GraphLab Conference 2014 Yucheng Low - Scalable Data Structures: SFrame & SGraph
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GraphLab Create uses a user-first architecture that optimizes for user interaction. It features SFrame for scalable tabular data manipulation and SGraph for scalable graph manipulation. These are built by data scientists for data scientists to easily translate between tabular and graph representations. SFrame uses a columnar format for efficient feature engineering and vectorized operations on large datasets.
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GraphLab Conference 2014 Yucheng Low - Scalable Data Structures: SFrame & SGraph
- 1. The Technology Behind Yucheng Low, PhD Chief Architect GraphLab Create
- 4. Architecture Systems User Systems-First Architectures Systems define constraints. Optimize for performance. PowerGraph
- 5. Architecture Systems User Users-First Architectures Users define constraints. Optimize for user interaction.
- 6. What is a Users-First Architecture for Data Science?
- 7. SFrame and SGraph Building on decades of database and systems research. Built by data scientists, for data scientists.
- 8. SFrame: Scalable Tabular Data Manipulation SGraph: Scalable Graph Manipulation User Com. Title Body User Disc.
- 9. Enabling users to easily and efficiently translate between both representations to get the best of both worlds.
- 10. SFrame: Scalable Tabular Data Manipulation SGraph: Scalable Graph Manipulation User Com. Title Body User Disc.
- 11. SFrame: Scalable Tabular Data Manipulation SGraph: Scalable Graph Manipulation User Com. Title Body User Disc.
- 12. SFrame Design Jobs fail because: • Machine run out of memory • Did not set Java Heap Size correctly • Resource Configuration X needs to be bigger. Pain Point #1: Resource Limits
- 13. SFrame Design • Graceful Degradation as 1st principle • Always Works Pain Point #2: Too Strict or Too Weak Schemas We want strong schema types. We also want weak schema types. Missing Values
- 14. SFrame Design • Graceful Degradation as 1st principle • Always Works • Rich Datatypes • Strong schema types: int, double, string... • Weak schema types: list, dictionary
- 15. SFrame Design • Graceful Degradation as 1st principle • Always Works • Rich Datatypes • Strong schema types: int, double, string... • Weak schema types: list, dictionary Pain Point #3: Feature Manipulation Difficult or costly to inspect existing features and create new features. Hard to perform data exploration.
- 16. SFrame Design • Graceful Degradation as 1st principle • Always Works • Rich Datatypes • Strong schema types: int, double, string... • Weak schema types: list, dictionary • Columnar Architecture • Easy feature engineering + Vectorized feature operations. • Immutable columns + Lazy evaluation • Statistics + visualization + sketches
- 17. SFrame Python API Example Make a little SFrame of 1 column and 5 values: sf = gl.SFrame({‘x’:[1,2,3,4,5]}) Normalizes the column x: sf[‘x’] = sf[‘x’] / sf[‘x’].sum() Uses a python lambda to create a new column: sf[‘x-squared’] = sf[‘x’].apply(lambda x: x*x) Create a new column using a vectorized operator: sf[‘x-cubed’] = sf[‘x-squared’] * sf[‘x’] Create a new SFrame taking only 2 of the columns: sf2 = sf[[‘x’,’x-squared’]]
- 18. SFrame Querying Supports most typical SQL SELECT operations using a Pythonic syntax. SQL SELECT Book.title AS title, COUNT(*) AS authors FROM Book JOIN Book_author ON Book.isbn = Book_author.isbn GROUP BY Book.title; SFrame Python Book.join(Book_author, on=‘isbn’) .groupby(‘title’, {‘authors’:gl.aggregate.COUNT})
- 19. SFrame Columnar Encoding user movie rating Netflix Dataset, 99M rows, 3 columns, ints 1.4GB raw 289MB gzip compressed
- 20. SFrame Columnar Encoding user movie rating Type aware compression: • Variable Bit length Encode • Frame Of Reference Encode • ZigZag Encode • Delta / Delta ZigZag Encode • Dictionary Encode • General Purpose LZ4 Netflix Dataset, 99M rows, 3 columns, ints 1.4GB raw 289MB gzip compressed SFrame File
- 21. SFrame Columnar Encoding user movie rating Type aware compression: • Variable Bit length Encode • Frame Of Reference Encode • ZigZag Encode • Delta / Delta ZigZag Encode • Dictionary Encode • General Purpose LZ4 Netflix Dataset, 99M rows, 3 columns, ints 1.4GB raw 289MB gzip compressed User 176 MB 14.2 bits/int SFrame File 0.02 bits/intMovie 257 KB 3.8 bits/intRating 47 MB ------------------------------- Total 223MB
- 22. SFrame Columnar Encoding user movie rating Type aware compression: • Variable Bit length Encode • Frame Of Reference Encode • ZigZag Encode • Delta / Delta ZigZag Encode • Dictionary Encode • General Purpose LZ4 Netflix Dataset, 99M rows, 3 columns, ints 1.4GB raw 289MB gzip compressed User 176 MB 14.2 bits/int SFrame File 0.02 bits/intMovie 257 KB 3.8 bits/intRating 47 MB ------------------------------- Total 223MB 10s
- 23. SFrames Distributed • Distributed Dataflow • Columnar Query Optimizations • Communicate columnar compressed blocks rather than row tuples. The choice of distributed or local execution is a question of query optimization.
- 24. SFrame: Scalable Tabular Data Manipulation SGraph: Scalable Graph Manipulation User Com. Title Body User Disc.
- 25. SFrame: Scalable Tabular Data Manipulation SGraph: Scalable Graph Manipulation User Com. Title Body User Disc.
- 26. SGraph • SFrame backed graph representation. Inherits SFrame properties. • Data types, External Memory, Columnar, compression, etc. • Layout optimized for batch external memory computation.
- 27. SGraph Layout 1 2 3 4 Vertex SFrames Vertices Partitioned into p = 4 SFrames.
- 28. SGraph Layout 1 2 3 4 Vertex SFrames __id Name Address ZipCode 1011 John … 98105 2131 Jack … 98102 Vertices Partitioned into p = 4 SFrames.
- 29. SGraph Layout 1 2 3 4 Vertex SFrames (1,2) (2,2) (3,2) (4,2) (1,1) (2,1) (3,1) (4,1) (1,4) (2,4) (3,4) (4,4) (1,3) (2,3) (3,3) (4,3) Edge SFrames Edges partitioned into p^2 = 16 SFrames.
- 30. SGraph Layout 1 2 3 4 Vertex SFrames (1,2) (2,2) (3,2) (4,2) (1,1) (2,1) (3,1) (4,1) (1,4) (2,4) (3,4) (4,4) (1,3) (2,3) (3,3) (4,3) Edge SFrames Edges partitioned into p^2 = 16 SFrames.
- 31. SGraph Layout 1 2 3 4 Vertex SFrames (1,2) (2,2) (3,2) (4,2) (1,1) (2,1) (3,1) (4,1) (1,4) (2,4) (3,4) (4,4) (1,3) (2,3) (3,3) (4,3) Edge SFrames Edges partitioned into p^2 = 16 SFrames.
- 37. Deep Integration of SFrames and SGraphs • Seamless interaction between graph data and table data. • Queries can be performed easily across graph and tables.
- 38. Demo
- 39. SFrame: Scalable Tabular Data Manipulation SGraph: Scalable Graph Manipulation User Com. Title Body User Disc. User-first architecture. Built by data scientists, for data scientists.
Editor's Notes
- My name is ... I am one of the co-founders and currently the chief architect at GraphLab. Talk about - architecture philosophy @ graphlab - and what we have built into GraphLab Create.
- The basic architecture philosophy at GraphLab is what I like to call “Users-First” architecture. What do I mean by that?
- The objective of a systems Architecture is to connect systems [] to users []. To provide users with a means to access data, compute resources, and so on.
- And of course, there are many ways to achieve this. [] Some architectures are designed with a bottom up nature: - Given particular systems constraints, what can we perform most efficiently? - Users can then try to develop whatever applications they need around the system.
- Other architectures are designed top down: - We begin by defining an interaction model with users. SQL for instance is a great example. - Then we figure out how to design an architecture that supports all these capabilities efficiently.
- The question we are trying to answer here at GraphLab is: “what is the Users-First Architecture for Data Science? For Machine Learning?” We think we have an answer. ----- Meeting Notes (7/21/14 03:15) ----- 1 min
- We designed two core datastructures we call... <T> Now what are SFrames and SGraphs?
- - SFrame is our scalable datastructure for table manipulation - SGraph is our scalable datastructure for graph manipulation.
- And one design objective is to enable ....
- I am going to first talk about the design of SFrames, our datastructure for table manipulation
- The SFrame design is governed by a series of common pain points we have observed. The first is fundamental. It is *extremely* annoying when we start a job / some task, have it run for a while, then have it fail. [] because... ----- Meeting Notes (7/21/14 03:15) ----- 2 min
- - graceful degradation as the first core principle in the SFrame design - instead of demanding more resources, we try to ensure that things always work even if there is insufficient memory. So we spent a lot of work on developing bounded memory algorithms to ensure that when there is insufficient memory, we might run slower, but we will always work. - We want strong types, because sometimes... It is *very* useful to have a priori guarantees that my “rating column” always contains an integer even in the 1billionth row. - We want weak types because sometime data is unstructured and I need some way to manage it.
- Our SFrames support a rich family of datatypes. From some strong types like int, double, string to weak types like arbitrary lists and dictionaries. Our lists and dictionaries are self-recursive and hence are expressive enough to hold arbitrary JSON. ----- Meeting Notes (7/21/14 03:15) ----- 4 min
- Key aspects of doing ML. I need to create new features, or delete new features. I need to be able to deeply explore a single feature or small sets of features at a time. ----- Meeting Notes (7/21/14 03:22) ----- efficiently create.
- This leads to the SFrame use of a columnar architecture. - By representing the data column-wise, we can support easy feature engineering. - By further using immutable columns and lazy evaluation, we can push through a large number of pipelining optimizations. - easily visualize or sketch statistics about single features
- The API looks somewhat Pandas like, and carry very similar ideas. For instance: It is as easy to load an SFrame with a billion rows as it is to construct a tiny SFrame here of 1 column and 5 values. 2) We can easily reassign the value of an entire column: here we normalize the column by the sum of the values. 3) We can easily create new columns by applying a python lambda operation to each entry. This lambda operation is parallelized behind the scenes 4) We can also create new columns by using the vectorized operators. 5) We can easily subselect columns to create new SFrames, And due to the immutable nature of columns, this operation is essentially free. So The SFrame can be used like a general purpose table, but having a carefully curated set of scalable operations.
- Further more, SFrames supports most of the key important query operators like groupby, join, etc. Most typical SQL Select operations will have a natural conversion to a pythonic syntax using SFrames
- I mentioned columnar architecture briefly in an earlier slide but I did not mention one of the fundamental benefits of columnar encoding: - aggressive compression is possible. But it is hard to understand how much compression can do without an actual demonstration. Data is 99M rows, 3 columns of integers of user, movie and ratings. This is ... Size ... ----- Meeting Notes (7/21/14 03:22) ----- 7 min
- - The SFrame encoder while ingressing the data, adaptively slicing the table up into blocks, targeted at a fixed block size after compression. - For compression, a collection of very high throughput columnar compression techniques are used to reduce the size of the data. Integers are particularly heavily compressed with a family of encoding algorithms. - The on disk SFrame representation ends up as ... (movie is sorted) - The total size is smaller than the gzip compression. - This allows us to do more on one machine. - Aggressive compression allows us to keep more in application cache / file system cache - faster, more throughput even though its external memory. - Oh, how long did it take to read the CSV and encode the entire dataset into an external memory, efficiently queryable SFrame? - 10s on a 4 core desktop. (i73770K )
- - The SFrame encoder while ingressing the data, adaptively slicing the table up into blocks, targeted at a fixed block size after compression. - For compression, a collection of very high throughput columnar compression techniques are used to reduce the size of the data. Integers are particularly heavily compressed with a family of encoding algorithms. - The on disk SFrame representation ends up as ... (movie is sorted) - The total size is smaller than the gzip compression. - This allows us to do more on one machine. - Aggressive compression allows us to keep more in application cache / file system cache - faster, more throughput even though its external memory. - Oh, how long did it take to read the CSV and encode the entire dataset into an external memory, efficiently queryable SFrame? - 10s on a 4 core desktop. (i73770K )
- - The SFrame encoder while ingressing the data, adaptively slicing the table up into blocks, targeted at a fixed block size after compression. - For compression, a collection of very high throughput columnar compression techniques are used to reduce the size of the data. Integers are particularly heavily compressed with a family of encoding algorithms. - The on disk SFrame representation ends up as ... (movie is sorted) - The total size is smaller than the gzip compression. - This allows us to do more on one machine. - Aggressive compression allows us to keep more in application cache / file system cache - faster, more throughput even though its external memory. - Oh, how long did it take to read the CSV and encode the entire dataset into an external memory, efficiently queryable SFrame? - 10s on a 4 core desktop. (i73770K )
- Now a natural question to bring up then is how about going Distributed? We take a somewhat novel perspective on this. The user facing Python API never changes. Instead, - In other words, the decision to go distributed is simply a question of query optimization. - If you are doing something small. It is going to be more efficient locally than to pay the distributed cost. - We are building a distributed dataflow system, taking advantage of columnar query optimizations. And when communication is necessary ,we can get reduce comms by communicating columnar compressed blocks rather than row tuples. ----- Meeting Notes (7/21/14 03:22) ----- 9 min – 10 min
- Next I will talk about SGraphs 10 min
- Our scalable datastructure for graph manipulation
- The layout works this way. Firstly, We partition the set of vertices into a collection of SFrames. This partitioning can be arbitrary, we use a simple hash function. Each vertex Sframe then contains the vertex ID and all the properties associated with the vertices. Note that this is an Sframe and hence the vertex attributes are stored column-wise.
- The layout works this way. Firstly, We partition the set of vertices into a collection of SFrames. This partitioning can be arbitrary, we use a simple hash function. Each vertex Sframe then contains the vertex ID and all the properties associated with the vertices. Note that this is an Sframe and hence the vertex attributes are stored column-wise.
- We next partition the edges into 16 Sframes, The layout is based on the adjacency matrix. For instance, edge partition (2,4) contains all the edges that connect between vertices in partition 2 and vertices in partition 4. This allows for instance, if computation is to be performed on edge partition (2,4), I only need vertex set 2 and vertex 4 in memory.
- We next partition the edges into 16 Sframes, The layout is based on the adjacency matrix. For instance, edge partition (2,4) contains all the edges that connect between vertices in partition 2 and vertices in partition 4. This allows for instance, if computation is to be performed on edge partition (2,4), I only need vertex set 2 and vertex 4 in memory.
- We next partition the edges into 16 Sframes, The layout is based on the adjacency matrix. For instance, edge partition (2,4) contains all the edges that connect between vertices in partition 2 and vertices in partition 4. This allows for instance, if computation is to be performed on edge partition (2,4), I only need vertex set 2 and vertex 4 in memory.
- The magic behind this layout is that ultimately, underlying the Sgraph is Sframes, which is stored in columnar fashion. This representation hence allows us to easily separate structure and data. For instance, we can without any copying, create new Graphs which shares the same structure, but with none of the data.
- The magic behind this layout is that ultimately, underlying the Sgraph is Sframes, which is stored in columnar fashion. This representation hence allows us to easily separate structure and data. For instance, we can without any copying, create new Graphs which shares the same structure, but with none of the data.
- The magic behind this layout is that ultimately, underlying the Sgraph is Sframes, which is stored in columnar fashion. This representation hence allows us to easily separate structure and data. For instance, we can without any copying, create new Graphs which shares the same structure, but with none of the data.
- Or introduce new features without rewriting anything. Finally, since the vertex and edge attributes are all simply Sframes, through a trick of lazy evaluation, we can make the both the vertices and edges appear as a single Sframe to the user.
- Or introduce new features without rewriting anything. Finally, since the vertex and edge attributes are all simply Sframes, through a trick of lazy evaluation, we can make the both the vertices and edges appear as a single Sframe to the user.
- This deep integration of SFrames and SGraphs allow seamless interaction between graph data and table data, and queries can be performed easily across both graphs and tables. Now, this is not so easy to understand just from slides, so I will give a quick demo.
- 13 min
- Now Lets briefly recap what we have just done during the demo. We have taken tabular data, converted it to graph and run a basic graph algorithm on it, and ask graph questions about it. And next we take the graph, and directly interpret it as a table: joining it with other tables to get some intelligence with very little code and very little friction.. All within a few lines of Python. This is what we have achieved by trying to understand data science from a user-first perspective. Ending up with a datastructure that is easy to use, powerful and enables our machine learning algorithms in GraphLab Create to scale easily to terabyte datasets on a single machine. Thank you.