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Mike, we are using Linux kernel 2.6.30, U-boot 1.3.4, AT91Bootstrap 1.14 and the Codesourcery GNU compiler toolchain (Linux i386 host to AT91Sam9 target). The CPU we use is the AT91SAM9G20 and we are having troubles with the USB Device Port also.
The test we run on the development board has run for over a day with no issue, but our board only runs for a few minutes before locking up. I assume our board layout is leading to more bad USB messages and the current Linux driver (patches for 2.6.30) does not respond properly to missed ACKs.
You might have to invest a lot of time to move to our environment... so I don't have a solution for you, but the Atmel USB device port does seem to work on the 9G20 (and earlier.)
Have you tried printing out the UDP_CSRx register contents, to see how the flags are responding to the communications with the host (PC)? That is what we have done to isolate our problem down to bad packets and bad timeout handling in the Linux driver.
JBond
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