flashxio / knorPy

# knor for Python

[![Build
Status](https://travis-ci.org/flashxio/knorPy.svg?branch=master)](https://travis-ci.org/flashxio/knorPy)

These are Python 2.7+ and Python 3 bindings for the standalone
machine in-memory portion of the clustering NUMA Optimized Routines. See the
full C++ library for details: https://github.com/flashxio/knor

## Supported OSes

The `knor` python package has been tested on the following OSes:
- Mac OSX Sierra, Mojave
- Ubuntu LTS 14.04, 16.04, 18.04
- Debian Linux

## Python Dependencies

- Numpy: `pip install -U numpy`
- Setuptools: `pip install -U setuptools`
- pybind11: `pip install -U pybind11`

## Mac Installation

```
pip install knor
```

## Linux installation

### Best Performance configuration

For the best performance make sure the `numa` system package is installed via

```
apt-get install -y libnuma-dbg libnuma-dev libnuma1
```

Then simply install the package via pip:

```
pip install knor
```

## Installation Errors

1.

```
  File “/Library/Python/2.7/site-packages/pip/utils/__init__.py”, line X, in
  call_subprocess
      % (command_desc, proc.returncode, cwd))
      InstallationError: Command “python setup.py egg_info” failed with error
      code 1 in /private/tmp/pip-build-vaASFl/knor/
```

### Solution

Update your `python` version to at least `2.7.10`

2.

```
    In file included from knor/cknor/libkcommon/clusters.cpp:23:
    knor/cknor/libkcommon/util.hpp:29:10: fatal error: ‘random’ file not found
    #include <random>
             ^
    1 error generated.
    error: command ‘/usr/bin/clang’ failed with exit status 1
```
### Solution
This usually occurs on Mac when your Xcode and Xcode command line tools are out of
date. Update then to at least Version 8

3.

```
unable to execute 'x86_64-linux-gnu-gcc': No such file or directory
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
```

### Solution
Install the `gcc` compiler via `apt-get install build-essential`

4.

```
 fatal error: Python.h: No such file or directory compilation terminated.
```

### Solution
Install the development headers for the version on Python you intend to install knor e.g

```
apt-get install python-dev  # for python2.x installs
apt-get install python3-dev  # for python3.x installs
```

5.
```
fatal error: 'pybind11/pybind11.h' file not found
#include <pybind11/pybind11.h>
         ^~~~~~~~~~~~~~~~~~~~~
ImportError: No module named pybind11
```

### Solution

This occurs on Mac and is best solved by utilizing virtual environments as
follows:

```
sudo pip install virtualenv
virtualenv -p <python-version> <desired-path>
source <desired-path>/bin/activate
```

Where `python-version` is either `python2.7` or `python3`.

Then install `pybind11` by `pip install pybind11` then attempt to install `knor`

6.
ImportError: No module named 'setuptools'
```

### Solution

Use a recent version of `setuptools` from `pip`

```
sudo apt remove python-setuptools python3-setuptool
pip install -U setuptools
pip3 install -U setuptools
```


## Documentation

```
from knor import *
help(Kmeans)
help(SKmeans)
help(KmeansPP)
help(FuzzyCMeans)
help(Kmedoids)
help(Xmeans)
help(Hmeans)
help(Gmeans)
```

## Example

```
import knor
import numpy as np
data = np.random.random((100, 10))
km = knor.Kmeans(k=5)
ret = km.fit(data)
print(ret)
```

## The `cluster_t` return object

The `cluster_t` return object has the following attributes:

- `k`: The number of clusters requested
- `nrow`: The number of rows/samples in the dataset
- `ncol`: Then number of columns/features in the dataset
- `sizes`: The number of samples in each cluster/centroid
- `iters`: The number of iterations performed
- `centroids`: A `list` where each row is a cluster center
- `clusters`: A `list` index for which cluster each sample falls into