- lots of containers running on a single host
- containers are each isolated in a VM (aka virtualized)
- workloads are not homogenous and change often (your neighbor today may not be your neighbor tomorrow)
I believe these are fair assumptions if you’re running on generic infrastructure with kubernetes.
In this setup, my concerns are pretty much noisy neighbors + throttling. You may get latency spikes out of nowhere and the cause could be any of:
- your neighbor is hogging IO (disk or network)
- your database spawned too many threads and got throttled by CFS
- CFS scheduled your DBs threads on a different CPU and you lost your cache lines
In short, the DB does not have stable, predictable performance, which are exactly the characteristics you want it to have. If you ran the DB on a dedicated host you avoid this whole suite of issues.
You can alleviate most of this if you make sure the DB’s container gets the entire host’s resources and doesn’t have neighbors.
Why are you assuming containers are virtualized? Is there some container runtime that does that as an added security measure? I thought they all use namespaces on Linux.
1. fsync. You cannot "divide" it between containers. Whoever does it, stalls I/O for everyone else.
2. Context switches. Unless you do a lot of configurations outside of container runtime, you cannot ensure exclusive access to the number of CPU cores you need.
3. Networking has the same problem. You would either have to dedicate a whole NIC or SRI-OV-style virtual NIC to your database server. Otherwise just the amount of chatter that goes on through the control plane of something like Kubernetes will be a noticeable disadvantage. Again, containers don't help here, they only get in the way as to get that kind of exclusive network access you need more configuration on the host, and, possible an CNI to deal with it.
4. kubelet is not optimized to get out of your way. It needs a lot of resources and may spike, hindering or outright stalling database process.
5. Kubernetes sucks at managing memory-intensive processes. It doesn't work (well or at all) with swap (which, again, cannot be properly divided between containers). It doesn't integrate well with OOM killer (it cannot replace it, so any configurations you make inside Kubernetes are kind of irrelevant, because system's OOM killer will do how it pleases, ignoring Kubernetes).
---
Bottom line... Kubernetes is lame from infrastructure perspective. It's written for Web developers. To make things appear simpler for them, while sacrificing a lot of resources and hiding a lot of actual complexity... which is impossible to hide, and which, in an even of failure will come to bite you. You don't want that kind of program near your database.
Would using direct-Io API’s fix most of the fsync issues? If workloads pin their stuff to specific cores can we incite some of the overhead here? (Assuming we’re only running a single dedicated workload + kubelet on the node).
> You would either have to dedicate a whole NIC or SRI-OV-style virtual NIC to your database server
Tbh I’ve no idea we could do this with commodity cloud servers, nor do I know how, but I’m terribly interested in knowing how, do you know if there’s like a “dummy’s guide to better networking”? Haha
> kubelet is not optimized to get out of your way...Kubernetes sucks at managing memory-intensive processes
Definitely agree on both these issues, I’ve blown up the kubelet by overallocating memory before, which basically borked the node until some watchdog process kicked in. Sounds like the better solution here is a kubelet rebuilt to operate more efficiently and more predictably? Is the solution a db-optimised kubelet/K8s?
Alway allocate whole cores, just mask them off
Dedicate physical IO devices for sensitive workloads
You can have per cgroup swap if you want, but imo swap is not useful
I think all of this is possible in k8s
If you're not in control of the system, and thus kubelet, obviously your hands are tied. I'm not sure anyone is suggesting that for a serious workload.
Now to dispell your myths:
1. You can assign dedicated storage devices to your database. Outside of mount operations you're not going to see much alien fsync activity. This is paranoid.
2. You can pin kubelet CPU cores. You can ensure exclusive access to the remaining ones. There are a number of advanced techniques that are not at all necessary if you want to be a control freak, such as creating your own cgroups. This isn't "outside" of the runtime. Kubernetes is designed to conform to your managed cgroups. That's the whole point. RTFM.
3. The general theme of your complaint has nothing to do with kubernetes. There's no beating a dedicated NIC and even network fabric. Some cloud providers even allow you to multi-NIC out of the box so this is pretty solvable. Also, like, the dumbest QoS rules can drastically minimize this problem generally. Who cares.
4. Nah. RTFM. This is total FUD.
5.a. I don't understand. Are you sharing resources on the node or not? If you're not, then swap works fine. If you are, then this smells like cognitive dissonance and maybe listen to your own advice, but also swap is still very doable. It's just disk. swapon to your heart's content. But also swap is almost entirely dumb these days. Are you suggesting swapping to your primary IO device? Come on. More FUD.
5.b. OOM killer does what it wants. What's a better alternative that integrates "well" with the OOM killer? Do you even understand how resource limits work? The OOM killer is only ever a problem if you either do not configure your workload properly (true regardless of execution environment) or you run out of actual memory.
Bottom line: come down off your high horse and acknowledge that dedicated resources and kernel tuning is the secret to extreme high performance. I don't care how you're orchestrating your workloads, the best practices are essentially universal.
And to be clear, I'm not recommending using Kubernetes to run a high performance database but it's not really any worse (today) than alternatives.
> It's written for Web developers. To make things appear simpler for them, while sacrificing a lot of resources and hiding a lot of actual complexity... which is impossible to hide, and which, in an even of failure will come to bite you.
What planet are you currently on? This makes no sense. It's a set of abstractions and patterns, the intent isn't to hide the complexity but to make it manageable at scale. I'd argue it succeeds at that.
Seriously, what is the alternative runtime you'd prefer here? systemd? hand rolled bash scripts? puppet and ansible? All of the above??
This is word salad. Do you even know what fsync is for? I'm not even asking if you know how it works... What is "alien" fsync activity? Mount is perhaps the one system call that has nothing to do with fsync... so, I wouldn't expect any fsync activity when calling mount...
Finally, I didn't say that you cannot allocate a dedicated storage device -- what I said is that Kubernetes or Docker or Singularity or containerd or... well, none of container (management) runtimes that I've ever used know how to do it. You need external tools to do it. The point isn't that you cannot, the point is that a container runtime will only stand in your way when you try to do it.
> You can pin kubelet CPU cores. You can ensure exclusive access to the remaining ones.
No you cannot. Not through Kubernetes. You need to do this on the node that hosts kubelet.
And... I don't have the time or the patience necessary to answer to the rest of the nonsense. Bottom line: you don't understand what you are replying to, and arguing with something I either didn't say, or just stringing meaningless words together.
I do, though perhaps an ignorant life would be simpler. "Alien" is a word with a definition. Perhaps "foreign" is a better word. Forgive me for attempting to wield the English language.
No one well will use your fucking disk if you mount it exclusively in a pod. Does that make sense? You must be a joy to work with.
> The point isn't that you cannot, the point is that a container runtime will only stand in your way when you try to do it.
I have no idea what this means. How does kubernetes stand in your way?
> No you cannot. Not through Kubernetes. You need to do this on the node that hosts kubelet.
This is incorrect. You can absolutely configure the kubelet to reserve cores and offer exclusive cores to pods by setting a CPU management policy. I know because I was waiting for this for a very long time for all of the reason in the discussion here. It works fine.
You clearly have an axe to grind and it seems pretty obvious you're not willing to do the work to understand what you're complaining about. It might help to start by googling what a container runtime even is, but I'm not optimistic.
Also, it brings nothing of value to the table, but requires a lot of dance around it to keep it going. I.e. if you are a decent DBA, you don't have a problem setting up a node to run your database of choice, you would be probably opposed to using pre-packaged Docker images anyways.
Also, Kubernetes sucks at managing storage... basically, it doesn't offer anything that'd be useful to a DBA. Things that might be useful come as CSI... and, obviously, it's better / easier to not use a CSI, but to interface directly with the storage you want instead.
That's not to say that storage products don't offer these CSI... so, a legitimate question would be why would anyone do that? -- and the answer is -- not because it's useful, but because a lot of people think they need / want it. Instead of fighting stupidity, why not make an extra buck?
If I run a db workload in K8s, it’s a tiny fraction of the operational overhead, and not a massively noticeable performance loss.
I would absolutely love a way to deploy and manage db’s as easily as K8s with fewer of the quite significant issues that have mentioned, so if you know of something that is better behaved around singular workloads, but keeps the simple deploys, the resiliency, the ease of networking and config deployments, the ease of monitoring, etc, I am all ears.
It's simple, until you hit a problem. And then it becomes a lot worse than if you had never touched it. You are now in the stage of a person who'd never made backups and never had a failure that required them to restore from backups, and you are wondering why would anyone do it. Adverse events are rare, and you may go like this for years, or, perhaps the rest of your life... unfortunately, your experience will not translate into a general advice.
But, again, you just might be in the camp where performance doesn't matter. Nor does uptime matter, nor does your data have very high value... and in that case it's OK to use tools that don't offer any of that, and save you some time. But, you cannot advise others based on that perspective. Or, at least, not w/o mentioning the downsides.
I am not sure what complexity Kubernetes adds in this situation. Anything Kubernetes can do to you, your cloud provider (or a poorly aimed fire extinguisher) can do to you. You have to be ready for a disaster no matter the platform.
Wrong. I wouldn't use kubelet at all. Kubernetes and good performance are not compatible. The goal of Kubernetes is to make it easier to deploy Web sites. Web is a very popular technology, so Kubernetes was adopted in many places where it's irrelevant / harmful because Web developers are plentiful and will help to power through the nonsense of this program. It's there because it makes trivial things even easier for less qualified personnel. It's not meant as a way to make things go faster, or to use less memory, or to use less persistent storage, or less network etc... it's the wheelchair of ops, not a highly-optimized professional-grade equipment.
Those who do that don't know what they are doing (even if they outnumber the other side hundred to one, they "don't count" because they aren't aiming for good performance anyways).
Well, maybe not quite... of course it's possible that someone would want to deploy a database in a container because of the convenience of assembling all dependencies in a single "package", however, they would never run database on the same node as applications -- that's insanity.
But, even the idea of deploying a database alongside something like kubelet service is cringe... This service is very "fat" and can spike in memory / CPU usage. I would be very strongly opposed to an idea of running a database on the same VM that runs Kubernetes or any container runtime that requires a service to run it.
Obviously, it says nothing about the number of processes that will run on the database node. At the minimum, you'd want to run some stuff for monitoring, that's beside all the system services... but I don't think GP meant "one process" literally. Neither that is realistic nor is it necessary.
The point was simply about other processes that could be competing for resources - CPU, memory, or I/O. It is expensive for a user-level process to perform accounting for all of these resources, and without such accounting you can't optimally allocate them.
If there are other apps that can suddenly spike memory usage then any careful buffer tuning you've done goes out the window. Likewise for any I/O scheduling you've done, etc.
(But just in containers, not in Kubernetes. I'm not crazy.)
And we are running them at the scale that most people can’t even imagine.
This is co-authored by Pavlo, Viktor Leiss, with feedback from Neumann. I'm sorry, but if someone on the internet claims to know better than those 3, you're going to need some monumental evidence of your credibility.
Additionally, what you link here:
> ... (See the slide at 21:25 into the video). Modern DBMSs spend 96% of their time managing buffers and locks, and only 4% doing actual useful work for the caller.
These databases represent a small portion of contemporary DBMS usage when compared to traditional RDBMS.
All you have to do is look at the bandwidth and reads/sec from the paper when using O_DIRECT "pread()"s versus mmap'ed IO.
(My understanding is that the GP wrote LMDB, works on openLDAP, and was a maintainer for BerkelyDB for a number of years. But even if he'd only written 'hello, world!' I'm much more interested in the specific arguments).
Andy and I have had this debate going for a long time already.
Isn't LMBD closer to an embedded key-value store than an RDBMS, though? Also there's a section in the paper that mentions it's single-writer.
- Queries can trigger blocking page faults when accessing (transparently) evicted pages, causing unexpected I/O stalls
- mmap() complicates transactionality and error-handling
- Page table contention, single-threaded page eviction, and TLB shootdowns become bottlenecks
2 - complexity? this is simply false. LMDB's ACID txns using MVCC are much simpler than any "traditional" approach.
3 - contention is a red herring since this approach is already single-writer, as is common for most embedded k/v stores these days. You lose more perf by trying to make the write path multi-threaded, in lock contention and cache thrashing.
Our experience with OpenLDAP was that multi-writer concurrency cost too much overhead. Even though you may be writing primary records to independent regions of the DB, if you're indexing any of that data (which all real DBs do, for query perf) you wind up getting a lot of contention in the indices. That leads to row locking conflicts, txn rollbacks, and retries. With a single writer txn model, you never get conflicts, never need rollbacks.
http://www.lmdb.tech/bench/hyperdex/
RAM is relatively cheap too, there's no real reason to be running multi-TB databases at greater than a 50x ratio.
> Now that the total database is 50 times larger than RAM, around half of the key lookups will require a disk I/O.
That is an insanely high cache hit rate, which should have probably set off your "unrepresentative benchmark" detector. I am also a little surprised at the lack of a random writes benchmark. I get that this is marketing material, though.
Eh? This was 20% random writes, 80% random reads. LMDB is for read-heavy workloads.
> That is an insanely high cache hit rate, which should have probably set off your "unrepresentative benchmark" detector.
No, that is normal for a B+tree; the root page and most of the branch pages will always be in cache. This is why you can get excellent efficiency and performance from a DB without tuning to a specific workload.
The page says "updates," not "writes." Updates are a constrained form of write where you are writing to an existing key. Updates, importantly, do not affect your index structure, while writes do.
> No, that is normal for a B+tree; the root page and most of the branch pages will always be in cache. This is why you can get excellent efficiency and performance from a DB without tuning to a specific workload.
It is normal for a small B+tree relative to the memory size available on the machine. The "small" was the unrepresentative part of the benchmark, not the "B+tree."
OK, I see your point. It would only have made things even worse for LevelDB here to do an Add/Delete workload because its garbage compaction passes would have had to do a lot more work.
> It is normal for a small B+tree relative to the memory size available on the machine. The "small" was the unrepresentative part of the benchmark, not the "B+tree."
This was 100 million records, and a 5-level deep tree. To get to 6 levels deep it would be about 10 billion records. Most of the branch pages would still fit in RAM; most queries would require at most 1 more I/O than the 5-level case. The cost is still better than any other approach.
This only works on systems with sufficiently slow storage. If your server has a bunch of NVMe, which is a pretty normal database config these days, you will be hard-pressed to get anywhere close to the theoretical throughput of the storage with a single writer. That requires 10+ GB/s sustained. It is a piece of cake with multiple writers and a good architecture.
Writes through indexing can be sustained at this rate (assuming appropriate data structures), most of the technical challenge is driving the network at the necessary rate in my experience.
> The database size for one warehouse is approximately 100 MB (we experiment with five warehouses for a total size of 500MB).
It is not surprising that when your database basically fits in RAM, serializing on one writer is worth doing, because it just plainly reduces contention. You basically gain nothing in a DB engine from multi-writer transactions when this is the case. A large part of a write (the vast majority of write latency) in many systems with a large database comes from reading the index up to the point where you plan to write. If that tree is in RAM, there is no work here, and you instead incur overhead on consistency of that tree by having multiple writers.
I'm not suggesting that these results are useless. They are useful for people whose databases are small because they are meaningfully better than RocksDB/LevelDB which implicitly assume that your database is a *lot* bigger than RAM.
Where are you getting that assumption from? LevelDB was built to be used in Google Chrome, not for multi-TB DBs. RocksDB was optimized specifically for in-memory workloads.
RocksDB is Facebook's offshoot of LevelDB, basically keeping the core architecture of the storage engine (but multithreading it), and is used internally at Facebook as the backing store for many of their database systems. I have never heard from anyone that RocksDB was optimized for in-memory workloads at all, and I think most benchmarks can conclusively say the opposite: both of those DB engines are pretty bad for workloads that fit in memory.
Was a PITA to optimise though; tons of options and little insight into which ones work.
Pretty much all storage libraries written in the past couple of decades are using single writer. Note that single writer doesn't mean single transaction. Merging transactions is easy and highly profitable, after all.
No "mainstream" database I'm aware of has a global single writer design.
Excuse me for a silly question, but whilst an I/O stall may be unavoidable, wouldn't a thread stall be avoidable if you're not using mmap?
Assuming that you're not swapping, you'll generally know if you've loaded something into memory or not, whilst mmap doesn't help you know if the relevant page is cached. If the data isn't in memory, you can send the I/O request to a thread to retrieve it, and the initiating thread can then move onto the next connection. I suspect this isn't doable under mmap based access?
We shouldn't apply a higher bar to the counterargument than we applied to the argument in the first place.
Interestingly, most of the reason for these problems has to do with theoretical limitations of cache replacement algorithms as drivers of I/O scheduling. There are alternative approaches to scheduling I/O that work much better in these cases but mmap() can’t express them, so in those cases bypassing mmap() offers large gains.
<<<There is one significant drawback that should not be understated. Algorithm design using topology manipulation can be enormously challenging to reason about. You are often taking a conceptually simple algorithm, like a nested loop or hash join, and replacing it with a much more efficient algorithm involving the non-trivial manipulation of complex high-dimensionality constraint spaces that effect the same result. Routinely reasoning about complex object relationships in greater than three dimensions, and constructing correct parallel algorithms that exploit them, becomes easier but never easy.>>>
There's nothing special about kernel programmers. In fact, if I had to compare, I'd go with storage people being the more experienced / knowledgeable ones. They have a highly competitive environment, which requires a lot more understanding and inventiveness to succeed, whereas kernel programmers proper don't compete -- Linux won many years ago. Kernel programmers who deal with stuff like drivers or various "extensions" are, largely, in the same group as storage (often time literally the same people).
As for "single process" argument... well, if you run a database inside an OS, then, obviously, that will never happen as OS has its own processes to run. But, if you ignore that -- no DBA worth their salt would put database in the environment where it has to share resources with applications. People who do that are, probably, Web developers who don't have high expectations from their database anyways and would have no idea how to configure / tune it for high performance, so, it doesn't matter how they run it, they aren't the target audience -- they are light years behind on what's possible to achieve with their resources.
This has nothing to do with mmap though. mmap shouldn't be used for storage applications for other reasons. mmap doesn't allow their users to precisely control the persistence aspect... which is kind of the central point of databases. So, it's a mostly worthless tool in that context. Maybe fine for some throw-away work, but definitely not for storing users' data or database's own data.
Yes, that was a shorthand generalization for "people who've studied computer architecture" - which most application developers never have.
> no DBA worth their salt would put database in the environment where it has to share resources with applications.
Most applications today are running on smartphones/mobile devices. That means they're running with local embedded databases - it's all about "edge computing". There's far more DBs in use in the world than there are DBAs managing them.
> mmap shouldn't be used for storage applications for other reasons. mmap doesn't allow their users to precisely control the persistence aspect... which is kind of the central point of databases. So, it's a mostly worthless tool in that context. Maybe fine for some throw-away work, but definitely not for storing users' data or database's own data.
Well, you're half right. That's why by default LMDB uses a read-only mmap and uses regular (p)write syscalls for writes. But the central point of databases is to be able to persist data such that it can be retrieved again in the future, efficiently. And that's where the read characteristics of using mmap are superior.
That's patently false. There are about 8 bn. people. Even if everyone has a smartphone or two, it's nothing compared to the total of all devices that can be called "computer". I think that "smart TV" alone will beat the number of smartphones. But even that is a drop in a bucket when it comes to the total of running programs on Earth / its orbit.
But, that's beside the point. Smartphones aren't designed to run database servers. Even if they indeed were the majority, they'd still be irrelevant for this conversation because they are a wrong platform for deploying databases. In other words, it doesn't matter how people deploy databases to smartphones -- they have no hopes of achieving good performance, and whether they use mmap or not is of no consequences -- they've lost the race before they even qualified for it.
> LMDB
Are we talking about this? https://en.wikipedia.org/wiki/Lightning_Memory-Mapped_Databa... If so, this is irrelevant for databases in general.
> LMDB databases may have only one writer at a time
(Taken from the page above) -- this isn't a serious contender for database server space. It's a toy database. You shouldn't give general advice based on whatever this system does or doesn't.
It's one of the databases compared in the paper
OP is one of the authors of LMDB
It's been a while since I've dealt with mmap(), but isn't this what msync() does? You can synchronously or asynchronously force dirty pages to be flushed to disk without waiting until munmap().
For fun, there is no guarantee in terms of writing a page in what order it is written. SQLite documents that they assume (but cannot verify) that _sector_ writes are linear, but not atomic. https://www.sqlite.org/atomiccommit.html
> If a power failure occurs in the middle of a sector write it might be that part of the sector was modified and another part was left unchanged. The key assumption by SQLite is that if any part of the sector gets changed, then either the first or the last bytes will be changed. So the hardware will never start writing a sector in the middle and work towards the ends. We do not know if this assumption is always true but it seems reasonable.
You are talking several levels higher than that, at the page level (composed of multiple sectors).
Assume that they reside in _different_ physical locations, and are written at different times. That's fun.
> Currently all hard drive/SSD manufacturers guarantee that 512 byte sector writes are atomic. As such, failure to write the 106 byte header is not something we account for in current LMDB releases. Also, failures of this type should result in ECC errors in the disk sector - it should be impossible to successfully read a sector that was written incorrectly in the ways you describe.
Even in extreme cases, the probability of failure to write the leading 128 out of 512 bytes of a sector is nearly nil - even on very old hard drives, before 512-byte sector write guarantees. We would have to go back nearly 30 years to find such a device, e.g.
https://archive.org/details/bitsavers_quantumQuaroductManual...
Page 23, Section 2.1 "No damage or loss of data will occur if power is applied or removed during drive operation, except that data may be lost in the sector being written at the time of power loss."
From the specs on page 15, the data transfer rate to/from the platters is
1.25MB/sec, so the time to write one full sector is 0.4096ms; the time to
write the leading 128 bytes of the sector is thus 1/4 of that: 0.10ms. You
would have to be very very unlucky to have a power failure hit the drive
within this .1ms window of time. Fast-forward to present day and it's simply
not an issue.
Assume 512 sectors ( I know those are rare ), but I don't think that there is any guarantees that 4KB page would be:
* Written atomically * Written in a particular order
If you are developing an DBMS and haven't studied computer architecture, the best idea is probably to ask more experienced people to help out with your ideas.
From my limited knowledge, I don't think the article is old enough to be obsolete, just that there's a lot more to it.
Not to be gatekeeping or anything, but it is a pretty well studied field with lots of very knowledgeable people around, who are probably more than keep to help. There aren't too many qualified jobs around and you probably have a budget if you are developing a database commercially.
The article is about DBMS developers. For DBMS developers, "in practice" (a) and (b) are usually true I think.
mmap works fine with small working sets.
Where did you look? This is a sample using DB 5x and 50x larger than RAM http://www.lmdb.tech/bench/hyperdex/
There are plenty of other larger-than-RAM benchmarks there.
Taking full control of your I/O and buffer management is great if (a) your developers are all smart and experienced enough to be kernel programmers and (b) your DBMS is the only process running on a machine. In practice, (a) is never true, and (b) is no longer true because everyone is running apps inside containers inside shared VMs. In the modern application/server environment, no user level process has accurate information about the total state of the machine, only the kernel (or hypervisor) does and it's an exercise in futility to try to manage paging etc at the user level.
As Dr. Michael Stonebraker put it: The Traditional RDBMS Wisdom is (Almost Certainly) All Wrong. https://slideshot.epfl.ch/play/suri_stonebraker (See the slide at 21:25 into the video). Modern DBMSs spend 96% of their time managing buffers and locks, and only 4% doing actual useful work for the caller.
Granted, even using mmap you still need to know wtf you're doing. MongoDB's original mmap backing store was a poster child for Doing It Wrong, getting all of the reliability problems and none of the performance benefits. LMDB is an example of doing it right: perfect crash-proof reliability, and perfect linear read scalability across arbitrarily many CPUs with zero-copy reads and no wasted effort, and a hot code path that fits into a CPU's 32KB L1 instruction cache.