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.
141 lines
5.5 KiB
ReStructuredText
141 lines
5.5 KiB
ReStructuredText
.. index:: timer
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timer command
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=============
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Syntax
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""""""
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.. parsed-literal::
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timer args
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* *args* = one or more of *off* or *loop* or *normal* or *full* or *sync* or *nosync* or *timeout* or *every*
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.. parsed-literal::
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*off* = do not collect or print any timing information
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*loop* = collect only the total time for the simulation loop
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*normal* = collect timer information broken down by sections (default)
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*full* = like *normal* but also include CPU and thread utilization
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*sync* = explicitly synchronize MPI tasks between sections
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*nosync* = do not synchronize MPI tasks between sections (default)
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*timeout* elapse = set wall time limit to *elapse*
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*every* Ncheck = perform timeout check every *Ncheck* steps
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Examples
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""""""""
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.. parsed-literal::
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timer full sync
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timer timeout 2:00:00 every 100
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timer loop
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Description
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"""""""""""
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Select the level of detail at which LAMMPS performs its CPU timings.
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Multiple keywords can be specified with the *timer* command. For
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keywords that are mutually exclusive, the last one specified takes
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precedence.
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During a simulation run LAMMPS collects information about how much
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time is spent in different sections of the code and thus can provide
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information for determining performance and load imbalance problems.
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This can be done at different levels of detail and accuracy. For more
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information about the timing output, see the :doc:`Run output <Run_output>` doc page.
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The *off* setting will turn all time measurements off. The *loop*
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setting will only measure the total time for a run and not collect any
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detailed per section information. With the *normal* setting, timing
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information for portions of the timestep (pairwise calculations,
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neighbor list construction, output, etc) are collected as well as
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information about load imbalances for those sections across
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processors. The *full* setting adds information about CPU
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utilization and thread utilization, when multi-threading is enabled.
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With the *sync* setting, all MPI tasks are synchronized at each timer
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call which measures load imbalance for each section more accurately,
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though it can also slow down the simulation by prohibiting overlapping
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independent computations on different MPI ranks Using the *nosync*
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setting (which is the default) turns this synchronization off.
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With the *timeout* keyword a wall time limit can be imposed, that
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affects the :doc:`run <run>` and :doc:`minimize <minimize>` commands.
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This can be convenient when calculations have to comply with execution
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time limits, e.g. when running under a batch system when you want to
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maximize the utilization of the batch time slot, especially for runs
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where the time per timestep varies much and thus it becomes difficult
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to predict how many steps a simulation can perform for a given wall time
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limit. This also applies for difficult to converge minimizations.
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The timeout *elapse* value should be somewhat smaller than the maximum
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wall time requested from the batch system, as there is usually
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some overhead to launch jobs, and it is advisable to write
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out a restart after terminating a run due to a timeout.
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The timeout timer starts when the command is issued. When the time
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limit is reached, the run or energy minimization will exit on the
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next step or iteration that is a multiple of the *Ncheck* value
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which can be set with the *every* keyword. Default is checking
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every 10 steps. After the timer timeout has expired all subsequent
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run or minimize commands in the input script will be skipped.
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The remaining time or timer status can be accessed with the
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:doc:`thermo <thermo_style>` variable *timeremain*\ , which will be
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zero, if the timeout is inactive (default setting), it will be
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negative, if the timeout time is expired and positive if there
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is time remaining and in this case the value of the variable are
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the number of seconds remaining.
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When the *timeout* key word is used a second time, the timer is
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restarted with a new time limit. The timeout *elapse* value can
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be specified as *off* or *unlimited* to impose a no timeout condition
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(which is the default). The *elapse* setting can be specified as
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a single number for seconds, two numbers separated by a colon (MM:SS)
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for minutes and seconds, or as three numbers separated by colons for
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hours, minutes, and seconds (H:MM:SS).
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The *every* keyword sets how frequently during a run or energy
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minimization the wall clock will be checked. This check count applies
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to the outer iterations or time steps during minimizations or :doc:`r-RESPA runs <run_style>`, respectively. Checking for timeout too often,
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can slow a calculation down. Checking too infrequently can make the
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timeout measurement less accurate, with the run being stopped later
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than desired.
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.. note::
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Using the *full* and *sync* options provides the most detailed
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and accurate timing information, but can also have a negative
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performance impact due to the overhead of the many required system
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calls. It is thus recommended to use these settings only when testing
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tests to identify performance bottlenecks. For calculations with few
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atoms or a very large number of processors, even the *normal* setting
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can have a measurable negative performance impact. In those cases you
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can just use the *loop* or *off* setting.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`run post no <run>`, :doc:`kspace\_modify fftbench <kspace_modify>`
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Default
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"""""""
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.. parsed-literal::
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timer normal nosync
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timer timeout off
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timer every 10
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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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