1, 566451, 1003, 1, 566575, 1003
    , 566871, 1003, 1, 566987, 1003, 1, 567231, 1003, 1, 567885, 1003, 1, 568059, 1003, 1, 568227, 1003,
    568493, 1003, 1, 569317, 1003, 1, 569449, 1003, 1, 569805, 1003, 1, 569859, 1003, 1, 570097, 1003,
    570547, 1003, 1, 570815, 1003, 1, 570863, 1003, 1, 570961, 1003, 1, 571089, 1003, 1, 571143, 1003, 1
    71669, 1003, 1, 572099, 1003, 1, 572195, 1003, 1, 572319, 1003, 1, 572425, 1003, 1, 572531, 1003, 1,
    2729, 1003, 1, 572929, 1003, 1, 573087, 1003, 1, 573137, 1003, 1, 573255, 1003, 1, 573611, 1003, 1,
    747, 1003, 1, 573813, 1003, 1, 574339, 1003, 1, 574425, 1003, 1, 574485, 1003, 1, 574579, 1003, 1, 5
    83, 1003, 1, 574925, 1003, 1, 575035, 1003, 1, 575211, 1003, 1, 575361, 1003, 1, 575803, 1003, 1, 57
    1, 1003, 1, 576015, 1003, 1, 576103, 1003, 1, 576203, 1003, 1, 576299, 1003, 1, 576759, 1003, 1, 576
    , 1003, 1, 577073, 1003, 1, 577277, 1003, 1, 577339, 1003, 1, 577463, 1003, 1, 577541, 1003, 1, 5777
    1003, 1, 578153, 1003, 1, 578301, 1003, 1, 578529, 1003, 1, 578737, 1003, 1, 578805, 1003, 1, 57893
    1003, 1, 579223, 1003, 1, 579353, 1003, 1, 579431, 1003, 1, 579491, 1003, 1, 579561, 1003, 1, 579629
    003, 1, 579735, 1003, 1, 579815, 1003, 1, 579857, 1003, 1, 580577, 1003, 1, 580803, 1003, 1, 580837,
    03, 1, 580997, 1003, 1, 581059, 1003, 1, 581367, 1003, 1, 581479, 1003, 1, 581547, 1003, 1, 581903,
    3, 1, 582299, 1003, 1, 582417, 1003, 1, 582729, 1003, 1, 582911, 1003, 1, 583379, 1003, 1, 583459, 1
    , 1, 583769, 1003, 1, 583951, 1003, 1, 584011, 1003, 1, 584057, 1003, 1, 584113, 1003, 1, 584211, 10
    1, 584437, 1003, 1, 584841, 1003, 1, 584859, 1003, 1, 585043, 1003, 1, 585277, 1003, 1, 585371, 100
    1, 585521, 1003, 1, 585625, 1003, 1, 585681, 1003, 1, 585815, 1003, 1, 586027, 1003, 1, 586149, 1003
    , 586623, 1003, 1, 586777, 1003, 1, 586819, 1003, 1, 586929, 1003, 1, 587171, 1003, 1, 587289, 1003,
    587823, 1003, 1, 587855, 1003, 1, 587983, 1003, 1, 588155, 1003, 1, 588321, 1003, 1, 588379, 1003,
    588547, 1003, 1, 588873, 1003, 1, 588939, 1003, 1, 588999, 1003, 1, 589347, 1003, 1, 589389, 1003, 1
    89643, 1003, 1, 589971, 1003, 1, 590289, 1003, 1, 590481, 1003, 1, 590565, 1003, 1, 590627, 1003, 1,
    0797, 1003, 1, 590877, 1003, 1, 590953, 1003, 1, 591033, 1003, 1, 591393, 1003, 1, 591703, 1003, 1,
    873, 1003, 1, 591917, 1003, 1, 592019, 1003, 1, 592047, 1003, 1, 592345, 1003, 1, 592461, 1003, 1, 5
    49, 1003, 1, 592689, 1003, 1, 592745, 1003, 1, 592783, 1003, 1, 592963, 1003, 1, 593009, 1003, 1, 59
    7, 1003, 1, 593415, 1003, 1, 593475, 1003, 1, 593513, 1003, 1, 593789, 1003, 1, 593915, 1003, 1, 593
    , 1003, 1, 594165, 1003, 1, 594215, 1003, 1, 594243, 1003, 1, 594311, 1003, 1, 594349, 1003, 1, 5944
    1003, 1, 594589, 1003, 1, 594825, 1003, 1, 595109, 1003, 1, 595139, 1003, 1, 595199, 1003, 1, 59534
    1003, 1, 595447, 1003, 1, 595611, 1003, 1, 595743, 1003, 1, 595811, 1003, 1, 595995, 1003, 1, 596097
    003, 1, 596239, 1003, 1, 596291, 1003, 1, 596445, 1003, 1, 596553, 1003, 1, 596625, 1003, 1, 596789,
    03, 1, 596877, 1003, 1, 596959, 1003, 1, 596993, 1003, 1, 597057, 1003, 1, 597181, 1003, 1, 597293,
    3, 1, 597459, 1003, 1, 597547, 1003, 1, 597651, 1003, 1, 597863, 1003, 1, 597999, 1003, 1, 598075, 1
    , 1, 598337, 1003, 1, 598379, 1003, 1, 598517, 1003, 1, 598547, 1003, 1, 598875, 1003, 1, 599093, 10
    1, 599201, 1003, 1, 599385, 1003, 1, 599491, 1003, 1, 599513, 1003, 1, 599649, 1003, 1, 599705, 100
    1, 600221, 1003, 1, 600255, 1003, 1, 600355, 1003, 1, 600461, 1003, 1, 600553, 1003, 1, 600617, 1003
    , 600737, 1003, 1, 600799, 1003, 1, 600825, 1003, 1, 600923, 1003, 1, 601157, 1003, 1, 601199, 1003,
    601281, 1003, 1, 601335, 1003, 1, 601471, 1003, 1, 601517, 1003, 1, 601725, 1003, 1, 601859, 1003,
    602315, 1003, 1, 602403, 1003, 1, 602577, 1003, 1, 602815, 1003, 1, 602909, 1003, 1, 603097, 1003, 1
    03275, 1003, 1, 603335, 1003, 1, 603357, 1003, 1, 603857, 1003, 1, 603941, 1003, 1, 604079, 1003, 1,
    4293, 1003, 1, 604377, 1003, 1, 604441, 1003, 1, 604537, 1003, 1, 604581, 1003, 1, 604749, 1003, 1,
    913, 1003, 1, 604997, 1003, 1, 605025, 1003, 1, 605103, 1003, 1, 605157, 1003, 1, 605241, 1003, 1, 6
    65, 1003, 1, 605443, 1003, 1, 605743, 1003, 1, 605929, 1003, 1, 606129, 1003, 1, 606203, 1003, 1, 60
    9, 1003, 1, 606635, 1003, 1, 606789, 1003, 1, 606849, 1003, 1, 606879, 1003, 1, 607021, 1003, 1, 607
    , 1003, 1, 607441, 1003, 1, 607629, 1003, 1, 607747, 1003, 1, 607819, 1003, 1, 607845, 1003, 1, 6079
    1003, 1, 608123, 1003, 1, 608177, 1003, 1, 608341, 1003, 1, 608389, 1003, 1, 608691, 1003, 1, 60879
    1003, 1, 608849, 1003, 1, 609019, 1003, 1, 609037, 1003, 1, 609233, 1003, 1, 609319, 1003, 1, 609373
    003, 1, 609671, 1003, 1, 609757, 1003, 1, 609857, 1003, 1, 609881, 1003, 1, 609907, 1003, 1, 609941,
    03, 1, 610051, 1003, 1, 610105, 1003, 1, 610215, 1003, 1, 610347, 1003, 1, 610463, 1003, 1, 610587,
    3, 1, 610797, 1003, 1, 610877, 1003, 1, 610903, 1003, 1, 610999, 1003, 1, 611371, 1003, 1, 611465, 1
    , 1, 611629, 1003, 1, 611659, 1003, 1, 611683, 1003, 1, 611831, 1003, 1, 611919, 1003, 1, 612049, 10
    1, 612153, 1003, 1, 612289, 1003, 1, 612411, 1003, 1, 612481, 1003, 1, 612509, 1003, 1, 612603, 100
    1, 612791, 1003, 1, 612813, 1003, 1, 612927, 1003, 1, 613015, 1003, 1, 613041, 1003, 1, 613085, 1003
    , 613245, 1003, 1, 613381, 1003, 1, 613411, 1003, 1, 613433, 1003, 1, 613459, 1003, 1, 613485, 1003,
    613809, 1003, 1, 613831, 1003, 1, 613909, 1003, 1, 613949, 1003, 1, 614049, 1003, 1, 614115, 1003,
    614407, 1003, 1, 614499, 1003, 1, 614613, 1003, 1, 614637, 1003, 1, 614687, 1003, 1, 614761, 1003, 1
    14803, 1003, 1, 614837, 1003, 1, 614909, 1003, 1, 614981, 1003, 1, 615011, 1003, 1, 615147, 1003, 1,
    5221, 1003, 1, 615303, 1003, 1, 615415, 1003, 1, 615435, 1003, 1, 615515, 1003, 1, 615601, 1003, 1,
    661, 1003, 1, 615729, 1003, 1, 615811, 1003, 1, 615865, 1003, 1, 615979, 1003, 1, 616065, 1003, 1, 6
    55, 1003, 1, 616413, 1003, 1, 616485, 1003, 1, 616593, 1003, 1, 616673, 1003, 1, 616759, 1003, 1, 61
    5, 1003, 1, 617001, 1003, 1, 617065, 1003, 1, 617117, 1003, 1, 617245, 1003, 1, 617327, 1003, 1, 617
    , 1003, 1, 617513, 1003, 1, 617633, 1003, 1, 617715, 1003, 1, 617783, 1003, 1, 617805, 1003, 1, 6178
    1003, 1, 618007, 1003, 1, 618085, 1003, 1, 618149, 1003, 1, 618167, 1003, 1, 618263, 1003, 1, 61832
    1003, 1, 618389, 1003, 1, 618463, 1003, 1, 618489, 1003, 1, 618511, 1003, 1, 618575, 1003, 1, 618603
    003, 1, 618739, 1003, 1, 618771, 1003, 1, 618867, 1003, 1, 618885, 1003, 1, 618943, 1003, 1, 619005,
    03, 1, 619115, 1003, 1, 619167, 1003, 1, 619243, 1003, 1, 619291, 1003, 1, 619335, 1003, 1, 619415,
    3, 1, 619507, 1003, 1, 619571, 1003, 1, 619597, 1003, 1, 619625, 1003, 1, 619745, 1003, 1, 619855, 1
    , 1, 619979, 1003, 1, 620025, 1003, 1, 620133, 1003, 1, 620193, 1003, 1, 620243, 1003, 1, 620411, 10
    1, 620535, 1003, 1, 620693, 1003, 1, 620747, 1003, 1, 620803, 1003, 1, 620865, 1003, 1, 620935, 100
    1, 621075, 1003, 1, 621149, 1003, 1, 621171, 1003, 1, 621197, 1003, 1, 621273, 1003, 1, 621349, 1003
    , 621441, 1003, 1, 621463, 1003, 1, 621583, 1003, 1, 621651, 1003, 1, 621701, 1003, 1, 621753, 1003,
    621911, 1003, 1, 621933, 1003, 1, 621989, 1003, 1, 622125, 1003, 1, 622183, 1003, 1, 622253, 1003,
    622337, 1003, 1, 622387, 1003, 1, 622415, 1003, 1, 622497, 1003, 1, 622545, 1003, 1, 622577, 1003, 1
    22641, 1003, 1, 622731, 1003, 1, 622795, 1003, 1, 622845, 1003, 1, 622893, 1003, 1, 622951, 1003, 1,
    3099, 1003, 1, 623163, 1003, 1, 623269, 1003, 1, 623345, 1003, 1, 623485, 1003, 1, 623541, 1003, 1,
    765, 1003, 1, 623829, 1003, 1, 623869, 1003, 1, 623931, 1003, 1, 623951, 1003, 1, 623967, 1003, 1, 6
    87, 1003, 1, 624143, 1003, 1, 624193, 1003, 1, 624363, 1003, 1, 624407, 1003, 1, 624447, 1003, 1, 62
    5, 1003, 1, 624601, 1003, 1, 624619, 1003, 1, 624675, 1003, 1, 624759, 1003, 1, 624817, 1003, 1, 624
    , 1003, 1, 625069, 1003, 1, 625099, 1003, 1, 625145, 1003, 1, 625181, 1003, 1, 625277, 1003, 1, 6253
    1003, 1, 625403, 1003, 1, 625453, 1003, 1, 625527, 1003, 1, 625585, 1003, 1, 625635, 1003, 1, 62568
    1003, 1, 625715, 1003, 1, 625775, 1003, 1, 625841, 1003, 1, 625855, 1003, 1, 626021, 1003, 1, 626079
    003, 1, 626167, 1003, 1, 626229, 1003, 1, 626307, 1003, 1, 626357, 1003, 1, 626423, 1003, 1, 626529,
    03, 1, 626651, 1003, 1, 626667, 1003, 1, 626737, 1003, 1, 626801, 1003, 1, 626867, 1003, 1, 626887,
    3, 1, 627123, 1003, 1, 627167, 1003, 1, 627185, 1003, 1, 627207, 1003, 1, 627225, 1003, 1, 627269, 1
    , 1, 627437, 1003, 1, 627483, 1003, 1, 627539, 1003, 1, 627657, 1003, 1, 627707, 1003, 1, 627721, 10
    1, 627817, 1003, 1, 627897, 1003, 1, 627961, 1003, 1, 628015, 1003, 1, 628127, 1003, 1, 628145, 100
    1, 628197, 1003, 1, 628237, 1003, 1, 628289, 1003, 1, 628345, 1003, 1, 628391, 1003, 1, 628457, 1003
    , 628533, 1003, 1, 628585, 1003, 1, 628611, 1003, 1, 628683, 1003, 1, 628735, 1003, 1, 628753, 1003,
    628823, 1003, 1, 628849, 1003, 1, 628919, 1003, 1, 628999, 1003, 1, 629031, 1003, 1, 629079, 1003,
    629115, 1003, 1, 629129, 1003, 1, 629179, 1003, 1, 629251, 1003, 1, 629295, 1003, 1, 629319, 1003, 1
    29567, 1003, 1, 629647, 1003, 1, 629681, 1003, 1, 629723, 1003, 1, 629765, 1003, 1, 629783, 1003, 1,
    9879, 1003, 1, 629895, 1003, 1, 629945, 1003, 1, 629995, 1003, 1, 630037, 1003, 1, 630093, 1003, 1,
    173, 1003, 1, 630217, 1003, 1, 630295, 1003, 1, 630371, 1003, 1, 630409, 1003, 1, 630465, 1003, 1, 6
    65, 1003, 1, 630623, 1003, 1, 630695, 1003, 1, 630737, 1003, 1, 630755, 1003, 1, 630803, 1003, 1, 63
    7, 1003, 1, 630931, 1003, 1, 630959, 1003, 1, 631037, 1003, 1, 631113, 1003, 1, 631205, 1003, 1, 631
    , 1003, 1, 631343, 1003, 1, 631361, 1003, 1, 631375, 1003, 1, 631389, 1003, 1, 631453, 1003, 1, 6314
    1003, 1, 631647, 1003, 1, 631715, 1003, 1, 631747, 1003, 1, 631791, 1003, 1, 631853, 1003, 1, 63186
    1003, 1, 631955, 1003, 1, 631989, 1003, 1, 632003, 1003, 1, 632067, 1003, 1, 632125, 1003, 1, 632165
    003, 1, 632273, 1003, 1, 632309, 1003, 1, 632323, 1003, 1, 632361, 1003, 1, 632399, 1003, 1, 632429,
    03, 1, 632493, 1003, 1, 632507, 1003, 1, 632575, 1003, 1, 632635, 1003, 1, 632665, 1003, 1, 632709,
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