Ruby wrappers for the XND project

Table of Contents

Introduction

Lack of stable and reliable scientific computing software has been a persistent problem for the Ruby community, making it hard for enthusiastic Ruby developers to use Ruby in everything from their web applications to their data analysis projects. One of the most important components of any successful scientific software stack is a well maintained and flexible array computation library that can act as a fast and simple way of storing in-memory data and interfacing it with various fast and battle-tested libraries like LAPACK and BLAS.

Various projects have attempted to make such libraries in the past (and some are still thriving and maintained). Some of the notable ones are numo, nmatrix, and more recently, numruby. These projects attempt to provide a simple Ruby-like API for creating and manipulating arrays of various types. All of them are able to easily interface with libraries like ATLAS, FFTW and LAPACK.

However, all of the above projects fall short in two major aspects:

  • Lack of extensibility to adapt to modern use cases (read Machine Learning).
  • Lack of a critical mass of developers to maintain a robust and fast array library.

The first problem is mainly due to the fact that they do not support very robust type systems. The available data types are limited and are hard to extend to more complex uses. Modern use cases like Machine Learning require a more robust type system (i.e. defining array shapes of arbitrary dimension on multiple devices), as has been demonstrated by the tensor implementations of various frameworks like Tensorflow and PyTorch.

The second problem is due to the fact that all of the aforementioned projects are community efforts that are maintained part-time by developers simply out of a sense of purpose and passion. Sustaining such complex projects for extended periods of time without expectation of any support is simply unfeasible even for the most driven engineers.

This is where the XND project comes in. The XND project is a project for building a common library that is able to meet the needs of the various data analysis and machine learning frameworks that have had to build their own array objects and programming languages. It is built with the premise of extending arrays with new types and various device types (CPUs, GPUs etc.) without loss of performance and ease of use.

The XND project as a whole is a product of three C libraries : ndtypes, xnd and gumath. They have been made such that they can work as standalone C libraries that can be interfaced with any language binding (currently supporting Ruby and Python). Ndtypes is used for defining the shape of data within memory, XND is a data container that holds that data and gumath provides a multiple dispatch mechanism for performing computations on data held in XND containers. We will elaborate on each of these in the post below.

The XND project presents the perfect answer to Ruby's lack of a mature array computation ecosystem. It is highly extensible, allows defining data types in almost any combination with a simple and intuitive interface, is built with performance in mind and is backed by a team consisting of experts who have vast experience in this domain for the Python scientific computing stack.

The biggest backer of XND as of now is Quansight, and I as a part-time engineer am responsible for maintaining the Ruby wrapper for XND. This post is a rather long and detailed introduction to the XND ruby wrapper. There will also be some details on the implementation of the wrapper and how it differs from the Python wrapper (which existed before the Ruby wrapper). Read on for further details.

All the source code can be found in the xnd-ruby repo.

Ndtypes

Ndtypes is the library that is used for defining the shape of data.

Run gem install ndtypes --pre for easily installing ndtypes onto your machine. It has been tested with Ruby 2.4.1 so far. The gem install will download the C sources and compile them by itself.

Usage

Basic initialization

The ndtypes Ruby wrapper provides a simple interface to the ndtypes C library for creating complex data shapes with extreme simplicity. For example, for creating an array of 10 int64 digits, all we need to do is create an instance of the NDT class:

t = NDT.new "10 * int64"

Not only can you create arrays, but also very complex types, for example a nested record (xnd terminology for a Ruby Hash) with the values as arrays of type float32 of size 25 each:

t = NDT.new "{x: 25 * float32, y: {a: 25 * float64, 25 * float64}}"

Concrete Vs. Abstract Types

Ndtypes distinguishes types depending on whether they are abstract or concrete. Abstract types can have symbolic values like dimension or type variables and are used for type checking. Concrete types additionally have full memory layout information like alignment and data size.

Some operations can be only performed on abstract types.

Typedefs

One can also define typedefs using the NDT#typedef function and then use them in place of the original type. Here's an example of using typedefs to define a graph type:

NDT.typedef "node", "int32"
NDT.typedef "cost", "int32"
NDT.typedef "graph", "var * var * (node, cost)"

Usage via The C API

Most of the C API functions of ndtypes deal with creating NDT Ruby objects or obtaining internal struct data of an NDT Ruby object. The complete specification can be found in the ruby_ndtypes.h file. This is the file you should include if you want to use the C API in any of your libraries.

Implementation

The Ruby wrapper is a wrapper over the libndtypes library. The NDT Ruby object is a wrapper over a C struct of type NdtObject that has the following definition:

typedef struct NdtObject {
  const ndt_t *ndt;                   /* type */
} NdtObject;

This simple struct stores a pointer to a struct of type const ndt_t * that is provided by libndtypes for representing an ndtype. The const ndt_t structs are allocated by various libndtypes functions like ndt_from_string() or ndt_alloc().

Internally libndtypes uses a reference counting mechanism for keeping track of ndt_t allocations that need to be destroyed. The reference count can be incremented using ndt_incref() or decremented using ndt_decref(). Once the refcount reaches the 0 the object is automatically destroyed by libndtypes. Of course, ndt_t structs allocated via calls to functions like ndt_alloc() already come with a refcount of 1.

Xnd

XND is the main storage library of the project. It uses types defined by ndtypes for defining the shape of data and allows users to read and write data into buffers that are of the shape of the data passed to it by ndtypes. It is responsible for maintaining the memory consistency of data and has provisions for various operations such as slicing, copying and interfacing data with 3rd party libraries like Apache Arrow. It also serves as a memory buffer for the functions that are defined within gumath (explained later in this post).

Similar to the ndtypes wrapper, the xnd Ruby wrapper can be installed with a call to gem install xnd --pre.

Basic Usage

The xnd Ruby wrapper is extremely simple to use and provides a single class XND for the user that interfaces with libxnd. In the simplest case, one can create an XND object as follows:

x = XND.new [1,2,3,4]
# => #<XND:47340720296980>
#    type= 4 * int64
#    value= [1, 2, 3, 4]

Since we have not specified the data type, it will be inferred as int64 since we are supplying an array composed entirely of integers. This can be seen using the XND#dtype function, which will return the NDT object that holds the type of this XND object:

x.dtype
# => #<NDTypes:47340721833280>
#   int64 

While XND#dtype gives the general type of the object, a more precise description of the data type (including shape etc.) can be obtained using the type method:

x.type
# => #<NDTypes:47340721846240>
#  4 * int64

The value within the XND object can be obtained as a Ruby Array (or Hash if it is a NDT record) using the XND#value method:

x.value
# => [1, 2, 3, 4]

We can also perform operations for checking equality between XND objects using the == or != operators:

a = XND.new [1,2,3,4]
x == a
# => true

A nice thing about XND is that it returns copy-free 'views' of data when you perform a slicing operation. So say we define a 2D tensor tensor_2d like this:

tensor_2d = XND.new(
  [
    [1,2,3,4,5],
    [1,2,3,4,5],
    [1,2,3,4,5],
    [1,2,3,4,5],
    [1,2,3,4,5]
  ]
)
tensor_2d.inspect
# => #<XND:47340720946720>
#    type= 5 * 5 * int64
#    value= [[1, 2, 3, 4, 5], [1, 2, 3, 4, 5], [1, 2, 3, 4, 5], [1, 2, 3, 4, 5], [1, 2, 3, 4, 5]]

We can obtain a slice (say the 2nd column) of the tensor using Ruby Range. Note that using INF is a shorthand for specifying the entire axis (usually denoted as 0..-1):

vector_view = tensor_2d[INF, 2]
# => #<XND:47340720380980>
#    type= 5 * int64
#    value= [3, 3, 3, 3, 3]

When using slices, XND will always return a 'view' of the original XND object. Changes made to this slice will reflect on the original XND object as well:

vector_view[2] = 666
tensor_2d.inspect
# => #<XND:47340720946720>
#    type= 5 * 5 * int64
#    value= [[1, 2, 3, 4, 5], [1, 2, 3, 4, 5], [1, 2, 666, 4, 5], [1, 2, 3, 4, 5], [1, 2, 3, 4, 5]]

However, the type of the view and the original object differ as they should:

vector_view.type
# => #<NDTypes:47340720381100>
#   5 * int64 
tensor_2d.type
# => #<NDTypes:47340720939360>
#   5 * 5 * int64

If you want a separate storage space for the view (i.e. do not want changes to the view to reflect on the parent object), you should use the XND#dup method and make a copy. You can also allocate a data container without storing any data into it using the XND.empty method as can be seen in the following examples.

Data Type Support

As a result of the flexibility provided by the ndtypes type definition interface, xnd is able to provide type support for far more flexible data shapes than simply for arrays with fixed dimensions. For example, you can use records for storing Ruby Hashes and performing operations on them:

require 'xnd'

x = XND.empty "{x: complex64, y: bytes, z: string}"
v = { 'x' => 1+20i, 'y' => "abc".b, 'z' => "any" }
x['x'] = v['x']
x['y'] = v['y']
x['z'] = v['z']
x
# => #<XND:47340721378580>
#    type= {x : complex64, y : bytes, z : string}
#    value= {"x"=>(1.0+20.0i), "y"=>"abc", "z"=>"any"}

Missing Values

XND also supports optional data (represented by nil). It can be created as follows:

x = XND.empty "2 * 4 * ?float64"
v = [[10.0, nil, 2.0, 100.12], [nil, nil, 6.0, 7.0]]
x[INF] = v # assign full slice
# => [[10.0, nil, 2.0, 100.12], [nil, nil, 6.0, 7.0]] 

Usage via The C API

The primary function of the XND Ruby C API is for creating and querying XND Ruby objects. The full API can be found in the ruby_xnd.h file.

Implementation

The implementation of the Ruby wrapper differs from the Python wrapper largely due to nature of the garbage collection algorithms employed by both these languages: Ruby uses a mark-and-sweep GC while Python uses a reference counted GC. Therefore, Ruby objects created within the C extension have to somehow be kept 'alive' such that the GC does not deallocate them thinking that they have gone out of scope and are no longer useful.

For this purpose we utilize a 'GC guard' structure (inspired by the implementation of @mrkn's matplotlib.rb gem). The GC guard is basically a global Ruby Hash that has the Ruby object created within the C extension as a key and something random as a value. We use a Hash because it provides lookups in O(1) time and we don't care about the value because we only want to save the object in some kind of a global store so that Ruby is aware of its presence (in case of NDT we use true for the value). XND uses three different GC guards for various internal objects, which can be found in the gc_guard.h file.

Gumath

While ndtypes and xnd allow us to define types and memory storage, gumath allows us to actually do something with them. The basic idea behind gumath is that it is a library that allows defining functions for various data types stored within an XND object and allows the user to transparently call them using a high level interface that uses multiple dispatch for calling the relevant function on the appropriate type. The Ruby interface is a wrapper over the libgumath C library.

Some functions (known as kernels) come bundled with libgumath and others can be written fairly easily. Similar to the xnd and ndtypes wrappers, the gumath Ruby wrapper can be installed with a call to gem install gumath --pre.

Usage

The Gumath class is a top level namespace for various modules that serve as namespaces for functions that come rolled in with the libgumath C library. These modules will keep expanding as more interfaces are added to libgumath. The Gumath::Functions module contains various such functions that are provided by libgumath by default.

Gumath functions accept XND objects as arguments and output XND objects with the result of the function. An example of a simple element-wise multiply kernel is the following:

require 'xnd'
require 'gumath'

x = XND.new [2,3,4,5,6,7,8,9], dtype: "float64"
y = XND.new [1,2,3,4,5,6,7,8], dtype: "float64"
z = Gumath::Functions.multiply x, y
# => #<XND:47340721458320>
#    type= 8 * float64
#    value= [2.0, 6.0, 12.0, 20.0, 30.0, 42.0, 56.0, 72.0]

Usage via The C API

Since the main purpose of the gumath C API is to allow adding kernels to a Ruby module, it provides a single function of the prototype:

int rb_gumath_add_functions(VALUE module, const gm_tbl_t *tbl);

The module parameter is a Ruby object, and tbl is a function table of gumath kernels.

Implementation

Compared to xnd and ndtypes, the gumath Ruby wrapper is much simpler since its primary function is to take functions from libgumath and add them as module functions to Ruby modules.

When the library is initially loaded using a call to require, the relevant libgumath kernels provided by default are loaded into the Ruby interpreter by interfacing each kernel with a Ruby object. Further details on the working of the method dispatch within Ruby can be found in the CONTRIBUTING file.

The most important part of the C implementation is the GufuncObject class which is a Ruby class defined within the C API that helps interface with a single gumath function. This class is basically a wrapper over a C struct GufuncObject that can be found in the gufunc_object.h file.

The struct has the following definition:

typedef struct {
  const gm_tbl_t *table;          /* kernel table */
  char *name;                     /* function name */
  uint32_t flags;                 /* memory target */
  VALUE identity;                 /* identity element */
} GufuncObject;

The table pointer is the pointer to the definition of the function within libgumath that holds information about the function that is used by gm_apply for making the actual call to the function with the data. name is a string holding the name of the function. flags signify whether the function is a CPU function or a CUDA function (or for that matter any other device that might be added in the future). identity is a Ruby object used for identifying this function. It is initially set to nil.

Automatic Kernel Generation

Writing kernels can be painstaking if you're not familiar with the various functionalities that libgumath provides for this purpose. Therefore we also provide a kernel generator called xndtools that allows writing gumath kernels by simply providing the function that needs to wrapped. However, this functionality has not yet been tested for Ruby.

Conclusion and Future Work

The current state of the Ruby XND wrappers makes them suitable for the XND libraries via Ruby, but what would be truly exciting would be have a more Ruby-like API that conforms to accepted Ruby idioms and creates a truly intuitive XND Ruby interface, rather than simply a one-on-one mapping of functions.

In the future we also plan to integrate XND with various Ruby libraries like rubyplot and daru and expand the uses of XND even further. For example, operators like multiplication in other scientific languages like MATLAB simply work with operator overloading by using the * operator between objects. Similarly overriding operators on XND and calling the underlying gumath kernel is a work in progress.

Similarly, have a 'Ruby-like' API that allows better method chaining in the sense of Rails or rspec should free up the programmer of having to 'think' of the interfaces and make array computations much more intuitive for programmers. These changes will of course be implemented after XND reaches a critical base of users who are willing to provide feedback and try out new interfaces. We plan to integrate XND into rubyplot to achieve this goal of more usage.

The C API for the wrapper is also quite limiting as of now, and it would be quite a pain for another Ruby gem to use XND via the C API. Therefore, improving the C API is also something that we will be seriously looking into in the future.