Debian-installer, mdadm configuration and the Bad Blocks Controversy

Updates! ^

Since this was posted on 2020-09-13 there was some interest in the comments and on Hacker News and I learned some things which required updates. I’ve tried to indicate them with struck out text.

Of particular note is the re-add method of removing BBLs.

MD and mdadm ^

MD is the Linux kernel driver that is used for running software RAID arrays. mdadm is the software that you run to manage MD devices. They are both part of the same project.

First, about the Bad Blocks List ^

Since about 2010, MD has had a bad blocks log (BBL) feature. When it fails to read from an underlying device it will (sometimes?) mark that block as bad and read the correct data from a different device, and then forever more redirect reads away from those bad blocks. This feature defaults to being on.

One problem with this feature is that read errors can occur for many reasons besides permanent failure of part of a storage device. For example, it could be a failure of the backplane or controller that causes many read errors on multiple devices, or the devices could be reached over a network of some sort and temporary network problems could propagate errors.

Even if the particular part of the device is unreadable, the operating system is supposed to try to write the correct data over the top. This write will either clear the problem or else be redirected to a spare sector on the drive by the drive’s firmware. The operating system is not supposed to be taking on this role, the drives are, and when the drives fail to do so then the redundancy of the array is supposed to save the day.

Even worse, there are apparently bugs somewhere in the BBL code that cause a device’s BBL to be copied onto a new device when the array is rebuilt or a device replaced. Clearly it does not make sense for a new device to get a copy of another device’s BBL because they are inherently a per-device thing. So far there has been no successful intentional reproduction of this, only people unwittingly hitting it at the worst possible moments. It has been reproduced that adding or replacing a device results in a BBL being copied. I am not aware of a formal bug report for this yet.

mdadm doesn’t even try particularly hard to warn you if a new bad block is found. Unlike when a device fails, it doesn’t send you an email. The MD driver writes in the syslog about the bad block(s). There’s also no change to /proc/mdstat. You have to examine some files in sysfs.

As a result the current situation is that:

No one seems to have made any progress on fixing any of this in 10 years.

Doing something about it ^

I’ll say right now that this story doesn’t (yet?) have a satisfying ending.

I’ve been aware of the “Bad Blocks Controversy” for about 5 years but I haven’t ever personally experienced any problems and it was always at the bottom of my list to look at. Roy’s recent thread spurred me into deciding that in future no MD array I created would have a BBL.

I also took the opportunity to deploy Sarah Newman’s Ansible role which checks all array components have an empty BBL. None of BitFolk‘s array components currently have any entries in their BBLs – phew!

Removing an existing BBL ^

Currently the only way to remove a BBL from an array component is to stop the array and then assemble it with an argument like this:

There are two ways to remove the BBL from the devices of existing arrays.

Fail and re-add each device with update

It doesn’t seem to be documented anywhere, but you can fail a device out of an array and re-add it with an update to remove the BBL on that device, like this:

# mdadm --fail /dev/md0 /dev/sdb1 \
        --remove /dev/sdb1 \
        --re-add /dev/sdb1 \
mdadm: set /dev/sdb1 faulty in /dev/md0                                              
mdadm: hot removed /dev/sdb1 from /dev/md0                   
mdadm: re-added /dev/sdb1

This will only work if your array has a bitmap, otherwise it will refuse to re-add. Most arrays do get a bitmap, but small arrays won’t by default. Fortunately you can easily add a bitmap like this:

# mdadm --grow --bitmap=internal /dev/md0

The downside of this approach is that your array will have reduced redundancy while it rebuilds. It should rebuild pretty quickly though as the bitmap will cause only changed parts to be rewritten.

(This won’t work if a BBL currently has any entries)

Stop the array and assemble again with update

The other way to remove BBL from devices is to stop the array and assemble it manually like this:

# mdadm --assemble /dev/mdX --update=no-bbl

The big problem with this is that stopping the array obviously causes downtime for whatever is using it. If your root filesystem is on an MD array (and why wouldn’t it be, if you use MD?) then that means the entire server, and you’re having to do this from sort of rescue environment.

I have suggested that a config option be added to remove a BBL on assembly, so that this will happen the next time the machine is rebooted. This does not appear to have provoked any interest.

This method is quicker since it operates on all devices and doesn’t require a rebuild, but personally I usually find downtime more painful so I’d be inclined to schedule an “at-risk” maintenance window and do it the re-add way.

Avoiding the BBL at creation time ^

So if the BBL cannot be easily removed, at least it can be prevented from ever existing, right? When Neil Brown, the previous MD maintainer, was asked in 2016 if the feature could be defaulted to off, Neil said that putting this in the config file was as good as that:

CREATE bbl=no

The thing is, it’s not as good as disabling it by default when you consider what many users’ experience is of running the mdadm command: they don’t run mdadm, something else runs it for them. I’d go as far as to say that the majority of uses of mdadm are done by helper scripts and installers, not by human beings.

If it’s a program that is running mdadm for you then you are going to have to find out how to set that mdadm.conf before it reads it.

Take for example my own process of installing Debian. I do it by booting the Debian Installer by PXE. I have some pre-seeding done to answer a lot of the installer questions, but actually I do still do the disk partitioning stage in the installer’s text interface.

So there I was thinking this is actually going to be quite simple, because the Debian Installer is really lovely about letting you execute a shell and poke around. Surely all I am going to need to do is open a shell once and edit /etc/mdadm/mdadm.conf and then go back into the mdcfg menu and carry on, right? Oh dear me no.

You can read the details of my wild ride that involved me uploading a binary of strace into the d-i to run mdadm under to work out what was going on, but just the relevant discoveries are in this article for those who’d rather not.

mdadm in d-i uses a config file at /tmp/mdadm.conf

After quite a bit of confusion over why even arrays I created manually with the mdadm command in the d-i shell still had a BBL, I discovered that the mdadm binary in d-i is compiled to have its config at /tmp/mdadm.conf. I don’t know why, but probably there is a good reason.

(At this point a number of people responded, “that’s because everything else will be set read-only.” That’s not the case with debian-installer which runs entirely off of a tmpfs. It’s all writeable.)

So just make the edit to /tmp/mdadm.conf then?

Oh ho ho no. Every time you go into the MD configuration section (mdcfg) it clobbers its own /tmp/mdadm.conf, and you can’t get to the “execute a shell” option without returning to the MD configuration section.

If you’re on something with multiple virtual consoles (like if you’re sitting in front of a conventional PC) then you could switch to one of those after you’ve entered the MD configuration part and modify /tmp/mdadm.conf then. I don’t have that option because I’m on a serial console.

I thought I didn’t have that option because I’m on a serial console, but it was pointed out to me that when the Debian installer detects it’s running in a serial console it runs itself under GNU Screen. So, by using the usual screen commands of ctrl+a n or ctrl+a p, one can switch backwards and forwards through the different virtual consoles. Neat!

There is also an earlier option to load an installer component that enables one to continue the installation process over SSH. If you select that then you can SSH in to the running installer system so if you do that after you’ve entered the MD configuration bit in your main console then I guess you can then edit the config file and continue.

By one of those methods of getting a shell, after you’ve already entered the array configuration part but before you’ve actually created any arrays, I think you could edit /tmp/mdadm.conf to have “CREATE bbl=no” and the installer’s mdadm binary would respect that when you switch back.

Alternatively you could just use the shell to create your arrays instead of using the Ddebian installer to do it. If it’s a simple case where you’ve just got an sda and an sdb disk identically partitioned and you want to make a bunch of arrays on them, it can be a fairly legible shell session like:

~ # mkdir -vp /etc/mdadm && echo "CREATE bbl=no" > /etc/mdadm/mdadm.conf
~ # for part in 1 2 3 5; do \
      mdadm --create \
            -v \
            --config=/etc/mdadm/mdadm.conf \
            /dev/md${part} \
            --level=1 \
            --raid-devices=2 \
            /dev/sd[ab]${part}; \

Do not try this until you understand exactly what it is doing.

It iterates the list 1, 2, 3, 5 (I use the 4th partition for something else) and makes arrays called mdX out of sdaX and sdbX. The mdadm binary is forced to use our config file that disables creation of a BBL.

You can verify that a BBL does not exist on any of the array components like this:

~ # mdadm --examine-badblocks /dev/sda1
No bad-blocks list configured on /dev/sda1

You should get identical output for every component. If a component did have a BBL it would output something like this:

~ # mdadm --examine-badblocks /dev/sda1
Bad-blocks list is empty in /dev/sda1

You can then exit the d-i shell and go back to the disk partitioning section. You won’t need the MD configuration part now but even if you do go into it, it should detect all your manually-created arrays.

How to make progress? ^

All of this isn’t great but at least it’s fairly easy to pause the Debian installer and take some manual action. I suspect users of other Linux distributions may not be so lucky, and so I too think it would be a good idea if this buggy feature was disabled by default, or at least if there were a way to tell mdadm to remove the BBL on assembly.

In fact I would very much like to be able to tell it to remove the BBL on assembly so that I can disable the BBL feature on all my existing servers.

mdadm actually gets called by udev from inside the initramfs in incremental assembly mode, so I think the incremental assembly code needs to look in the config file for this “remove all the BBLs” directive and do it then during assembly as if update=no-bbl had been specified on a command line.

It should be possible to write a script that:

  1. Looks in /sys/block/md* to find device components of all arrays.
  2. Checks each one to see if it has a BBL.
  3. If any are found, add a bitmap if necessary.
  4. Do the fail/remove/re-add trick on each one in turn, waiting for the array to go back into sync each time.

i.e. it should be possible to automate this and run it at the end of an install so the entire install process can remain automated, or run it on a host any time after it’s been provisioned.

When is a 64-bit counter not a 64-bit counter?

…when you run a Xen device backend (commonly dom0) on a kernel version earlier than 4.10, e.g. Debian stable.


Xen netback devices used 32-bit counters until that bug was fixed and released in kernel version 4.10.

On a kernel with that bug you will see counter wraps much sooner than you would expect, and if the interface is doing enough traffic for there to be multiple wraps in 5 minutes, your monitoring will no longer be accurate.

The problem ^

A high-bandwidth VPS customer reported that the bandwidth figures presented by BitFolk’s monitoring bore no resemblance to their own statistics gathered from inside their VPS. Their figures were a lot higher.

About octet counters ^

The Linux kernel maintains byte/octet counters for its network interfaces. You can view them in /sys/class/net/<interface>/statistics/*_bytes.

They’re a simple count of bytes transferred, and so the count always goes up. Typically these are 64-bit unsigned integers so their maximum value would be 18,446,744,073,709,551,615 (264-1).

When you’re monitoring bandwidth use the monitoring system records the value and the timestamp. The difference in value over a known period allows the monitoring system to work out the rate.

Wrapping ^

Monitoring of network devices is often done using SNMP. SNMP has 32-bit and 64-bit counters.

The maximum value that can be held in a 32-bit counter is 4,294,967,295. As that is a byte count, that represents 34,359,738,368 bits or 34,359.74 megabits. Divide that by 300 (seconds in 5 minutes) and you get 114.5. Therefore if the average bandwidth is above 114.5Mbit/s for 5 minutes, you will overflow a 32-bit counter. When the counter overflows it wraps back through zero.

Wrapping a counter once is fine. We have to expect that a counter will wrap eventually, and as counters never decrease, if a new value is smaller than the previous one then we know it has wrapped and can still work out what the rate should be.

The problem comes when the counter wraps more than once. There is no way to tell how many times it has wrapped so the monitoring system will have to assume the answer is once. Once traffic reaches ~229Mbit/s the counters will be wrapping at least twice in 5 minutes and the statistics become meaningless.

64-bit counters to the rescue ^

For that reason, network traffic is normally monitored using 64-bit counters. You would have to have a traffic rate of almost 492 Petabit/s to wrap a 64-bit byte counter in 5 minutes.

The thing is, I was already using 64-bit SNMP counters.

Examining the sysfs files ^

I decided to remove SNMP from the equation by going to the source of the data that SNMP uses: the kernel on the device being monitored.

As mentioned, the kernel’s interface byte counters are exposed in sysfs at /sys/class/net/<interface>/statistics/*_bytes. I dumped out those values every 10 seconds and watched them scroll in a terminal session.

What I observed was that these counters, for that particular customer, were wrapping every couple of minutes. I never observed a value greater than 8,469,862,875. That’s larger than a 32-bit counter would hold, but very close to what a 33 bit counter would hold (8,589,934,591).

64-bit counters not to the rescue ^

Once I realised that the kernel’s own counters were wrapping every couple of minutes inside the kernel it became clear that using 64-bit counters in SNMP was not going to help at all, and multiple wraps would be seen in 5 minutes.

What a difference a minute makes ^

To test the hypothesis I switched to 1-minute polling. Here’s what 12 hours of real data looks like under both 5- and 1-minute polling.

As you can see that is a pretty dramatic difference.

The bug ^

By this point, I’d realised that there must be a bug in Xen’s netback driver (the thing that makes virtual network interfaces in dom0).

I went searching through the source of the kernel and found that the counters had changed from an unsigned long in kernel version 4.9 to a u64 in kernel version 4.10.

Of course, once I knew what to search for it was easy to unearth a previous bug report. If I’d found that at the time of the initial report that would have saved 2 days of investigation!

Even so, the fix for this was only committed in February of this year so, unfortunately, is not present in the kernel in use by the current Debian stable. Nor in many other current distributions.

For Xen set-ups on Debian the bug could be avoided by using a backports kernel or packaging an upstream kernel.

Or you could do 1-minute polling as that would only wrap one time at an average bandwidth of ~572Mbit/s and should be safe from multiple wraps up to ~1.1Gbit/s.

Inside the VPS the counters are 64-bit so it isn’t an issue for guest administrators.

Tracking down the lvmcache fix

Background ^

In the previous article I covered how, in order to get decent performance out of lvmcache with a packaged Debian kernel, you’d have to use the 4.12.2-1~exp1 kernel from experimental. The kernels packaged in sid, testing (buster) and stable (stretch) aren’t new enough.

I decided to bisect the Linux kernel upstream git repository to find out exactly which commit(s) fixed things.

Results ^

Here’s a graph showing the IOPS over time for baseline SSD and lvmcache with a full cache under several different kernel versions. As in previous articles, the lines are actually Bezier curves fitted to the data which is scattered all over the place from 500ms averages.

What we can see here is that performance starts to improve with commit 4d44ec5ab751 authored by Joe Thornber:

dm cache policy smq: put newly promoted entries at the top of the multiqueue

This stops entries bouncing in and out of the cache quickly.

This is part of a set of commits authored by Joe Thornber on the drivers/md/dm-cache-policy-smq.c file and committed on 2017-05-14. By the time we reach commit 6cf4cc8f8b3b we have the long-term good performance that we were looking for.

The first of Joe Thornber’s commits on that day in the dm-cache area was 072792dcdfc8 and stepping back to the commit immediately prior to that one (2ea659a9ef48) we get a kernel representing the moment that Linus designated the v4.12-rc1 tag. Joe’s commits went into -rc1, and without them the performance of lvmcache under these test conditions isn’t much better than baseline HDD.

It seems like some of Joe’s changes helped a lot and then the last one really provided the long term performance.

git bisect procedure ^

Normally when you do a git bisect you’re starting with something that works and you’re looking for the commit that introduced a bug. In this case I was starting off with a known-good state and was interested in which commit(s) got me there. The normal bisect key words of “good” and “bad” in this case would be backwards to what I wanted. Dominic gave me the tip that I could alias the terms in order to reduce my confusion:

$ git bisect start --term-old broken --term-new fixed

From here on, when I encountered a test run that produced poor results I would issue:

$ git bisect broken

and when I had a test run with good results I would issue:

$ git bisect fixed

As I knew that the tag v4.13-rc1 produced a good run and v4.11 was bad, I could start off with:

$ git bisect reset v4.13-rc1
$ git bisect fixed
$ git bisect broken v4.11

git would then keep bisecting the search space of commits until I would find the one(s) that resulted in the high performance I was looking for.

Good and bad? ^

As before I’m using fio to conduct the testing, with the same job specification:


The only difference from the other articles was that the run time was reduced to 15 minutes as all of the interesting behaviour happened within the first 11 minutes.

To recap, this fio job specification lays out two 2GiB files of random data and then starts two processes that perform 4kiB-sized reads against the files. Direct IO is used, in order to bypass the page cache.

A Zipfian distribution with a factor of 1.2 is used; this gives a 90/10 split where about 90% of the reads should come from about 10% of the data. The purpose of this is to simulate the hot spots of popular data that occur in real life. If the access pattern were to be perfectly and uniformly random then caching would not be effective.

In previous tests we had observed that dramatically different performance would be seen on the first run against an empty cache device compared to all other subsequent runs against what would be a full cache device. In the tests using kernels with the fix present the IOPS achieved would converge towards baseline SSD performance, whereas in kernels without the fix the performance would remain down near the level of baseline HDD. Therefore the fio tests were carried out twice.

Where to next? ^

I think I am going to see what happens when the cache device is pretty small in comparison to the working data.

All of the tests so far have used a 4GiB cache with 4GiB of data, so if everything got promoted it would entirely fit in cache. Not only that but the Zipf distribution makes most of the hits come from 10% of the data, so it’s actually just ~400MiB of hot data. I think it would be interesting to see what happens when the hot 10% is bigger than the cache device.

git bisect progress and test output ^

Unless you are particularly interested in the fio output and why I considered each one to be either fixed or broken, you probably want to stop reading now.

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