Hi there,
I know your question is kinda old, but since I am working with NetApp gear on a daily basis I think I can help you a bit
You are correct that amber is a caused because of an error of some kind.
It can be abler on the disks, on the shelf (at the front), on the PSU's at the back, and on the IOM modules... ๐
If I were you I would start out with two PSU's (for the DS4246) you only need four PSUs if you are using SAS 10k drives... NetApp ships them with SATA/NL-SAS 7.2k drives and two PSUs.... Also only use one of the IOM6 modules (to top one), remove the lower IOM module, you can only use this if all your drives are SAS drives as they are dual-ported, which SATA drives are not. (NetApp use a little converter board which converts SATA to SAS)... but basically forget about getting dual-path working with anything else than a NetApp controller
If you have to connect more shelfs together you have to connect them to the right ports... on the IOM6 modules you have a port with a circle and one with a square...
You want to connect your HBA to the first shelf using the square port, then connect the circle port from that shelf to the square port on the other shelf you want to link...
And yes the shelfs have to have different IDs... yet I'm not sure if anything else than a NetApp controller cares about that... and even with a loop with same ID shelfs, a NetApp controller can see all disks, they will just be numbered with a strange ID...
Power the shelfs on... id anything lights up amber now, identify which amber light it is...
Amber disk = Faulty disk (duh!)
Amber PSU = No power, not turned on, or faulty PSU (replace it)
Amber IOM module = Most likely faulty IOM module, or possibly faulty cabeling (check that no circle is connected to another circle on the other shelf, and the same with the square port...) if it is still amber, replace the IOM module.
Amber shelf = This can be caused but the temperature sensors, faulty fans, or faulty voltages
You can check some of the issues above with the sg3-utils package for Linux... I cannot remember the commands, and it is kinda hairy... so if you have an old NetApp Controller handy, it will be much easier to troubleshoot it by just booting it into maint. mode and issuing a "environment status" command and it should tell you what's wrong ๐
The DS shelfs from NetApp are in general very stable! I have customers that have shelfs that are 7-8 years old now and still going strong... we have replaced disks and the odd PSU and IOM module, but never a whole shelf.... in my 15+ years working with NetApp gear I have replaced a whole shelf two or three times... one of which NetApp support wasn't even sure what was wrong, and they just replaced it to be sure...
I hope you figure it out...
Another thing you might want to know, is that it is that as it was possible to upgrade your shelf from IOM3 modules to IOM6, it is also possible to upgrade to IOM12...
Of cause it only makes sense if you have SAS drives capable of 12G speeds... and of cause a HBA that can do 12G... (this all uses different cables too... MiniSAS HD compared to QSFP for 3G and 6G)... (and remember that it is till Quad 12G per cable which confuses some people) so there are four SAS lanes in the shelf.
Only problem with the IOM12, is that it is pricy at the moment... (about $1.000 used)
Good luck ๐
/B