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How can I improve overall system performance?

I used to work in a computer (Dell Inspiron) with 2GB RAM, 80GB dd and Intel Core Processor with Ubuntu 10 under Gnome, and went well. It went slow when I had a Virtual Machine (VirtualBox with 512-1024 RAM) open, a big IDE from Tibco (say like Netbeans using 600MB RAM) and Firefox.

Then I installed Ubuntu 12.04 in another computer (Dell Inspiron too) Intel Core 2 Duo, 4Gb RAM, 500GB dd and I can only run the same programs and it gets really slow. Even worse than with the previous machine. I first tried with Ubuntu 64 bits and it was too slow, then I moved to Ubuntu 12.04 32 bits and is a little faster.

Even worse, sometimes I'm not doing anything and I see the disk drive reading a lot. When I list the processes all the processes are using like 2% of the CPU and the memory is below the 3GB used.

I don't know what to do. I have changed the swapiness (now is 10, before was 60), I have tested it with Unity 3D and 2D, I have installed preload and other programs alike but nothing.

I'm thinking it could be the partitions in the disk drive, but I don't know why it makes so many disks operations.

Thanks in advance for your help. What else can I do? Is something with Unity? is my computer configuration

Edit: (DMA output)

 Timing cached reads:   5236 MB in  2.00 seconds = 2624.56 MB/sec
 Timing buffered disk reads: 240 MB in  3.01 seconds =  79.84 MB/sec

sudo dmesg |grep DMA
[    0.000000]   DMA      0x00000010 -> 0x00001000
[    0.000000]   DMA zone: 32 pages used for memmap
[    0.000000]   DMA zone: 0 pages reserved
[    0.000000]   DMA zone: 3951 pages, LIFO batch:0
[    0.790649] ata1: SATA max UDMA/133 cmd 0x1f0 ctl 0x3f6 bmdma 0xbfa0 irq 14
[    0.790652] ata2: PATA max UDMA/100 cmd 0x170 ctl 0x376 bmdma 0xbfa8 irq 15
[    0.952622] ata2.00: ATAPI: SONY CD-RW/DVD-ROM CRX880A, KD09, max UDMA/33
[    0.953649] ata1.00: ATA-8: WDC WD5000BEVT-00A03T0, 01.01A01, max UDMA/133
[    0.960633] ata1.00: configured for UDMA/133
[    0.968317] ata2.00: configured for UDMA/33
[    1.208604] mmc0: SDHCI controller on PCI [0000:02:01.1] using DMA
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