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sjplimp
@ -277,35 +277,14 @@ 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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There are several Python packages available that purport to wrap MPI
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as a library and allow MPI functions to be called from Python.
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as a library and allow MPI functions to be called from Python. However,
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development on most of them seems to be halted except on:
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These include
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"mpi4py"_https://bitbucket.org/mpi4py/mpi4py
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"PyPar"_https://github.com/daleroberts/pypar :ul
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"pyMPI"_http://pympi.sourceforge.net/
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"maroonmpi"_http://code.google.com/p/maroonmpi/
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"mpi4py"_http://code.google.com/p/mpi4py/
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"myMPI"_http://nbcr.sdsc.edu/forum/viewtopic.php?t=89&sid=c997fefc3933bd66204875b436940f16
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"Pypar"_http://code.google.com/p/pypar :ul
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All of these except pyMPI work by wrapping the MPI library and
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exposing (some portion of) its interface to your Python script. This
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means Python cannot be used interactively in parallel, since they do
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not address the issue of interactive input to multiple instances of
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Python running on different processors. The one exception is pyMPI,
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which alters the Python interpreter to address this issue, and (I
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believe) creates a new alternate executable (in place of "python"
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itself) as a result.
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In principle any of these Python/MPI packages should work to invoke
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LAMMPS in parallel and to make MPI calls themselves from a Python
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script which is itself running in parallel. However, when I
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downloaded and looked at a few of them, their documentation was
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incomplete and I had trouble with their installation. It's not clear
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if some of the packages are still being actively developed and
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supported.
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The packages Pypar and mpi4py have both been successfully tested with
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LAMMPS. Pypar is simpler and easy to set up and use, but supports
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Both packages, PyPar and mpi4py have been successfully tested with
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LAMMPS. PyPar is simpler and easy to set up and use, but supports
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only a subset of MPI. Mpi4py is more MPI-feature complete, but also a
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bit more complex to use. As of version 2.0.0, mpi4py is the only
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python MPI wrapper that allows passing a custom MPI communicator to
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@ -314,7 +293,7 @@ LAMMPS instances on subsets of the total MPI ranks.
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:line
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Pypar requires the ubiquitous "Numpy package"_http://numpy.scipy.org
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PyPar requires the ubiquitous "Numpy package"_http://numpy.scipy.org
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be installed in your Python. After launching Python, type
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import numpy :pre
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@ -329,16 +308,16 @@ sudo python setup.py install :pre
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The "sudo" is only needed if required to copy Numpy files into your
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Python distribution's site-packages directory.
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To install Pypar (version pypar-2.1.4_94 as of Aug 2012), unpack it
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To install PyPar (version pypar-2.1.4_94 as of Aug 2012), unpack it
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and from its "source" directory, type
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python setup.py build
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sudo python setup.py install :pre
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Again, the "sudo" is only needed if required to copy Pypar files into
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Again, the "sudo" is only needed if required to copy PyPar files into
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your Python distribution's site-packages directory.
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If you have successully installed Pypar, you should be able to run
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If you have successully installed PyPar, you should be able to run
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Python and type
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import pypar :pre
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@ -355,17 +334,17 @@ print "Proc %d out of %d procs" % (pypar.rank(),pypar.size()) :pre
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and see one line of output for each processor you run on.
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NOTE: To use Pypar and LAMMPS in parallel from Python, you must insure
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NOTE: To use PyPar and LAMMPS in parallel from Python, you must insure
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both are using the same version of MPI. If you only have one MPI
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installed on your system, this is not an issue, but it can be if you
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have multiple MPIs. Your LAMMPS build is explicit about which MPI it
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is using, since you specify the details in your lo-level
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src/MAKE/Makefile.foo file. Pypar uses the "mpicc" command to find
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src/MAKE/Makefile.foo file. PyPar 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 Pypar 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 Pypar finds
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both PyPar 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 PyPar finds
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the right one.
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:line
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@ -467,8 +446,8 @@ lmp_g++ -in in.lj :pre
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[Test LAMMPS and Python in parallel:] :h5
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To run LAMMPS in parallel, assuming you have installed the
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"Pypar"_Pypar package as discussed above, create a test.py file
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containing these lines:
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"PyPar"_https://github.com/daleroberts/pypar package as discussed
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above, create a test.py file containing these lines:
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import pypar
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from lammps import lammps
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@ -478,8 +457,8 @@ print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp
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pypar.finalize() :pre
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To run LAMMPS in parallel, assuming you have installed the
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"mpi4py"_mpi4py package as discussed above, create a test.py file
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containing these lines:
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"mpi4py"_https://bitbucket.org/mpi4py/mpi4py package as discussed
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above, create a test.py file containing these lines:
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from mpi4py import MPI
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from lammps import lammps
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@ -498,17 +477,17 @@ and you should see the same output as if you had typed
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% mpirun -np 4 lmp_g++ -in in.lj :pre
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Note that if you leave out the 3 lines from test.py that specify Pypar
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Note that if you leave out the 3 lines from test.py that specify PyPar
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commands you will instantiate and run LAMMPS independently on each of
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the P processors specified in the mpirun command. In this case you
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should get 4 sets of output, each showing that a LAMMPS run was made
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on a single processor, instead of one set of output showing that
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LAMMPS ran on 4 processors. If the 1-processor outputs occur, it
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means that Pypar is not working correctly.
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means that PyPar is not working correctly.
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Also note that once you import the PyPar module, Pypar initializes MPI
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Also note that once you import the PyPar module, PyPar initializes MPI
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for you, and you can use MPI calls directly in your Python script, as
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described in the Pypar documentation. The last line of your Python
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described in the PyPar documentation. The last line of your Python
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script should be pypar.finalize(), to insure MPI is shut down
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correctly.
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@ -761,7 +740,8 @@ Add a wrapper method to python/lammps.py for this interface
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function. :l
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You should now be able to invoke the new interface function from a
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Python script. Isn't ctypes amazing? :l,ule
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Python script. Isn't ctypes amazing? :l
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:ule
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:line
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:line
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