I recently had user colicstew comment that they could not get Freenas 9.10.2 U3 to see drives on his LSI2116. Luckily I have some unused 2TB Drives and LSI 2116 Controller as part of my Xeon D Lab.
First step was to passthrough my LSI2116 Controller and Reboot the Server. You should see Enabled/Active for the LSI Controller which we do
Next I created a VM. 
I chose to install the OS on one of my VMware Datastores.
On the Hardware Settings I set as shown.
Then I clicked Add other device -> PCI Device and Add the LSI Controller
Finally I added a CD-ROM Drive and attached the Freenas ISO downloaded from here.
Finally we boot the VM
Then we select Install at the first Screen
One of the oddities I ran into while creating this tutorial was the key sequence to release the mouse from the VMWare Remote Console was the escape key in the Freenas installer that bounces you back to Initial Setup Screen, so the remaining pictures are via my phone.
On the next screen you will be warned about only having 4GB of memory. Since I’m only using this as a test system, I am not concerned. If you were running this as an actual file server you would want at a minimum 1GB of Memory per TB of storage.
On the this screen we see five drives. One is our drive we will install FreeNAS OS to, and the other four are 2TB Hitachi Drives I attached to the Xeon D Board.
Next you are warned that FreeNAS will clear the drive you are installing to.
Next you are asked to set the root password.
Finally you are asked to choose a BIOS Mode.
At this point, I went to install the system, but no matter what I did, it would not install the OS, failing with the below error.
The problem here is that the drive that we are installing the OS to is thin provisioned. FreeNAS does not like this.
Fix is to create the disk as “Thick provisioned, eagerly zeroed”.
Once that was fixed, the OS installation continued without issue.
Once completed, you will see the following success message.
Then, I chose option four to shutdown the system. Be sure to remove the DVD Drive, or the system will continue to boot from the Installer. Once that is completed your system will work as expected.
Unfortunately, I had no issues getting the system up and running. colicstew feel free to email me via the contact method and we can see about troubleshooting this issue. I would start with verifying you have the correct breakout cable. I used one of the four breakout cables from the Motherboard.
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