I have a freshly built, updated EL6 system and am having problems with USB stability – at boot everything works fine but within a few hours, USB devices start disappearing randomly. At first I though the USB
devices were suspect, but removing the suspect devices and an accessory PCIE USB card hasn’t changed anything. As of now, a single USB device is working. (which is lucky, it hosts the OS) I’ve rebooted the server several times trying to diagnose the problem. After a reboot, everything works great – for a while. Is this a driver issue or just a bum motherboard/chipset?

The system is built based on the SUPERMICRO MBD-X9SCM-F-O available here:
http://www.newegg.com/Product/Product.aspx?Item=N82E16813182253

According to the OS compatibility matrix, the most recent CentOS 6.5 is supported:
http://www.supermicro.com/support/resources/OS/C204.cfm and all yum updates have been applied.

I have the output of /var/log/messages since the last reboot here:
http://hal.schoolpathways.com/lastboot.txt

Notes: Everything was working after the boot. Devices read/wrote fine.

ata9.00 HD errors are known, it’s the old ATA O/S drive.

Jun 11 01:07:36: Problem begins shortly after leaving for the day,

Jun 11 03:35:44 sdi goes offline, it’s one of the two USB boot devices and is plugged into the USB port directly on the main board. (IE: It’s not a bad cable)

Jun 11 15:53:43 b2012 goes offline, it’s mounted USB.

Here’s the output of lspci (Note, this is when the system is having a problem)
00:00.0 Host bridge: Intel Corporation Xeon E3-1200 v2/3rd Gen Core processor DRAM Controller (rev 09)
00:19.0 Ethernet controller: Intel Corporation 82579LM Gigabit Network Connection (rev 05)
00:1a.0 USB controller: Intel Corporation 6 Series/C200 Series Chipset Family USB Enhanced Host Controller #2 (rev 05)
00:1c.0 PCI bridge: Intel Corporation 6 Series/C200 Series Chipset Family PCI Express Root Port 1 (rev b5)
00:1c.4 PCI bridge: Intel Corporation 6 Series/C200 Series Chipset Family PCI Express Root Port 5 (rev b5)
00:1d.0 USB controller: Intel Corporation 6 Series/C200 Series Chipset Family USB Enhanced Host Controller #1 (rev 05)
00:1e.0 PCI bridge: Intel Corporation 82801 PCI Bridge (rev a5)
00:1f.0 ISA bridge: Intel Corporation C204 Chipset Family LPC Controller
(rev 05)
00:1f.2 SATA controller: Intel Corporation 6 Series/C200 Series Chipset Family SATA AHCI Controller (rev 05)
00:1f.3 SMBus: Intel Corporation 6 Series/C200 Series Chipset Family SMBus Controller (rev 05)
01:00.0 SATA controller: JMicron Technology Corp. JMB363 SATA/IDE
Controller (rev 03)
01:00.1 IDE interface: JMicron Technology Corp. JMB363 SATA/IDE
Controller (rev 03)
02:00.0 Ethernet controller: Intel Corporation 82574L Gigabit Network Connection
03:03.0 VGA compatible controller: Matrox Electronics Systems Ltd. MGA
G200eW WPCM450 (rev 0a)

And here is the output of lsusb: (Again, after the problem appears)
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub Bus 001 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub Bus 001 Device 003: ID 0557:2221 ATEN International Co., Ltd Winbond Hermon Bus 001 Device 004: ID 13fe:5200 Kingston Technology Company Inc. Bus 001 Device 005: ID 05e3:0608 Genesys Logic, Inc. USB-2.0 4-Port HUB

I plan on verifying/updating the BIOS tonight. Is there any other information that I could provide to help diagnose this?

-Ben