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Considering I made an architecture to do some specific thing, wrote in vhdl, for example.
Can I 'burn' it in a fpga chip, forever? Or how should I do it, protecting the intelectual property knowing the fact it can be read from the serial flash memory?
Xilinx Spartan 3AN FPGA's have internal flash making them nonvolatile. Your question is actually multiple questions.
1) Are FPGA's volatile or non-volatile? Most are volatile, requiring the configuration bitstream to be read into the FPGA from an external nonvolatile storage device at every power on. There are some that are nonvolatile. Like the Xilinx S3AN I mention.
2) How do you protect the configuaration bitstream? There are multiple answers to this question.
You can encrypt the bitstream; which means to say that the bitstream that is stored on the above discussed nonvolatile storage device is a unique ciphertext that can only be decrypted by the single fpga with the appropriate key. This will protect the bitstream's functionality from being discovered by reverse engineering. That is to say that even if the enciphered bitstream is able to be extracted from the nonvolatile storage device, either in-situ or more destructive means, sense will not be able to be made from the extracted file since it is encrypted.
You can also set the bitstream to be prohibited from being readback. The JTAG interface that one uses to program an FPGA at debug time can generally be used to read the configuration bitstream back out of the fpga. Setting the NO_READBACK option prohibits this.
It is possible to find FPGAs with an integrated non-volatile program memory. For example, Microsemi (formerly Actel) specializes in this type of device.
Other vendors offer the option to mask-program an FPGA. For example, Xilinx calls their mask-programmed devices "EasyPath" FPGAs. This does require an NRE payment, as far as I know, so it isn't appropriate for situations where you might need to update your design. (Hat tip to alex.forencich for the correction)
I can at least speak for altera, I assume Xilinx will have something similar. They have the option of encrypting the file you put into external flash or EEPROM. Then you load the decryption key into the altera part, using its non volatile or battery backed key storage.
Since you can't read the key out it protects your ip. They were losing design wins to Asics because they couldn't protect peoples IP so this is a pretty common feature.
http://www.altera.com/devices/fpga/stratix-fpgas/about/security/stx-design-security.html
The only way you could accomplish this is by purchasing a separate Flash module (if you dont already have one on the PGA) and loading your code into ram, however this is not recommended for all the hassle, just purchase something like a CPLD if you plan on reprogramming at a later point or a ASIC if you have no intentions of reprogramming it again.
