Linux Software RAID and SATA Hot Swap

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Why Software RAID?

I know there are a million pages online about Linux Software RAID, but I wanted to record my own experience with it.

My home server has a lot of storage:

  • a 160GB RAID1 array, for my boot volume, on one of the motherboard's RAID controllers
  • a 500GB RAID1 array, for backups and pictures, again on a RAID controller
  • a 2TB RAID1 array, for home directories and virtual machines, on a RAID controller
  • a 3TB RAID1 array, for other stuff, using software RAID.
  • a single 3TB drive, for daily backups of my 3TB array

My motherboard is a number of years old now, and the onboard controllers could not do RAID for 3TB drives, as they only recognized them as 873GB. So I left these as standard drives, and set them up in software RAID.

My goal for this endeavor was to convert my 500GB and 2TB over to software RAID. The reasons being:

  • Actually getting notifications regarding any issues
  • Control over rebuilds, being able to add/remove disks
  • Not being tied to a specific RAID controller with a specific firmware version. If the motherboard were to die, I can easily move the drives.
  • No reboots required to work with the drives
  • Linux can do SATA hot swap, so I don't need to power down to swap a disk

The minor performance hit isn't an issue, so the pros far outweigh the cons.


Fiasco #1: The 500GB Array

I decided to do the 500GB array first, since it was small and quick to work with.

I moved the data off the drive, rebooted the server to get into the BIOS, deleted the array, then booted the server back up. Then I (not showing any of these steps, you'll see why...):

  • partitioned the drives using fdisk
  • created the RAID1 array and waited for it to sync
  • formatted it
  • mounted the drive
  • put all my files back on

Then I rebooted the server, and what do I get? NO OPERATING SYSTEM FOUND

I shut down the server and unplugged the two 500GB drives, and it found the operating system just fine. The 3TB array is using software RAID, but didn't trigger the same issue. Why? To have drives >2.2TB, you need a GUID Partition Table (GPT) [1] on the drive, not the standard msdos partition table. My motherboard won't attempt to boot from a GPT drive.

Now to rebuild the array using GPT drives...

Rebuilding The Array

I could not boot the server with the drives plugged in, and running them on USB to SATA converters is just horrible. What to do? Linux supports SATA hot swap! I booted the server up, then just plugged the drives in. They are instantly recognized by the system, and added in as sd[x] devices.

  • Reenable the array
mdadm -A /dev/md1
  • Mount the drive
mount /dev/md1 /mnt/500GB-array
  • Move all the data off the drive
  • Stop the array, zero the superblocks and remove the array
mdadm -S /dev/md1
mdadm --zero-superblock /dev/sdi1
mdadm --zero-superblock /dev/sdh1
mdadm --remove /dev/md1
rm /dev/md1
  • Create a new partition table and partitions using parted on the first drive
[root@fileserver dev]# parted sdi
GNU Parted 1.8.1
Using /dev/sdi
Welcome to GNU Parted! Type 'help' to view a list of commands.
(parted) print

Model: ATA ST3500630AS (scsi)
Disk /dev/sdi: 500GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos

Number  Start   End    Size   Type     File system  Flags
 1      32.3kB  500GB  500GB  primary               raid

(parted) rm 1
(parted) print

Model: ATA ST3500630AS (scsi)
Disk /dev/sdi: 500GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos

Number  Start  End  Size  Type  File system  Flags

(parted) mklabel
Warning: The existing disk label on /dev/sdi will be destroyed and all data on this disk will be lost. Do you want to
continue?
Yes/No? yes
New disk label type?  [msdos]? gpt
(parted) unit GB
(parted) mkpart primary 0.00GB 500.0GB
(parted) print

Model: ATA ST3500630AS (scsi)
Disk /dev/sdi: 500GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt

Number  Start   End    Size   File system  Name     Flags
 1      0.00GB  500GB  500GB               primary

(parted) quit
  • Do the same thing on the second drive
  • Create the array
[root@fileserver dev]# mdadm --create /dev/md1 --level=1 --metadata=1.2 --raid-devices=2 /dev/sdh1 /dev/sdi1
mdadm: metadata format 1.02 unknown, ignored.
mdadm: metadata format 1.02 unknown, ignored.
mdadm: array /dev/md1 started.
[root@fileserver dev]# cat /proc/mdstat
Personalities : [raid6] [raid5] [raid4] [raid1]
md1 : active raid1 sdi1[1] sdh1[0]
      488386414 blocks super 1.2 [2/2] [UU]
      [>....................]  resync =  0.1% (783360/488386414) finish=103.7min speed=78336K/sec

md0 : active raid1 sdc1[0] sdd1[1]
      5860532736 blocks super 1.2 [2/2] [UU]

unused devices: <none>
  • At any point during the resync, you can format the drive, mount it, and start using it. Obviously, it will not have working redundancy until it has fully synced.

To have the array detected during bootup, save the config like this: 

mdadm -Q --detail --brief /dev/md1 > /etc/mdadm.conf

It's also a good idea to add this line to your /etc/mdadm.conf file: 

MAILADDR you@yourdomain.com

Obviously, put your email address in there. Then you will get notifications of any RAID events.

By default, Linux reserves 5% of a drive for the root user. This really adds up, as drives get bigger. For example, 5% of 3TB is 150GB. You can adjust this using tune2fs. 

tune2fs -m 0.5 /dev/sda1

The 0.5 is the percentage of the drive. It can be any integer or decimal.


Fiasco #2: The 2TB Array

Next on the agenda was to make the 2TB RAID1 array into a software array.

One of my motivators behind this project was to correct the 37 bad sectors that showed up on one of my 2TB drives. I figured I would work that in, between deleting the hardware array and creating the software array. I was going to use the linux program badblocks to verify and fix the drive.

Using badblocks

Badblocks is a handy program, similar to Spinrite. It works by taking 4 passes over the drive (by default):

  • The first pass writes the pattern "10101010" to all bits on the drive, then it reads it back to verify
  • The second pass writes the pattern "01010101" to all the bits, then verifies
  • The third pass writes all ones to the drive, and verifies.
  • The final pass writes all zeroes to the drive, and verifies.

If there are no issues with the drive, it takes about 24 hours to run. And at the end, you have a completely zeroed drive.

When it's successful, it looks like this: 

[root@fileserver /]# badblocks -wvs /dev/sda
Checking for bad blocks in read-write mode
From block 0 to 390711384
Testing with pattern 0xaa: done
Reading and comparing: done
Testing with pattern 0x55: done
Reading and comparing: done
Testing with pattern 0xff: done
Reading and comparing: done
Testing with pattern 0x00: done
Reading and comparing: done
Pass completed, 0 bad blocks found.

To my dismay, my drive had more than 37 bad sectors. A lot more. The output looked like this: 

[root@fileserver mnt]# badblocks -wvs /dev/sda
Checking for bad blocks in read-write mode
From block 0 to 1953514584
Testing with pattern 0xaa: done
Reading and comparing: 1113920 1113920/     1953514584
1115128 1115128/     1953514584
1115248 1115248/     1953514584
1116392 1116392/     1953514584
1118944 1118944/     1953514584
2340632 2340632/     1953514584
2350736 2350736/     1953514584
2356936 2356936/     1953514584
2362000 2362000/     1953514584
2399560 2399560/     1953514584
2413312 2413312/     1953514584
2430776 2430776/     1953514584

Badblocks only managed to get 5% done its first pass in the span of five days. I decided to pull that drive and make the remaining 2TB drive into a standalone, without RAID. Getting a replacement drive for it was cost prohibitive, so I needed to find a new solution for redundant storage for my virtual machines.

SATA Hot Swap

Linux makes it really easy to hot swap SATA drives:

  • Make sure that a drive is not mounted or part of an active array
  • Use this command (change sda to the appropriate drive):
echo 1 > /sys/block/sda/device/delete
  • Unplug the drive


Fiasco #3: The Surprise Array

I decided to repurpose the standalone 3TB drive, and upgrade my 3TB RAID1 array to a 6TB RAID5 array.

The first issue I ran in to is that when I went to delete the partitions and recreate them, it would always show the original file system that was on the disk. So to wipe them out, I used: 

dd if=/dev/zero of=/dev/sdg bs=512 count=100000 conv=notrunc

That zeroed out the first 50MB of the drive, and allowed me to create the partition and filesystem from scratch.

Afterwards, the procedure was largely the same as making a RAID1 array. The only differences were:

  • In parted, I set the unit as TB instead of GB, as I was working with 3TB drives.
  • To create the array, I used this command:
mdadm --create --verbose /dev/md0 --level=5 --metadata=1.2 --raid-devices=3 /dev/sdc1 /dev/sdd1 /dev/sdg1
  • I added it to the mdadm.conf file like this:
mdadm -Q --detail --brief /dev/md0 >> /etc/mdadm.conf
  • I changed the reserved space to 0.2% (12GB)
tune2fs -m 0.2 /dev/md0

Afterwards, I got this email: 

This is an automatically generated mail message from mdadm
running on fileserver.home

A SparesMissing event had been detected on md device /dev/md0.

Faithfully yours, etc.

P.S. The /proc/mdstat file currently contains the following:

Personalities : [raid6] [raid5] [raid4]
md0 : active raid5 sdc1[0] sdg1[3] sdd1[1]
      5860532736 blocks super 1.2 level 5, 64k chunk, algorithm 2 [3/3] [UUU]

unused devices: <none>

To fix that, I edited /etc/mdadm.conf and change this line: 

ARRAY /dev/md0 level=raid5 num-devices=3 metadata=1.02 spares=1 name=0 UUID=0036f465:a16a0eb0:2c35cd8e:079dfacb

to this: 

ARRAY /dev/md0 level=raid5 num-devices=3 metadata=1.02 spares=0 name=0 UUID=0036f465:a16a0eb0:2c35cd8e:079dfacb


Dénouement

Everything is finally built, synced, and data stored where it should be. I stuck an extra 400GB drive in, to make up for some of the space I lost by not having a 3TB backup drive.

My home server now looks like this:

  • a 160GB RAID1 array, for my boot volume, using hardware RAID
  • a 500GB RAID1 array, for backups and pictures, using software RAID
  • a 6TB RAID5 array, for home directories, virtual machines, and other stuff, using software RAID.
  • a 2TB standalone drive, for daily backups from the 6TB array
  • a 400GB standalone drive, for daily backups of the 6TB array


Update: Repairing A Faulty RAID5 Array

I had one of the 3TB disks suddenty discover 46,000 bad sectors. Luckily, I had an extra matching disk.

Mdadm had not yet notice the drive was faulty, so I faulted it manually: 

mdadm --manage /dev/md124 -f /dev/sdb1

[root@fileserver done]# mdadm --detail /dev/md124
/dev/md124:
        Version : 1.2
  Creation Time : Sun May  8 16:05:48 2016
     Raid Level : raid5
     Array Size : 5860268032 (5588.79 GiB 6000.91 GB)
  Used Dev Size : 2930134016 (2794.39 GiB 3000.46 GB)
   Raid Devices : 3
  Total Devices : 3
    Persistence : Superblock is persistent

  Intent Bitmap : Internal

    Update Time : Wed Mar 15 22:27:51 2017
          State : clean, degraded
 Active Devices : 2
Working Devices : 2
 Failed Devices : 1
  Spare Devices : 0

         Layout : left-symmetric
     Chunk Size : 512K

           Name : fileserver.local:124  (local to host fileserver.local)
           UUID : a84efac6:0742aae1:46f6f79b:bff11d2c
         Events : 20570

    Number   Major   Minor   RaidDevice State
       -       0        0        0      removed
       1       8       33        1      active sync   /dev/sdc1
       3       8       49        2      active sync   /dev/sdd1

       0       8       17        -      faulty   /dev/sdb1

Then I removed it from the array: 

mdadm --manage /dev/md124 -r /dev/sdb1

Then I soft disconnected the drive: 

echo 1 > /sys/block/sdb/device/delete

Then removed the physical disk from the server and plugged in the replacement.

I then set up the GPT partition table and single partition, using the procedure above.

Then I added the new partition into the array: 

mdadm --manage -a /dev/md124 /dev/sdb1

[root@fileserver done]# mdadm --detail /dev/md124
/dev/md124:
        Version : 1.2
  Creation Time : Sun May  8 16:05:48 2016
     Raid Level : raid5
     Array Size : 5860268032 (5588.79 GiB 6000.91 GB)
  Used Dev Size : 2930134016 (2794.39 GiB 3000.46 GB)
   Raid Devices : 3
  Total Devices : 3
    Persistence : Superblock is persistent

  Intent Bitmap : Internal

    Update Time : Wed Mar 15 22:51:25 2017
          State : clean, degraded, recovering
 Active Devices : 2
Working Devices : 3
 Failed Devices : 0
  Spare Devices : 1

         Layout : left-symmetric
     Chunk Size : 512K

 Rebuild Status : 0% complete

           Name : fileserver.local:124  (local to host fileserver.local)
           UUID : a84efac6:0742aae1:46f6f79b:bff11d2c
         Events : 20586

    Number   Major   Minor   RaidDevice State
       4       8       17        0      spare rebuilding   /dev/sdb1
       1       8       33        1      active sync   /dev/sdc1
       3       8       49        2      active sync   /dev/sdd1

Now to wait five hours until it rebuilds...


Update: Expanding A RAID5 Array

This is to add another drive to the RAID5 array to expand capacity.

Use parted as shown above.

Add the drive to the array. Note the (S) after the newly added drive (sdf1). That indicates it is a spare, which is only used when one of the other three drives fails. 

[root@fileserver ~]# mdadm --add /dev/md124 /dev/sdf1
mdadm: added /dev/sdf1
[root@fileserver ~]# cat /proc/mdstat
Personalities : [raid1] [raid6] [raid5] [raid4]
md124 : active raid5 sdf1[5](S) sdc1[4] sdd1[1] sde1[3]
      5860268032 blocks super 1.2 level 5, 512k chunk, algorithm 2 [3/3] [UUU]
      bitmap: 0/22 pages [0KB], 65536KB chunk

unused devices: <none>

Grow the array to use the additional disk. Note that it is now reshaping. 

[root@fileserver ~]# mdadm --grow --raid-devices=4 /dev/md124
[root@fileserver ~]# cat /proc/mdstat
Personalities : [raid1] [raid6] [raid5] [raid4]
md124 : active raid5 sdf1[5] sdc1[4] sdd1[1] sde1[3]
      5860268032 blocks super 1.2 level 5, 512k chunk, algorithm 2 [4/4] [UUUU]
      [>....................]  reshape =  0.0% (10240/2930134016) finish=9523.2min speed=5120K/sec
      bitmap: 0/22 pages [0KB], 65536KB chunk

unused devices: <none>

To improve the reshape speed, do the following: 

[root@fileserver ~]# echo 40000 > /proc/sys/dev/raid/speed_limit_min
[root@fileserver ~]# echo 0 > /proc/sys/dev/raid/speed_limit_max
[root@fileserver ~]# echo 32768 > /sys/block/md124/md/stripe_cache_size


Next, resize the md partition.

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