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If I have an I2C Master with multiple I2C Slaves all on separate 3V3 lines (i.e. 3v3_Master, 3V3_Slave1, 3V3_Slave2... etc.) does it matter which 3V3 line the pull-up resistors on the line connect to?
I've looked through the I2C Manual here but couldn't find the answer.
No it doesn't matter. It will work as long as the micro and pullups both have power. It makes no difference where the voltage comes from - both sides will see 3.3V when no device is pulling down the lines.
With multiple rails, the order that your power rails come up at power-on can sometimes be troublesome. But the good news is that according to the I2C specification, I2C devices and masters are required to use true open-drain outputs, so they won't be damaged or affect communications when they have no power. For example, there are 3 possible states of the micro+pull-up power rails at any given moment for your circuit:
(All of this assumes I2C compliance, which is not always complete, so as always, testing will tell you for sure.)
In my opinion, it does matter. The concerns mentioned by other commenters as well do lead to system integration issues, with possible nasty, stochastic bugs.
Nathan is correct that by I2C specification the open drain drivers do not have protection diodes, which may result to the pull-ups powering a 3.3V rail if that rail is not up by the time the rail driving the pull-ups is already up. This may result to occasional brown-out conditions, and a slave or master booting incorrectly.
If the system has removable components, such as sensors connected via external connectors, ESD mitigation may require the use of TVS diodes. If zener diodes are used above rated above the rail voltage, this is not an issue. If reverse biased diodes are used, then the pull-ups need to be on the rail that comes up last. This is typically a good strategy, given:
With a variable configuration (removable slaves), if the pull-ups are on the slaves, multiple sets of pull-ups may lead to unpredictable conditions. In this case, the pull-ups may be powered from the master's side, and each slave can use a re-driver, or level translator, such as https://www.nxp.com/docs/en/data-sheet/PCA9509P.pdf, with one supply coming from the master side rail, one from the slave. This is probably the safest solution, especially if there is significant difference between the rise times of the rails.
