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.
171 lines
4.5 KiB
ReStructuredText
171 lines
4.5 KiB
ReStructuredText
Test the Python/LAMMPS interface
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================================
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To test if LAMMPS is callable from Python, launch Python interactively
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and type:
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.. parsed-literal::
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>>> from lammps import lammps
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>>> lmp = lammps()
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If you get no errors, you're ready to use LAMMPS from Python. If the
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2nd command fails, the most common error to see is
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.. parsed-literal::
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OSError: Could not load LAMMPS dynamic library
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which means Python was unable to load the LAMMPS shared library. This
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typically occurs if the system can't find the LAMMPS shared library or
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one of the auxiliary shared libraries it depends on, or if something
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about the library is incompatible with your Python. The error message
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should give you an indication of what went wrong.
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You can also test the load directly in Python as follows, without
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first importing from the lammps.py file:
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.. parsed-literal::
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>>> from ctypes import CDLL
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>>> CDLL("liblammps.so")
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If an error occurs, carefully go through the steps on the
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:doc:`Build\_basics <Build_basics>` doc page about building a shared
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library and the :doc:`Python\_install <Python_install>` doc page about
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insuring Python can find the necessary two files it needs.
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**Test LAMMPS and Python in serial:**
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-------------------------------------
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To run a LAMMPS test in serial, type these lines into Python
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interactively from the bench directory:
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.. parsed-literal::
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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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.. parsed-literal::
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% python 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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lmp_g++ -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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.. parsed-literal::
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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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To run LAMMPS in parallel, assuming you have installed the
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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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.. parsed-literal::
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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 either script in parallel as:
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.. parsed-literal::
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% mpirun -np 4 python test.py
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and you should see the same output as if you had typed
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.. parsed-literal::
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% mpirun -np 4 lmp_g++ -in in.lj
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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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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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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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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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.. parsed-literal::
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% python foo.script
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% python -i foo.script
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% foo.script
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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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.. parsed-literal::
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#!/usr/local/bin/python
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#!/usr/local/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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.. parsed-literal::
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% chmod +x foo.script
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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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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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