I am currently running Android and an RTOS together using OKL4 Hypervisor to virtualize both of them on a Pandaboard (OMAP4430). At some point during power up it seems like the Linux Kernel somehow causes all the GPIO banks on the board to be unmapped from memory, even the physical address is unreachable (Through JTAG). This seems to be temporary since it is only a problem when the Hypervisor interrupts Android in this state and lets the RTOS run. I have tried disabling power management in the Linux kernel and that didn't seem to make a difference, I also checked all the clocks on the Pandaboard using the test points and they look fine, The Hypervisor reports that all pages are mapped correctly. I am looking for any help in finding out what possible configuration on the Pandaboard or OMAP could cause all GPIO banks to disappear from memory. Thanks a lot
The interface and functionnal clock needs to be enabled for some register to be available. I don't know for the 4430, but for the 3730, two register control the functionnal and interface clok for the GPIO banks :
CM_ICLKEN_PER
CM_FCLKEN_PER
Look for these in the TRM of your omap, and see if you can fix your JTAG access problem with them. This not really programming related