Any chance of an idiots guide to doing this as i know nothing about configuring switches.Also see if you can enable STP on your switches this should hopefully prevent loops bringing the entire network down, or at least contain the problem to one or two switches.
Spanning Tree is good for preventing loops but you do need to configure it properly. For example it sould only be configured for ports that connects to other switches or routers, it should not be enabled on ports that are connected to servers or workstations.
For connectivity problems such as GPO not assigning properly and scripts not running could be because the port that the workstations is connecting is still checking for loops. The thing to is like i said turn of spanning tree for ports that connects to workstations. In cisco switches its called portfast which basically tells the switch to immediatly move to forwarding state rather than checking for loops.
Now you may ask what if someone connects a patch leads to two network data points in this case the loop would occur but the switch will not let this propergate it to other switches because the port that connects to other switch(s) will have STP enabled on it.
For multiple vlan scenario, rapid spanning tree might be ideal however you do need to calculate the root switch, and the path cost etc. to make it work correctly.
Loops can also occur if spanning tree is turned on espically when configuring port trunking or link aggregation or etherchannel as cisco calls it. However if configured correctly the etherchannel is seen as one link to STP instance.
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