Hi MRJG,
The FlexPod environment will also include the Cisco UCS Compute layer along with the NetApp Storage and Nexus switches.
The FEX can be used to connect the Cisco UCS C-series Rack Mount servers to the Fabric Interconnects.
We do not use the FEX ports for Storage connectivity primarily because there is enough availability of ports on the Nexus 5K, as these switches are not shared outside the FlexPod environment.
I am not aware of a written statement that recommends for or against connecting NetApp Storage to a FEX, I will check on this and let you know.
In the meanwhile, you can try to improve the performance by increasing the number of uplinks from the FEX to the Nexus 5K. (If you have not done that already
)
As you know, you will not be able to acheive the same level of performance with the FEX when compared to the 5Ks. All the traffic will need to go upstream to the 5K irrespective of the initiator/target being connected to the same FEX or otherwise. Thus, affecting the throughput of your uplinks.
Thanks
Arvind.