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https://github.com/uqfoundation/pathos
parallel graph management and execution in heterogeneous computing
https://github.com/uqfoundation/pathos
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parallel graph management and execution in heterogeneous computing
- Host: GitHub
- URL: https://github.com/uqfoundation/pathos
- Owner: uqfoundation
- License: other
- Created: 2013-06-28T06:31:38.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2024-10-02T02:52:37.000Z (about 1 month ago)
- Last Synced: 2024-10-12T08:30:57.448Z (about 1 month ago)
- Language: Python
- Homepage: http://pathos.rtfd.io
- Size: 1.76 MB
- Stars: 1,382
- Watchers: 35
- Forks: 89
- Open Issues: 71
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
pathos
======
parallel graph management and execution in heterogeneous computing
About the Pathos Framework
--------------------------
``pathos`` is a framework for heterogeneous computing. It provides a consistent
high-level interface for configuring and launching parallel computations
across heterogeneous resources. ``pathos`` provides configurable launchers for
parallel and distributed computing, where each launcher contains the
syntactic logic to configure and launch jobs in an execution environment.
Examples of launchers that plug into ``pathos`` are: a queue-less MPI-based
launcher (in ``pyina``), a ssh-based launcher (in ``pathos``), and a multi-process
launcher (in ``multiprocess``).
``pathos`` provides a consistent interface for parallel and/or distributed
versions of ``map`` and ``apply`` for each launcher, thus lowering the barrier
for users to extend their code to parallel and/or distributed resources.
The guiding design principle behind ``pathos`` is that ``map`` and ``apply``
should be drop-in replacements in otherwise serial code, and thus switching
to one or more of the ``pathos`` launchers is all that is needed to enable
code to leverage the selected parallel or distributed computing resource.
This not only greatly reduces the time to convert a code to parallel, but it
also enables a single code-base to be maintained instead of requiring
parallel, serial, and distributed versions of a code. ``pathos`` maps can be
nested, thus hierarchical heterogeneous computing is possible by merely
selecting the desired hierarchy of ``map`` and ``pipe`` (``apply``) objects.
The ``pathos`` framework is composed of several interoperating packages:
* ``dill``: serialize all of Python
* ``pox``: utilities for filesystem exploration and automated builds
* ``klepto``: persistent caching to memory, disk, or database
* ``multiprocess``: better multiprocessing and multithreading in Python
* ``ppft``: distributed and parallel Python
* ``pyina``: MPI parallel ``map`` and cluster scheduling
* ``pathos``: graph management and execution in heterogeneous computing
About Pathos
------------
The ``pathos`` package provides a few basic tools to make parallel and
distributed computing more accessible to the end user. The goal of ``pathos``
is to enable the user to extend their own code to parallel and distributed
computing with minimal refactoring.
``pathos`` provides methods for configuring, launching, monitoring, and
controlling a service on a remote host. One of the most basic features
of ``pathos`` is the ability to configure and launch a RPC-based service
on a remote host. ``pathos`` seeds the remote host with the ``portpicker``
script, which allows the remote host to inform the localhost of a port
that is available for communication.
Beyond the ability to establish a RPC service, and then post requests,
is the ability to launch code in parallel. Unlike parallel computing
performed at the node level (typically with MPI), ``pathos`` enables the
user to launch jobs in parallel across heterogeneous distributed resources.
``pathos`` provides distributed ``map`` and ``pipe`` algorithms, where a mix of
local processors and distributed workers can be selected. ``pathos``
also provides a very basic automated load balancing service, as well as
the ability for the user to directly select the resources.
The high-level ``pool.map`` interface, yields a ``map`` implementation that
hides the RPC internals from the user. With ``pool.map``, the user can launch
their code in parallel, and as a distributed service, using standard Python
and without writing a line of server or parallel batch code.
RPC servers and communication in general is known to be insecure. However,
instead of attempting to make the RPC communication itself secure, ``pathos``
provides the ability to automatically wrap any distributes service or
communication in a ssh-tunnel. Ssh is a universally trusted method.
Using ssh-tunnels, ``pathos`` has launched several distributed calculations
on national lab clusters, and to date has performed test calculations
that utilize node-to-node communication between several national lab clusters
and a user's laptop. ``pathos`` allows the user to configure and launch
at a very atomistic level, through raw access to ssh and scp.
``pathos`` is the core of a Python framework for heterogeneous computing.
``pathos`` is in active development, so any user feedback, bug reports, comments,
or suggestions are highly appreciated. A list of issues is located at https://github.com/uqfoundation/pathos/issues, with a legacy list maintained at https://uqfoundation.github.io/project/pathos/query.
Major Features
--------------
``pathos`` provides a configurable distributed parallel ``map`` interface
to launching RPC service calls, with:
* a ``map`` interface that meets and extends the Python ``map`` standard
* the ability to submit service requests to a selection of servers
* the ability to tunnel server communications with ssh
The ``pathos`` core is built on low-level communication to remote hosts using
ssh. The interface to ssh, scp, and ssh-tunneled connections can:
* configure and launch remote processes with ssh
* configure and copy file objects with scp
* establish an tear-down a ssh-tunnel
To get up and running quickly, ``pathos`` also provides infrastructure to:
* easily establish a ssh-tunneled connection to a RPC server
Current Release
[](https://pepy.tech/project/pathos)
[](https://anaconda.org/conda-forge/pathos)
[](https://stackoverflow.com/questions/tagged/pathos)
---------------
The latest released version of ``pathos`` is available from:
https://pypi.org/project/pathos
``pathos`` is distributed under a 3-clause BSD license.
Development Version
[](http://www.uqfoundation.org/pages/donate.html)
[](https://pathos.readthedocs.io/en/latest/?badge=latest)
[](https://app.travis-ci.com/github/uqfoundation/pathos)
[](https://codecov.io/gh/uqfoundation/pathos)
-------------------
You can get the latest development version with all the shiny new features at:
https://github.com/uqfoundation
If you have a new contribution, please submit a pull request.
Installation
------------
``pathos`` can be installed with ``pip``::
$ pip install pathos
Requirements
------------
``pathos`` requires:
* ``python`` (or ``pypy``), **>=3.8**
* ``setuptools``, **>=42**
* ``pox``, **>=0.3.5**
* ``dill``, **>=0.3.9**
* ``ppft``, **>=1.7.6.9**
* ``multiprocess``, **>=0.70.17**
More Information
----------------
Probably the best way to get started is to look at the documentation at
http://pathos.rtfd.io. Also see ``pathos.tests`` and https://github.com/uqfoundation/pathos/tree/master/examples for a set of scripts that demonstrate the
configuration and launching of communications with ssh and scp, and demonstrate
the configuration and execution of jobs in a hierarchical parallel workflow.
You can run the test suite with ``python -m pathos.tests``. Tunnels and other
connections to remote servers can be established with the ``pathos_connect``
script (or with ``python -m pathos``). See ``pathos_connect --help`` for more
information. ``pathos`` also provides a ``portpicker`` script to select an
open port (also available with ``python -m pathos.portpicker``). The source
code is generally well documented, so further questions may be resolved by
inspecting the code itself. Please feel free to submit a ticket on github,
or ask a question on stackoverflow (**@Mike McKerns**). If you would like to
share how you use ``pathos`` in your work, please send an email (to **mmckerns
at uqfoundation dot org**).
Important classes and functions are found here:
* ``pathos.abstract_launcher`` [the worker pool API definition]
* ``pathos.pools`` [all of the pathos worker pools]
* ``pathos.core`` [the high-level command interface]
* ``pathos.hosts`` [the hostname registry interface]
* ``pathos.serial.SerialPool`` [the serial Python worker pool]
* ``pathos.parallel.ParallelPool`` [the parallelpython worker pool]
* ``pathos.multiprocessing.ProcessPool`` [the multiprocessing worker pool]
* ``pathos.threading.ThreadPool`` [the multithreading worker pool]
* ``pathos.connection.Pipe`` [the launcher base class]
* ``pathos.secure.Pipe`` [the secure launcher base class]
* ``pathos.secure.Copier`` [the secure copier base class]
* ``pathos.secure.Tunnel`` [the secure tunnel base class]
* ``pathos.selector.Selector`` [the selector base class]
* ``pathos.server.Server`` [the server base class]
* ``pathos.profile`` [profiling in threads and processes]
* ``pathos.maps`` [standalone map instances]
``pathos`` also provides two convenience scripts that are used to establish
secure distributed connections. These scripts are installed to a directory
on the user's ``$PATH``, and thus can be run from anywhere:
* ``portpicker`` [get the portnumber of an open port]
* ``pathos_connect`` [establish tunnel and/or RPC server]
Typing ``--help`` as an argument to any of the above scripts will print out an
instructive help message.
Citation
--------
If you use ``pathos`` to do research that leads to publication, we ask that you
acknowledge use of ``pathos`` by citing the following in your publication::
M.M. McKerns, L. Strand, T. Sullivan, A. Fang, M.A.G. Aivazis,
"Building a framework for predictive science", Proceedings of
the 10th Python in Science Conference, 2011;
http://arxiv.org/pdf/1202.1056
Michael McKerns and Michael Aivazis,
"pathos: a framework for heterogeneous computing", 2010- ;
https://uqfoundation.github.io/project/pathos
Please see https://uqfoundation.github.io/project/pathos or
http://arxiv.org/pdf/1202.1056 for further information.