vertica/ddR

The 'ddR' package aims to provide an unified R interface for writing parallel and distributed applications. Our goal is to ensure that R programs written using the 'ddR' API work across different distributed backends, therefore, reducing the effort required by users to understand and program on different backends. Currently 'ddR' programs can be executed on R's default 'parallel' package as well as the open source HP Distributed R. We plan to add support for SparkR. This package is an outcome of feedback and collaboration across different companies and R-core members!

Through funding provided by the R-consortium this package is under active development for the summer of 2016. Check out the mailing list to see the latest discussions.

'ddR' is an API, and includes a default execution engine, to express and execute distributed applications. Users can declare distributed objects (i.e., dlist, dframe, darray), and execute parallel operations on these data structures using R-style apply functions. It also allows different backends (that support ddR, and have ddR "drivers" written for them) to be dynamically activated in the R user's environment to execute applications

Please refer to the user guide under vignettes/ for a detailed description on how to use the package.

Some quick examples

library(ddR)

By default, the parallel backend is used with all the cores present on the machine. You can switch backends or specify the number of cores to use with the useBackend function. For example, you can specify that the parallel backend should be used with only 4 cores by executing useBackend(parallel, executors=4).

Initializing a distributed list (dlist):

a <- dmapply(function(x) { x }, rep(3,5))
collect(a)

## [[1]]
## [1] 3
## 
## [[2]]
## [1] 3
## 
## [[3]]
## [1] 3
## 
## [[4]]
## [1] 3
## 
## [[5]]
## [1] 3

Printing a:

a

## 
## ddR Distributed Object
## Type: dlist
## # of partitions: 5
## Partitions per dimension: 5x1
## Partition sizes: [1], [1], [1], [1], [1]
## Length: 5
## Backend: parallel

a is a distributed object in ddR. Note that we did not specify the number of partitions of the output, but by default it is equal to the length of the inputs (5). Use the parameter nparts to specify how the output should be partitioned:

Below is the code to add 1 to the first element of a, 2 to the second, etc. The syntax of dmapply is similar to R's standard mapply function.

b <- dmapply(function(x,y) { x + y }, a, 1:5,nparts=1)
b

## 
## ddR Distributed Object
## Type: dlist
## # of partitions: 1
## Partitions per dimension: 1x1
## Partition sizes: [5]
## Length: 5
## Backend: parallel

Since we specified nparts=1 in dmapply, b only has one partition of 5 elements. Note that the argument nparts is optional, and a user can always ignore it.

collect(b)

## [[1]]
## [1] 4
## 
## [[2]]
## [1] 5
## 
## [[3]]
## [1] 6
## 
## [[4]]
## [1] 7
## 
## [[5]]
## [1] 8

Some other operations: `

Adding a to b, and then subtracting a constant value

addThenSubtract <- function(x,y,z) {
  x + y - z
}
c <- dmapply(addThenSubtract,a,b,MoreArgs=list(z=5))
collect(c)

## [[1]]
## [1] 2
## 
## [[2]]
## [1] 3
## 
## [[3]]
## [1] 4
## 
## [[4]]
## [1] 5
## 
## [[5]]
## [1] 6

We can also process distributed objects partitionwise. Below is an example where we calculate the length of each partition:

d <- dmapply(function(x) length(x),parts(a))
collect(d)

## [[1]]
## [1] 1
## 
## [[2]]
## [1] 1
## 
## [[3]]
## [1] 1
## 
## [[4]]
## [1] 1
## 
## [[5]]
## [1] 1

We partitioned a with 5 parts and it had 5 elements, so the length of each partition is 1.

However, b only had one partition, so that one partition should be of length 5:

e <- dmapply(function(x) length(x),parts(b))
collect(e)

## [[1]]
## [1] 5

Note that parts() and non-parts arguments can be used in any combination to dmapply. parts(dobj) returns a list of the partitions of that dobject, which can be passed into dmapply like any other list. parts(dobj,index), where index is a list, vector, or scalar, returns a specific partition or range of partitions of dobj.

We also have support for darrays and dframes. Check vignettes/ on how to use them.

For more interesting parallel machine learning algorithms, you may view (and run) the example scripts under /examples.

Using the Distributed R backend

To use the Distributed R library for ddR, first install distributedR.ddR and then load it:

library(distributedR.ddR)

## Loading required package: distributedR
## Loading required package: Rcpp
## Loading required package: RInside
## Loading required package: XML
## Loading required package: ddR
## 
## Attaching package: 'ddR'
## 
## The following objects are masked from 'package:distributedR':
## 
##     darray, dframe, dlist, is.dlist

useBackend(distributedR)

Now you can try the different list examples which were used with the 'parallel' backend.

How to Contribute

You can help us in different ways:

1. Reporting issues.
2. Contributing code and sending a Pull Request.

In order to contribute the code base of this project, you must agree to the Developer Certificate of Origin (DCO) 1.1 for this project under GPLv2+:

By making a contribution to this project, I certify that:

(a) The contribution was created in whole or in part by me and I have the 
    right to submit it under the open source license indicated in the file; or
(b) The contribution is based upon previous work that, to the best of my 
    knowledge, is covered under an appropriate open source license and I 
    have the right under that license to submit that work with modifications, 
    whether created in whole or in part by me, under the same open source 
    license (unless I am permitted to submit under a different license), 
    as indicated in the file; or
(c) The contribution was provided directly to me by some other person who 
    certified (a), (b) or (c) and I have not modified it.
(d) I understand and agree that this project and the contribution are public and
    that a record of the contribution (including all personal information I submit 
    with it, including my sign-off) is maintained indefinitely and may be 
    redistributed consistent with this project or the open source license(s) involved.

To indicate acceptance of the DCO you need to add a Signed-off-by line to every commit. E.g.:

Signed-off-by: John Doe <[email protected]>

To automatically add that line use the -s switch when running git commit:

$ git commit -s