@mtx512rk @stylon A quick update. I’ve finally managed to get the board working with both pcie slots!
rock@rock-5b:~$ lspci -tvb
-±[0004:40]—00.0-[41]----00.0 Realtek Semiconductor Co., Ltd. RTL8125 2.5GbE Controller
±[0002:20]—00.0-[21]----00.0 JMicron Technology Corp. JMB58x AHCI SATA controller
±[0001:10]—00.0-[11]----00.0 Intel Corporation SSD Pro 7600p/760p/E 6100p Series
-[0000:00]—00.0-[01-ff]----00.0 Yangtze Memory Technologies Co.,Ltd Device 0001
Both of the nvme SSD connected to the m-key slot and they are working now.
rock@rock-5b:~$ sudo hdparm -Tt /dev/nvme0n1p1
/dev/nvme0n1p1:
Timing cached reads: 5438 MB in 2.00 seconds = 2720.40 MB/sec
Timing buffered disk reads: 4296 MB in 3.00 seconds = 1431.83 MB/sec
rock@rock-5b:~$ sudo hdparm -Tt /dev/nvme1n1p1
/dev/nvme1n1p1:
Timing cached reads: 3702 MB in 2.00 seconds = 1851.65 MB/sec
Timing buffered disk reads: 2628 MB in 3.00 seconds = 875.51 MB/sec
After inspecting the board and schematic carefully, the problem was the bifurcation board utilized different GPIO pin from the development guide for perst signal.