You may try out the uClinux on your Altera Nios dev board before compiling anything. You can learn how to run a compiled program on your board. It is a very basic and important step. The kernel image was built from uClinux-dist with the default config. Both the sof and ptf files come from the example project, and there is no change. The sof and kernel image version must match, otherwise it will not run.

Please check UClinuxDist for booting up message and usage. After you get uClinux boot up successfully, you can build the kernel image with the ptf file of the same hardware project.

You will need Quartus and Nios2eds installed. Download the sof and zImage files for your board to a working dir, eg c:download on Windows or ~/download on Linux. Note the drives mapping in Nios II command shell (cygwin), drive c: is named as /cygdrive/c/ and c:download is /cygdrive/c/download. 

Open a Nios II command shell on Windows from Windows Start-->Programs-->Altera-->Nios II 7.2 -->Nios II Command Shell, and change to the download dir.
cd /cygdrive/c/download

Or open a shell terminal on Linux and change to the download dir.
cd ~/download

Note: If you don't have a Nios II license and have generated the .sof file yourself then its usage will be restricted. Follow the following instructions but run the nios2-configure-sof instruction from one command shell and run the nios2-download and nios2-terminal instructions from another. This allows the nios2-configure-sof to keep in contact with the processor so as to allow it to keep running.

For DE2  2C35 dev board

step 1. Configure the FPGA,
nios2-configure-sof  DE2_NIOS_HOST_MOUSE_VGA.sof
step 2. Download and run the kernel image,
nios2-download -g zImage_DE2_NIOS_HOST_MOUSE_VGA_v1.6
nios2-terminal

The kernel image was built with DE2_NIOS_HOST_MOUSE_VGA.ptf (was system_0.ptf) in the project DE2_System_v1.6/DE2_demonstrations/DE2_NIOS_HOST_MOUSE_VGA of the DE2 v1.6 CD.

For DE2-70 dev board

step 1. Configure the FPGA,
nios2-configure-sof  DE2_70_NIOS_HOST_MOUSE_VGA.sof
step 2. Download and run the kernel image,
nios2-download -g zImage_DE2_70_NIOS_HOST_MOUSE_VGA_v1.1
nios2-terminal

The kernel image was built with DE2_70_NIOS_HOST_MOUSE_VGA.ptf (was DE2_70_SOPC.ptf) in the project DE2_70_SYSTEM_cd_v1.1/DE2_70_demonstrations/DE2_70_NIOS_HOST_MOUSE_VGA of the DE2-70 v1.1 CD.

For DE1 dev board

step 1. Configure the FPGA,
nios2-configure-sof  DE1_SD_Card_Audio.sof
step 2. Download and run the kernel image,
nios2-download -g zImage_DE1_SD_Card_Audio_v0.6
nios2-terminal

The kernel image was built with DE1_SD_Card_Audio.ptf (was system_0.ptf) in the project DE1_CD_v0.6/DE1_demonstrations/DE1_SD_Card_Audio of the DE1 v0.6 CD.

For Nios II Embedded Evaluation Kit, Cyclone III Edition, including Cyclone III starter kit (aka the "NEEK")

Easiest way to run Linux on the NEEK:

step 1: Copy the unzipped content of the NEEK-uCLinux-eek.zip file as a subdirectory ("uCLinux") into the "Altera_EEK_Applications" directory on the SD-card provided with the kit.
step 2: With the Application Selector you now can select and start "uCLinux"
View the embedded file info.txt (e.g. in the Application Selector) to see what it can do and how it's done.

Another Application Selector Application is SLS_Console.zip uploaded with permission of SLS Corp. This distribution shows the Linux starting messages on the NEEK's LCD screen and opens a shell that is displayed on the LCD screen and can be used with a PS2 keyboard attached to the NEEK.


Without using the SD-Card you can do this:

step 1. Configure the FPGA,
nios2-configure-sof  cycloneIII_embedded_evaluation_kit_web_server.sof
step 2. Download and run the kernel image,
nios2-download -g zImage_cycloneIII_embedded_evaluation_kit_web_server
nios2-terminal

The kernel image was built with cycloneIII_embedded_evaluation_kit_web_server_sopc.ptf in the Cyclone III Embedded Evaluation Kit Web Server files.
However, the TSE MAC driver is not ready yet, and the ethernet won't work.

For Cyclone III starter kit only

step 1. Configure the FPGA,
nios2-configure-sof  cycloneIII_embedded_evaluation_kit_web_server.sof
step 2. Download and run the kernel image,
nios2-download -g zImage_cycloneIII_embedded_evaluation_kit_web_server
nios2-terminal

The kernel image was built with cycloneIII_embedded_evaluation_kit_web_server_sopc.ptf in the Cyclone III Embedded Evaluation Kit Web Server files.
However, the ethernet won't work as there isn't one on this board.
Useful wiki page: Cyclone III - Nios II - Starter board

For Altera Nios dev board 2C35 edition (not DSP board 2C35)

step 1. Configure the FPGA,
nios2-configure-sof NiosII_cycloneII_2c35_full_featured.sof
step 2. Download and run the kernel image,
nios2-download -g zImage_NiosII_cycloneII_2c35_full_featured_v7.2
nios2-terminal

The kernel image was built with NiosII_cycloneII_2c35_full_featured_sopc.ptf in the Nios2eds v7.2 installation dir, nios2eds/examples/verilog/niosII_cycloneII_2c35/full_featured .

For Altera Nios dev board 1C20 edition

step 1. Configure the FPGA,
nios2-configure-sof NiosII_cyclone_1c20_full_featured.sof
step 2. Download and run the kernel image,
nios2-download -g zImage_NiosII_cyclone_1c20_full_featured_v7.2
nios2-terminal

The kernel image was built with NiosII_cyclone_1c20_full_featured_sopc.ptf in the Nios2eds v7.2 installation dir, nios2eds/examples/verilog/niosII_cyclone_1c20/full_featured .

For Altera Nios dev board 2S60 ROHS edition

step 1. Configure the FPGA,
nios2-configure-sof NiosII_stratixII_2s60_RoHS_full_featured.sof
step 2. Download and run the kernel image,
nios2-download -g zImage_NiosII_stratixII_2s60_RoHS_full_featured_v7.2
nios2-terminal

The kernel image was built with NiosII_stratixII_2s60_RoHS_full_featured_sopc.ptf in the Nios2eds v7.2 installation dir, nios2eds/examples/verilog/niosII_stratixII_2s60_RoHS/full_featured .
But the ethernet port on 2S60 may not work , due an issue in the design file v7.2.

For Altera Nios dev board 1S10 edition

step 1. Configure the FPGA,
nios2-configure-sof NiosII_stratix_1s10_full_featured.sof
step 2. Download and run the kernel image,
nios2-download -g zImage_NiosII_stratix_1s10_full_featured_v7.2
nios2-terminal

The kernel image was built with NiosII_stratix_1s40_full_featured.ptf in the Nios2eds v7.2 installation dir, nios2eds/examples/verilog/niosII_stratix_1s10/full_featured .

For Altera Nios dev board 1S40 edition

step 1. Configure the FPGA,
nios2-configure-sof NiosII_stratix_1s40_full_featured.sof
step 2. Download and run the kernel image,
nios2-download -g zImage_NiosII_stratix_1s40_full_featured_v7.2
nios2-terminal

The kernel image was built with NiosII_stratix_1s40_full_featured.ptf in the Nios2eds v7.2 installation dir, nios2eds/examples/verilog/niosII_stratix_1s40/full_featured .

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If you are using time-limited sof , read opencore plus,

http://www.altera.com/literature/an/an320.pdf

Tethered Mode

Tethered mode requires an Altera serial joint test actions group (JTAG)
cable connected between the JTAG port on your board and the host
computer, which runs the Quartus II Programmer for the duration of the
hardware evaluation period. The Quartus II Programmer only requires a
minimum installation of the Quartus II software—no license is required.