May
07
2017
How a slow disk affects your system

The problem

The last couple weeks, a backup server I am managing is failing to make backups!

The backup procedure (a script via cron daemon) is to rsync data from a primary server to it’s /backup directory. I was getting cron errors via email, informing me that the previous rsync script hasnt already finished when the new one was starting (by checking a lock file). This was strange as the time duration is 12hours. 12 hours werent enough to perform a ~200M data transfer over a 100Mb/s network port. That was really strange.

This is the second time in less than a year that this server is making problems. A couple months ago I had to remove a faulty disk from the software raid setup and check the system again. My notes on the matter, can be found here:

https://balaskas.gr/blog/2016/10/17/linux-raid-mdadm-md0/


Identify the problem

So let us start to identify the problem. A slow rsync can mean a lot of things, especially over ssh. Replacing network cables, viewing dmesg messages, rebooting servers or even changing the filesystem werent changing any things for the better. Time to move on the disks.


Manage and Monitor software RAID devices

On this server, I use raid5 with four hard disks:

# mdadm --verbose --detail /dev/md0


/dev/md0:
        Version : 1.2
  Creation Time : Wed Feb 26 21:00:17 2014
     Raid Level : raid5
     Array Size : 2929893888 (2794.16 GiB 3000.21 GB)
  Used Dev Size : 976631296 (931.39 GiB 1000.07 GB)
   Raid Devices : 4
  Total Devices : 4
    Persistence : Superblock is persistent

    Update Time : Sun May  7 11:00:32 2017
          State : clean
 Active Devices : 4
Working Devices : 4
 Failed Devices : 0
  Spare Devices : 0

         Layout : left-symmetric
     Chunk Size : 512K

           Name : ServerTwo:0  (local to host ServerTwo)
           UUID : ef5da4df:3e53572e:c3fe1191:925b24cf
         Events : 10496

    Number   Major   Minor   RaidDevice State
       4       8       16        0      active sync   /dev/sdb
       1       8       32        1      active sync   /dev/sdc
       6       8       48        2      active sync   /dev/sdd
       5       8        0        3      active sync   /dev/sda


View hardware parameters of hard disk drive

aka test the hard disks:

# hdparm -Tt /dev/sda


/dev/sda:
 Timing cached reads:   2490 MB in  2.00 seconds = 1245.06 MB/sec
 Timing buffered disk reads: 580 MB in  3.01 seconds = 192.93 MB/sec

# hdparm -Tt /dev/sdb


/dev/sdb:
 Timing cached reads:   2520 MB in  2.00 seconds = 1259.76 MB/sec
 Timing buffered disk reads: 610 MB in  3.00 seconds = 203.07 MB/sec

# hdparm -Tt /dev/sdc

/dev/sdc:
 Timing cached reads:   2512 MB in  2.00 seconds = 1255.43 MB/sec
 Timing buffered disk reads: 570 MB in  3.01 seconds = 189.60 MB/sec

# hdparm -Tt /dev/sdd

/dev/sdd:
 Timing cached reads:     2 MB in  7.19 seconds = 285.00 kB/sec
 Timing buffered disk reads:   2 MB in  5.73 seconds = 357.18 kB/sec


Root Cause

Seems that one of the disks (/dev/sdd) in raid5 setup, is not performing as well as the others. The same hard disk had a problem a few months ago.

What I did the previous time, was to remove the disk, reformatting it in Low Level Format and add it again in the same setup. The system rebuild the raid5 and after 24hours everything was performing fine.

However the same hard disk seems that still has some issues . Now it is time for me to remove it and find a replacement disk.


Remove Faulty disk

I need to manually fail and then remove the faulty disk from the raid setup.

Failing the disk

Failing the disk manually, means that mdadm is not recognizing the disk as failed (as it did previously). I need to tell mdadm that this specific disk is a faulty one:

# mdadm --manage /dev/md0 --fail /dev/sdd
mdadm: set /dev/sdd faulty in /dev/md0

Removing the disk

now it is time to remove the faulty disk from our raid setup:

# mdadm --manage /dev/md0 --remove  /dev/sdd
mdadm: hot removed /dev/sdd from /dev/md0


Show details

# mdadm --verbose --detail /dev/md0

/dev/md0:
        Version : 1.2
  Creation Time : Wed Feb 26 21:00:17 2014
     Raid Level : raid5
     Array Size : 2929893888 (2794.16 GiB 3000.21 GB)
  Used Dev Size : 976631296 (931.39 GiB 1000.07 GB)
   Raid Devices : 4
  Total Devices : 3
    Persistence : Superblock is persistent

    Update Time : Sun May  7 11:08:44 2017
          State : clean, degraded
 Active Devices : 3
Working Devices : 3
 Failed Devices : 0
  Spare Devices : 0

         Layout : left-symmetric
     Chunk Size : 512K

           Name : ServerTwo:0  (local to host ServerTwo)
           UUID : ef5da4df:3e53572e:c3fe1191:925b24cf
         Events : 10499

    Number   Major   Minor   RaidDevice State
       4       8       16        0      active sync   /dev/sdb
       1       8       32        1      active sync   /dev/sdc
       4       0        0        4      removed
       5       8        0        3      active sync   /dev/sda


Mounting the Backup

Now it’s time to re-mount the backup directory and re-run the rsync script

mount /backup/

and run the rsync with verbose and progress parameters to review the status of syncing

/usr/bin/rsync -zravxP --safe-links --delete-before --partial --protect-args -e ssh 192.168.2.1:/backup/ /backup/

Everything seems ok.

A replacement order has already been placed.

Rsync times manage to hit ~ 10.27MB/s again!

rsync time for a daily (12h) diff is now again in normal rates:

real    15m18.112s
user    0m34.414s
sys     0m36.850s
Tag(s): linux, mdadm, md0
Oct
17
2016
Linux Raid mdadm md0

Linux Raid

This blog post is created as a mental note for future reference

Linux Raid is the de-facto way for decades in the linux-world on how to create and use a software raid. RAID stands for: Redundant Array of Independent Disks. Some people use the I for inexpensive disks, I guess that works too!

In simple terms, you can use a lot of hard disks to behave as one disk with special capabilities!

You can use your own inexpensive/independent hard disks as long as they have the same geometry and you can do almost everything. Also it’s pretty easy to learn and use linux raid. If you dont have the same geometry, then linux raid will use the smallest one from your disks. Modern methods, like LVM and BTRFS can provide an abstract layer with more capabilities to their users, but some times (or because something you have built a loooong time ago) you need to go back to basics.

And every time -EVERY time- I am searching online for all these cool commands that those cool kids are using. Cause what’s more exciting than replacing your -a decade ago- linux raid setup this typical Saturday night?

Identify your Hard Disks


% find /sys/devices/ -type f -name model -exec cat {} \;
ST1000DX001-1CM1
ST1000DX001-1CM1
ST1000DX001-1CM1

% lsblk
NAME   MAJ:MIN RM   SIZE RO TYPE  MOUNTPOINT
sda      8:0    0 931.5G  0 disk
sdb      8:16   0 931.5G  0 disk
sdc      8:32   0 931.5G  0 disk  

% lsblk -io KNAME,TYPE,SIZE,MODEL

KNAME TYPE    SIZE MODEL
sda   disk  931.5G ST1000DX001-1CM1
sdb   disk  931.5G ST1000DX001-1CM1
sdc   disk  931.5G ST1000DX001-1CM1

Create a RAID-5 with 3 Disks

Having 3 hard disks of 1T size, we are going to use the raid-5 Level . That means that we have 2T of disk usage and the third disk with keep the parity of the first two disks. Raid5 provides us with the benefit of loosing one hard disk without loosing any data from our hard disk scheme.

raid5.png


% mdadm -C -v /dev/md0 --level=5 --raid-devices=3 /dev/sda /dev/sdb /dev/sdc 

mdadm: layout defaults to left-symmetric
mdadm: layout defaults to left-symmetric
mdadm: chunk size defaults to 512K
mdadm: sze set to 5238784K
mdadm: Defaulting to version 1.2 metadata
md/raid:md0 raid level 5 active with 2 our of 3 devices, algorithm 2
mdadm: array /dev/md0 started.

% cat /proc/mdstat

Personalities : [raid6] [raid5] [raid4]
md0: active raid5 sdc[3] sdb[2] sda[1]
        10477568 blocks super 1.2 level 5, 512k chink, algorith 2 [3/3] [UUU]

unused devices: <none>

running lsblk will show us our new scheme:

# lsblk -io KNAME,TYPE,SIZE,MODEL
KNAME TYPE    SIZE MODEL
sda   disk  931.5G ST1000DX001-1CM1
md0   raid5   1.8T
sdb   disk  931.5G ST1000DX001-1CM1
md0   raid5   1.8T
sdc   disk  931.5G ST1000DX001-1CM1
md0   raid5   1.8T

Save the Linux Raid configuration into a file

Software linux raid means that the raid configuration is actually ON the hard disks. You can take those 3 disks and put them to another linux box and everything will be there!! If you are keeping your operating system to another harddisk, you can also change your linux distro from one to another and your data will be on your linux raid5 and you can access them without any extra software from your new linux distro.

But it is a good idea to keep the basic conf to a specific configuration file, so if you have hardware problems your machine could understand what type of linux raid level you need to have on those broken disks!


% mdadm --detail --scan >> /etc/mdadm.conf

% cat /etc/mdadm.conf
ARRAY /dev/md0 metadata=1.2 name=MyServer:0 UUID=ef5da4df:3e53572e:c3fe1191:925b24cf

UUID - Universally Unique IDentifier

Be very careful that the above UUID is the UUID of the linux raid on your disks.
We have not yet created a filesystem over this new disk /dev/md0 and if you need to add this filesystem under your fstab file you can not use the UUID of the linux raid md0 disk.

Below there is an example on my system:

% blkid
/dev/sda: UUID="ef5da4df-3e53-572e-c3fe-1191925b24cf" UUID_SUB="f4e1da17-e4ff-74f0-b1cf-6ec86eca3df1" LABEL="MyServer:0" TYPE="linux_raid_member"
/dev/sdb: UUID="ef5da4df-3e53-572e-c3fe-1191925b24cf" UUID_SUB="ad7315e5-56ce-bd8c-75c5-0a72893a63db" LABEL="MyServer:0" TYPE="linux_raid_member"
/dev/sdc: UUID="ef5da4df-3e53-572e-c3fe-1191925b24cf" UUID_SUB="a90e317e-4384-8f30-0de1-ee77f8912610" LABEL="MyServer:0" TYPE="linux_raid_member" 

/dev/md0: LABEL="data" UUID="48fc963a-2128-4d35-85fb-b79e2546dce7" TYPE="ext4" 

% cat /etc/fstab

UUID=48fc963a-2128-4d35-85fb-b79e2546dce7   /backup auto    defaults    0   0

Replacing a hard disk

Hard disks will fail you. This is a fact that every sysadmin knows from day one. Systems will fail at some point in the future. So be prepared and keep backups !!

Failing a disk

Now it’s time to fail (if not already) the disk we want to replace:

% mdadm --manage /dev/md0 --fail /dev/sdb
mdadm: set /dev/sdb faulty in /dev/md0

Remove a broken disk

Here is a simple way to remove a broken disk from your linux raid configuration. Remember with raid5 level we can manage with 2 hard disks.

% mdadm --manage /dev/md0 --remove /dev/sdb
mdadm: hot removed /dev/sdb from /dev/md0

% cat /proc/mdstat
Personalities : [raid6] [raid5] [raid4]
md0 : active raid5 sda[1] sdc[3]
      1953262592 blocks super 1.2 level 5, 512k chunk, algorithm 2 [3/2] [_UU]

unused devices: <none>

dmesg shows:


% dmesg | tail

md: data-check of RAID array md0
md: minimum _guaranteed_  speed: 1000 KB/sec/disk.
md: using maximum available idle IO bandwidth (but not more than 200000 KB/sec) for data-check.
md: using 128k window, over a total of 976631296k.
md: md0: data-check done.
md/raid:md0: Disk failure on sdb, disabling device.
md/raid:md0: Operation continuing on 2 devices.
RAID conf printout:
 --- level:5 rd:3 wd:2
 disk 0, o:0, dev:sda
 disk 1, o:1, dev:sdb
 disk 2, o:1, dev:sdc
RAID conf printout:
 --- level:5 rd:3 wd:2
 disk 0, o:0, dev:sda
 disk 2, o:1, dev:sdc
md: unbind<sdb>
md: export_rdev(sdb)

Adding a new disk - replacing a broken one

Now it’s time to add a new and (if possible) clean hard disk. Just to be sure, I always wipe with dd the first few kilobytes of every disk with zeros.

Using mdadm to add this new disk:


# mdadm --manage /dev/md0 --add /dev/sdb
mdadm: added /dev/sdb

% cat /proc/mdstat
Personalities : [raid6] [raid5] [raid4]
md0 : active raid5 sdb[4] sda[1] sdc[3]
      1953262592 blocks super 1.2 level 5, 512k chunk, algorithm 2 [3/2] [_UU]
      [>....................]  recovery =  0.2% (2753372/976631296) finish=189.9min speed=85436K/sec

unused devices: <none>

For a 1T Hard Disk is about 3h of recovering data. Keep that in mind on scheduling the maintenance window.

after a few minutes:

% cat /proc/mdstat
Personalities : [raid6] [raid5] [raid4]
md0 : active raid5 sdb[4] sda[1] sdc[3]
      1953262592 blocks super 1.2 level 5, 512k chunk, algorithm 2 [3/2] [_UU]
      [>....................]  recovery =  4.8% (47825800/976631296) finish=158.3min speed=97781K/sec

unused devices: <none>

mdadm shows:

% mdadm --detail /dev/md0 

/dev/md0:
        Version : 1.2
  Creation Time : Wed Feb 26 21:00:17 2014
     Raid Level : raid5
     Array Size : 1953262592 (1862.78 GiB 2000.14 GB)
  Used Dev Size : 976631296 (931.39 GiB 1000.07 GB)
   Raid Devices : 3
  Total Devices : 3
    Persistence : Superblock is persistent

    Update Time : Mon Oct 17 21:52:05 2016
          State : clean, degraded, recovering
 Active Devices : 2
Working Devices : 3
 Failed Devices : 0
  Spare Devices : 1

         Layout : left-symmetric
     Chunk Size : 512K

 Rebuild Status : 58% complete

           Name : MyServer:0  (local to host MyServer)
           UUID : ef5da4df:3e53572e:c3fe1191:925b24cf
         Events : 554

    Number   Major   Minor   RaidDevice State
       1       8       16        1      active sync   /dev/sda
       4       8       32        0      spare rebuilding   /dev/sdb
       3       8       48        2      active sync   /dev/sdc

You can use watch command that refreshes every two seconds your terminal with the output :


# watch cat /proc/mdstat

Every 2.0s: cat /proc/mdstat                                                                                               Mon Oct 17 21:53:34 2016

Personalities : [raid6] [raid5] [raid4]
md0 : active raid5 sdb[4] sda[1] sdc[3]
      1953262592 blocks super 1.2 level 5, 512k chunk, algorithm 2 [3/2] [_UU]
      [===========>.........]  recovery = 59.4% (580918844/976631296) finish=69.2min speed=95229K/sec

unused devices: <none>

Growing a Linux Raid

Even so … 2T is not a lot of disk usage these days! If you need to grow-extend your linux raid, then you need hard disks with the same geometry (or larger).

Steps on growing your linux raid are also simply:

# Umount the linux raid device:
% umount /dev/md0

# Add the new disk
% mdadm --add /dev/md0 /dev/sdd

# Check mdstat
% cat /proc/mdstat

# Grow linux raid by one device
%  mdadm --grow /dev/md0 --raid-devices=4

# watch mdstat for reshaping to complete - also 3h+ something
% watch cat /proc/mdstat

# Filesystem check your linux raid device
% fsck -y /dev/md0

# Resize - Important
% resize2fs /dev/md0

But sometimes life happens …

Need 1 spare to avoid degraded array, and only have 0.

mdadm: Need 1 spare to avoid degraded array, and only have 0.

or

mdadm: Failed to initiate reshape!

Sometimes you get an error that informs you that you can not grow your linux raid device! It’s not time to panic or flee the scene. You’ve got this. You have already kept a recent backup before you started and you also reading this blog post!

You need a (an extra) backup-file !


% mdadm --grow --raid-devices=4 --backup-file=/tmp/backup.file /dev/md0
mdadm: Need to backup 3072K of critical section..

% cat /proc/mdstat
Personalities : [linear] [multipath] [raid0] [raid1] [raid6] [raid5] [raid4] [raid10]
md0 : active raid5 sda[4] sdb[0] sdd[3] sdc[1]
      1953262592 blocks super 1.2 level 5, 512k chunk, algorithm 2 [4/4] [UUUU]
      [>....................]  reshape =  0.0

% (66460/976631296) finish=1224.4min speed=13292K/sec

unused devices: <none>

1224.4min seems a lot !!!

dmesg shows:


% dmesg
[   36.477638] md: Autodetecting RAID arrays.
[   36.477649] md: Scanned 0 and added 0 devices.
[   36.477654] md: autorun ...
[   36.477658] md: ... autorun DONE.

[  602.987144] md: bind<sda>
[  603.219025] RAID conf printout:
[  603.219036]  --- level:5 rd:3 wd:3
[  603.219044]  disk 0, o:1, dev:sdb
[  603.219050]  disk 1, o:1, dev:sdc
[  603.219055]  disk 2, o:1, dev:sdd
[  608.650884] RAID conf printout:
[  608.650896]  --- level:5 rd:3 wd:3
[  608.650903]  disk 0, o:1, dev:sdb
[  608.650910]  disk 1, o:1, dev:sdc
[  608.650915]  disk 2, o:1, dev:sdd
[  684.308820] RAID conf printout:
[  684.308832]  --- level:5 rd:4 wd:4
[  684.308840]  disk 0, o:1, dev:sdb
[  684.308846]  disk 1, o:1, dev:sdc
[  684.308851]  disk 2, o:1, dev:sdd
[  684.308855]  disk 3, o:1, dev:sda
[  684.309079] md: reshape of RAID array md0
[  684.309089] md: minimum _guaranteed_  speed: 1000 KB/sec/disk.
[  684.309094] md: using maximum available idle IO bandwidth (but not more than 200000 KB/sec) for reshape.
[  684.309105] md: using 128k window, over a total of 976631296k.

mdstat

% cat /proc/mdstat
Personalities : [linear] [multipath] [raid0] [raid1] [raid6] [raid5] [raid4] [raid10]
md0 : active raid5 sda[4] sdb[0] sdd[3] sdc[1]
      1953262592 blocks super 1.2 level 5, 512k chunk, algorithm 2 [4/4] [UUUU]
      [>....................]  reshape =  0.0

% (349696/976631296) finish=697.9min speed=23313K/sec

unused devices: <none>

ok it’s now 670minutes

Time to use watch:

(after a while)

% watch cat /proc/mdstat

Personalities : [linear] [multipath] [raid0] [raid1] [raid6] [raid5] [raid4] [raid10]
md0 : active raid5 sda[4] sdb[0] sdd[3] sdc[1]
      1953262592 blocks super 1.2 level 5, 512k chunk, algorithm 2 [4/4] [UUUU]
      [===========>......]  reshape = 66.1% (646514752/976631296) finish=157.4min speed=60171K/sec

unused devices: <none>

mdadm shows:


% mdadm --detail /dev/md0

/dev/md0:
        Version : 1.2
  Creation Time : Thu Feb  6 13:06:34 2014
     Raid Level : raid5
     Array Size : 1953262592 (1862.78 GiB 2000.14 GB)
  Used Dev Size : 976631296 (931.39 GiB 1000.07 GB)
   Raid Devices : 4
  Total Devices : 4
    Persistence : Superblock is persistent

    Update Time : Sat Oct 22 14:59:33 2016
          State : clean, reshaping
 Active Devices : 4
Working Devices : 4
 Failed Devices : 0
  Spare Devices : 0

         Layout : left-symmetric
     Chunk Size : 512K

 Reshape Status : 66% complete
  Delta Devices : 1, (3->4)

           Name : MyServer:0
           UUID : d635095e:50457059:7e6ccdaf:7da91c9b
         Events : 1536

    Number   Major   Minor   RaidDevice State
       0       8       16        0      active sync   /dev/sdb
       1       8       32        1      active sync   /dev/sdc
       3       8       48        2      active sync   /dev/sdd
       4       8        0        3      active sync   /dev/sda

be patient and keep an aye on mdstat under proc.

So basically those are the steps, hopefuly you will find them useful.

Tag(s): md0, mdadm, linux, raid