Hi Tunjun,
Have you tried to remove spine S03 for approximately 1 min from the chassis then re-insert it and see if it boots and is seen properly without errors.I looked at the attached logs and it looks like the I2C management buss is stuck and is not properly seeing the S03 slot.Also there are other tell tale signs of I2C buss stuck issues.If your not on the latest SW which is 1.1.2700 for the IS56XX chassis based systems I suggest a "cold boot" removing power for the whole chassis for ~ 1min then once rebooted see if all cards show up with a "show inventory" then upgrade to 1.1.2700 which helps mitigate known buss sticking issues in earlier SW revs.