diff --git a/doc/src/Run_basics.rst b/doc/src/Run_basics.rst index 02adfe038c..22cec5858b 100644 --- a/doc/src/Run_basics.rst +++ b/doc/src/Run_basics.rst @@ -2,8 +2,8 @@ Basics of running LAMMPS ======================== LAMMPS is run from the command line, reading commands from a file via -the -in command line flag, or from standard input. Using the "-in -in.file" variant is recommended (see note below). The name of the +the ``-in`` command line flag, or from standard input. Using the ``-in +in.file`` variant is recommended (see note below). The name of the LAMMPS executable is either ``lmp`` or ``lmp_`` with `` being the machine string used when compiling LAMMPS. This is required when compiling LAMMPS with the traditional build system @@ -35,7 +35,7 @@ executable itself can be placed elsewhere. form is required. As LAMMPS runs it prints info to the screen and a logfile named -*log.lammps*\ . More info about output is given on the :doc:`screen and +``log.lammps``. More info about output is given on the :doc:`screen and logfile output ` page. If LAMMPS encounters errors in the input script or while running a @@ -69,12 +69,12 @@ defaults are often adequate. For example, it is often important to bind MPI tasks (processes) to physical cores (processor affinity), so that the operating system does not migrate them during a simulation. If this is not the default -behavior on your machine, the mpirun option "--bind-to core" (OpenMPI) -or "-bind-to core" (MPICH) can be used. +behavior on your machine, the mpirun option ``--bind-to core`` (OpenMPI) +or ``-bind-to core`` (MPICH) can be used. If the LAMMPS command(s) you are using support multi-threading, you can set the number of threads per MPI task via the environment -variable OMP_NUM_THREADS, before you launch LAMMPS: +variable ``OMP_NUM_THREADS``, before you launch LAMMPS: .. code-block:: bash @@ -91,7 +91,7 @@ packages and which commands support multi-threading. You can experiment with running LAMMPS using any of the input scripts provided in the examples or bench directory. Input scripts are named -in.\* and sample outputs are named log.\*.P where P is the number of +``in.*`` and sample outputs are named ``log.*.P`` where P is the number of processors it was run on. Some of the examples or benchmarks require LAMMPS to be built with diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index ff466d3b8a..86e8e47626 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -275,13 +275,13 @@ impact can be significant, especially for large parallel runs. Invoke the :doc:`package ` command with style and args. The syntax is the same as if the command appeared at the top of the input -script. For example "-package gpu 2" or "-pk gpu 2" is the same as +script. For example ``-package gpu 2`` or ``-pk gpu 2`` is the same as :doc:`package gpu 2 ` in the input script. The possible styles and args are documented on the :doc:`package ` doc page. This switch can be used multiple times, e.g. to set options for the INTEL and OPENMP packages which can be used together. -Along with the "-suffix" command-line switch, this is a convenient +Along with the ``-suffix`` command-line switch, this is a convenient mechanism for invoking accelerator packages and their options without having to edit an input script. @@ -300,7 +300,7 @@ specify the number of processors in each partition. Arguments of the form MxN mean M partitions, each with N processors. Arguments of the form N mean a single partition with N processors. The sum of processors in all partitions must equal P. Thus the command -"-partition 8x2 4 5" has 10 partitions and runs on a total of 25 +``-partition 8x2 4 5`` has 10 partitions and runs on a total of 25 processors. Running with multiple partitions can be useful for running @@ -378,8 +378,8 @@ processors will be in the first partition, the second set in the second partition. The -reorder command-line switch can alter this so that the first N procs in the first partition and one proc in the second partition will be ordered consecutively, e.g. as the cores on one physical node. -This can boost performance. For example, if you use "-reorder nth 4" -and "-partition 9 3" and you are running on 12 processors, the +This can boost performance. For example, if you use ``-reorder nth 4`` +and ``-partition 9 3`` and you are running on 12 processors, the processors will be reordered from .. parsed-literal:: @@ -584,11 +584,11 @@ style that accepts arguments. It allows for two packages to be specified. The first package specified is the default and will be used if it is available. If no style is available for the first package, the style for the second package will be used if available. For -example, "-suffix hybrid intel omp" will use styles from the +example, ``-suffix hybrid intel omp`` will use styles from the INTEL package if they are installed and available, but styles for the OPENMP package otherwise. -Along with the "-package" command-line switch, this is a convenient +Along with the ``-package`` command-line switch, this is a convenient mechanism for invoking accelerator packages and their options without having to edit an input script. @@ -605,30 +605,30 @@ variant version does not exist, the standard version is created. For the GPU package, using this command-line switch also invokes the default GPU settings, as if the command "package gpu 1" were used at the top of your input script. These settings can be changed by using -the "-package gpu" command-line switch or the :doc:`package gpu ` command in your script. +the ``-package gpu`` command-line switch or the :doc:`package gpu ` command in your script. For the INTEL package, using this command-line switch also invokes the default INTEL settings, as if the command "package intel 1" were used at the top of your input script. These settings -can be changed by using the "-package intel" command-line switch or +can be changed by using the ``-package intel`` command-line switch or the :doc:`package intel ` command in your script. If the OPENMP package is also installed, the hybrid style with "intel omp" arguments can be used to make the omp suffix a second choice, if a requested style is not available in the INTEL package. It will also invoke the default OPENMP settings, as if the command "package omp 0" were used at the top of your input script. These settings can -be changed by using the "-package omp" command-line switch or the +be changed by using the ``-package omp`` command-line switch or the :doc:`package omp ` command in your script. For the KOKKOS package, using this command-line switch also invokes the default KOKKOS settings, as if the command "package kokkos" were used at the top of your input script. These settings can be changed -by using the "-package kokkos" command-line switch or the :doc:`package kokkos ` command in your script. +by using the ``-package kokkos`` command-line switch or the :doc:`package kokkos ` command in your script. For the OMP package, using this command-line switch also invokes the default OMP settings, as if the command "package omp 0" were used at the top of your input script. These settings can be changed by using -the "-package omp" command-line switch or the :doc:`package omp ` command in your script. +the ``-package omp`` command-line switch or the :doc:`package omp ` command in your script. The :doc:`suffix ` command can also be used within an input script to set a suffix, or to turn off or back on any suffix setting