Update Python docs
This commit is contained in:
Richard Berger
@ -5,9 +5,9 @@ Running LAMMPS and Python in serial:
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-------------------------------------
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To run a LAMMPS in serial, type these lines into Python
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interactively from the bench directory:
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interactively from the ``bench`` directory:
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.. parsed-literal::
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.. code-block:: python
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>>> from lammps import lammps
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>>> lmp = lammps()
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@ -17,35 +17,22 @@ Or put the same lines in the file ``test.py`` and run it as
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.. code-block:: bash
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% python test.py
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$ python3 test.py
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Either way, you should see the results of running the ``in.lj`` benchmark
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on a single processor appear on the screen, the same as if you had
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typed something like:
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.. parsed-literal::
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.. code-block:: bash
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lmp_serial -in in.lj
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Test LAMMPS and Python in parallel:
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---------------------------------------
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To run LAMMPS in parallel, assuming you have installed the
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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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.. code-block:: python
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import pypar
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from lammps import lammps
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lmp = lammps()
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lmp.file("in.lj")
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print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp
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pypar.finalize()
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Running LAMMPS and Python in parallel with MPI (mpi4py)
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-------------------------------------------------------
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To run LAMMPS in parallel, assuming you have installed the
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`mpi4py <https://mpi4py.readthedocs.io>`_ package as discussed
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above, create a ``test.py`` file containing these lines:
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:ref:`python_install_mpi4py`, create a ``test.py`` file containing these lines:
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.. code-block:: python
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@ -55,14 +42,61 @@ above, create a ``test.py`` file containing these lines:
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lmp.file("in.lj")
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me = MPI.COMM_WORLD.Get_rank()
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nprocs = MPI.COMM_WORLD.Get_size()
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print "Proc %d out of %d procs has" % (me,nprocs),lmp
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print("Proc %d out of %d procs has" % (me,nprocs),lmp)
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MPI.Finalize()
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You can run either script in parallel as:
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You can run the script in parallel as:
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.. code-block:: bash
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$ mpirun -np 4 python test.py
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$ mpirun -np 4 python3 test.py
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and you should see the same output as if you had typed
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.. code-block:: bash
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$ mpirun -np 4 lmp_mpi -in in.lj
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Note that without the mpi4py specific lines from ``test.py``
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.. code-block::
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from lammps import lammps
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lmp = lammps()
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lmp.file("in.lj")
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running the script with ``mpirun`` on :math:`P` processors would lead to
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:math:`P` independent simulations to run parallel, each with a single
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processor. Therefore, if you use the mpi4py lines and you see multiple LAMMPS
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single processor outputs. that means mpi4py isn't working correctly.
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Also note that once you import the mpi4py module, mpi4py 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 mpi4py documentation. The last line of your Python
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script should be ``MPI.finalize()``, to insure MPI is shut down
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correctly.
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Running LAMMPS and Python in parallel with MPI (pypar)
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------------------------------------------------------
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To run LAMMPS in parallel, assuming you have installed the
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`PyPar <https://github.com/daleroberts/pypar>`_ package as discussed
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in :ref:`python_install_mpi4py`, create a ``test.py`` file containing these lines:
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.. code-block:: python
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import pypar
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from lammps import lammps
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lmp = lammps()
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lmp.file("in.lj")
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print("Proc %d out of %d procs has" % (pypar.rank(),pypar.size()), lmp)
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pypar.finalize()
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You can run the script in parallel as:
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.. code-block:: bash
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$ mpirun -np 4 python3 test.py
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and you should see the same output as if you had typed
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@ -72,7 +106,7 @@ and you should see the same output as if you had typed
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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 :math:`P` processors specified in the mpirun command. In this case you
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the :math:`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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@ -84,8 +118,8 @@ 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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Running Python scripts:
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---------------------------
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Running Python scripts
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----------------------
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Note that any Python script (not just for LAMMPS) can be invoked in
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one of several ways:
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