docs/source/parallelz/parallel_process.txt

.. _parallel_process:

===========================================
Starting the IPython controller and engines
===========================================

To use IPython for parallel computing, you need to start one instance of
the controller and one or more instances of the engine. The controller
and each engine can run on different machines or on the same machine.
Because of this, there are many different possibilities.

Broadly speaking, there are two ways of going about starting a controller and engines:

* In an automated manner using the :command:`ipclusterz` command.
* In a more manual way using the :command:`ipcontrollerz` and 
  :command:`ipenginez` commands.

This document describes both of these methods. We recommend that new users
start with the :command:`ipclusterz` command as it simplifies many common usage
cases.

General considerations
======================

Before delving into the details about how you can start a controller and
engines using the various methods, we outline some of the general issues that
come up when starting the controller and engines. These things come up no
matter which method you use to start your IPython cluster.

Let's say that you want to start the controller on ``host0`` and engines on
hosts ``host1``-``hostn``. The following steps are then required:

1. Start the controller on ``host0`` by running :command:`ipcontrollerz` on
   ``host0``.
2. Move the JSON file (:file:`ipcontroller-engine.json`) created by the 
   controller from ``host0`` to hosts ``host1``-``hostn``.
3. Start the engines on hosts ``host1``-``hostn`` by running 
   :command:`ipenginez`.  This command has to be told where the JSON file 
   (:file:`ipcontroller-engine.json`) is located.

At this point, the controller and engines will be connected. By default, the JSON files
created by the controller are put into the :file:`~/.ipython/clusterz_default/security`
directory. If the engines share a filesystem with the controller, step 2 can be skipped as
the engines will automatically look at that location.

The final step required to actually use the running controller from a client is to move
the JSON file :file:`ipcontroller-client.json` from ``host0`` to any host where clients
will be run. If these file are put into the :file:`~/.ipython/clusterz_default/security`
directory of the client's host, they will be found automatically. Otherwise, the full path
to them has to be passed to the client's constructor.

Using :command:`ipclusterz`
==========================

The :command:`ipclusterz` command provides a simple way of starting a
controller and engines in the following situations:

1. When the controller and engines are all run on localhost. This is useful
   for testing or running on a multicore computer.
2. When engines are started using the :command:`mpirun` command that comes 
   with most MPI [MPI]_ implementations
3. When engines are started using the PBS [PBS]_ batch system.
4. When the controller is started on localhost and the engines are started on 
   remote nodes using :command:`ssh`.

.. note::

    It is also possible for advanced users to add support to
    :command:`ipclusterz` for starting controllers and engines using other
    methods (like Sun's Grid Engine for example).

.. note::

    Currently :command:`ipclusterz` requires that the
    :file:`~/.ipython/cluster_<profile>/security` directory live on a shared filesystem that is
    seen by both the controller and engines. If you don't have a shared file
    system you will need to use :command:`ipcontrollerz` and
    :command:`ipenginez` directly.  This constraint can be relaxed if you are 
    using the :command:`ssh` method to start the cluster.

Under the hood, :command:`ipclusterz` just uses :command:`ipcontrollerz`
and :command:`ipenginez` to perform the steps described above.

Using :command:`ipclusterz` in local mode
----------------------------------------

To start one controller and 4 engines on localhost, just do::

    $ ipclusterz start -n 4

To see other command line options for the local mode, do::

    $ ipclusterz -h

.. note::

    The remainder of this section refers to the 0.10 clusterfile model, no longer in use.
    skip to 

Using :command:`ipclusterz` in mpiexec/mpirun mode
-------------------------------------------------

.. note::

    This section is out of date for IPython 0.11


The mpiexec/mpirun mode is useful if you:

1. Have MPI installed.
2. Your systems are configured to use the :command:`mpiexec` or
   :command:`mpirun` commands to start MPI processes.

.. note::

    The preferred command to use is :command:`mpiexec`.  However, we also 
    support :command:`mpirun` for backwards compatibility.  The underlying
    logic used is exactly the same, the only difference being the name of the 
    command line program that is called.

If these are satisfied, you can start an IPython cluster using::

    $ ipclusterz mpiexec -n 4

This does the following:

1. Starts the IPython controller on current host.
2. Uses :command:`mpiexec` to start 4 engines.

On newer MPI implementations (such as OpenMPI), this will work even if you
don't make any calls to MPI or call :func:`MPI_Init`. However, older MPI
implementations actually require each process to call :func:`MPI_Init` upon
starting. The easiest way of having this done is to install the mpi4py
[mpi4py]_ package and then call ipclusterz with the ``--mpi`` option::

    $ ipclusterz mpiexec -n 4 --mpi=mpi4py

Unfortunately, even this won't work for some MPI implementations. If you are
having problems with this, you will likely have to use a custom Python
executable that itself calls :func:`MPI_Init` at the appropriate time.
Fortunately, mpi4py comes with such a custom Python executable that is easy to
install and use. However, this custom Python executable approach will not work
with :command:`ipclusterz` currently.

Additional command line options for this mode can be found by doing::

    $ ipclusterz mpiexec -h

More details on using MPI with IPython can be found :ref:`here <parallelmpi>`.


Using :command:`ipclusterz` in PBS mode
--------------------------------------

.. note::

    This section is out of date for IPython 0.11


The PBS mode uses the Portable Batch System [PBS]_ to start the engines. To
use this mode, you first need to create a PBS script template that will be
used to start the engines. Here is a sample PBS script template:

.. sourcecode:: bash

    #PBS -N ipython
    #PBS -j oe
    #PBS -l walltime=00:10:00
    #PBS -l nodes=${n/4}:ppn=4
    #PBS -q parallel

    cd $$PBS_O_WORKDIR
    export PATH=$$HOME/usr/local/bin
    export PYTHONPATH=$$HOME/usr/local/lib/python2.4/site-packages
    /usr/local/bin/mpiexec -n ${n} ipengine --logfile=$$PBS_O_WORKDIR/ipengine

There are a few important points about this template:

1. This template will be rendered at runtime using IPython's :mod:`Itpl` 
   template engine.

2. Instead of putting in the actual number of engines, use the notation
   ``${n}`` to indicate the number of engines to be started. You can also uses
   expressions like ``${n/4}`` in the template to indicate the number of 
   nodes.

3. Because ``$`` is a special character used by the template engine, you must  
   escape any ``$`` by using ``$$``.  This is important when referring to 
   environment variables in the template.

4. Any options to :command:`ipenginez` should be given in the batch script 
   template.

5. Depending on the configuration of you system, you may have to set 
   environment variables in the script template.

Once you have created such a script, save it with a name like
:file:`pbs.template`. Now you are ready to start your job::

    $ ipclusterz pbs -n 128 --pbs-script=pbs.template

Additional command line options for this mode can be found by doing::

    $ ipclusterz pbs -h

Using :command:`ipclusterz` in SSH mode
--------------------------------------

.. note::

    This section is out of date for IPython 0.11


The SSH mode uses :command:`ssh` to execute :command:`ipenginez` on remote
nodes and the :command:`ipcontrollerz` on localhost.

When using using this mode it highly recommended that you have set up SSH keys
and are using ssh-agent [SSH]_ for password-less logins.

To use this mode you need a python file describing the cluster, here is an
example of such a "clusterfile":

.. sourcecode:: python
    
    send_furl = True
    engines = { 'host1.example.com' : 2,
                'host2.example.com' : 5,
                'host3.example.com' : 1,
                'host4.example.com' : 8 }

Since this is a regular python file usual python syntax applies. Things to
note:

* The `engines` dict, where the keys is the host we want to run engines on and
  the value is the number of engines to run on that host.
* send_furl can either be `True` or `False`, if `True` it will copy over the
  furl needed for :command:`ipenginez` to each host.

The ``--clusterfile`` command line option lets you specify the file to use for
the cluster definition. Once you have your cluster file and you can
:command:`ssh` into the remote hosts with out an password you are ready to
start your cluster like so:

.. sourcecode:: bash 

   $ ipclusterz ssh --clusterfile /path/to/my/clusterfile.py


Two helper shell scripts are used to start and stop :command:`ipenginez` on
remote hosts:

* sshx.sh 
* engine_killer.sh

Defaults for both of these are contained in the source code for
:command:`ipclusterz`. The default scripts are written to a local file in a
tmep directory and then copied to a temp directory on the remote host and
executed from there. On most Unix, Linux and OS X systems this is /tmp.

The default sshx.sh is the following:

.. sourcecode:: bash

   #!/bin/sh
   "$@" &> /dev/null &
   echo $!

If you want to use a custom sshx.sh script you need to use the ``--sshx``
option and specify the file to use. Using a custom sshx.sh file could be
helpful when you need to setup the environment on the remote host before
executing :command:`ipenginez`.

For a detailed options list:

.. sourcecode:: bash

   $ ipclusterz ssh -h

Current limitations of the SSH mode of :command:`ipclusterz` are:

* Untested on Windows. Would require a working :command:`ssh` on Windows.
  Also, we are using shell scripts to setup and execute commands on remote
  hosts.
* :command:`ipcontrollerz` is started on localhost, with no option to start it
  on a remote node.

Using the :command:`ipcontrollerz` and :command:`ipenginez` commands
====================================================================

It is also possible to use the :command:`ipcontrollerz` and :command:`ipenginez`
commands to start your controller and engines. This approach gives you full
control over all aspects of the startup process.

Starting the controller and engine on your local machine
--------------------------------------------------------

To use :command:`ipcontrollerz` and :command:`ipenginez` to start things on your
local machine, do the following.

First start the controller::

	$ ipcontrollerz
	
Next, start however many instances of the engine you want using (repeatedly)
the command::

	$ ipenginez

The engines should start and automatically connect to the controller using the
JSON files in :file:`~/.ipython/cluster_<profile>/security`. You are now ready to use the
controller and engines from IPython.

.. warning:: 
	
	The order of the above operations may be important.  You *must*
	start the controller before the engines, unless you are manually specifying
	the ports on which to connect, in which case ordering is not important.

.. note::

    On some platforms (OS X), to put the controller and engine into the
    background you may need to give these commands in the form ``(ipcontroller
    &)`` and ``(ipengine &)`` (with the parentheses) for them to work
    properly.

Starting the controller and engines on different hosts
------------------------------------------------------

When the controller and engines are running on different hosts, things are
slightly more complicated, but the underlying ideas are the same:

1. Start the controller on a host using :command:`ipcontrollerz`.
2. Copy :file:`ipcontroller-engine.json` from :file:`~/.ipython/cluster_<profile>/security` on
   the controller's host to the host where the engines will run.
3. Use :command:`ipenginez` on the engine's hosts to start the engines.

The only thing you have to be careful of is to tell :command:`ipenginez` where
the :file:`ipcontroller-engine.json` file is located. There are two ways you
can do this:

* Put :file:`ipcontroller-engine.json` in the :file:`~/.ipython/cluster_<profile>/security`
  directory on the engine's host, where it will be found automatically.
* Call :command:`ipenginez` with the ``--file=full_path_to_the_file``
  flag.

The ``--file`` flag works like this::

    $ ipengine --file=/path/to/my/ipcontroller-engine.json

.. note::
    
    If the controller's and engine's hosts all have a shared file system  
    (:file:`~/.ipython/cluster_<profile>/security` is the same on all of them), then things
    will just work!

Make JSON files persistent
---------------------------

At fist glance it may seem that that managing the JSON files is a bit
annoying. Going back to the house and key analogy, copying the JSON around
each time you start the controller is like having to make a new key every time
you want to unlock the door and enter your house. As with your house, you want
to be able to create the key (or JSON file) once, and then simply use it at
any point in the future.

This is possible, but before you do this, you **must** remove any old JSON
files in the :file:`~/.ipython/cluster_<profile>/security` directory.

.. warning::

    You **must** remove old JSON files before using persistent JSON files.

Then, the only thing you have to do is specify the registration port, so that
the connection information in the JSON files remains accurate::

    $ ipcontrollerz -r --regport 12345


Then, just copy the JSON files over the first time and you are set. You can
start and stop the controller and engines any many times as you want in the
future, just make sure to tell the controller to use the *same* ports.

.. note::

    You may ask the question: what ports does the controller listen on if you
    don't tell is to use specific ones? The default is to use high random port
    numbers. We do this for two reasons: i) to increase security through
    obscurity and ii) to multiple controllers on a given host to start and
    automatically use different ports.

Log files
---------

All of the components of IPython have log files associated with them.
These log files can be extremely useful in debugging problems with
IPython and can be found in the directory :file:`~/.ipython/cluster_<profile>/log`.
Sending the log files to us will often help us to debug any problems.


.. [PBS] Portable Batch System.  http://www.openpbs.org/
.. [SSH] SSH-Agent http://en.wikipedia.org/wiki/Ssh-agent