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MPI parallel map and cluster scheduling

Project description

About Pyina

The pyina package provides several basic tools to make MPI-based parallel computing more accessable to the end user. The goal of pyina is to allow the user to extend their own code to MPI-based parallel computing with minimal refactoring.

The central element of pyina is the parallel map algorithm. pyina currently provides two strategies for executing the parallel-map, where a strategy is the algorithm for distributing the work list of jobs across the availble nodes. These strategies can be used “in-the-raw” (i.e. directly) to provide the map algorithm to a user’s own mpi-aware code. Further, in pyina.mpi pyina provides pipe and map implementations (known as “easy map”) that hide the MPI internals from the user. With the “easy map”, the user can launch their code in parallel batch mode – using standard python and without ever having to write a line of MPI code.

There are several ways that a user would typically launch their code in parallel – directly with mpirun or mpiexec, or through the use of a scheduler such as torque or slurm. pyina encapsulates several of these “launchers”, and provides a common interface to the different methods of launching a MPI job.

pyina is part of pathos, a python framework for heterogeneous computing. pyina is in active development, so any user feedback, bug reports, comments, or suggestions are highly appreciated. A list of known issues is maintained at http://trac.mystic.cacr.caltech.edu/project/pathos/query.html, with a public ticket list at https://github.com/uqfoundation/pyina/issues.

Major Features

pyina provides a highly configurable parallel map interface to running MPI jobs, with:

  • a map interface that extends the python map standard
  • the ability to submit batch jobs to a selection of schedulers
  • the ability to customize node and process launch configurations
  • the ability to launch parallel MPI jobs with standard python
  • ease in selecting different strategies for processing a work list

Current Release

This documentation is for version pyina-0.2.0.

The latest released version of pyina is available at:

https://pypi.org/project/pyina

pyina is distributed under a 3-clause BSD license.

>>> import pyina
>>> print (pyina.license())

Development Version

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

pyina is packaged to install from source, so you must download the tarball, unzip, and run the installer:

[download]
$ tar -xvzf pyina-0.2.0.tar.gz
$ cd pyina-0.2.0
$ python setup py build
$ python setup py install

You will be warned of any missing dependencies and/or settings after you run the “build” step above. pyina depends on dill, pox, pathos, and mpi4py, so you should install them first. A version of MPI must also be installed. Launchers in pyina that submit to a scheduler will throw errors if the underlying scheduler is not available, however a scheduler is not required for pyina to execute.

Alternately, pyina can be installed with pip or easy_install:

$ pip install pyina

Requirements

pyina requires:

  • python, version >= 2.6 or version >= 3.3
  • numpy, version >= 1.0
  • mpi4py, version >= 1.2.1
  • dill, version >= 0.2.8.1
  • pox, version >= 0.2.4
  • pathos, version >= 0.2.2

Optional requirements:

  • setuptools, version >= 0.6
  • pyre, version == 0.8
  • mystic, version >= 0.3.1

More Information

Probably the best way to get started is to look at the documentation at http://pyina.rtfd.io. Also see pyina.examples and pyina.tests for a set of scripts that demonstrate the configuration and launching of mpi-based parallel jobs using the “easy map” interface. Also see pyina.examples_other for a set of scripts that test the more raw internals of pyina. You can run the tests with python -m pyina.tests. A script is included for querying, setting up, and tearing down an MPI environment, see python -m pyina for more information. 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 pyina in your work, please send an email (to mmckerns at uqfoundation dot org).

Important classes and functions are found here:

  • pyina.mpi [the map API definition]
  • pyina.schedulers [all available schedulers]
  • pyina.launchers [all available launchers]

Mapping strategies are found here:

  • pyina.mpi_scatter [the scatter-gather strategy]
  • pyina.mpi_pool [the worker pool strategy]

pyina also provides a convience script that helps navigate the MPI environment. This script can be run from anywhere with:

$ mpi_world

If may also be convienent to set a shell alias for the launch of ‘raw’ mpi-python jobs. Set something like the following (for bash):

$ alias mpython1='mpiexec -np 1 `which python`'
$ alias mpython2='mpiexec -np 2 `which python`'
$ ...

Citation

If you use pyina to do research that leads to publication, we ask that you acknowledge use of pyina 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- ;
http://trac.mystic.cacr.caltech.edu/project/pathos

Please see http://trac.mystic.cacr.caltech.edu/project/pathos or http://arxiv.org/pdf/1202.1056 for further information.

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