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README.md

Juniper Kernel

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An R kernel for Jupyter built with Xeus and Rcpp.

The development of JuniperKernel is sponsored by Bloomberg.

Install from CRAN

> install.packages("JuniperKernel")
> library(JuniperKernel)
> installJuniper(useJupyterDefault = TRUE)  # install into default Jupyter kernel location

Install via Conda

Availability is architecture dependent, see:

  • conda install -c conda-forge r-juniperkernel or
  • conda install -c conda-forge/label/gcc7 r-juniperkernel

Building

Requirements

If you're going to build from scratch, then these packages will be necessary to fetch:

  • R packages: BH, Rcpp (>= 0.11.0), gdtools (>= 0.1.6), pbdZMQ (>= 0.3-0), roxygen2, jsonlite, repr, data.table

Other necessary bacon bits (fetched automatically--c.f. Makevars/Makevars.win):

  • zeromq (4.4.2)
  • xeus (0.7.0)
  • xtl (0.3.1)

Devtools Build and Install from Github

Installing from github is probably the easiest option.

Loop through the requirements, and then do:

devtools::install_github("JuniperKernel/JuniperKernel")

Building on Windows

Supported compilers:

  • mingw32/64 (bundled with Rtools)
  • no other compilers are officially supported (though you may have success via cygwin)

Supported architectures:

  • 32/64 bit arch

To build and install the Juniper kernel run the following from a cmd prompt:

cmd /c mk.bat

Alternatively, you can run the build from RStudio.

You should see the following compilation output:

C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.1/include" -DNDEBUG -I../inst/include -I. -Wno-conversion-null -I"C:/Program Files/R/R-3.4.1/library/Rcpp/include" -I"C:/Program Files/R/R-3.4.1/library/gdtools/include" -I"C:/Program Files/R/R-3.4.1/library/BH/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.1/include" -DNDEBUG -I../inst/include -I. -Wno-conversion-null -I"C:/Program Files/R/R-3.4.1/library/Rcpp/include" -I"C:/Program Files/R/R-3.4.1/library/gdtools/include" -I"C:/Program Files/R/R-3.4.1/library/BH/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2 -c juniper.cpp -o juniper.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o JuniperKernel.dll tmp.def RcppExports.o juniper.o -lzmq -Lx64 -Ld:/Compiler/gcc-4.9.3/local330/lib/x64 -Ld:/Compiler/gcc-4.9.3/local330/lib -LC:/PROGRA~1/R/R-34~1.1/bin/x64 -lR
installing to C:/Program Files/R/R-3.4.1/library/JuniperKernel/libs/x64
** R
** inst
** preparing package for lazy loading
No man pages found in package  'JuniperKernel' 
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (JuniperKernel)

Building on macOS

You may install via RStudio, or via terminal with

$ make
$ make install

which produces the following output:

* installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* installing *source* package ‘JuniperKernel’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I../inst/include/xeus -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdtools/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I../inst/include/xeus -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdtools/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c juniper.cpp -o juniper.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o JuniperKernel.so RcppExports.o juniper.o -lzmq -L../inst/zmq -Wl,-rpath,/Library/Frameworks/R.framework/Resources/library/JuniperKernel/zmq -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/JuniperKernel/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* creating tarball
packaged installation of ‘JuniperKernel’ as ‘JuniperKernel_0.0.0.1.tgz’
* DONE (JuniperKernel)

Installing the Juniper Kernel

Jupyter Requirements

These are the notebook versions that are compatible with the Juniper kernel:

notebook version: 5.0.0
jupyter_client version: 5.1.0
jupyter_core version: 4.3.0

If you want to also enable widgets, this is the compatible version:

widgetsnbextension version: 3.0.2

Note also that Juniper installation depends on jupyter kernelspec being available:

$ jupyter kernelspec --version
5.1.0
Juniper Kernel Installation

The Juniper kernel is installed via the R package that was just built and installed:

$ R
> library(JuniperKernel)
> installJuniper()
[InstallKernelSpec] Installed kernelspec juniper_r3.4.1 in /PATH/TO/jupyter/kernels/juniper_r3.4.1

You may also install into a virtual environment, provide your own names, and install under different R versions. To list all of the available kernels you may run:

$ jupyter kernelspec list

or you can do it from the R package:

> JuniperKernel::listKernels()

Juniper In Action

Juniper Screenshot:

xwidgets demo:

xwidgets integration screenshot:

Architecture Overview

Juniper is a from-scratch Jupyter kernel implementing the 5.2 Jupyter messaging protocol and extending xeus for custom messaging. The zeromq architecture handles R stdout/stderr in a novel way by listening on regular TCP sockets that R scribbles in via socketConnections.

Here's a diagram of the architecture:

Despite the number of arrows and boxes in the diagram, the architecture is about as straightfoward as you'd expect it to be after a read-through of the docs. There's a client that connects to five sockets exposed by the kernel (heartbeat, iopub, shell, ctrl, stdin), a request handler, and two internal sockets to handle ipc. Green boxes represent independent threads: heartbeat gets its own thread; IOPub gets its own thread; and shell, ctrl, stdin all share the same thread. The need for the signaller and internal publisher may not be obvious; but a read-through of both the Jupyter and ZeroMQ docs make it evident that if you're going to have a multi-threaded zmq architecture, you'll need a mechanism of ipc (with the additional wrinkle of portability). Practically speaking you'll need some way of sending shutdowns to socket pollers (the signaller's job); and you'll need a way of ack'ing client requests with a 'busy' signal over IOPub or sending partial results (since you can't just magically reach into that thread and say iopub_sock.send('busy'), and so you have the internal publisher pass the message along).

In order to start the kernel, a client forks off a new process with some JSON in a connection_file. Primarily this file instructs the kernel about the transport mechanism (tcp, ipc, etc.), ip address, and ports for all sockets:

 // sample connection_file
{
 "iopub_port": 59992,
 "stdin_port": 59993,
 "key": "8de88e2a-05ef-4ac8-9af0-000d6389cbc8",
 "shell_port": 59991,
 "transport": "tcp",
 "hb_port": 59995,
 "ip": "127.0.0.1",
 "control_port": 59994,
 "signature_scheme": "hmac-sha256"
}

More details in the docs. The kernel boot sequence goes like this:

  1. Read connection_file
  2. Bind the internal pub/sig sockets
  3. Start the heartbeat/iopub threads
  4. Bind the ctrl/shell sockets
  5. Poll the ctrl/shell sockets forever

The heartbeat and iopub threads do exactly what the main thread does in binding sockets to the right ports, connecting to the necessary inproc topics, and properly breaking out of an infinite poll loop when signalled. By decree of the ZMQ docs, each thread is responsible for its own socket creation/teardown; therefore, it should strike you that since all of the logic is the same, all of the startup/poll/shutdown code should be shared. And to a large degree it is. You do need some individuality so that messages can be ushered to the right handlers, but a generic solution is helpful for maintenance.

Request Handling and Execution

ctrl and shell receive the preponderance of client requests, and these are all handled in a single-threaded fashion. Heartbeats are implemented with a plain-old echo socket that pongs back whatever binary data the client pings the kernel with. It's worth noting that if your kernel doesn't support a multithreaded model, then your kernel will run into hot water when launching code-execution requests that require execution times on the order of the elapsed time between heartbeats; from the client's perspective the kernel looks non-responsive since your kernel has no way of saying it's not just stuck in 'busy' and doing real work.

When a request comes in over a channel, there's some boilerplate handling to decode the message, do validation, read off its type bits, create a reply, and finally ship the reply back over the channel to the client. Reply content is created by doing some work in the language-specific engine (e.g., plot(x,y) or hist(data)) and then handing back any results to be packaged for client consumption. The request handler, therefore, is the most appropriate place to draw a boundary where the zeromq architecture can be abstracted away from the code-exec'ing one.

Version Notes

Release versions will be of the form <odd/even>.<even>.<patch>.0

Dev versions will be of the form <odd/even>.<odd/even>.<patch>.<dev>

The major version always increments.

<patch> numbers increment always and dev versions will match patched versions.

For example:
1.0.0.0 is a release version 1.1.0.0 is a dev version next minor: 1.2.0.0 is the next minor release version 1.3.0.0 is the next minor dev version next major: 2.0.0.0 is the next major release version 2.1.0.0 is the next major dev version

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