Aligning my web server with devops practices: part 1 (backups)

post by VipulNaik · 2022-11-27T18:38:38.244Z · LW · GW · 0 comments

Contents

  Recommendations for others (transferable learnings)
  Considerations when evaluating backup strategies
    Considerations for the process of making backups
    Considerations for backup storage
    Considerations for restoration process
  Full disk backups
    What these are
    What I use full disk backups for
    Evaluating full disk backups
      Consideration for the process of making backups: integrity of the backup process and backup output (good)
      Consideration for the process of making backups: time taken for backup (good)
      Consideration for the process of making backups: impact of making the backup on other processes (good)
      Consideration for the process of making backups: cost of making the backup (meh)
      Consideration for backup storage: security of backups (good)
      Consideration for backup storage: independence of backups in terms of geography and provider (bad)
      Consideration for backup storage: cost of storing the backup (meh)
      Consideration for restoration process: well-defined process to restore from backups (good)
      Consideration for restoration process: time taken for restoration (bad)
      Consideration for restoration process: cost of restoration (meh)
  Cloud storage backups
    Mechanics of backup script for code
    Mechanics of backup script for SQL
    Mechanics of backup script for logs
    Evaluating cloud storage backups
      Consideration for the process of making backups: integrity of the backup process and backup output (probably good)
      Consideration for the process of making backups: time taken for backups (probably good)
      Consideration for the process of making backups: impact of making the backup on other processes (probably good)
      Consideration for the process of making backups: cost of making the backup (probably good)
      Consideration for backup storage: security of backups (probably good)
      Consideration for backup storage: independence of backups in terms of geography and provider (good)
      Consideration for backup storage: cost of storing the backup (good)
      Consideration for restoration process: well-defined process to restore from backups (getting to good; work in progress)
      Consideration for restoration process: time taken for restoration (getting to good)
      Consideration for restoration process: cost of restoration (good)
  Not quite a backup but serves some of the functions of a backup: git and GitHub
    What's good about git and GitHub?
    What's bad about git and GitHub?
  Postmortem regarding my checks missing things
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UPDATE: Part 2 is now published here [LW · GW].

I have a web server that serves a double-digit number of different domains and subdomains, such as contractwork.vipulnaik.com and groupprops.subwiki.org. I originally set it up in 2013, and more recently upgraded it a few years ago. Back when I did the original setup, I had no knowledge or experience of the principles of devops (I didn't even have any experience with software engineering, though I had done some programming for academic and personal purposes).

Over time, as part of my job as a data scientist and machine learning engineer, I acquired deeper familiarity with software engineering and devops. However, for the most part, I didn't have the time or energy to apply this knowledge to my personal web server setup. As a result, my web server continued to basically be a snowflake -- a special hodgepodge of stuff that would be hard to regenerate from scratch -- and the thought of regenerating it from scratch was terrifying. The time commitment to do so was big enough that I didn't have enough time away from my job to do so.

In the past year, I've finally started work on desnowflaking my web server and formulating a set of recipes that could be used to build it from scratch, assembling all the websites and turning them on. This work only happens in the spare time from my day job, and competes with other personal projects, so progress is slow, but I've made a lot of it.

This series of posts talks about various choices I made in setting up various pieces of the system. Many of these pieces already existed prior to my systematic efforts this year, but I had to add several other pieces.

This particular post focuses on backups.

Recommendations for others (transferable learnings)

These are some of the key learnings that I expect to transfer to other contexts, and that are sufficiently non-obvious and that may not come to your attention until it is too late:

• Establish monitoring of the backups so that you can be confident that they're happening as expected, and get notified if they aren't. If using a managed service, make sure you are subscribed to notifications for the status page of the service so that you get notified if there are any issues with backups.

• Establish a well-defined process to restore from backups, and fire-drill it so that you know it works.

• This may seem irrelevant to you if your budget is way higher than the expected cost of backups, but it's important (in at least some cases) to keep an eye on the cost of backups. In particular, considerations such as backup size, frequency, and retention period affect the cost of making, storing, and recovering from backups.

The rest of the stuff is also pretty important, so I do recommend reading the whole post.

Considerations when evaluating backup strategies

Backup strategies need to be evaluated along a variety of dimensions. Some of these are listed below. Different considerations come to the forefront for different kinds of backups, as we see in later parts of the post.

Considerations for the process of making backups

• Integrity of the backup process and backup output: Given their role as a failsafe, backups should be done properly; in particular, the backup process should not fail, and even more importantly, should not fail silently.

  This is particularly important, because most of the time, we don't need backups, so we may not notice that backups are failing, unless we set up active monitoring around the existence of backups.

• Time taken for backup: We want backups that can be executed relatively quickly (e.g., over a period of minutes, rather than hours or days).

• Impact of making the backup on other processes: Particularly for backups of production servers, we want the backup to operate in a way that has minimal impact on the rest of the server.

• Cost of making the backup: All else equal, we want making backups to be cheap! In general, the cost of making the backup depends on the size of the backup as well as the frequency. One thing to keep in mind when thinking about size is whether the underlying data being backed up is growing organically in a significant way. This isn't an issue for my sites, but is worth thinking about in other contexts.

Considerations for backup storage

• Security of backups: We don't want the backup to leak to the public, and we also want to make sure that the backup is hard to destroy even if the machine is compromised somehow.

• Independence of backups in terms of geography and provider: We ideally want backups that are as independent as possible from the thing being backed up, to minimize the risk of both going down together.

• Cost of storing the backup: All else equal, we want backup storage to be cheap! In general, the cost of storing the backup depends on the size, frequency, and retention policy of the backup. Having a retention policy that deletes sufficiently old backups is important for containing costs. One thing to keep in mind when thinking about size is whether the underlying data being backed up is growing organically in a significant way. This isn't an issue for my sites, but is worth thinking about in other contexts.

Considerations for restoration process

• Well-defined process to restore from backups: We very rarely need to restore from backups, but when we do, time is of the essence, and we lack a lot of contextual information (for instance, if restoring from backup because the server got hacked or had a hardware failure). Formulating a well-defined process to restore from backups, and fire-drilling this process so that it can be applied quickly in stressful situations, is important.

• Time taken for restoration: All else equal, we prefer backups that we can restore from relatively quickly.

• Cost of restoration: All else equal, we prefer backups that are cheap to restore from.

Full disk backups

What these are

The crudest kind of backup is that of the full disk. My VPS provider, Linode, offers managed backups for 25% of the cost of the server (see here for more). The backups are done daily, and at any time I can access three recent backups, the most recent being the one in the last ~24 hours, and two others within the past two weeks.

The full disk backup includes basically the whole filesystem. In particular, it includes the operating system, all the packages, all the configurations, all the websites, everything.

What I use full disk backups for

I use full disk backups as a final layer of redundancy: I try to design things in a way that I never have to use them. I basically only use them when doing a fire drill to make sure I can restore from them.

Full disk backups are also a fallback solution for recovering something that was on disk at the time of the backup but is no longer on disk, perhaps due to accidental deletion or a bad upgrade. In most cases, I don't want to rely on a full disk backup for this purpose (due to the time and cost), but it's good to have it available as a fallback solution, if all else fails.

Evaluating full disk backups

I now evaluate full disk backups based on considerations described earlier in the post.

Consideration for the process of making backups: integrity of the backup process and backup output (good)

Full disk backups are managed by my VPS as part of its Backups service; information on this is reported on the Linode status page. I have subscribed to notifications on this page via both email and Slack.

I also have the ability to log in at any time and check what full disk backups are available to restore from, but I don't do this regularly.

Consideration for the process of making backups: time taken for backup (good)

I'm not sure how long the backup takes, but it appears to be done asynchronously.

Consideration for the process of making backups: impact of making the backup on other processes (good)

As far as I can make out, the backup doesn't affect the performance of production servers.

I do have the ability to configure when in the day the backup process will run so if impact on other processes ever becomes an issue, I can try to configure the timing to minimize that impact.

Consideration for the process of making backups: cost of making the backup (meh)

Making the backups is not broken down as a cost item; the total cost of full disk backups is 25% of the machine cost, and it's offered as a package deal. There aren't any knobs to tweak to optimize cost here.

Consideration for backup storage: security of backups (good)

Access to the backups is gated by access to my account, so they're as secure as my account. This is good (to the extent I believe my account is secure). In particular, it's stricter than access to the server itself; if the server were to get hacked, the already-taken backups would not be compromised.

Consideration for backup storage: independence of backups in terms of geography and provider (bad)

The managed backups are hosted by the same provider and in the same region as the stuff being backed up, so in that sense they are not very independent (Linode's guide confirms this).

Consideration for backup storage: cost of storing the backup (meh)

Storing the backups is not broken down as a cost item; the total cost of full disk backups is 25% of the machine cost, and it's offered as a package deal. There aren't any knobs to tweak to optimize cost here. With that said, the cost here is comparable to or less than the cost of just the storage portion if I were backing up the full disk to S3.

Consideration for restoration process: well-defined process to restore from backups (good)

Linode offers a clear process to restore from the backup either to the same machine or to a new machine; I've tried their option of restoring to a new machine. However, this is not the full restoration process for a production server because there are additional steps (such as updating DNS records) that I did not undertake. It is, however, the bulk of the process (and the only part I'm comfortable testing) and I have a reasonably clear sense of the remaining steps.

Consideration for restoration process: time taken for restoration (bad)

My last attempt to restore from backup (done for a fire drill) took 4 hours. Since then, I've reduced the amount of stuff on my disk, so I expect the restoration from backup to take less time, but likely still over 1 hour (probably closer to 2 hours). This is not great, but it's not terrible to use as a last resort. However, it's not small enough to use as a matter of course for time-sensitive recovery of individual files that I carelessly delete or overwrite.

Consideration for restoration process: cost of restoration (meh)

The main cost associated with restoring from backup is the cost of running the new server I'm restoring to, for the duration prior to the restoration being complete. At a few hours, this comes to well above 1 cent but under 1 dollar. The cost is small enough for a genuine emergency, but not small enough to be negligible and to use as a matter of course just to recover individual files that I carelessly delete or overwrite. Overall, though, the cost scales with time, and the downside based on cost is less than the downside based on time, so it makes sense to just focus on the time angle.

Cloud storage backups

I back up relevant stuff (code files and SQL database dumps) to a chosen location in Amazon Simple Storage Service (S3). I describe briefly the mechanics of the scripts I use for these backups, then talk about their advantages and disadvantages.

Mechanics of backup script for code

The backup script for code works as follows:

• It takes in a bunch of arguments specifying what site to run it for, what folder to copy from, specific subfolders to exclude, etc.

• It copies stuff from the source folder into a local folder inside a code backups folder that includes the site and the current date in its file path. The copying is done using rsync and excludes any specified subfolders to exclude.

• The stuff in the local folder is now synced to a folder in S3 with a parallel naming structure. This uses aws s3 sync.

• While we're at it, some older local backups are deleted based on their date (the goal is to have about two recent backups in the server's code backups folder; older backups are only in S3).

Mechanics of backup script for SQL

The backup script for SQL works as follows:

• It takes in a bunch of arguments specifying what database to back up, what site it's for, and any specific instructions on tables to exclude from the backup process.

• It runs mysqldump on the database to back up, with exclusions of tables specified, and saves it in a SQL backup folder.

• It then compresses the SQL file obtained using bzip2.

• The bz2 file is now copied over to a parallel location in S3.

• While we're at it, some older local backups are deleted based on their date (the goal is to have about two recent backups in the server's SQL backups folder; older backups are only in S3).

Mechanics of backup script for logs

I also back up the access logs and error logs for the sites regularly. This actually uses the same script as for code backups, just with different parameters, with the source now the log file and the target file slightly different.

Evaluating cloud storage backups

I now evaluate cloud storage backups based on considerations described earlier in the post. I also talk of tweaks I made to improve the way I did cloud storage backups in order to score better on the various considerations.

Consideration for the process of making backups: integrity of the backup process and backup output (probably good)

There were a bunch of considerations related to the integrity of the backups; some of these actually occurred and others were identified by me before they occurred. I think I'm in a good position here, but since this is basically just my own set of scripts, I need to monitor for a little longer to be confident that things are working well.

• The backup process could fail silently, ending up not sending output to S3: I fixed this two-fold, albeit one piece of the fix is still pending:

  • I had the backup script do extensive error-checking and report to a private Slack workspace I own, both in case of success and in case of error; in case of error, I would also get tagged. I eyeball the Slack channel occasionally.

  • I wrote a script that runs daily to check if recent backups exist in S3 and reports success to Slack (without tagging me); any missing backups are also reported and tag me. I investigate any tagged messages quickly, and also monitor the channel semi-regularly to make sure that the script that checks if recent backups exist has been running.

• The SQL backup process could just miss some tables or err in some other weird way while still outputting stuff that seems legitimate: This happened with one of my sites; mysqldump stopped whenever it got to specific tables, so all tables after those were omitted from the backups. I fixed this multi-fold:

  • ADDED 2023-05-10 (a few months after writing the post): I added a check for the status code from mysqldump and a channel-tagged notification if there was a nonzero status code; I also saved the mysqldump error log to a file for further examination. I should have done this earlier (and well before the writing of the post) but I somehow skipped the step of trying to capture the mysqldump status code! Because I hadn't done this, I was more reliant than I should have been on my other layers, and poor thinking regarding those layers led to me missing genuine issues.

  • I added a verification for significant changes to the size of the SQL backup file. In case of detection of a significant size change, I'd get tagged in a Slack message.

    ADDED 2023-05-10: Although this notification did work to catch major changes to the size of backup files, the downside of the notification logic is that it triggers on only the one day that the backup file size changes, so if I miss the notification on that one day, then I am unaware of the issue with the backup file size. This actually happened to me in some cases. Based on this, I updated the logic to include both a notification for a relative size change, and a notification if the size is less than an absolute threshold of 10000 bytes (the smallest of my legitimate backup files is over 15000 bytes). I also included the latter size check in the independent script that I run daily to check if my backups have happened properly; since that script outputs to a different, less noisy, Slack channel, and runs at a different time, I have another layer of notification redundancy.

  • I investigated what tables were choking the SQL backup for the site where I saw the choking, then manually excluded those tables from the backup after confirming that this would be okay.

• There were potential filename clashes between backups being run from my production server and backups being done from dev servers I was setting up (to possibly replace the production server, or just to test the setup process): I updated the path generation logic to include an identifier for the machine in the path, so that two diferent machines should give non-colliding backup file paths.

Consideration for the process of making backups: time taken for backups (probably good)

For some sites, the backups were large in size and took a lot of time. The time taken was directly related to their size, so reducing the size was a good strategy for reducing the time taken.

• In one case, the huge amount of space was due to the creation of several spam accounts even though the spam accounts couldn't actually post spam because they didn't have edit access; I had to manually clean up the spam accounts.

• In another case, a few tables were creating problems and I had to manually exclude them from the backup after confirming that they are derivative tables and can be reconstructed. Specifically, on MediaWiki sites, I confirmed that the objectcache table and l10n_cache table can be excluded from backups.

• Similar to the above, for code backups, I switched from using cp to using rsync because it's easier in rsync to exclude a set of paths from the copy process. I was then able to exclude a variety of paths, including paths for autogenerated images, cache files, and logs.

In addition to reducing the time, I also decided to start monitoring the time for backups. To do this, I set up Slack messaging for the start and end of backups. At some point, I might also start adding tagging for backups that take longer than a threshold amount of time.

Consideration for the process of making backups: impact of making the backup on other processes (probably good)

First off, reducing the size of backups (that I did in order to reduce the time taken for backup) had a ripple effect on the impact of backups: when the backup process had to do less work, it had less impact on the server as well. However, there were a couple of other ways I tried to mitigate the impact of the backup process:

• I switched to running all backup jobs with nice -n 20 in order to play nicely with the rest of the server and to interfere as little as possible with production serving.

• In order to reduce the size of backups on disk on the server, I set up automatic deletion of older backups that I ran along with the backup script. My initial approach had been a find <old enough backup files> and rm them. This fix worked to address the disk space, but it ended up often taking a lot of time when there was a large search space.

  I later switched to a fix of directly deleting backup subfolders based on the expected dates in those subfolders. This worked much faster than find and has less performance implications.

Consideration for the process of making backups: cost of making the backup (probably good)

The cost of making the backup is essentially proportional to the size of the backup, so the points of the preceding section also helped with reducing the cost of making backups. With that said, the cost of making the backup is relatively small compared to the cost of storing the backups.

Consideration for backup storage: security of backups (probably good)

In order to upload the backup files to S3, I needed AWS credentials with access to S3 to be stored on the server.

Having the S3 credentials on the server led to the risk of a hack on the server leading to a compromise of the S3 data, or of some error in the script causing the data in S3 to get overridden. This is a serious risk, because S3 is intended as a layer of redundancy if Linode fails. I took two steps to address this:

• I reduced the permissions (using AWS Identity and Access Management (IAM)) on the AWS keys on the server, so that they had access to only a specific bucket, and could only GET and PUT stuff, not DELETE stuff. This still didn't make things fully secure; it is still possible to effectively delete every file by manually writing a new version of the file. However, it did cut down significantly the risk of accidental data deletion.

• I created a separate bucket that isn't accessible at all with these AWS keys, and created a process that runs outside of the Linode that copies a few of the backups to this bucket. For instance, one backup every 3 or 6 months, depending on the frequency of content changing. These backups serve as an additional layer of protection.

Consideration for backup storage: independence of backups in terms of geography and provider (good)

The backups are stored on Amazon S3. This is a different provider than my VPS (Linode). Also, the AWS region where the backups are stored is not geographically very close to the region where my Linode is stored. Therefore, we have independence of both geography and provider.

Consideration for backup storage: cost of storing the backup (good)

The number of backup files grew linearly with time, and even assuming that the backups were not growing in size from one day to the next (a reasonable approximation, as most sites didn't have huge growth in content), we still get a linear increase in S3 cost. This wasn't acceptable.

In order to address this, I implemented a lifecycle policy in S3 for the bucket with the primary backups that expired old code backups and SQL backups after a few months. This made sure that costs largely stabilized.

I also did some further optimization around costs: essentially, for older backups that I don't expect to access frequently but that I maintain just in case, I don't need them to be easily available. So, in my lifecycle policy, I migrated backups that were somewhat old to Glacier, S3's storage / cold storage. Glacier is cheaper than regular S3 but also needs more time to access.

Consideration for restoration process: well-defined process to restore from backups (getting to good; work in progress)

I have a set of scripts to recreate all my sites on a new server based on a mix of data from GitHub and S3. For those sites of mine that are not fully restorable from GitHub (and this includes the MediaWiki and Wordpress sites) I use the code and database backups in S3 as part of my process for recreating the sites on a new server.

It shouldn't be too hard to modify the scripts to fully restore from S3 even if I don't have access to GitHub at all, but I haven't done so yet (it doesn't seem worth the effort to figure this out in advance, since I expect that the chances of losing access to both my existing server and GitHub at the same time are low).

Consideration for restoration process: time taken for restoration (getting to good)

As of now, the total time taken to restore all sites is comparable to the time for a restore of a full disk backup, but this is largely because there are still pieces I am working through automating (most of these are pieces around testing; the actual downloading from S3 is pretty streamlined).

However, the time taken to fix and restore a single site, or a few sites, is way less than for a full disk backup. Full disk backups are all-or-nothing: you need to fully restore to access any data. In contrast, with S3 backups, it's possible to access just the data for a particular site, or even more specifically, just a particular file.

I expect that the restoration process will get more streamlined over time, as I'm using the same scripts to recreate all my sites on a new server -- something that is going to be extremely useful for OS upgrades.

Consideration for restoration process: cost of restoration (good)

Restoration is relatively cheap: the only cost is that of downloading the backup from S3, which is relatively small. Moreover, because I can selectively restore only the sites or even the files that I need to restore, I only incur the costs associated with those specific sites or files.

Not quite a backup but serves some of the functions of a backup: git and GitHub

Some of my websites are fully on GitHub, and can be fully reconstructed from the corresponding git repository. In this case, the setup process for the website is mostly just a process of git cloning followed by the execution of various steps as documented in the README (and many of these have Makefiles, so it's just about executing specific make commands).

Some other websites are mostly on GitHub, in the sense that for the most part, they can be reconstructed from what's on GitHub. But there are some pieces of information that are not on GitHub, and either (a) cannot be reconstructed based on what's on GitHub, or (b) can be reconstructed based on what's on GitHub, but the process is long and tedious.

A combined example of both phenomena: the GitHub code for analytics.vipulnaik.com includes the logic to fetch analytics data, but a secret key is needed to actually be able to fetch that data. Therefore, what's on GitHub isn't sufficient to set up the repository; I also need to fetch the secret key. However, fetching the secret key and then redownloading all the data is time-consuming and expensive, so my setup script instead downloads an existing database backup to jumpstart itself to the data already downloaded on the previous server, after which the secret key can be used to download additional data.

What's good about git and GitHub?

• The great thing about the git protocol is that it facilitates both version control and ease of duplication across machines. This includes not just my servers, but also my laptop where I can keep a copy of the repositories and also work on changes locally.

• GitHub also stores a copy of the content on its own servers, which offers an additional layer of redundancy.

• GitHub makes it easy to give other selected people access to the repository, which facilitates collaboration.

• The GitHub UI has a bunch of other functionality for exploring the code and data.

What's bad about git and GitHub?

• GitHub does not recommend the use of git for storing secret keys and credentials. For public repositories in particular, it doesn't make sense to store any credential information along with the repository, but GitHub discourages this even for private repositories. This isn't a bad thing about git per se, but it does indicate a limitation; when restoring from a git repository, additional logic is needed to populate the credentials.

• Git and GitHub aren't great with large files, and in particular, it therefore makes sense to exclude a bunch of large files from the git repository. This makes it unsuitable for some kinds of backups.

• For sites that use other software such as MediaWiki or Wordpress, it's hard to square both the code side and the database side of it with git.

Postmortem regarding my checks missing things

On 2023-05-10, I fixed a few holes in my checks. Here's what happened:

• The backup process for one of my sites had been broken for a while, resulting in a backup size of less than 2000 bytes. I hadn't given this a lot of thought at the time, becaause the size didn't seem so low as to trip alarm bells in my head (though it should have!).

  Had I been looking at the mysqldump status code in my code, I would have spotted the error a long time ago. But I didn't, even though I had investigated mysqldump failures for other sites.

• On 2023-01-25, the mysqldump for several of my sites broke on my dev machine, resulting in mysqldump outputing very small files that didn't have any of the actual stuff. This triggered the day-over-day size change notifications in Slack, but I somehow missed the Slack notifications on that day. No notifications triggered in later days, because there were no day-over-day changes after that. Miraculously, the problem reversed itself on 2023-05-10, triggering day-over-day change notifications again, and this time I did catch the notifications. This led me to make the various fixes. Unfortunately, I don't know the details of the specific mysqldump issue because it self-resolved.

  Had I been looking at the mysqldump status code in my code, I would have received Slack notifications every day that it remained broken (so every day from 2023-01-25 and before 2023-05-10) rather than just the day of transition (2023-01-25). So even if I missed the notifications on one day, I would have seen them another day and acted on them.

  Had I had an absolute size check (that I instituted on 2023-05-10 after noticing this), I would have received Slack notifications every day that it remained broken (so every day from 2023-01-25 and before 2023-05-10) rather than just the day of transition (2023-01-25). So even if I missed the notifications on one day, I would have seen them another day and acted on them.

  Had I been doing the size check as part of the independent checking script, and notifying Slack, I would have had a further layer of redundancy (different time of notification, diferent channel being notified). Also, I would have received Slack notifications every day that it remained broken (so every day from 2023-01-25 and before 2023-05-10) rather than just the day of transition (2023-01-25). So even if I missed the notifications on one day, I would have seen them another day and acted on them.

As we can see, my thought process around designing robust notifications was not as thorough as I had thought. My direction of thinking wasn't wrong; I just didn't go far enough. This is a lesson in humility.

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