Change doc folder src -> txt, rst -> src

doc/src/Python_mpi.rst

@@ -0,0 +1,79 @@
+Extending Python to run in parallel
+===================================
+
+If you wish to run LAMMPS in parallel from Python, you need to extend
+your Python with an interface to MPI.  This also allows you to
+make MPI calls directly from Python in your script, if you desire.
+
+We recommend use of mpi4py:
+
+* `PyPar <https://github.com/daleroberts/pypar>`_
+
+As of version 2.0.0 it allows passing a custom MPI communicator to
+the LAMMPS constructor, which means one can easily run one or more
+LAMMPS instances on subsets of the total MPI ranks.
+
+To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it
+and from its main directory, type
+
+
+.. parsed-literal::
+
+   python setup.py build
+   sudo python setup.py install
+
+Again, the "sudo" is only needed if required to copy mpi4py files into
+your Python distribution's site-packages directory. To install with
+user privilege into the user local directory type
+
+
+.. parsed-literal::
+
+   python setup.py install --user
+
+If you have successfully installed mpi4py, you should be able to run
+Python and type
+
+
+.. parsed-literal::
+
+   from mpi4py import MPI
+
+without error.  You should also be able to run python in parallel
+on a simple test script
+
+
+.. parsed-literal::
+
+   % mpirun -np 4 python test.py
+
+where test.py contains the lines
+
+
+.. parsed-literal::
+
+   from mpi4py import MPI
+   comm = MPI.COMM_WORLD
+   print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size())
+
+and see one line of output for each processor you run on.
+
+.. note::
+
+   To use mpi4py and LAMMPS in parallel from Python, you must
+   insure both are using the same version of MPI.  If you only have one
+   MPI installed on your system, this is not an issue, but it can be if
+   you have multiple MPIs.  Your LAMMPS build is explicit about which MPI
+   it is using, since you specify the details in your lo-level
+   src/MAKE/Makefile.foo file.  Mpi4py uses the "mpicc" command to find
+   information about the MPI it uses to build against.  And it tries to
+   load "libmpi.so" from the LD\_LIBRARY\_PATH.  This may or may not find
+   the MPI library that LAMMPS is using.  If you have problems running
+   both mpi4py and LAMMPS together, this is an issue you may need to
+   address, e.g. by moving other MPI installations so that mpi4py finds
+   the right one.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html