arkouda 2020.7.7
Parallel, distributed NumPy-like arrays backed by Chapel
Requires Python: >=3.6
Keywords: HPC workflow exploratory analysis parallel distribute arrays Chapel

# Arkouda (αρκούδα): NumPy-like arrays at massive scale backed by Chapel.
## _NOTE_: Arkouda is under the MIT license.

## Gitter channels
[Arkouda Gitter channel](https://gitter.im/ArkoudaProject/community)

[Chapel Gitter channel](https://gitter.im/chapel-lang/chapel)

## Talks on Arkouda
[Mike Merrill's CHIUW 2019 talk](https://chapel-lang.org/CHIUW/2019/Merrill.pdf)

[Bill Reus' CLSAC 2019 talk](http://www.clsac.org/uploads/5/0/6/3/50633811/2019-reus-arkuda.pdf)

(PAW-ATM) [talk](https://github.com/sourceryinstitute/PAW/raw/gh-pages/PAW-ATM19/presentations/PAW-ATM2019_talk11.pdf) 
and [abstract](https://github.com/sourceryinstitute/PAW/raw/gh-pages/PAW-ATM19/extendedAbstracts/PAW-ATM2019_abstract5.pdf)

## Abstract:
Exploratory data analysis (EDA) is a prerequisite for all data
science, as illustrated by the ubiquity of Jupyter notebooks, the
preferred interface for EDA among data scientists. The operations
involved in exploring and transforming the data are often at least as
computationally intensive as downstream applications (e.g. machine
learning algorithms), and as datasets grow, so does the need for HPC-enabled
EDA. However, the inherently interactive and open-ended nature of
EDA does not mesh well with current HPC usage models. Meanwhile, several
existing projects from outside the traditional HPC space attempt to
combine interactivity and
distributed computation using programming paradigms and tools from
cloud computing, but none of these projects have come close to meeting
our needs for high-performance EDA.

To fill this gap, we have
developed a software package, called Arkouda, which allows a user to
interactively issue massively parallel computations on distributed
data using functions and syntax that mimic NumPy, the underlying
computational library used in the vast majority of Python data science
workflows. The computational heart of Arkouda is a Chapel interpreter
that
accepts a pre-defined set of commands from a client (currently
implemented in Python) and
uses Chapel's built-in machinery for multi-locale and multithreaded
execution. Arkouda has benefited greatly from Chapel's distinctive
features and has also helped guide the development of the language.

In early applications, users of Arkouda have tended to iterate rapidly
between multi-node execution with Arkouda and single-node analysis in
Python, relying on Arkouda to filter a large dataset down to a smaller
collection suitable for analysis in Python, and then feeding the results
back into Arkouda computations on the full dataset. This paradigm has
already proved very fruitful for EDA. Our goal is to enable users to
progress seamlessly from EDA to specialized algorithms by making Arkouda
an integration point for HPC implementations of expensive kernels like
FFTs, sparse linear algebra, and graph traversal. With Arkouda serving
the role of a shell, a data scientist could explore, prepare, and call
optimized HPC libraries on massive datasets, all within the same
interactive session.

## Installation

### Requirements:
 * requires chapel 1.22.0
 * requires zeromq version >= 4.2.5, tested with 4.2.5 and 4.3.1
 * requires hdf5 
 * requires python 3.6 or greater
 * requires numpy
 * requires Sphinx and sphinx-argparse to build python documentation
 * requires pytest and pytest-env to execute the Python test harness

### MacOS Environment Installation

It is usually very simple to get things going on a mac:

```bash
brew install zeromq

brew install hdf5

brew install chapel

# Although not required, is is highly recommended to install Anaconda to provide a 
# Python 3 environment and manage Python dependencies:
wget https://repo.anaconda.com/archive/Anaconda3-2020.02-Linux-x86_64.sh
sh Anaconda3-2020.02-Linux-x86_64.sh
source ~/.bashrc

# Otherwise, Python 3 can be installed with brew
brew install python3
# !!! the standard way of installing through pip3 installs an old version of arkouda
# !!! the arkouda python client is available via pip
# !!! pip will automatically install python dependencies (zmq and numpy)
# !!! however, pip will not build the arkouda server (see below)
# !!!pip3 install arkouda
#
# install the version of the arkouda python package which came with the arkouda_server
# if you plan on editing the arkouda python package use the -e flag
# from the local arkouda repo/directory run...
pip3 install -e .
#
# these packages are nice but not a requirement
pip3 install pandas
pip3 install jupyter
```

If it is preferred to build Chapel instead of using the brew install, the process is as follows:

```bash

# on my mac build chapel in my home directory with these settings...
export CHPL_HOME=~/chapel/chapel-1.22.0
source $CHPL_HOME/util/setchplenv.bash
export CHPL_COMM=gasnet
export CHPL_COMM_SUBSTRATE=smp
export CHPL_TARGET_CPU=native
export GASNET_QUIET=Y
export CHPL_RT_OVERSUBSCRIBED=yes
cd $CHPL_HOME
make

# Build chpldoc to enable generation of Arkouda docs
make chpldoc

# Add the Chapel executable (chpl) to PATH either in ~/.bashrc (single user) 
# or /etc/environment (all users):

export PATH=$CHPL_HOME/bin/linux64-x86_64/:$PATH
```

### Linux Environment Installation

There is no Linux Chapel install, so the first two steps in the Linux Arkouda install are 
to install the Chapel dependencies followed by downloading and building Chapel:

```
# Update Linux kernel and install Chapel dependencies
sudo apt-get update
sudo apt-get install gcc g++ m4 perl python python-dev python-setuptools bash make mawk git pkg-config

# Download latest Chapel release, explode archive, and navigate to source root directory
wget https://github.com/chapel-lang/chapel/releases/download/1.22.0/chapel-1.22.0.tar.gz
tar xvf chapel-1.22.0.tar.gz
cd chapel-1.22.0/

# Set CHPL_HOME
export CHPL_HOME=$PWD

# Add chpl to PATH
source $CHPL_HOME/util/setchplenv.bash

# Set remaining env variables and execute make
export CHPL_COMM=gasnet
export CHPL_COMM_SUBSTRATE=smp
export CHPL_TARGET_CPU=native
export GASNET_QUIET=Y
export CHPL_RT_OVERSUBSCRIBED=yes
cd $CHPL_HOME
make

# Build chpldoc to enable generation of Arkouda docs
make chpldoc

# Optionally add the Chapel executable (chpl) to the PATH for all users: /etc/environment
export PATH=$CHPL_HOME/bin/linux64-x86_64/:$PATH
```

As is the case with the MacOS install, it is highly recommended to install Anaconda to provide a Python environment 
and manage Python dependencies:

```
 wget https://repo.anaconda.com/archive/Anaconda3-2020.02-Linux-x86_64.sh
 sh Anaconda3-2020.02-Linux-x86_64.sh
 source ~/.bashrc
```

## Building Arkouda

Download, clone, or fork the [arkouda repo](https://github.com/mhmerrill/arkouda). Further instructions assume that 
the current directory is the top-level directory of the repo.

If your environment requires non-system paths to find dependencies (e.g.,
if using the ZMQ and HDF5 bundled with [Anaconda]), append each path to a new file `Makefile.paths` like so:

```make
# Makefile.paths

# Custom Anaconda environment for Arkouda
$(eval $(call add-path,/home/user/anaconda3/envs/arkouda))
#                      ^ Note: No space after comma.
```

The `chpl` compiler will be executed with `-I`, `-L` and an `-rpath` to each path.

```
# If zmq and hdf5 have not been installed previously, execute make install-deps
make install-deps

# Run make to build the arkouda_server executable
make
```

Now that the arkouda_server is built and tested, install the Python library

## Installing the Arkouda Python Library

```
 pip3 install -e .
```

## Testing Arkouda

There are two unit test suites for Arkouda, one for Python and one for Chapel. As mentioned above, the Arkouda Python 
test harness leverages the [pytest](https://docs.pytest.org/en/latest/) and [pytest-env](https://pypi.org/project/pytest-env/) 
libraries, whereas the Chapel test harness does not require any external librares.

For more details regarding Arkouda testing, please consult the Python test [README](tests/README.md) and Chapel test
[README](test/README.md), respectively.

## Building the Arkouda documentation

Make sure you've installed the Sphinx and sphinx-argparse packages (e.g. `pip3 install -U Sphinx sphinx-argparse`). _Important: if you've built Chapel, you must execute make chpldoc as detailed above._

Run `make doc` to build both the Arkouda python documentation and the Chapel server documentation

The output is currently in subdirectories of the `arkouda/doc`
```
arkouda/doc/python # python frontend documentation
arkouda/doc/server # chapel backend server documentation 
```

To view the documentation for the Arkouda python client, point your browser to `file:///path/to/arkouda/doc/python/index.html`, 
substituting the appropriate path for your configuration.

## Running arkouda_server

The command-line invocation depends on whether you built a single-locale version (with `CHPL_COMM=none`) or 
multi-locale version (with `CHPL_COMM` set).

Single-locale startup:

```bash
./arkouda_server
```

Multi-locale startup (user selects the number of locales):

```bash
./arkouda_server -nl 2
```
Also can run server with memory checking turned on using

```bash
./arkouda_server --memTrack=true
```

By default, the server listens on port `5555` and prints verbose output. These options can be changed with command-line 
flags `--ServerPort=1234` and `--v=false`

Memory checking is turned off by default and turned on by using `--memTrack=true`

Logging messages are turned on by default and turned off by using `--logging=false`

Verbose messages are turned on by default and turned off by using  `--v=false`

Other command line options are available, view them by using `--help`

## Testing arkouda_server

To sanity check the arkouda server, you can run

```bash
make check
```

This will start the server, run a few computations, and shut the server down. In addition, the check script can be executed 
against a running server by running the following Python command:

```bash
python3 tests/check.py localhost 5555
```

## Contributing to Arkouda

If you'd like to contribute, please see [CONTRIBUTING.md](CONTRIBUTING.md).