92 lines
3.6 KiB
ReStructuredText
92 lines
3.6 KiB
ReStructuredText
Basics of running LAMMPS
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========================
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LAMMPS is run from the command line, reading commands from a
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file via the -in command line flag, or from standard input.
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Using the "-in in.file" variant is recommended:
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.. parsed-literal::
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lmp_serial < in.file
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lmp_serial -in in.file
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/path/to/lammps/src/lmp_serial < in.file
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mpirun -np 4 lmp_mpi -in in.file
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mpirun -np 8 /path/to//lammps/src/lmp_mpi -in in.file
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mpirun -np 6 /usr/local/bin/lmp -in in.file
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You normally run the LAMMPS command in the directory where your
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input script is located. That is also where output files are
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produced by default, unless you provide specific other paths in
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your input script or on the command line. As in some of the
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examples above, the LAMMPS executable itself can be placed elsewhere.
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.. note::
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The redirection operator "<" will not always work when running
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in parallel with mpirun; for those systems the -in form is required.
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As LAMMPS runs it prints info to the screen and a logfile named
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log.lammps. More info about output is given on the :doc:`Run output <Run_output>` doc page.
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If LAMMPS encounters errors in the input script or while running a
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simulation it will print an ERROR message and stop or a WARNING
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message and continue. See the :doc:`Errors <Errors>` doc page for a
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discussion of the various kinds of errors LAMMPS can or can't detect,
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a list of all ERROR and WARNING messages, and what to do about them.
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----------
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LAMMPS can run the same problem on any number of processors, including
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a single processor. In theory you should get identical answers on any
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number of processors and on any machine. In practice, numerical
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round-off can cause slight differences and eventual divergence of
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molecular dynamics phase space trajectories. See the :doc:`Errors common <Errors_common>` doc page for discussion of this.
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LAMMPS can run as large a problem as will fit in the physical memory
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of one or more processors. If you run out of memory, you must run on
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more processors or define a smaller problem.
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If you run LAMMPS in parallel via mpirun, you should be aware of the
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:doc:`processors <processors>` command which controls how MPI tasks are
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mapped to the simulation box, as well as mpirun options that control
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how MPI tasks are assigned to physical cores of the node(s) of the
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machine you are running on. These settings can improve performance,
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though the defaults are often adequate.
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For example, it is often important to bind MPI tasks (processes) to
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physical cores (processor affinity), so that the operating system does
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not migrate them during a simulation. If this is not the default
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behavior on your machine, the mpirun option "--bind-to core" (OpenMPI)
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or "-bind-to core" (MPICH) can be used.
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If the LAMMPS command(s) you are using support multi-threading, you
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can set the number of threads per MPI task via the environment
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variable OMP\_NUM\_THREADS, before you launch LAMMPS:
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.. parsed-literal::
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export OMP_NUM_THREADS=2 # bash
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setenv OMP_NUM_THREADS 2 # csh or tcsh
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This can also be done via the :doc:`package <package>` command or via
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the :doc:`-pk command-line switch <Run_options>` which invokes the
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package command. See the :doc:`package <package>` command or
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:doc:`Speed <Speed>` doc pages for more details about which accelerator
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packages and which commands support multi-threading.
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----------
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You can experiment with running LAMMPS using any of the input scripts
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provided in the examples or bench directory. Input scripts are named
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in.\* and sample outputs are named log.\*.P where P is the number of
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processors it was run on.
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Some of the examples or benchmarks require LAMMPS to be built with
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optional packages.
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