MPI parallel map and cluster scheduling
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 issues is located at https://github.com/uqfoundation/pyina/issues, with a legacy list maintained at https://uqfoundation.github.io/project/pathos/query.
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
The latest released version of pyina
is available at:
https://pypi.org/project/pyina
pyina
is distributed under a 3-clause BSD license.
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.
pyina
can be installed with pip
::
$ pip install pyina
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.
pyina
requires:
python
(orpypy
), >=3.8setuptools
, >=42cython
, >=0.29.30numpy
, >=1.0mpi4py
, >=1.3dill
, >=0.3.8pox
, >=0.3.4pathos
, >=0.3.2
Probably the best way to get started is to look at the documentation at
http://pyina.rtfd.io. Also see https://github.com/uqfoundation/pyina/tree/master/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. 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`'
$ ...
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- ;
https://uqfoundation.github.io/project/pathos
Please see https://uqfoundation.github.io/project/pathos or http://arxiv.org/pdf/1202.1056 for further information.