I’m building a “control processor”, it’s a custom made board with the AT91SAM9260. It will be installed on ships for automation purposes. It’s a project for my graduation and it must run on Linux OS. I need to write the boot program and install Linux on the Nor Flash memory. I’m kind of stuck thus I’m asking for tips and advice. Thanks.

Ok, but where exactly you're stuck?

It’s a custom made board with 64MB flash. For example we have another custom board with Intel i386, with Red Boot we are able to download Linux OS on the flash memory via JTAG. This new board with the AT91SAM9260 will replace the i386, but how can I load Linux OS on the flash memory?

I see, newcomer

This page have all the answers you may have so far:
http://www.linux4sam.org/twiki/bin/view ... ingStarted

where are going to store bootstrap u-boot? these two can be stored only atmel nor. we could not do in spansion s29gl512 because off its timings.
Anyway, you can do everything with SAM-ICE jtag or similar

Mentorel is correct. I hope you designed your board with Atmel's NOR flash, so you can store u-boot there.
Note, that latest u-boot don't require you to initialize from bootstrap, as it does all the initialization and relocation stuff by itself (can be switch off if required). At least our AT91RM9200 based board does this, don't know AT91SAM9260 situation though.

rybo, what exact version of u-boot do you imply "the latest"? Denx reports 1.3.0 as the latest. buildroot can compile only 1.2.0 please clarify

Mentorel,
actually the latest u-boot is 1.3.3: check this out.

I have tried a lot of u-boot versions during development..
Recent tested versions include 1.2.0, 1.3.0, 1.3.1 and 1.3.2:
1.2.0 was coming with devkit (Atmel's patch). 1.2.2 with also Atmel's patch won't work on our board (don't know why, probably defines), and I haven't played a lot with it - jumped directly to 1.3.x

I believe that u-boot support for low level initializing (for AT91) appeared in 1.3.0, maybe i'm wrong though, maybe it was earlier..

After development start I have ported 1.3.0 to support our platform hardware. The same patch where applied to 1.3.1 and to 1.3.2. Currently board have u-boot 1.3.2 and it's running perfectly, so as the other 1.3.x versions.

This is one of the reasons I don't use buildroot - I prefer the latest versions.

One more note regarding booting with u-boot with no bootstrap :

Props:
- Only one booting app - no need to have both.
- Faster booting times (u-boot is not gzipped)
Cons:
- U-boot is bigger than bootstrap + compressed u-boot

Also, if you decide to get this feature to work, you will have to compile two different versions of u-boot - one is flash version with low level initializing, another without it if you want to load it via xmodem when flash is erased or BMS is high, or the board will simply hang.
Another possibility is to write a patch (as I have done) to skip low-level initializing when u-boot has started from RAM.

Hope this helps.

P.S. If you need that patch, just let me know, I'll post it here.
P.P.S. Не за что.