2017-01-18 Speeding up a distributed computation in Haskell

This blog post originally appeared on the FP Complete blog.


While helping a client ship a medical device we were tasked to make its response time bearable. This was no easy feat, given that each request to this device requires running a simulation that takes hours if ran on a single CPU. This long response time would make it impossible for doctors to use this device interactively, which in turn would make the device much less desirable – think of a doctor having to wait hours between inputting the patient data and getting results, as opposed to getting results immediately as the data is available.

Luckily the simulations in question are embarrassingly parallel, and thus one obvious path to reduce the response time is to run it on multiple CPUs.

At the core of this device sits a Haskell program that performs the simulation. Thus the first step was to exploit Haskell built-in multi-core parallelism to achieve the parallelization. However the results were unsatisfactory, since we were unable to scale decently beyond 7 to 10 CPUs. Thus we created a custom distribution algorithm where separate Haskell runtimes communicate with TCP sockets, similar to what happens in Erlang. This also allowed us to scale beyond a single machine. We’ve described this effort in the past, see the report Scaling Up a Scientific Computation and the talk Parallelizing and distributing scientific software in Haskell.

This first effort allowed us to run simulations in a much shorter time, but it still did not allow us to scale nicely to hundreds of CPUs. This article describes how we fixed that by bypassing one of the high level facilities that Haskell provides.

High level languages are all about offering such facilities, to be able to write correct programs quicker. Haskell offers a great number of abstractions to help in this regard, such as garbage collection and laziness, and GHC also is full of tools on top of the language itself to write an ever greater number of programs in a more comfortable way.

One of the features that makes GHC stand out is the sophistication of the runtime it provides. Apart from being an impressive piece of work even just for implementing Haskell efficiently, it also offers features that are very useful for the kind of systems programming that writing a distributed application requires. Specifically, green threads and the GHC event manager make writing a fast multi-threaded server much easier than in other languages. For example the first versions of Warp, Haskell’s most popular web server, outperformed most web servers in just 500 lines of code, largely thanks to these facilities.1 Warp has since grown in code size to add new features, but the core is still using the same facilities and performing well.

Since the core of the software that we built is a server coordinating the work of many slaves, for our first version we reached for these facilities to write it. The server was reasonably fast and served us for a while, but we hit a ceiling pretty quickly beyond which we were unable to scale.

However, a nice thing about GHC Haskell is that it’s very easy to drop down to a lower level programming style when needed. This can be accomplished through the excellent foreign function interface to C paired with the low-level utilities in base. By doing so we were able to scale to hundreds of cores and run simulations up to 5 times faster then the best time we achieved with the previous version.

The program

As mentioned, the server in question is the master process in a distributed computing application. The application is essentially a particle filter, distributed across many processes which might be on different machines. Since we want multi-machine distribution, we use TCP sockets to communicate between the processes doing the computation.

At the core of the program logic we have a function taking some State and some Input, and generating some new states and an output associated with each one:

type Evolve = State -> Input -> [(State, Output)]

Note that a single state and input pair generates multiple states and output.2 We need to run one such function on thousands of inputs:

-- Apply the `Evolve` to every given `State`, return
-- the new states and output.
evolveMany :: Evolve -> [State] -> [Input] -> [[(State, Output)]]
evolveMany f = zipWith f

Given this initial specification, there are a couple of adjustments we need to make if we want to be able to distribute the computation. First, the function will have to live in IO, since communication will happen through Sockets. Second, we won’t refer to the states directly, but rather refer to them using tokens provided by the system. At the beginning we’ll provide the initial states and get back tokens in result, and at each call to evolveMany we’ll get – instead of new States – new tokens.

We can do this because we do not care about the content of the states (while we care about the outputs) and referring to them with tokens rather than directly we can avoid transferring them to other processes each time we need to operate on them, saving a lot of bandwidth and speeding up the computation greatly.

Thus, we’ll also need to book-keep which slave processes are holding which state.

Finally, we’ll need Sockets to communicate with the slave processes.

This gives us a new API:

-- We use `Map` and `Set` from `containers` for illustrative purposes, `HashMap`
-- from `unordered-containers` or a mutable hash table from `hashtables`
-- will most likely be more performant.
import Data.Map (Map)
import qualified Data.Map as Map
import Data.Set (Set)
import qualified Data.Set as Set

-- Some token representing a `State` on some slave.
data StateId

-- Some token representing a slave.
data SlaveId

-- Reset the states in the system to the given ones, returns a
-- 'StateId' for each state.
resetStates ::
     Map SlaveId Socket -- Connection to the slaves
  -> [State]
  -> IO (Map SlaveId (Set StateId), [StateId])
  -- Returns how the states have been repartitioned on the slaves
  -- and a list to know which `StateId` corresponds to which `State`.

-- Evolves the states with the given inputs, returns the outputs and
-- the new 'StateId's resulting from the evolution. 
evolveMany ::
     Map SlaveId Socket -- Connections to the slaves
  -> Map SlaveId (Set StateId) -- Which states are on which slave
  -> Map StateId Input -- Inputs to each state
  -> IO (Map SlaveId (Set StateId), Map StateId [(StateId, Output)])
  -- Returns the new mapping from slaves to states, and
  -- the outputs.

When using this API, the usual pattern is to call resetStates at the beginning with the initial states and then a series of evolveMany afterwards, each using the StateIds returned from resetStates the first time and evolveMany afterwards.

The challenge is to implement evolveMany as efficiently as possible.

To give an idea of the time involved, we usually have around 2000 states, a few tens of calls to evolveMany, and each call to Evolve takes a few tenths of seconds to complete, giving a single-threaded run time of a few hours, e.g.

 2000 * -- Number of states
   80 * -- number of calls to evolveMany
0.03s = -- Evolve time 
1h 20m  -- Total running time

High level overview of the implementation

resetStates just assigns a unique StateId to each state, and then splits up and uploads the states evenly between the slaves.

All the complexity lies in evolveMany: the goal is to utilize the slaves as efficiently as possible.

We found pretty early that naively evolving the states present on each slave would not work, because:

More concretely, imagine a situation with 10 states, where 9 of the states take 1 second while there is an odd state that takes 10 seconds. If we have 2 slaves at our disposal, the most efficient distribution is to assign the slow state to one slave, and all the others to another slave, with one slave taking 10 seconds and the other taking 9. If we just distribute the states evenly between the slaves, 1 slave will take 14 seconds and one 5. Since the total runtime will be constrained by the slowest slave, we must be careful to avoid such long tails.

So we switched to a simple but effective method to utilize the slaves efficiently. The master process keeps track of the states present on each slave, and asks the slaves to process them in batches, say of 5. When a slave finishes its batch, it sends the output back to the master and waits for further instructions. If the slave still has states to evolve, the master sends a request for a new batch to be evolved. If the slave does not have states to update the master will search for a slave with states to spare, and request them. When a slave receives such a request it sends back the states to the master, which will forward them to the needy slave. When there are no more states to update, evolveMany is done.

The algorithm can be summed up as two state machines, one for the master and one for the slave:

-- This is what the master sends to the slave.
data Request
  -- Evolve the selected states
  = EvolveStates [StateId]
  -- Add the given states
  | AddStates [(StateId, State)]
  -- Remove the requested states, and return them to the master
  | RemoveStates [StateId]

-- This is what the slaves reply to the master.
data Response
  = StatesEvolved [(StateId, [(StateId, Output)])]
  | StatesAdded
  | StatesRemoved [(StateId, State)]

-- The slave has a set of `State`s indexed by `StateId`, and it updates
-- it at each request from the master.
slaveStateMachine :: Map StateId State -> Request -> (Map StateId State, Response)

-- Some type to refer to slaves uniquely.
data SlaveId

-- The master keeps track of which states each slave has, and will update
-- it. It also records the outputs we have received from the slaves so far.
data MasterState = MasterState
  { msSlavesStates :: Map SlaveId (Set StateId)
  , msStatesToEvolve :: Map StateId Input
  , msEvolvedStates :: Map StateId [(StateId, Output)]
  }

-- At each response from a slave the master updates its state and then
-- might reply with a new `Request`. Note that the `Request` might not
-- be directed at the same slave that sent the `Response`, since sometimes
-- we need to steal slaves from other slaves since the slave at hand does
-- not have states to update.
masterStateMachine ::
     MasterState -> SlaveId -> Response
  -> (MasterState, Maybe (SlaveId, Request))

The most common pattern of interaction between slave and master will be of a loop of EvolveStates and StatesEvolved:

EvolveStates and StatesEvolved

This interaction between slave and master will continue until one slave will runs out of states to evolve. In that case, the master will have to reach out to some other slave to be able to provide the needy slave with something to evolve. For example, this is what will happen if slave 3 runs out of states and the master decides to ship some states to it from slave 2:

Running out of states

The exact implementation of the state machines is not relevant, but given their types what’s to note is that:

First attempt, and performance

Now that we have abstracted out the logic of the master and the slaves in self-contained state machines, we can describe the slave and master processes. We’ll assume IO functions to send and receive messages.

The slave implementation is trivial and won’t change:

-- These functions will use `recv`/`send` to work with the `Socket`s,
-- and the `store` library to efficiently deserialize and serialize
-- the requests and responses.
receiveRequest :: Socket -> IO Request
sendResponse :: Socket -> Response -> IO ()

slave ::
     Socket -- Connection to master
  -> IO a
slave sock = loop mempty -- No states at the beginning
  where
    loop :: Map StateId State -> IO (Map StateId State)
    loop states = do
      req <- receiveFromMaster sock
      (states', resp) <- slaveStateMachine states req
      sendToMaster sock resp

Note that a slave process is not bound to a single call to evolveMany, it just takes requests from a master.

The master on the other hand is essentially the implementation of evolveMany, and we have a lot more options to implement it. Our first version is a pretty idiomatic Haskell program, using one thread per slave so that we can wait on all of them at once, with the master state stored in an MVar that can be accessed from all the slave threads:

First implementation

Each slave thread will run code waiting on a slave, modifying the shared state using the master state machine:

import Control.Concurrent.MVar

receiveResponse :: Socket -> IO Response
sendRequest :: Socket -> Request -> IO ()

-- Terminates when there is nothing left to do.
slaveThread :: Map SlaveId Socket -> MVar MasterState -> SlaveId -> IO ()
slaveThread slaveSockets masterStateVar slaveId = do
  resp <- receiveResponse (slaveSockets Map.! slaveId)
  (masterState, mbReq) <- modifyMVar masterStateVar $ \masterState ->
    let (masterState', mbReq) =
          masterStateMachine masterState slaveId resp
    return (masterState', (masterState', mbReq))
  -- Send the request if needed
  mapM_
    (\(slaveId, req) -> sendRequest (slaveSockets Map.! slaveId) req)
    mbReq 
  -- Continue if there are still slates to evolve
  unless (Map.null (msStatesToEvolve masterState)) $
    slaveThread masterStateVar slaveId

-- Runs the provided actions in separate threads, returns as
-- soon as any exists
raceMany_ :: [IO ()] -> IO ()
raceMany_ xs0 = case xs0 of
  -- `race_` is from the `async` package.
  [] -> return ()
  [x] -> x
  x : xs -> race_ x (raceMany_ xs)
 
evolveMany ::
     Map SlaveId Socket
  -> Map SlaveId (Set StateId)
  -> Map StateId Input 
  -> IO (Map SlaveId (Set StateId), Map StateId [(StateId, Output)])
evolveMany slaveSockets slaveStates inputs = do
  masterStateVar <- newMVar MasterState
    { msSlavesStates = slaveStates
    , msStatesToEvolve = inputs
    , msEvolvedStates = mempty
    }
  -- Run one thread per slave until one receives the response
  -- after which there are no states to evolve
  raceMany_ (map (slaveThread masterStateVar) (Map.keys slaveStates))
  -- Return the results in the `MasterState`
  masterState <- readMVar masterStateVar
  return (msSlavesStates masterState, msEvolvedStates masterState)

This implementation is simple and quite obviously correct, and it’s also pretty fast. In fact, we were able to scale up to around 20 slaves quite well with it:

Performance up to 17 slaves, first implementation

Note that both axes for this and every other plot in this article are logarithmic: if we scaled perfectly we’d get a straight line, which we’re pretty close to.

However, things go downhill if we try to scale beyond 20 slaves. Here is a sample of the runtime with up to 450 slaves for six different scenarios:

Performance up to 450 slaves, first implementation

These measurements were all taken on clusters of c4.8xlarge AWS instances with 18 physical cores, with up to 30 machines running at once.3

It’s evident that the distribution does not scale beyond around 40 slaves, and stalls completely between 50 and 100 slaves, after which adding slaves is detrimental to the runtime. Note that for the scenarios taking more time the scaling is better: this is because for those scenarios each individual call to the Evolve function takes longer, and thus the overhead of the distribution is less substantial. This is the case for scenario D, which starts out being the slowest with 17 slaves, taking more than 4000 seconds rather than 800-1000 seconds, but scaling much better.

From this data it was clear that if we wanted to be able to leverage a large number of machines to run our simulations in a minute or less we had to improve the performance of evolveMany.

Small aside: note how these plots contains a line “with taskset” and one without, with the one without performing noticeably worse. The line with taskset indicates measurements taken where each Haskell process is pinned to a physical CPU core: this improves performance substantially compared to letting the kernel schedule them.4 After finding this out we ran all subsequent tests pinning slave processes to physical cores. Hyperthreading was also detrimental to the runtime, since the increased distribution overhead far outweighed the gained CPU time; so we used only one process per physical CPU core and avoided hyperthreading.

Second attempt

By measuring how much time each slave spent working and how much time it spent waiting for instructions from the master, it became clear that the program was getting slower because the slaves spent more and more time waiting for instructions, rather than actually working. Thus, if we wanted proper scaling, we needed to lower the latency between the time a response reached the master and the time the slave received the next request.

Now, we tried to gain conclusive evidence of why our first version of evolveMany is slow, but profiling these sort of applications is quite hard unless you’re intimately familiar with the Haskell runtime – which is almost like saying “if you are Simon Marlow”.

We had however some hypotheses of why our program was slow. One possibility is that the event manager can simply not handle hundreds of connections at the same time efficiently, at least in our use case.

Another suspicion is that the multi-threadedness of the first version played at our disadvantage since there would be a lot of pointless context-switches while one thread was already modifying the MVar MasterState. In other words, any context switch between slave threads while one slave thread is already holding the MVar MasterState is (almost) wasted, since it’ll be blocked on the MVar MasterState right after receiving a slave response and will yield, delaying the completion of the loop body in the thread that was already processing the MasterState.

While our second version was based on these hypotheses we were quite short on time and did not want to take the risk of rewriting the program to find that we still could not scale as we desired. Thus, we set ourselves to write the fastest possible version of evolveMany that we could think of.

The main change we wanted was to turn the server from a multi-threaded server multiplexing through the event manager to a single-threaded application multiplexing the sockets directly.

In Linux, the epoll set of syscalls exist for this exact reason: you can register multiple sockets to wait on with epoll_ctl, and then wait for any of them to be ready using epoll_wait.

However in Haskell epoll is abstracted over by the GHC event manager, so there is no library to use these facilities directly. The GHC event manager does offer an interface to it in the form of GHC.Event.registerFd. However all these functions are callback based – they take a function that will be called in a green thread when the socket is ready. Thus we cannot easily write a single threaded program directly using it. If we want to write a single-threaded loop we’re forced to go through an additional synchronization primitive such an MVar to signal that a socket is ready to be read from in the callback provided to registerFd.5 We tried this approach and got no performance improvement.

Thus we decided to just write the loop using epoll directly, which proved very painless given that the GHC codebase already contains bindings to the epoll functions, as part of the event manager. We released a simple library for people that need to do the same, simple-poll. Right now it only supports epoll, and is thus limited to Linux, but it should be easy to extend to other platforms by copy-pasting other bits of code from the GHC event manager.

Updating the old loop to an explicit multiplexing style, we have:

-- `System.Poll.EPoll` comes from the `simple-poll` package
import System.Poll.EPoll (EPoll)
import qualified System.Poll.EPoll as EPoll
import Network.Socket (Socket(MkSocket))
import System.Posix.Types (Fd(Fd))

-- Receives first responses to arrive from any of the slaves.
-- This amounts to calling `EPoll.wait` to get back a list of
-- sockets to read from, and then draining them in turn to
-- decode the `Response`.
-- 
-- Note that draining them might still not give us a response,
-- since the full response might not be available all at once,
-- and thus in the full version of the software this function will have
-- to hold somes state holding partially read messages.
-- 
-- Also note that in the real software it's much better to return
-- a list of `(SlaveId, Response)` pairs. We have it return only
-- one for simplicity.
receiveFromAnySlave ::
     EPoll
  -> Map Fd SlaveId
  -- Reverse lookup table from `Fd`s to `SlaveId`s. We need it
  -- since `EPoll.wait` gives us the `Fd`s which are ready to
  -- be read from, and from that we need to get back which
  -- `SlaveId` it corresponds to, to return it.
  -> IO (SlaveId, Response)

-- Utility to get a file descriptor out of a `Socket`
socketFd :: Socket -> Fd
socketFd (MkSocket fd _ _ _ _) = Fd fd

evolveMany ::
     Map SlaveId Socket -- All the connections to the slaves
  -> Map SlaveId (Set StateId) -- The states held by each slave
  -> Map StateId Input -- The inputs to each state
  -> IO (Map SlaveId (Set StateId), Map StateId [(StateId, Output)])
evolveMany slaveSockets slaveStates inputs = EPoll.with 256 $ \epoll -> do
  -- First register all the sockets with `epoll_ctl`. `epollIn` is to
  -- indicate that we want to be notified when a socket can be read from.
  forM_ slaveSockets $ \socket ->
    EPoll.control epoll Epoll.controlOpAdd (socketFd socket) EPoll.epollIn
  -- Then start the event loop
  masterState <- loop epoll MasterState
    { msSlavesStates = slaveStates
    , msStatesToEvolve = inputs
    , msEvolvedStates = mempty
    }
  return (msSlavesStates masterState, msEvolvedStates masterState)
  where
    fdToSlaveIds :: Map Fd SlaveId
    fdToSlaveIds =
      Map.fromList [(socketFd sock, slaveId) | (slaveId, sock) <- Map.toList slaveSockets]
    
    loop :: EPoll -> MasterState -> IO (Map StateId [(StateId, Output)])
    loop epoll masterState = do
      -- Get a response from some slave
      (slaveId, resp) <- receiveFromAnySlave epoll slaveSockets
      -- Update the state accordingly
      let (masterState', mbResp) =
            masterStateMachine masterState slaveId resp
      -- Send the new requests
      mapM_ (uncurry sendToSlave) mbResp
      -- Continue if we're not done
      unless (Map.null (msStatesToEvolve masterState')) (loop masterState')

Once we did this, the performance increased dramatically, fulfilling our current scaling needs and probably getting quite close to optimal scaling for our use case, although we have not researched what more margin for improvements we have since we do not need them for now.

Going back to the original set of plots, the blue line shows the improved performance with our second implementation:

Improved performance

The plots clearly show a much nicer scaling pattern as the number of slaves increases, and runtimes of often 100 seconds of less, which represent a 2x to 5x improvement compared to the first version.

We also integrated other micro optimizations that yielded less substantial improvements (in the 5 to 10%) range, such as

Conclusion

Our biggest takeaway from this experience is that in Haskell we can have the confidence that we’ll always be able to write the task at hand to be as fast as possible with relative ease. Writing the epoll based version took around a day, including factoring out the bindings from the GHC event manager into a library.

Moreover, it’s important to remember that the normal facilities for fast IO in Haskell (green threads + transparent evented IO) is fast enough for the overwhelming majority of cases, and much easier to manage and think about than manual evented IO. Michael Snoyman recently compared green threads to garbage collection, an apt comparison. Our software is one of the cases where the abstraction prevents performance, and thus we need to work without it.

Finally, it would be great to gain hard evidence on why the first program was slow, rather than just hypotheses. We tried quite hard to understand it but could not reach conclusive evidence in the time we had. We hope to get to the bottom of this issue when we have the time, and maybe make profiling these kind of programs easier in the meantime.

Acknowledgments

The work described was performed with Philipp Kant and Niklas Hambüchen. Thanks to Michael Snoyman, Philipp Kant, and Niklas Hambüchen for reviewing drafts of this blog post.


  1. You can find more info about the Warp web server and how the features that GHC provided enabled it on this report: http://steve.vinoski.net/pdf/IC-Warp_a_Haskell_Web_Server.pdf

  2. The multiple outputs are due to the fact that in a particle filter each state (or rather each “particle”) can be sampled 0 or multiple times.

  3. The benchmarking was automated using terraform, which was invaluable when evaluating the improvements.

  4. Keep in mind that since we’re distributing the work manually using TCP sockets each slave is a separate OS process that runs a dedicated Haskell runtime, which is why it makes sense to pin it to a single core.

  5. Note that the normal blocking read for Haskell sockets is implemented using threadWaitRead, which uses registerFd in exactly this way, by having the callback to fill in an MVar that threadWaitRead will wait on.