I get lost in all the options for parallel computing on the cheap. I summarise for myself here.
My emphasis is strictly on doing large computations. I don’t care about serving webpages or streaming your videos or whatever.
Fashion dictates this should be “cloud” computing, although I’m also interested in using the same methods without a cloud, as such. In fact, I would prefer frictionless switching between such things according to debugging and processing power needs.
Emphasis for now is on embarrassingly parallel computation, which is what I as a statistician mostly do. Mostly in python, sometimes in other things. That is, I run many calculations/simulations with absolutely no shared state and aggregate them in some way at the end. This avoids much of graph computing complexity.
Let’s say, I want “easy, optionally local, shared-nothing parallel computing”.
Additional material to this theme under scientific computation workflow (for the actual job management software) and stream processing. I might need to consider how to store my data.
Algorithms, implementations thereof, and providers of parallel processing services are all coupled closely. Nonetheless I’ll try to draw a distinction between the three.
Since I am not a startup trying to do machine-learning on the cheap, but a grad student implementing algorithms, it’s essential what whatever I use can get me access “under the hood”; I can’t just hand in someone else’s library as my dissertation.
airflow is Airbnb’s hybrid parallel-happy workflow tool:
While you can get up and running with Airflow in just a few commands, the complete architecture has the following components:
- The job definitions, in source control.
- A rich CLI (command line interface) to test, run, backfill, describe and clear parts of your DAGs.
- A web application, to explore your DAGs’ definition, their dependencies, progress, metadata and logs. The web server is packaged with Airflow and is built on top of the Flask Python web framework.
- A metadata repository, typically a MySQL or Postgres database that Airflow uses to keep track of task job statuses and other persistent information.
- An array of workers, running the jobs task instances in a distributed fashion.
- Scheduler processes, that fire up the task instances that are ready to run.
SystemML created by IBM, now run by the Apache Foundation:
SystemML provides declarative large-scale machine learning (ML) that aims at flexible specification of ML algorithms and automatic generation of hybrid runtime plans ranging from single-node, in-memory computations, to distributed computations on Apache Hadoop and Apache Spark.
Tensorflow is the hot new Google one, coming from the training of artificial neural networks, but more broadly applicable. See my notes It handles general optimisation problems, especially for neural networks. Listed here as a parallel option because it has some parallel support, especially on google’ own infrastructure.. C++/Python.
Turi (formerly Dato (formally Graphlab)) claims to automate this stuff, using their own libraries, which are a little… opaque. (update - recently they opensourced a bunch so perhaps this has changed?) They have similar, but not identical, APIs to python’s scikit-learn. Their (open source) Tensorflow competitor mxnet claims to the the fastest thingy ever times whatever you said plus one.
…an open-source cluster computing framework originally developed in the AMPLab at UC Berkeley. […]By allowing user programs to load data into a cluster’s memory and query it repeatedly, Spark is well suited to machine learning algorithms.
Spark requires a cluster manager and a distributed storage system. […] Spark also supports a pseudo-distributed mode, usually used only for development or testing purposes, where distributed storage is not required and the local file system can be used instead; in the scenario, Spark is running on a single machine with one worker per CPU core.
Spark had over 465 contributors in 2014, making it the most active project in the Apache Software Foundation and among Big Data open source projects.
Sounds lavishly well-endowed with a community. Not an option for me, since the supercomputer I use has its own weird proprietary job management system. Although possibly I could set up temporary multiprocess clusters on our cluster? It does support python, for example.
- Standalone – a simple cluster manager included with Spark that makes it easy to set up a private cluster.
- Apache Mesos – a general cluster manager that can also run Hadoop MapReduce and service applications.
- Hadoop YARN – the resource manager in Hadoop 2.
- basic EC2 launch scripts for free, btw
Interesting application: Communication-Efficient Distributed Dual Coordinate Ascent (CoCoA):
By leveraging the primal-dual structure of these optimization problems, COCOA effectively combines partial results from local computation while avoiding conflict with updates simultaneously computed on other machines. In each round, COCOA employs steps of an arbitrary dual optimization method on the local data on each machine, in parallel. A single update vector is then communicated to the master node.
i.e. cunning optimisation stunts to do efficient distribution of optimisation problems over various machines.
Spark integrates with scikit-learn via spark-sklearn:
This package distributes simple tasks like grid-search cross-validation. It does not distribute individual learning algorithms (unlike Spark MLlib).
i.e. this one is for when your data fits in memory, but the optimisation over hyperparameters needs to be parallelised.
Dataflow/Beam is google’s job handling as used in google cloud (see below), but they open-sourced this bit. Comparison with spark. The claim has been made that Beam subsumes Spark. It’s not clear how easy it is to make a cluster of these things, but it can also use Apache Spark for processing. Here’s an example using docker. Java only, for now.
dispy is a comprehensive, yet easy to use framework for creating and using compute clusters to execute computations in parallel across multiple processors in a single machine (SMP), among many machines in a cluster, grid or cloud. dispy is well suited for data parallel (SIMD) paradigm where a computation (Python function or standalone program) is evaluated with different (large) datasets independently with no communication among computation tasks (except for computation tasks sending Provisional/Intermediate Results or Transferring Files to the client
dask seems to parallelize certain python tasks well and claims to scale up elastically. It’s purely for python.
Thunder does time series and image analysis - seems to be a python/spark gig specialising in certain operations but at scale:
Spatial and temporal data is all around us, whether images from satellites or time series from electronic or biological sensors. These kinds of data are also the bread and butter of neuroscience. Almost all raw neural data consists of electrophysiological time series, or time-varying images of fluorescence or resonance.
Thunder is a library for analyzing large spatial and temporal data. Its core components are:
- Methods for loading distributed collections of images and time series data
- Data structures and methods for working with these data types
- Analysis methods for extracting patterns from these data
It is built on top of the Spark distributed computing platform. The API is broadly organized into:
Not clear how easy it is to extend to do more advanced operations.
The Tessera computational environment is powered by a statistical approach, Divide and Recombine. At the front end, the analyst programs in R. At the back end is a distributed parallel computational environment such as Hadoop. In between are three Tessera packages: datadr, Trelliscope, and RHIPE. These packages enable the data scientist to communicate with the back end with simple R commands.
Thrill s a C++ framework for distributed Big Data batch computations on a cluster of machines. It is currently being designed and developed as a research project at Karlsruhe Institute of Technology and is in early testing.
Some of the main goals for the design are:
- To create a high-performance Big Data batch processing framework.
- Expose a powerful C++ user interface, that is efficiently tied to the framework’s internals. The interface supports the Map/Reduce paradigm, but also versatile “dataflow graph” style computations like Apache Spark or Apache Flink with host language control flow.[…]
- Leverage newest C++11 and C++14 features like lambda functions and auto types to make writing user programs easy and convenient.
- Enable compilation of binary programs with full compile-time optimization runnable directly on hardware without a virtual machine interpreter. Exploit cache effects due to less indirections than in Java and other languages. Save energy and money by reducing computation overhead.
- Due to the zero-overhead concept of C++, enable applications to process small datatypes efficiently with no overhead.
Computation node suppliers
- Cloud, n.
- A place of terror and dismay, a mysterious digital onslaught, into which we all quietly moved.
- A fictitious place where dreams are stored. Once believed to be free and nebulous, now colonized and managed by monsters. See ‘Castle in the Air’.[…]
- […] other peoples’ computers
via Bryan Alexander’s Devil’s Dictionary of educational computing
If you want a GPU this all becomes incredibly tedious. Anyway…
Sciencecluster claims fast and easy deployment too.
databricks, spun off from the apache spark team, does automated spark deployment. The product looks tasty, but has a crazy high baseline rate for a solo seveloper of USD99/month
Amazon has stepped up the ease of doing this recently. See my Amazon Cloud notes
Google cloud might interoperate well with a bunch of google products, such as Tensorflow, although it has weirdnesses like relying on esoteric google APIs so it’s hard to do offline. See my google cloud notes.
yhat aims at deploying real-timeish analytics for large scale production use; the marketing folks have got at their front page and made their precise product offerings impossibly hard to discern. It’s possible they sell flash animation about machine learning services rather than actual machine learning services.
Oh wait, there are yhat docs hidden two links deep. Looks like they especially do model-prediction calls? But this is frustrating if the bottleneck is fitting the model, surely? And isn’t that usually the bottleneck? Confused.
Turi is also in this business, I think? I’ve grown tired of trying to keep track of their doohickeys. I’m sure they are lovely.
Parallel tasks on your awful ancient “High Performance” computing cluster that you hate but your campus spent lots of money on and it IS free so uh…
hanythingondemand provides a set of scripts to easily set up an ad-hoc Hadoop cluster through PBS jobs.
Holy crap, someone procrastinated. Andrea Zonca wrote a script that allows spawning on your PlatformLSF/Torque legacy HPC monstrosity. It’s called remotespawner. This is the most thankless kind of task.
A more ad hoc, probably-slower-but-more-robust approach: Easily distributing a parallel IPython Notebook on a cluster:
Have you ever asked yourself: “Do I want to spend 2 days adjusting this analysis to run on the cluster and wait 2 days for the jobs to finish or do I just run it locally with no extra work and just wait a week.”
Why yes, I have.
“Quickly and easily parallelize Python functions using IPython on a cluster, supporting multiple schedulers. Optimizes IPython defaults to handle larger clusters and simultaneous processes.”[…]
ipython-cluster-helper creates a throwaway parallel IPython profile, launches a cluster and returns a view. On program exit it shuts the cluster down and deletes the throwaway profile.
works on on Platform LSF, Sun Grid Engine, Torque, SLURM.
I do not at all understand how you get data back from this; I guess you run it in situ. Strictly python.
Local parallel tasks with pytyhon.
See also build tools.
pathos is one general tool here.
ipyparallel is the built-in jupyter option with less pluggability but much ease.
dispy claims to do this too.
You could also launch spark jobs.