574e4067dc
This is the first step for moving the documentation format from *.txt to the *.rst format. In the last years we've been automatically converting txt files from Steve's markup into RST to generate the documentation pages via Sphinx. The decision has now been made to fully migrate to RST and avoid the conversion in the future. This will enable us to fully use RST and Sphinx to improve the documentation. For the intermediate period, while there are still pending PRs with documentation changes, we will keep both source files and update the RST files accordingly.
80 lines
2.3 KiB
ReStructuredText
80 lines
2.3 KiB
ReStructuredText
Extending Python to run in parallel
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===================================
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If you wish to run LAMMPS in parallel from Python, you need to extend
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your Python with an interface to MPI. This also allows you to
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make MPI calls directly from Python in your script, if you desire.
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We recommend use of mpi4py:
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* `PyPar <https://github.com/daleroberts/pypar>`_
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As of version 2.0.0 it allows passing a custom MPI communicator to
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the LAMMPS constructor, which means one can easily run one or more
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LAMMPS instances on subsets of the total MPI ranks.
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To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it
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and from its main directory, type
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.. parsed-literal::
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python setup.py build
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sudo python setup.py install
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Again, the "sudo" is only needed if required to copy mpi4py files into
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your Python distribution's site-packages directory. To install with
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user privilege into the user local directory type
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.. parsed-literal::
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python setup.py install --user
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If you have successfully installed mpi4py, you should be able to run
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Python and type
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.. parsed-literal::
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from mpi4py import MPI
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without error. You should also be able to run python in parallel
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on a simple test script
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.. parsed-literal::
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% mpirun -np 4 python test.py
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where test.py contains the lines
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.. parsed-literal::
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from mpi4py import MPI
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comm = MPI.COMM_WORLD
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print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size())
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and see one line of output for each processor you run on.
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.. note::
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To use mpi4py and LAMMPS in parallel from Python, you must
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insure both are using the same version of MPI. If you only have one
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MPI installed on your system, this is not an issue, but it can be if
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you have multiple MPIs. Your LAMMPS build is explicit about which MPI
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it is using, since you specify the details in your lo-level
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src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find
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information about the MPI it uses to build against. And it tries to
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load "libmpi.so" from the LD\_LIBRARY\_PATH. This may or may not find
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the MPI library that LAMMPS is using. If you have problems running
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both mpi4py and LAMMPS together, this is an issue you may need to
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address, e.g. by moving other MPI installations so that mpi4py finds
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the right one.
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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