Installing a HighPoint RocketRAID 2300 SATA controller on a motherboard ASUS E35M1-M may cause you problem. In the long term, the performance is horrible. The maximum read speed for a disk was 2.6MB/sec. A reboot solved the problem, but only for a while. Further investigation lead me to the following lines in /var/log/syslog:

kernel: [58995.098814] irq 16: nobody cared (try booting with the "irqpoll" option)
kernel: [58995.098967] Pid: 0, comm: swapper/0 Not tainted 3.2.0-29-generic #46-Ubuntu
kernel: [58995.098975] Call Trace:
kernel: [58995.098981]    [] __report_bad_irq+0x3d/0xe0
kernel: [58995.099010]  [] note_interrupt+0x135/0x190
kernel: [58995.099022]  [] handle_irq_event_percpu+0xa9/0x220
kernel: [58995.099033]  [] handle_irq_event+0x51/0x80
kernel: [58995.099044]  [] handle_fasteoi_irq+0x6a/0x110
kernel: [58995.099056]  [] handle_irq+0x22/0x40
kernel: [58995.099068]  [] do_IRQ+0x5a/0xe0
kernel: [58995.099079]  [] common_interrupt+0x6e/0x6e
kernel: [58995.099084]    [] ? arch_local_irq_enable+0x8/0xd
kernel: [58995.099106]  [] ? sched_clock_idle_wakeup_event+0x1a/0x20
kernel: [58995.099117]  [] acpi_idle_enter_simple+0xd3/0x115
kernel: [58995.099128]  [] cpuidle_idle_call+0xc1/0x280
kernel: [58995.099139]  [] cpu_idle+0xca/0x120
kernel: [58995.099151]  [] rest_init+0x72/0x74
kernel: [58995.099163]  [] start_kernel+0x3b0/0x3bd
kernel: [58995.099174]  [] x86_64_start_reservations+0x132/0x136
kernel: [58995.099185]  [] ? early_idt_handlers+0x140/0x140
kernel: [58995.099195]  [] x86_64_start_kernel+0xcd/0xdc
kernel: [58995.099202] handlers:
kernel: [58995.099279] [] mv_interrupt
kernel: [58995.099375] [] irq_handler
kernel: [58995.099462] Disabling IRQ #16

It appears the firewire controller and the Highpoint RocketRaid controller are sharing the same IRQ causing the problem. The solution is very simple: as I don’t need firewire, I disabled it from the BIOS.

cat /proc/interrupts | grep 16
16:      52234       1362   IO-APIC-fasteoi   sata_mv, firewire_ohci