parallel_winhpc.txt

============================================
Getting started with Windows HPC Server 2008
============================================

Introduction
============

The Python programming language is an increasingly popular language for
numerical computing. This is due to a unique combination of factors. First,
Python is a high-level and *interactive* language that is well matched to
interactive numerical work. Second, it is easy (often times trivial) to
integrate legacy C/C++/Fortran code into Python. Third, a large number of
high-quality open source projects provide all the needed building blocks for
numerical computing: numerical arrays (NumPy), algorithms (SciPy), 2D/3D
Visualization (Matplotlib, Mayavi, Chaco), Symbolic Mathematics (Sage, Sympy)
and others.

The IPython project is a core part of this open-source toolchain and is
focused on creating a comprehensive environment for interactive and
exploratory computing in the Python programming language. It enables all of
the above tools to be used interactively and consists of two main components:

* An enhanced interactive Python shell with support for interactive plotting
  and visualization.
* An architecture for interactive parallel computing.

With these components, it is possible to perform all aspects of a parallel
computation interactively. This type of workflow is particularly relevant in
scientific and numerical computing where algorithms, code and data are
continually evolving as the user/developer explores a problem. The broad
treads in computing (commodity clusters, multicore, cloud computing, etc.)
make these capabilities of IPython particularly relevant.

While IPython is a cross platform tool, it has particularly strong support for
Windows based compute clusters running Windows HPC Server 2008. This document
describes how to get started with IPython on Windows HPC Server 2008. The
content and emphasis here is practical: installing IPython, configuring
IPython to use the Windows job scheduler and running example parallel programs
interactively. A more complete description of IPython's parallel computing
capabilities can be found in IPython's online documentation
(http://ipython.org/documentation.html).

Setting up your Windows cluster
===============================

This document assumes that you already have a cluster running Windows
HPC Server 2008. Here is a broad overview of what is involved with setting up
such a cluster:

1. Install Windows Server 2008 on the head and compute nodes in the cluster.
2. Setup the network configuration on each host. Each host should have a 
   static IP address.
3. On the head node, activate the "Active Directory Domain Services" role 
   and make the head node the domain controller.
4. Join the compute nodes to the newly created Active Directory (AD) domain.
5. Setup user accounts in the domain with shared home directories.
6. Install the HPC Pack 2008 on the head node to create a cluster.
7. Install the HPC Pack 2008 on the compute nodes.

More details about installing and configuring Windows HPC Server 2008 can be
found on the Windows HPC Home Page (http://www.microsoft.com/hpc). Regardless
of what steps you follow to set up your cluster, the remainder of this
document will assume that:

* There are domain users that can log on to the AD domain and submit jobs
  to the cluster scheduler.
* These domain users have shared home directories. While shared home
  directories are not required to use IPython, they make it much easier to
  use IPython.

Installation of IPython and its dependencies
============================================

IPython and all of its dependencies are freely available and open source.
These packages provide a powerful and cost-effective approach to numerical and
scientific computing on Windows. The following dependencies are needed to run
IPython on Windows:

* Python 2.6 or 2.7 (http://www.python.org)
* pywin32 (http://sourceforge.net/projects/pywin32/)
* PyReadline (https://launchpad.net/pyreadline)
* pyzmq (http://github.com/zeromq/pyzmq/downloads)
* IPython (http://ipython.org)

In addition, the following dependencies are needed to run the demos described
in this document.

* NumPy and SciPy (http://www.scipy.org)
* Matplotlib (http://matplotlib.sourceforge.net/)

The easiest way of obtaining these dependencies is through the Enthought
Python Distribution (EPD) (http://www.enthought.com/products/epd.php). EPD is
produced by Enthought, Inc. and contains all of these packages and others in a
single installer and is available free for academic users. While it is also
possible to download and install each package individually, this is a tedious
process. Thus, we highly recommend using EPD to install these packages on
Windows.

Regardless of how you install the dependencies, here are the steps you will
need to follow:

1. Install all of the packages listed above, either individually or using EPD
   on the head node, compute nodes and user workstations.

2. Make sure that :file:`C:\\Python27` and :file:`C:\\Python27\\Scripts` are
   in the system :envvar:`%PATH%` variable on each node.

3. Install the latest development version of IPython. This can be done by
   downloading the the development version from the IPython website
   (http://ipython.org) and following the installation instructions.

Further details about installing IPython or its dependencies can be found in
the online IPython documentation (http://ipython.org/documentation.html)
Once you are finished with the installation, you can try IPython out by
opening a Windows Command Prompt and typing ``ipython``. This will
start IPython's interactive shell and you should see something like the
following::

    Microsoft Windows [Version 6.0.6001]
    Copyright (c) 2006 Microsoft Corporation.  All rights reserved.

    Z:\>ipython
    Python 2.7.2 (default, Jun 12 2011, 15:08:59) [MSC v.1500 32 bit (Intel)]
    Type "copyright", "credits" or "license" for more information.

    IPython 0.12.dev -- An enhanced Interactive Python.
    ?         -> Introduction and overview of IPython's features.
    %quickref -> Quick reference.
    help      -> Python's own help system.
    object?   -> Details about 'object', use 'object??' for extra details.

    In [1]:


Starting an IPython cluster
===========================

To use IPython's parallel computing capabilities, you will need to start an
IPython cluster. An IPython cluster consists of one controller and multiple
engines:

IPython controller
    The IPython controller manages the engines and acts as a gateway between 
    the engines and the client, which runs in the user's interactive IPython
    session. The controller is started using the :command:`ipcontroller`
    command.

IPython engine
    IPython engines run a user's Python code in parallel on the compute nodes. 
    Engines are starting using the :command:`ipengine` command.

Once these processes are started, a user can run Python code interactively and
in parallel on the engines from within the IPython shell using an appropriate
client. This includes the ability to interact with, plot and visualize data
from the engines.

IPython has a command line program called :command:`ipcluster` that automates
all aspects of starting the controller and engines on the compute nodes.
:command:`ipcluster` has full support for the Windows HPC job scheduler,
meaning that :command:`ipcluster` can use this job scheduler to start the
controller and engines. In our experience, the Windows HPC job scheduler is
particularly well suited for interactive applications, such as IPython. Once
:command:`ipcluster` is configured properly, a user can start an IPython
cluster from their local workstation almost instantly, without having to log
on to the head node (as is typically required by Unix based job schedulers).
This enables a user to move seamlessly between serial and parallel
computations.

In this section we show how to use :command:`ipcluster` to start an IPython
cluster using the Windows HPC Server 2008 job scheduler. To make sure that
:command:`ipcluster` is installed and working properly, you should first try
to start an IPython cluster on your local host. To do this, open a Windows
Command Prompt and type the following command::

    ipcluster start -n 2

You should see a number of messages printed to the screen.
The result should look something like this::

    Microsoft Windows [Version 6.1.7600]
    Copyright (c) 2009 Microsoft Corporation.  All rights reserved.

    Z:\>ipcluster start --profile=mycluster
    [IPClusterStart] Using existing profile dir: u'\\\\blue\\domainusers$\\bgranger\\.ipython\\profile_mycluster'
    [IPClusterStart] Starting ipcluster with [daemon=False]
    [IPClusterStart] Creating pid file: \\blue\domainusers$\bgranger\.ipython\profile_mycluster\pid\ipcluster.pid
    [IPClusterStart] Writing job description file: \\blue\domainusers$\bgranger\.ipython\profile_mycluster\ipcontroller_job.xml
    [IPClusterStart] Starting Win HPC Job: job submit /jobfile:\\blue\domainusers$\bgranger\.ipython\profile_mycluster\ipcontroller_job.xml /scheduler:HEADNODE
    [IPClusterStart] Starting 15 engines
    [IPClusterStart] Writing job description file: \\blue\domainusers$\bgranger\.ipython\profile_mycluster\ipcontroller_job.xml
    [IPClusterStart] Starting Win HPC Job: job submit /jobfile:\\blue\domainusers$\bgranger\.ipython\profile_mycluster\ipengineset_job.xml /scheduler:HEADNODE
    

At this point, the controller and two engines are running on your local host.
This configuration is useful for testing and for situations where you want to
take advantage of multiple cores on your local computer. 

Now that we have confirmed that :command:`ipcluster` is working properly, we
describe how to configure and run an IPython cluster on an actual compute
cluster running Windows HPC Server 2008. Here is an outline of the needed
steps:

1. Create a cluster profile using: ``ipython profile create mycluster --parallel``

2. Edit configuration files in the directory :file:`.ipython\\cluster_mycluster`

3. Start the cluster using: ``ipcluster start --profile=mycluster -n 32``

Creating a cluster profile
--------------------------

In most cases, you will have to create a cluster profile to use IPython on a
cluster. A cluster profile is a name (like "mycluster") that is associated
with a particular cluster configuration. The profile name is used by
:command:`ipcluster` when working with the cluster.

Associated with each cluster profile is a cluster directory. This cluster
directory is a specially named directory (typically located in the
:file:`.ipython` subdirectory of your home directory) that contains the
configuration files for a particular cluster profile, as well as log files and
security keys. The naming convention for cluster directories is:
:file:`profile_<profile name>`. Thus, the cluster directory for a profile named
"foo" would be :file:`.ipython\\cluster_foo`.

To create a new cluster profile (named "mycluster") and the associated cluster
directory, type the following command at the Windows Command Prompt::

    ipython profile create --parallel --profile=mycluster

The output of this command is shown in the screenshot below. Notice how
:command:`ipcluster` prints out the location of the newly created profile
directory::

    Z:\>ipython profile create mycluster --parallel
    [ProfileCreate] Generating default config file: u'\\\\blue\\domainusers$\\bgranger\\.ipython\\profile_mycluster\\ipython_config.py'
    [ProfileCreate] Generating default config file: u'\\\\blue\\domainusers$\\bgranger\\.ipython\\profile_mycluster\\ipcontroller_config.py'
    [ProfileCreate] Generating default config file: u'\\\\blue\\domainusers$\\bgranger\\.ipython\\profile_mycluster\\ipengine_config.py'
    [ProfileCreate] Generating default config file: u'\\\\blue\\domainusers$\\bgranger\\.ipython\\profile_mycluster\\ipcluster_config.py'
    [ProfileCreate] Generating default config file: u'\\\\blue\\domainusers$\\bgranger\\.ipython\\profile_mycluster\\iplogger_config.py'

    Z:\>

Configuring a cluster profile
-----------------------------

Next, you will need to configure the newly created cluster profile by editing
the following configuration files in the cluster directory:

* :file:`ipcluster_config.py`
* :file:`ipcontroller_config.py`
* :file:`ipengine_config.py`

When :command:`ipcluster` is run, these configuration files are used to 
determine how the engines and controller will be started. In most cases,
you will only have to set a few of the attributes in these files.

To configure :command:`ipcluster` to use the Windows HPC job scheduler, you
will need to edit the following attributes in the file
:file:`ipcluster_config.py`::

    # Set these at the top of the file to tell ipcluster to use the
    # Windows HPC job scheduler.
    c.IPClusterStart.controller_launcher_class = 'WindowsHPCControllerLauncher'
    c.IPClusterEngines.engine_launcher_class = 'WindowsHPCEngineSetLauncher'

    # Set these to the host name of the scheduler (head node) of your cluster.
    c.WindowsHPCControllerLauncher.scheduler = 'HEADNODE'
    c.WindowsHPCEngineSetLauncher.scheduler = 'HEADNODE'

There are a number of other configuration attributes that can be set, but
in most cases these will be sufficient to get you started.

.. warning::
    If any of your configuration attributes involve specifying the location
    of shared directories or files, you must make sure that you use UNC paths
    like :file:`\\\\host\\share`. It is helpful to specify
    these paths using raw Python strings: ``r'\\host\share'`` to make sure
    that the backslashes are properly escaped.

Starting the cluster profile
----------------------------

Once a cluster profile has been configured, starting an IPython cluster using
the profile is simple::

    ipcluster start --profile=mycluster -n 32

The ``-n`` option tells :command:`ipcluster` how many engines to start (in
this case 32). Stopping the cluster is as simple as typing Control-C.

Using the HPC Job Manager
-------------------------
føø
When ``ipcluster start`` is run the first time, :command:`ipcluster` creates
two XML job description files in the cluster directory:

* :file:`ipcontroller_job.xml`
* :file:`ipengineset_job.xml`

Once these files have been created, they can be imported into the HPC Job
Manager application. Then, the controller and engines for that profile can be
started using the HPC Job Manager directly, without using :command:`ipcluster`.
However, anytime the cluster profile is re-configured, ``ipcluster start``
must be run again to regenerate the XML job description files. The
following screenshot shows what the HPC Job Manager interface looks like
with a running IPython cluster.

.. image:: figs/hpc_job_manager.*

Performing a simple interactive parallel computation
====================================================

Once you have started your IPython cluster, you can start to use it. To do
this, open up a new Windows Command Prompt and start up IPython's interactive
shell by typing::

    ipython

Then you can create a :class:`DirectView` instance for your profile and
use the resulting instance to do a simple interactive parallel computation. In
the code and screenshot that follows, we take a simple Python function and
apply it to each element of an array of integers in parallel using the
:meth:`DirectView.map` method:

.. sourcecode:: ipython

    In [1]: from IPython.parallel import *

    In [2]: c = Client(profile='mycluster')

    In [3]: view = c[:]

    In [4]: c.ids
    Out[4]: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14]

    In [5]: def f(x):
       ...:     return x**10

    In [6]: view.map(f, range(15))  # f is applied in parallel
    Out[6]:
    [0,
     1,
     1024,
     59049,
     1048576,
     9765625,
     60466176,
     282475249,
     1073741824,
     3486784401L,
     10000000000L,
     25937424601L,
     61917364224L,
     137858491849L,
     289254654976L]

The :meth:`map` method has the same signature as Python's builtin :func:`map`
function, but runs the calculation in parallel. More involved examples of using
:class:`DirectView` are provided in the examples that follow.