Using ConnectX-3 you can't reach an aggregate BW of 2xFDR.
the two ports are consider as an high availability solution of one active and one standby.
You can reach the 2xFDR full BW by using Connect-IB.
What gadis said.
If for no other reason then PCIe3 x8 has a theoretical max bandwidth of about 56Gbps.
X16 should give you better ability with both ports - the card can. it is what's underneath it that is limiting us. :-)