Windows Server 2012, Intel S5520HC, poor disk to disk transfer performance

I am trying to install Server 2012 64 R2 onto a WD Velociraptor 1 TB hard drive, the mainboard is an Intel S5520HC, 16 GB ECC non-registered RAM (2x8).  I installed the OS and then reattach the 500 GB WD Velociraptor that was the main drive with SBS2003 installed.
This machine was a upgrade (failed server) in September of 2011.

When I start to copy data from WD 500 GB drive, the transfer starts out 200 mbps plus and quickly falls to nothing.

I first attempted this install 05/01-05/02, the performance was so bad I pulled the installation and place the server back as SBS 2003.

I contacted WD and they thought the drive was the issue... I purchased a new WD 1TB Velociraptor as well as a WD1003FBYZ Enterprise drive.

I attempted the install this morning to the new Velociraptor, configured DNS, DHCP and Active Directory.  I then restarted and attached the WD 500 Velociraptor.  Same issue, transfer rate falls to less that 1 mbps all the way to zero and then continually pauses, poor transfer rate.

I then attempted the WD1003 drive and did the OS install only, connected the WD 500 Velo. drive and copied 115 GB, took about 45 min... not great but averaged over 50 mbps.  I then configured AD DS and the poor transfer performance reappeared.


I contacted Intel Wednesday about the issue and received the response below... BTW, I searched and found where others are using the S5520HC mainboard with Server 2012.  I have a 10 year old server I am running Server 2012 on.

Any help greatly appreciated.  Thanks in Adanvce.

Dear Customer,
 
Intel Customer Support Service Request Management request # 8001118865 has been updated.
 
Agent Comments:
Good Afternoon Phil,

Thank you for contacting Intel Technical Support.
We have found that the Operating System Windows Sever 2012 is not
supported by this board, so, in this case if you want to update the
Operating System you can download the Windows Server 2008.

You can find the Operating Systems supported by this board in the
following link:

http://www.intel.com/support/motherboards/server/s5520hc/sb/CS-030222.ht

m

You can get the driver for your server board at the following link:

https://downloadcenter.intel.com/product/36599/Intel-Server-Board-S5520H

C

In the other hand, in regards the issue you got with the performance
when transferring data from the old drive to the new drive, we would
like to know if you have a RAID configuration or you are just using a
single drive without any RAID configuration.

Important Note: if you need additional help with your request, we would
appreciate it if you answered this e-mail and not writing a new email,
unless it is an entirely different matter.


Kind Regards

Carlos
Intel Technical Support
frdbadfAsked:
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Lionel MMSmall Business IT ConsultantCommented:
SO when you have 2003 installed the performance (with all the same hardware, disks, raid controllers, ram) was fine, fast enough? But when you install 2012 it drops to unacceptable levels? What RAID controller do you have? If you are using an "on-board" controller on the motherboard you may have to consider installing an add-on controller as my guess is the issue is with an on-board controller and Win 2012. Is 2008 a feasible option for you as suggested by Intel?
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Davis McCarnOwnerCommented:
Lurking in the background, the Windoze storage drivers will automatically slow down the access rate whenever they think the drive has problems with the slowest rate being PIO1 (ala early 1990's) and 3MBps.  Add the 10+ retries on each problem read or write and the performance absolutely s*cks.
I also suspect that if you let the copying continue, you'd hit a read error and the process would abort.
To check, get the free trial version of HDTune Pro, run it, change the selected drive to the WD 500, and look at the Health tab.  If the data column shows anything but 0 (zero) for (05) Reallocated sector count or (C5) Pending, you found your culprit: http://www.hdtune.com/
The way you overcome it is to clone the failing drive to another which does not have hardware problems using something like Rawcopy: http://www.roadkil.net/program.php?ProgramID=22
Choose the physical disks in the source and destination pulldowns (being VERY careful!!!) and it often helps to check the box to start at the end of the drive first.  After it has finished, shutdown, disconnect the failing drive, reboot, and copy from the clone.
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pgm554Commented:
Looking at the downloads I see that there are drivers for 2012 ,so that is a red herring.
I would get a hold of the WDDiag from WD and run it.
It's a whole lot more through than HD Tune .
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frdbadfAuthor Commented:
At first I suspected that possibly something was wrong with WD450.  I did some testing copying/pasting folders to same drive rather that disk to disk.  On the new WD1000 Velos, they show the same symptoms.  The Velo 450 acceptable performance.  I am in the process of setting up the WD1000s as a RAID using the embedded Intel controller.  Then I am going to try and update the RAID driver to the 2012 version Intel has released, other than MGT console downloads  for 2012, that is the only 2012 driver (released 2015) I see.

2008 R2 may be an alternative.  I will look at all the suggestions, keep you posted.

thanks,
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pgm554Commented:
The embedded raid on most mobo's is fake raid and not real reliable.
Seen many a failure or performance issue with those types of controllers(especially on vm's).
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kevinhsiehCommented:
Windows disables disk write caching when Active Directory is installed. Poor write performance is to be expected.

https://social.technet.microsoft.com/forums/windowsserver/en-US/16352eee-6bc6-4858-8642-12b2496d39ee/how-to-enable-write-caching-on-domain-controller
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frdbadfAuthor Commented:
Sorry for leaving the question abandoned so long... long story short.  I gave up on using the existing server as a platform for Server 2012 and Exchange 2013.

In CMOS I configured the SATA as SW RAID and installed the 2 1 TB WD Velos as a RAID 1 and the performance did improve.  
However all SATA ports were used in the SW RAID and I could not transfer the data from the existing WD 450 Velo by connecting directly.  That and in lieu of the following email from Intel asking if I could jumper and slow the new WD Velos to 3 GBPS led me to go with a new server.  Thanks for your suggestions.

Agent Comments:
Good Afternoon Phil,

Is there a jumper in the hard drive to force the speed to 3 Gb/s so it
will meet the speed from the SATA ports in the server board?

The drivers are available; our recommendation is to proceed with the
upgrade.

ESRT2 RAID driver for Windows
You can modify the following configuration in the BIOS and it might
improve the data transfer rate:
• Go to the BIOS > Advanced Tab > PCI configuration > PCI AER Support
should be Disabled.

On the other hand, regarding the issue that you are getting with the
detection of the WD Velociraptor 500 GB drive, the SATA ports are
currently configured to support RAID arrays, which give you the option
to  configure a single hard drive as RAID 0; however, this procedure
could affect the data inside the hard drive since we are changing the
read/write properties.

The best option will be to copy the information from the hard drive by
using a different machine without RAID configurations.

Please let us know the results of the steps provided.

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frdbadfAuthor Commented:
Maybe you are right but Intel said this board was not supported for Server 2012 R2.  Too many issues encountered.

thanks anyway.
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