Ok thanks. Just found this picture which seems to match up with what you said. Does it matter what red ports I use?
It does not as long as you use a separate cable fo each side of your miner. This is because, as mentioned several times, that particular supply has individual 30A 12v rails (360w per) and the antminer needs 360w total, so to keep things at 80% utilization on your power supply AND so your cables don't fry out (cause fires), it is safest to load up two separate rails.
Awesome, thank you your help. This is my first miner so this all new to me. Do you think it will be safe to run a second S3s with this power supply? (one with the native cables and then a new one with the two modular cables I will get) You mentioned fires and the PSU only having two 12v rails at 360w per.
Yes, you Will be fine to run two S3 units from this 1000w supply, one using the two PCI E connectors built-in, and two plugged into the modular section running the other.
Wrong
Only one per rail so to run two machines all four rails must be used.
This mean the three red jacks are needed and the attached none remove able cable should be the fourth rail
Using all four rails is a must on this psu to do two miners.
@ op. Buy or get three remove able cables if you want to do two miners
This may be correct, it is hard to tell without a schematic. I am sorry for any mis-ionformation, looking at the .pdf of the offered specs for this power supply it is unclear how the rails are wired, it may well be that one internal rail provides both MB 12v power AND powers the 2 integral PCI-E connectors, I would hope not, but this may be the case.
The chart for the 1000w suppyl shows TWO 'native' connectors, and TWO modular ones, and I would suppose that each of these FOUR would be on a separate rail, (with the MB connectors sharing one, but we would not be drawing off of this) however the picture appears to have THREE of said red connectors, so I have no idea how these might be wired internally, as the pictures offered do not match the chart!
If your wires are getting very warm to the touch, you are drawing near the limit of power and should explore alternative configurations, this supply, as others with 30A rails MAY be able to power an S3 one one rail (I've seen it many times, and consider it a fire hazard), but your wires would be getting quite warm and your supply's capacitors and transformer(s) would be over-taxed and this is not a good thing.
All that said, your supply has FOUR individual 12v rails, which should be independent of each other, if you are handy with a multimeter, you may be able to figure out which is which, otherwise dig for more specs or examine the docs for your PSU and each of these rails should power ONE hashing board, or one SIDE of each miner. If you can get one rail per board, you will be solid.
Good luck!
Edit:
Looking back at the pic in the op, IF the cable pictured that represents the TWO 'native' PCI-E connectors listed is of the BRANCHED type, meaning that it is just a short jumper that provides the second connector, then it is highly likely that, as mentioned, all THREE modular connectors would be required to run two S3 units from this power supply.