Can some Guru help me with the starting point to communicate with spartan-6 FPGA on Nexys 3 board using USB. I need to send large amount of data using software to the FPGA , so UART solution will be really slow.
You can't use connector J4 to communicate with the FPGA.
It's used only as a USB HID controller.
Other then that, you can use the Ethernet port, but this will require implementing (or using an IP) Ethernet MAC on the FPGA - which I think isn't a project for beginners.
J13 is connected to a USB to UART IC - I think you'll be able to communicate at about 1Mbps using this interface.
You can't use connector J4 to communicate with the FPGA.
It's used only as a USB HID controller.
Other then that, you can use the Ethernet port, but this will require implementing (or using an IP) Ethernet MAC on the FPGA - which I think isn't a project for beginners.
J13 is connected to a USB to UART IC - I think you'll be able to communicate at about 1Mbps using this interface.
No.
UARTs can go much faster then that. The maximum speed will depend upon the capabilities of the physical layer (rise/fall time of the buffers, voltage levels, quality and length of cabling) and the accuracy of the internal clocks of the communicating devices.
For example, I implemented a custom 11bit UART on a Spartan 3 that ran at speed of 5MHz.
However, the communicating devices where on the same PCB and the I/O standard was LVCMOS 3.3V (not RS232...).