Is it possible to configure an FPGA design that uses the FPGA2SDRAM (F2S) port on a Cyclone® V SoC / Arria® V SoC after booting Linux from the Hard Processor System (HPS) side?

The ability to set the applycfg bit is implemented in Uboot, and setting the applycfg bit from Linux is not supported due to the restriction that the SDRAM must be idle to set the applycfg bit.

FogBugz #158537: Updating U-Boot FPGA2SDRAM driver
https://github.com/altera-opensource/u-boot-socfpga/commit/75905816ec95b0ccd515700b 922628d7aa9036f8

If you need to configure the FPGA on Linux, please do so after you have configured the FPGA configuration and the applycfg bit in Uboot.

As an example, you can execute unzip command in Uboot.
Please add the following to include/configs/socfpga_common.h in Uboot and build it.
#define CONFIG_CMD_UNZIP

Please issue the following command in Uboot.
fatload mmc 0 0x2000000 your_rbf.gz unzip 0x2000000 0x2800000
fpga load 0 0x2800000 $filesize

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Category: SoC
Tools: SoC EDS
Devices: Arria® V / Cyclone® V