Unreadable partition and GPT error problems

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refreshx2
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Joined: 2013/06/11 00:39:06

Unreadable partition and GPT error problems

Post by refreshx2 » 2013/06/11 01:13:20

Hello,

Apologies in advance if I have not provided enough system info. As we cannot install CentOS, I don't think I can get the getinfo.sh that is requested. I will give you any information you request as soon as possible.

We are trying to set up a cluster. We are installing ROCKS 5.5 on it which uses CentOS 5.8 as an operating system and uses CentOS's partition manager (which is where we are having problems) during the installation.

We are using three 2TB hard drives which came in GPT format (not MBR). We have the hard drives set up in RAID 5.

Here is what we did, what our problem is, and how we have tried to fix it:
We set the hard drives up in RAID 5 and boot from the dvd to install ROCKS. All goes well until we try to create our partitions. After setting up the '/', 'var', 'swap', and '/export' partitions (following the ROCKS installation guide) to be created, we click "Next" and get the error:
[code]“Your boot partition is on a disk using the GPT partitioning scheme but this machine cannot boot using GPT”.[/code]
So we used a rescue system cd to change the GPT to MBR using parted on all three hard drives indiviually and on the RAID 5 configured virtual drive as well using:
[code]parted /dev/sda
mklabel msdos
quit[/code]
and doing the same thing for /dev/sdb, sdc, and sdd. (Note that /dev/sda is the RAID 5 drive and the other three are the individual hard drives).
Our drives now should be in MBR format and not GPT (gdisk confirms this as well).

Now we rebooted and again tried to install ROCKS 5.5 (CentOS 5.8).
Just before we get to the partitioning screen we now get the error:
[code]"The partition table on device sda was unreadable. To create new partitions, it must be initialized, causing the loss of ALL DATA on the drive. Would you like to initialize this drive?"[/code]
Saying No stops the installation, but saying Yes reconfigures the hard drives back into GPT format and we get the 1st error I mentioned above (and will repeat here for clarity) after trying to set up the partitions:
[code]“Your boot partition is on a disk using the GPT partitioning scheme but this machine cannot boot using GPT”.[/code]

So basically, CentoOS 5.8 won't let us use GPT format on our harddrives but changing the harddrives manually to MBR using parted gives us an unreadable partition table error. Fixing this error during the CentOS installation reverts the hard drives back to GPT format.

Any advice on how to go about properly fixing this problem?

Thanks in advance!
Jason

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TrevorH
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Re: Unreadable partition and GPT error problems

Post by TrevorH » 2013/06/11 11:25:54

Are you using hardware RAID 5 or software?

First, you cannot boot from software RAID 5 - the /boot partition can be on a software RAID 1 set but not on RAID 0 or 5.

If you are using hardware RAID then I suspect the individual partition tables on each disk are ignored (and probably wiped) and the device on /dev/sda will be presented by the RAID controller as a single drive of 4TB. If you use parted on a device with 4TB I am pretty sure it will ignore what you tell it and put a GPT label on it.

refreshx2
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Joined: 2013/06/11 00:39:06

Re: Unreadable partition and GPT error problems

Post by refreshx2 » 2013/06/11 13:34:04

Hi Trevor,

We are using a hardware RAID 5. If the partition tables on the individual disks are ignored or wiped during the creation of RAID 5 then that is just fine. Creating the RAID 5 with the three 2TB drives does indeed put a GPT label on it. However, we used parted to change the GPT label to MBR:
[code]parted /dev/sda
mklabel msdos
quit[/code]
This did seem to work correctly because 'gdisk /dev/sda' printed:
[code]MBR: present
BSD: not present
APM: not present
GPT: not present[/code]
Maybe that does not mean it actually worked.

Either way, we are still stuck with the problem.
(Pasted from the tl;dr in the first post with a correction): CentoOS 5.8 won't let us use GPT format on our harddrives but changing the harddrives manually to MBR using parted gives us an unreadable partition table error. Fixing this error during the CentOS installation reverts the RAID config (although not the harddrives individually) back to GPT format.

gerald_clark
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Unreadable partition and GPT error problems

Post by gerald_clark » 2013/06/11 14:19:28

You will need to boot from a drive < 2T in size.
Can you configure your RAID controller to present your drives a one smaller drive and one larger drive?

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TrevorH
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Re: Unreadable partition and GPT error problems

Post by TrevorH » 2013/06/11 15:29:01

The since support of UEFI and GPT was one of the bullet points in the CentOS 6 release notes, I suspect that CentOS 5 does not support it. [b]Gerald[/b] has the best answer.

refreshx2
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Joined: 2013/06/11 00:39:06

Re: Unreadable partition and GPT error problems

Post by refreshx2 » 2013/06/11 23:39:54

Gerald did indeed help me fix my issues. Below I will detail exactly what I did for anyone in the future having the same problem.

We have four 2TB hard drives that we are making into RAID 5.

Using the hardware RAID controller, configure the RAID (Alt+3 during boot) to RAID 5, set the stripe to 256kb, and make the boot disk 250 (GB). The rest will be make into another partition (5.7TB). Note: 256kb striping is the maximum. We can also do 64kb striping which may be better if we have smaller file sizes. If our files are usually over 256kb then the 256kb is what we want. However, it may only be a minor speed improvement, I don't know.

During this installation, sda was the RAID 5 250GB disk and sdb was the remainder of the RAID 5 config (5.7TB).

Boot using a rescue cd with 'parted' on it.

For /dev/sdb: (the
parted /dev/sdb
(parted) mklabel gpt
(parted) mkpart primary 0 -0 ****** I'm fairly certain I had to type this command but now I can't remember exactly. ******
quit
mkfs.xfs /dev/sdb1

For /dev/sda:
parted /dev/sda
mklabel msdos
quit

reboot

Put in the ROCKS install DVD and enter any necessary information until you get to the partitioning option.

Select manual partitioning and create the following:
On the 250GB disk ONLY (uncheck the other boxs for the following 4 partitions) create:
/boot with 256MB (ext4)
swap with 32768MB (swap)
/var with 32768MB (ext4)
/ with the remaining space on the 250GB disk (ext4)
On the other RAID disk DO NOT change the type, simple write in the name/label: /state/partition1
Click Next and ROCKS should download and install the OS. It takes a bit, maybe 20-30 min. It will then reboot automatically and, having ejected the disk, will boot into ROCKS. ***You might get an error here. I did - it was an "Unhandled exception" error. I just decided to scrap ROCKS 5.5 at that point and install ROCKS 6.1 instead. After that I didn't get the unhandled exception error and everything installed fine.***

You now how a functional CentOS 6.3 installation with ROCKS 6.1!
Login using 'root' as the username and the password you specified during installation.

kaiyara
Posts: 1
Joined: 2013/07/04 12:26:04

Re: Unreadable partition and GPT error problems

Post by kaiyara » 2013/07/04 12:28:47

I have CentOS 5.7 installed on HP Z620.
And I found the problem(?) with access indicator light .

The light stays on after the OS started. (Not blinking. Untill shutdown.)

I checked Applications(about Memory, CPU, ...etc),but they do not seem to have problems.

If possible, I want to repair it without changing the OS.
Or, I want to know whether it is OK even if I continue using it.

Is it not good to use OS5.7 on this PC?
Could anyone tell me the way to repair without changing the OS?

Any help would be appreciated.

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TrevorH
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Re: Unreadable partition and GPT error problems

Post by TrevorH » 2013/07/04 14:37:35

Please do not hijack threads and post unrelated content on them. Start your own thread with a descriptive subject and people will help you if they know how.

This thread is locked.

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