109 lines
2.9 KiB
ReStructuredText
109 lines
2.9 KiB
ReStructuredText
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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.. code-block:: python
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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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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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$ 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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.. code-block:: bash
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lmp_serial -in in.lj
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Running LAMMPS and Python in parallel with MPI
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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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:ref:`python_install_mpi4py`, create a ``test.py`` file containing these lines:
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.. code-block:: python
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from mpi4py import MPI
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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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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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MPI.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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.. 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:: python
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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, mpi4py is not 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 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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.. code-block:: bash
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$ python script.py
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$ python -i script.py
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$ ./script.py
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The last command requires that the first line of the script be
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something like this:
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.. code-block:: bash
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#!/usr/bin/python
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#!/usr/bin/python -i
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where the path points to where you have Python installed, and that you
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have made the script file executable:
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.. code-block:: bash
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$ chmod +x script.py
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Without the ``-i`` flag, Python will exit when the script finishes.
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With the ``-i`` flag, you will be left in the Python interpreter when
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the script finishes, so you can type subsequent commands. As
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mentioned above, you can only run Python interactively when running
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Python on a single processor, not in parallel.
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