Lenovo ThinkStation Probs: BIOS Issues & Windows7 Boot Install on M.2 SSD

Have a Lenovo ThinkStation Desktop P500, P700, or P900 with an M.2 SSD drive?

Having trouble getting Windows 7 (or other OS) to install as boot drive?

I’ll walk you through updating the BIOS and reinstalling the OS, which solved my problem.

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See End of Post for Review of Lenovo ThinkStation P500 as 3D CAD Workstation, and Details on How I Configured the Machine

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Nature of this Problem: PCIe SSD Not Factory Installed as Boot Drive (or) A Minor BIOS Change Makes Computer Unable To Find Boot Drive

I recently got a new 3D CAD workstation desktop, a Lenovo P500 ThinkStation. I ordered an option that I’ve never used before, a 250GB M.2 SSD card. It interfaces with a “Flex Adapter” riser board plugged into a PCI express 4x lane slot. (Well, I found out it’s not JUST a PCIe x4 slot, it’s a “FLEX CONNECTOR,” and also can handle USB signals or something – more on that in the last section). This was to be set up as my boot drive, with Windows 7 x64 as the operating system (“downgrade rights” from Windows 8.1 Pro).

Well, I’m not sure what all happened with the ordering of this configuration through our IT dept., but apparently this step didn’t happen at the factory. So we had to get the M.2 SSD going and install Win7 on it as the boot drive. This turned out to be an odyssey of mythical proportions. And I’m not going to get into most of the stuff that happened (I’ll just say there were no Sirens to speak of).

Zooming in to show the PCIe “FLEX ADAPTER” mezzanine board with a M.2 PCIe SSD installed (the other M.2 SSD slot next to it is for SATA type M.2 SSD cards)

Dead Giveaway Tip That Your BIOS Needs Updating: It Doesn’t Know The Boot Drive’s Name

Usually, installing any hard drive in any computer is not a daunting task, and takes about 10 minutes. But installing this SSD was one thing. Getting the computer to recognize it, another.

This is the “after” pic of the boot sequence screen. Before, even when the OS was installed sort of successfully, the mezzanine drive wasn’t being named in BIOS. This is weird. There was an OS installed on it; when you pushed the power button, the computer booted into this drive. But the BIOS didn’t show that there was a drive installed at that port. It didn’t show anything at all. In this pic, after the BIOS upgrade, it now shows a description of the drive. If there’s no name assigned to your drive, you probably need to update your BIOS.

What does “Mezz” mean? Because these Lenovo workstation computers have a new hardware expandability scheme of adding in certain components to the PCIe x4 bus, they use “Mezzanine cards” to create the interface do it. I’ve also seen them referred to as riser cards or daughter boards.

The first OS install was achieved after days of tries and calls to Lenovo tech support by our IT person. I then started to use the computer. When it wasn’t booting as fast as I expected, and I was having some new software errors, I got into the BIOS to change something that should’ve been minor and reversible. But the delicate sensibilities of the computer system were devastated nonetheless. It then would throw the “Error 1962: No operating system found. Boot sequence will automatically repeat.” It would no longer boot to the Windows install.

Wondering why the OS would no longer boot after a simple BIOS option change that was then changed back, I started trying many other changes and researching the problem. There wasn’t much help out there, which is why I write this now.

It Matters Whether You Want to Install Windows 8.1 or 7 (UEFI vs. Legacy BIOS)

I’m assuming this would’ve been a different (shorter) story if I’d just deigned to use Windows 8.1, but I prefer 7. There came a point where I changed my mind and decided to try to install the 8.1 from some other Lenovo recovery discs I found lying around (lots of Lenovo machines in the office). But it didn’t want to work.

Why the distinction? Because the motherboard BIOS program has a fancy UEFI BIOS – I say “fancy” because if you’re not familiar, see the difference between UEFI BIOS and Legacy BIOS below. But UEFI (I say YOO-Fee) BIOS supposedly only works for Windows 8. Windows 7 needs to have the Legacy BIOS settings selected.

Here’s the age old legacy BIOS we’ve all known and loved.

Here’s the shiny new UEFI BIOS that Legacy BIOS looks at and shouts “YOU BIOS GET OFFA MY LAWN!!!”

If you’re installing Win7, another thing to keep in mind: You’ll want to install a disc that is already up to date of Windows7 SP1 (Service Pack One). I think it’s got the drivers that can understand and install to an M.2 NGFF SSD (Next Generation Form Factor) interface.

MAKE SURE THE BIOS IS UPDATED TO THE LATEST VERSION. FIRST!

Legacy vs. UEFI wasn’t really the issue here, though. Instead of wasting hours fiddling with BIOS settings and recovery discs, I wish I had just done this in the first place: MAKE SURE THE BIOS IS UPDATED TO THE LATEST VERSION. FIRST!

I’m guessing Lenovo decided to make this workstation so bleeding edge, insofar as mass market corporate workstations go, that they pushed it out the door with some half-baked options. It happens. It’s not easy to make configurable products and not have any mistakes, nor test for all design flaws that create unknown malfunctions. At least it looks like Lenovo is trying to fix the issues.

There may be other glitches that were impeding my progress, but here’s a rundown of the BIOS update fixes to date that caught my eye. (Click for PDF)

I’m sure that second one got me. I tried that “optimized” setting when the computer had its 1st OS install, because it was booting unimpressively slow and I wanted to get everything “optimal.” And then I set the Legacy/UEFI settings back to Legacy, because I knew Windows7 likes it that way. And then I saved the settings. It proved to be a punishing “optimization”, and changing the settings back to how they were didn’t help the computer find the boot drive again.

How To Update BIOS to Latest Version (For Novices)

• Go to Google, type in “lenovo p500 thinkstation bios update” (or p700, p900).
• Once you’re on this page, sort for “BIOS” and then sort for your Operating System.

• Download a format of update. I chose the CD/DVD version.
  • I was in the situation where I couldn’t use the ThinkStation to make media as it wouldn’t boot to an OS. So I downloaded this CD/DVD vsn to my laptop, and burnt a disc.
  • You can also choose the USB option for this situation, but I didn’t have a thumb drive lying around that I wanted to take the time to clear off. And when it comes to BIOS updates, you want the BIOS software to be THE ONLY FILE on the media. You don’t want some weird file confusion to brick your motherboard.
• Insert blank CD or DVD in your burner on your non-ThinkStation machine, if your ThinkStation machine is out of order at the time.
• If you have Windows 7, download this file to your desktop or wherever, right-click and choose “Burn Disc image” (other versions of Windows may have different commands for burning disc images).

• When the CD is ready, put it into the ThinkStation’s DVD drive.
• Restart your ThinkStation.
  • If it’s messed up and keeps going through the boot sequence over and over, try CTRL-ALT-DELETE to restart, or just push the power button on the tower until it shuts off.
• When the computer restarts, push ENTER either once, or several times until a menu opens.
  • Push ENTER (or whatever button pauses the countdown) if you need more than 10 seconds to make a choice.

• Push F12 to choose a different boot device.

• Choose the DVD drive.
  • If there’s a UEFI version and a Legacy version, try Legacy.
    • I’m not sure if this matters for BIOS updating, but it seems to for later when you install a Windows OS.
  • The pic below doesn’t show 2 vsns of the DVD drive, I think it’s just whatever drive you’ve designated as the primary boot drive at the time that shows 2 versions.

• Your computer should now boot into the update DVD. Leave the machine alone unless prompted to make choices. You do not want to restart or mess up the machine when it’s rewriting motherboard firmware.
  • I was asked 2 questions during my update, right at the start, which was remarkable as I’d never seen that before on a BIOS update.
    • I was asked something about if I wanted to change the serial number and then if I wanted to change the machine model name. I typed “N” for “no” each time.
  • Then it goes through a process of overwriting the firmware. This should take a minute or three. Let it go. The computer will probably restart itself when it’s done.
  • After the computer restarts itself, it may not be done, so don’t just take the DVD out yet. It will tell you when. When I did it, I was surprised to see the update go through a whole other series of processes after it restarted. So, again, these are sensitive processes and should be left to their own devices.
• When you’re sure it’s all done with the BIOS update, or it actually says it is, you can take the disc out.

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Theoretically, after installing the BIOS updates, I probably could’ve then rebooted and witnessed the computer boot into its long-lost love, the boot drive that had the OS installed!

But I had burnt that bridge by trying several botched Recovery Media installs of OSs in the hopes of fixing the computer. So at this point, you can see if your computer works again, or if you need to install an OS.

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Prepping BIOS for Win7 OS Install:

Go into the BIOS and Make These Choices (If Not Already Set)

• Go into the BIOS menu:
  • Reboot
  • Press Enter until you get a menu
  • Press F1 or select it and Enter to go into BIOS settings
• Go to Devices tab
  • If not already, set Boot Agent to Disabled
    • Honestly, I don’t know much about this, but I think it’s for if you’re booting into a server image, and if you’re worried about installing an OS on your local machine, you probably are not booting over a network. When I had this set to default of PXE, it added a lot more boot time and sometimes threw errors about finding a boot disc.
• Go to Save & Exit tab,
  • For installing Windows 7: Make sure OS Optimized Defaults is set to Disabled.
    • This optimizes for Win 8.
• Go to Startup tab,
  • Set CSM to Enabled
  • Set Boot Priority to Legacy First
• That step  should automatically change the Secure Boot choice to Disabled, which is how it needs to be.
  • If Security tab > Secure Boot is not disabled, set to Disabled.
• Press “F10” to save and exit BIOS Settings.

Now Reboot, and Boot Into Your DVD or USB Drive (ASSUMING You Have Recovery Media Already)

• As shown before, hit Enter until you get a menu, then hit F12 and choose to boot into your DVD drive (choose Legacy DVD if option)
• It should start installing your OS. It may tell you to change discs periodically and then press “Enter” after doing so.
  • If you need to insert the Lenovo Windows recovery discs and get to the point in the OS reinstall/repair process where it asks you if you want to partition the drive with MBR or GPT, choose GPT. I say this only because it says it’s “faster”.

If you DO NOT have recovery media, see next.

Reinstalling or Repairing your OS: Locate (or Make) Compatible Lenovo Recovery Discs

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Make:

Need Them NOW?! If you didn’t get these discs with your computer, you may be able to find compatible versions and download them from one of those torrent / file sharing sites, and burn them. Be very wary of this idea though. I say it only because I’m very impatient, and would probably balk at ordering $30 (or whatever priced discs) and having to wait for a week or two for arrival. Also, in this day and age, I would hope you can purchase a download from Lenovo and get them faster, but haven’t looked it up.

And if you stumbled upon this post because you’re being proactive, and you don’t have these discs, but you DO HAVE a new ThinkStation that’s working, I believe you can make these Recovery discs from your current OS install, so you’ll have them in case you’re in this situation. You’ll have to look it up.

Otherwise, here’s what I found in a quick search:

Note: On the Windows 7 operating system, you can create recovery media using discs or external USB storage devices

To create recovery media on the Windows 7 operating system, click Start ➙ All Programs ➙ Lenovo ThinkVantage Tools ➙ Factory Recovery Disks. Then, follow the instructions on the screen.

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Locate:

If you’re like me, you ruined your OS install and will need to redo it. And since you ruined your install, you won’t have that nice recovery partition already on your disc that you can hit F11 and boot into it.

• So get out your Lenovo Recovery Media (I assume these are still always discs, and not USB drives or anything?).
• Make sure they’re actually for your machine, in case you’ve got multiple different Lenovo machines around, with different sets of discs (as I had).
  • I kept sticking the wrong discs in the drive, and thinking the computer was even more screwed up than it was, because it DOES NOTHING AT ALL when you stick in incompatible recovery discs. It doesn’t TELL YOU IT’S INCOMPATIBLE. It just sits on its metaphorical thumb and counts the hairs as they fall from your frustrated scalp.
    • See the red outlined blowup of a disk writing in the photo below – it’s for a P500 ThinkStation. I was trying discs for a different Lenovo model before, thinking it couldn’t really matter much. But it did.
• You must load the discs in order.
  • with the number 1 in the circle, and a much smaller “Disc 1 of 1” underneath it, you’ll know to stick that one in first.
    • It will tell you which ones to put in after that. If it asks you if you have a “supplemental disc” to put in (and if you don’t) then it’s okay to click “no”. You’re probably not actually missing something.
• Notice how the Operating System recovery disc says Windows 7 Professional SP 1.
  • That SP 1 is apparently important if you want to install to an M.2 form factor, as previous discs didn’t have the drivers to manage that advanced hardware.

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And here’s just a bunch of pics of Lenovo ThinkStation P500 BIOS menus, in case that’s helpful for some reason:

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Lastly: After All That Trouble, I’m Moving the M.2 SSD from the Flex Connector

So, because of the confusion with the ordering of this computer, I didn’t receive it how I had configured it on the Lenovo site. The IT person ordered it with a RAID card option, which led to having “Blind Connect Assemblies” (BCAs) with SAS cables that need to be connected to a RAID card. Fortunately, the configuration change also included the “FLEX RAID Adapter” card. But it wants to be plugged into the only Flex Connector/adapter/whatever slot that comes on a P500 or P700 motherboard. I asked Lenovo support forums if I could just move this other card to another PCIe x16 slot and secure it with a zip tie (since it wouldn’t have a bracket elsewhere on the board), but they said no, that other signals have to go through that flex slot, and only the FLEX PCIe slot is set up to handle that, or something. I actually do believe the Lenovo staff forum person, because it’s clear they know their stuff from other posts I’ve read.

The BCA boards are really a cool idea for sliding in drives, although completely unnecessary. But now that I have them, I want to make them work, instead of just removing them and using SATA cables and power cords from the PSU. If you’re not understanding what I’m saying, these are little SATA and power slots in the back of the drive bays, and you place a 3.5″ or 2 x 2.5″ or even a 3.5″ and a 2.5″ in one of the little drawers that fit in the bays, and then you can just slide it in all the way, and it’s connected. No more messing with cables, aside from the initial plugging in and routing of the BCA boards.

I’m going to move the M.2 SSD drive from the M.2 Flex mezzanine card, add it to an Addonics-brand PCIe 3.0 x4 card called the “ADM2PX4,” and install it into a different PCIe slot on the board. Then I’ll remove the M.2 Flex mezzanine card. Then I’ll take the Flex RAID mezzanine card that had up until now been gathering dust on the parts table, and install it in the now-open Flex slot. I’ll then plug the mini SAS cables into it to transfer data from expansion drives. I will also plug the BAC boards into the 4-pin power connectors on the mobo. When I get this going next week, assume all is wonderful unless I come back and update this post with bad news.

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Last Lastly: Endorsement – This is kindofa ThinkStation-P500-as-3D-CAD-Workstation Review

I’ve only been using this computer as a CAD workstation for a short time, but I really like it. It s the snappiest workstation I’ve yet had the privilege of using. I attribute the brute-force, ravenous, crushing speed to the following hardware:

• Scary fast Intel Xeon E5-1630 v3 3.7GHz 10MB cache CPU
  • Samsung M.2 PCIe SSD drive interfacing with PCIe 3.0 x4 lanes
• 10GB NIC card with corresponding 10GB card in the server
  • (this was our IT person’s idea, and it’s made a noticeable difference in dealing with CAD files stored on our server, something I used to complain about incessantly)
• W7100 AMD FirePro graphics card
  • This has made a noticeable difference with manipulating large CAD assemblies. There’s been some quirks with it in SolidWorks, but I think I’ve already figured them mostly out.
• ECC RAM, DDR4
  • For all the people that tell themselves (AND EVERYONE ELSE) ECC RAM and Xeon procs are wastes of money (or even that a gamer graphics card will do everything a pro card will for 3D CAD software at 1/4th the price), I am here to roll my eyes and scoff at you.

Why am I a “Sucker” for Pro-Grade Hardware?

I just have fewer crashes; fewer “weird” computer issues or artifacts; and faster, smoother work sessions when I use professional hardware than when I’m using other (lesser) equipment. This is something I’ve picked up over thousands of hours of professional CAD software use on both high-end consumer-grade computers and professional workstation computers.

There’s truly a more down-to-business, cleaner experience to using a Xeon CPU/ECC RAM/”Pro” Samsung or Intel SSD/Quadro or FirePro graphics card vs. using a Intel I7/Reg RAM/Consumer SSD/and hey–keep the pro graphics–it’s still hobbled by the other consumer hardware.

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Hucksters: You’re On Notice!

I’ve seen hucksters on YouTube try to convince they’ll show how to make a “value workstation” every bit as good as, say, an Apple MacPro Desktop**, but for half the price (or less). As soon as they equate “Workstation*” with regular RAM, I7 or AMD desktop CPUs, and gamer graphics, it’s illegitimate and makes them look like either they’re very unqualified to host shows about computer hardware. And/or they think everyone who uses the equipment is moronic and inexperienced.

*(asterisked ‘Workstation’ because I realize many “Workstation” laptops are still outfitted with I7 chips, and therefore reg RAM, although probably still pro-grade mobile graphics. Sacrifices must still be made for compact mobile form factors. That still doesn’t excuse confused computer “pros” [gamers who don’t actually “work” on computers] for being so extremely wrong in their concepts of “value”.)

**FYI: I don’t like Apple OS, and I can’t really use it with much of the software I must use on a daily basis. But I tried to make a build for less money using New Egg parts that would beat or match performance of their MacPro Desktops (the “cannister” vsns starting out in 2014), and couldn’t do it at all. It blew away my preconceptions of them as merely an obscenely priced style shop, there’s a lot of value in some of their products.

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In other words, I really like this ThinkStation Desktop machine, and recommend it with my current configuration.