Dask for Institutions

Datetime:2016-08-23 05:29:14          Topic: DataBase           Share

This work is supported by Continuum Analytics

tl;dr

Institutions use software differently than individuals. Over the last few months I’ve had dozens of conversations about using Dask within larger organizations like universities, research labs, private companies, and non-profit learning systems. This post provides a very coarse summary of those conversations and extracts common questions. I’ll then try to answer those questions.

Note: some of this post will be necessarily vague at points. Some companies prefer privacy. All details here are either in public Dask issues or have come up with enough institutions (say at least five) that I’m comfortable listing the problem here.

Common story

Institution X, a university/research lab/company/… has many scientists/analysts/modelers who develop models and analyze data with Python, the PyData stack like NumPy/Pandas/SKLearn, and a large amount of custom code. These models/data sometimes grow to be large enough to need a moderately large amount of parallel computing.

Fortunately, Institution X has an in-house cluster acquired for exactly this purpose of accelerating modeling and analysis of large computations and datasets. Users can submit jobs to the cluster using a job scheduler like SGE/LSF/Mesos/Other.

However the cluster is still under-utilized and the users are still asking for help with parallel computing. Either users aren’t comfortable using the SGE/LSF/Mesos/Other interface, it doesn’t support sufficiently complex/dynamic workloads, or the interaction times aren’t good enough for the interactive use that users appreciate.

There was an internal effort to build a more complex/interactive/Pythonic system on top of SGE/LSF/Mesos/Other but it’s not particularly mature and definitely isn’t something that Institution X wants to pursue. It turned out to be a harder problem than expected to design/build/maintain such a system in-house. They’d love to find an open source solution that was well featured and maintained by a community.

The Dask.distributed scheduler looks like it’s 90% of the system that Institution X needs. However there are a few open questions:

  • How do we integrate dask.distributed with the SGE/LSF/Mesos/Other job scheduler?
  • How can we grow and shrink the cluster dynamically based on use?
  • How do users manage software environments on the workers?
  • How secure is the distributed scheduler?
  • Dask is resilient to worker failure, how about scheduler failure?
  • What happens if dask-worker s are in two different data centers? Can we scale in an asymmetric way?
  • How do we handle multiple concurrent users and priorities?
  • How does this compare with Spark?

So for the rest of this post I’m going to answer these questions. As usual, few of answers will be of the form “Yes Dask can solve all of your problems.” These are open questions, not the questions that were easy to answer. We’ll get into what’s possible today and how we might solve these problems in the future.

How do we integrate dask.distributed with SGE/LSF/Mesos/Other?

It’s not difficult to deploy dask.distributed at scale within an existing cluster using a tool like SGE/LSF/Mesos/Other. In many cases there is already a researcher within the institution doing this manually by running dask-scheduler on some static node in the cluster and launching dask-worker a few hundred times with their job scheduler and a small job script.

The goal now is how to formalize this process for the individual version of SGE/LSF/Mesos/Other used within the institution while also developing and maintaining a standard Pythonic interface so that all of these tools can be maintained cheaply by Dask developers into the foreseeable future. In some cases Institution X is happy to pay for the development of a convenient “start dask on my job scheduler” tool, but they are less excited about paying to maintain it forever.

We want Python users to be able to say something like the following:

from dask.distributed import Executor, SGECluster

c = SGECluster(nworkers=200, **options)
e = Executor(c)

… and have this same interface be standardized across different job schedulers.

How can we grow and shrink the cluster dynamically based on use?

Alternatively, we could have a single dask.distributed deployment running 24/7 that scales itself up and down dynamically based on current load. Again, this is entirely possible today if you want to do it manually (you can add and remove workers on the fly) but we should add some signals to the scheduler like the following:

  • “I’m under duress, please add workers”
  • “I’ve been idling for a while, please reclaim workers”

and connect these signals to a manager that talks to the job scheduler. This removes an element of control from the users and places it in the hands of a policy that IT can tune to play more nicely with their other services on the same network.

How do users manage software environments on the workers?

Today Dask assumes that all users and workers share the exact same software environment. There are some small tools to send updated .py and .egg files to the workers but that’s it.

Generally Dask trusts that the full software environment will be handled by something else. This might be a network file system (NFS) mount on traditional cluster setups, or it might be handled by moving docker or conda environments around by some other tool like knit for YARN deployments or something more custom. For example Continuum sells proprietary software that does this.

Getting the standard software environment setup generally isn’t such a big deal for institutions. They typically have some system in place to handle this already. Where things become interesting is when users want to use drastically different environments from the system environment, like using Python 2 vs Python 3 or installing a bleeding-edge scikit-learn version. They may also want to change the software environment many times in a single session.

The best solution I can think of here is to pass around fully downloaded conda environments using the dask.distributed network (it’s good at moving large binary blobs throughout the network) and then teaching the dask-worker s to bootstrap themselves within this environment. We should be able to tear everything down and restart things within a small number of seconds. This requires some work; first to make relocatable conda binaries (which is usually fine but is not always fool-proof due to links) and then to help the dask-workers learn to bootstrap themselves.

Somewhat related, Hussain Sultan of Capital One recently contributed a dask-submit command to run scripts on the cluster: http://distributed.readthedocs.io/en/latest/submitting-applications.html

How secure is the distributed scheduler?

Dask.distributed is incredibly insecure. It allows anyone with network access to the scheduler to execute arbitrary code in an unprotected environment. Data is sent in the clear. Any malicious actor can both steal your secrets and then cripple your cluster.

This is entirely the norm however. Security is usually handled by other services that manage computational frameworks like Dask.

For example we might rely on Docker to isolate workers from destroying their surrounding environment and rely on network access controls to protect data access.

Because Dask runs on Tornado, a serious networking library and web framework, there are some things we can do easily like enabling SSL, authentication, etc.. However I hesitate to jump into providing “just a little bit of security” without going all the way for fear of providing a false sense of security. In short, I have no plans to work on this without a lot of encouragement. Even then I would strongly recommend that institutions couple Dask with tools intended for security. I believe that is common practice for distributed computational systems generally.

Dask is resilient to worker failure, how about scheduler failure?

Workers can come and go. Clients can come and go. The state in the scheduler is currently irreplaceable and no attempt is made to back it up. There are a few things you could imagine here:

  1. Backup state and recent events to some persistent storage so that state can be recovered in case of catastrophic loss
  2. Having a hot failover node that gets a copy of every action that the scheduler takes
  3. Have multiple peer schedulers operate simultaneously in a way that they can pick up slack from lost peers
  4. Have clients remember what they have submitted and resubmit when a scheduler comes back online

Currently option 4 is currently the most feasible and gets us most of the way there. However options 2 or 3 would probably be necessary if Dask were to ever run as critical infrastructure in a giant institution. We’re not there yet.

As of recent work spurred on by Stefan van der walt at UC Berkeley/BIDS the scheduler can now die and come back and everyone will reconnect. The state for computations in flight is entirely lost but the computational infrastructure remains intact so that people can resubmit jobs without significant loss of service.

Dask has a bit of a harder time with this topic because it offers a persistent stateful interface. This problem is much easier for distributed database projects that just run ephemeral queries of off some persistent store, return the results, and then clear out state.

What happens if dask-workers are in two different data centers? Can we scale in an asymmetric way?

The short answer is no. Other than number of cores and available RAM all workers are considered equal to each other (except when the user explicitly specifies otherwise ).

However this problem and problems like it have come up a lot lately. Here are a few examples of similar cases:

  1. Multiple data centers geographically distributed around the country
  2. Multiple racks within a single data center
  3. Multiple workers that have GPUs that can move data between each other easily
  4. Multiple processes on a single machine

Having some notion of hierarchical worker group membership is probably inevitable long term. As with all distributed scheduling questions the hard part isn’t deciding that this is useful, or even coming up with a sensible design, but rather figuring out how to make decisions on the sensible design that are foolproof and operate in constant time. I don’t personally have a good approach here yet.

How do we handle multiple concurrent users and priorities?

There are several sub-questions here:

  • Can multiple users use Dask on my cluster at the same time?

Yes, either by spinning up separate scheduler/worker sets or by sharing the same set.

  • If they’re sharing the same workers then won’t they clobber each other’s data?

This is very unlikely. Dask is careful about naming tasks, so it’s very unlikely that the two users will submit conflicting computations that compute to different values but occupy the same key in memory. However if they both submit computations that overlap somewhat then the scheduler will nicely avoid recomputation. This can be very nice when you have many people doing slightly different computations on the same hardware. This works in the same way that Git works.

  • If they’re sharing the same workers then won’t they clobber each other’s resources?

Yes, this is definitely possible. If you’re concerned about this then you should give everyone their own scheduler/workers (which is easy and standard practice). There is not currently much user management built into Dask.

How does this compare with Spark?

At an institutional level Spark seems to primarily target ETL + Database-like computations. While Dask modules like Dask.bag and Dask.dataframe can happily play in this space this doesn’t seem to be the focus of recent conversations.

Recent conversations are almost entirely around supporting interactive custom parallelism (lots of small tasks with complex dependencies between them) rather than the big Map->Filter->Groupby->Join abstractions you often find in a database or Spark. That’s not to say that these operations aren’t hugely important; there is a lot of selection bias here. The people I talk to are people for whom Spark/Databases are clearly not an appropriate fit. They are tackling problems that are way more complex, more heterogeneous, and with a broader variety of users.

I usually describe this situation with an analogy comparing “Big data” systems to human transportation mechanisms in a city. Here we go:

  • A Database is like a train : it goes between a set of well defined points with great efficiency, speed, and predictability. These are popular and profitable routes that many people travel between (e.g. business analytics). You do have to get from home to the train station on your own (ETL), but once you’re in the database/train you’re quite comfortable.
  • Spark is like an automobile : it takes you door-to-door from your home to your destination with a single tool. While this may not be as fast as the train for the long-distance portion, it can be extremely convenient to do ETL, Database work, and some machine learning all from the comfort of a single system.
  • Dask is like an all-terrain-vehicle : it takes you out of town on rough ground that hasn’t been properly explored before. This is a good match for the Python community, which typically does a lot of exploration into new approaches. You can also drive your ATV around town and you’ll be just fine, but if you want to do thousands of SQL queries then you should probably invest in a proper database or in Spark.

Again, there is a lot of selection bias here, if what you want is a database then you should probably get a database. Dask is not a database.

This is also wildly over-simplifying things. Databases like Oracle have lots of ETL and analytics tools, Spark is known to go off road, etc.. I obviously have a bias towards Dask. You really should never trust an author of a project to give a fair and unbiased view of the capabilities of the tools in the surrounding landscape.

Conclusion

That’s a rough sketch of current conversations and open problems for “How Dask might evolve to support institutional use cases.” It’s really quite surprising just how prevalent this story is among the full spectrum from universities to hedge funds.

The problems listed above are by no means halting adoption. I’m not listing the 100 or so questions that are answered with “yes, that’s already supported quite well”. Right now I’m seeing Dask being adopted by individuals and small groups within various institutions. Those individuals and small groups are pushing that interest up the stack. It’s still several months before any 1000+ person organization adopts Dask as infrastructure, but the speed at which momentum is building is quite encouraging.

I’d also like to thank the several nameless people who exercise Dask on various infrastructures at various scales on interesting problems and have reported serious bugs. These people don’t show up on the GitHub issue tracker but their utility in flushing out bugs is invaluable.

As interest in Dask grows it’s interesting to see how it will evolve. Culturally Dask has managed to simultaneously cater to both the open source science crowd as well as the private-sector crowd. The project gets both financial support and open source contributions from each side. So far there hasn’t been any conflict of interest (everyone is pushing in roughly the same direction) which has been a really fruitful experience for all involved I think.





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