Merge branch 'develop' into collected-small-fixes
This commit is contained in:
Axel Kohlmeyer
@ -268,6 +268,12 @@ molecule can be specified in the molecule file. See the
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required to be in this file are the coordinates and types of atoms in
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the molecule.
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.. note::
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If you are using the *mol* keyword in combination with the
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:doc:`atom style template <atom_style>` command, they must use
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the same molecule template-ID.
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Using a lattice to add molecules, e.g. via the *box* or *region* or
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*single* styles, is exactly the same as adding atoms on lattice
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points, except that entire molecules are added at each point, i.e. on
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@ -74,7 +74,7 @@ Syntax
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*no_affinity* values = none
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*kokkos* args = keyword value ...
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zero or more keyword/value pairs may be appended
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keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *neigh/transpose* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* or *comm/pair/forward* or *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *sort* or *gpu/aware* or *pair/only*
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keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *neigh/transpose* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* or *comm/pair/forward* or *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *sort* or *atom/map* or *gpu/aware* or *pair/only*
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*neigh* value = *full* or *half*
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full = full neighbor list
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half = half neighbor list built in thread-safe manner
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@ -108,6 +108,9 @@ Syntax
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*sort* value = *no* or *device*
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*no* = perform atom sorting in non-KOKKOS mode
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*device* = perform atom sorting on device (e.g. on GPU)
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*atom/map* value = *no* or *device*
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*no* = build atom map in non-KOKKOS mode
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*device* = build atom map on device (e.g. on GPU)
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*gpu/aware* = *off* or *on*
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*off* = do not use GPU-aware MPI
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*on* = use GPU-aware MPI (default)
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@ -566,15 +569,19 @@ performing the exchange pack/unpack on the host CPU can give speedup
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since it reduces the number of CUDA kernel launches.
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The *sort* keyword determines whether the host or device performs atom
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sorting, see the :doc:`atom_modify sort <atom_modify>` command. The
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value options for the *sort* keyword are *no* or *device* similar to the
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*comm* keywords above. If a value of *host* is used it will be
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automatically be changed to *no* since the *sort* keyword does not
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support *host* mode. The value of *no* will also always be used when
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running on the CPU, i.e. setting the value to *device* will have no
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effect if the simulation is running on the CPU. Not all fix styles with
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extra atom data support *device* mode and in that case a warning will be
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given and atom sorting will run in *no* mode instead.
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sorting, see the :doc:`atom_modify sort <atom_modify>` command. The value
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options for the *sort* keyword are *no* or *device* similar to the *comm*
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keywords above. If a value of *host* is used it will be automatically be
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changed to *no* since the *sort* keyword does not support *host* mode. Not
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all fix styles with extra atom data support *device* mode and in that case
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a warning will be given and atom sorting will run in *no* mode instead.
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.. versionadded:: TBD
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The *atom/map* keyword determines whether the host or device builds the
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atom_map, see the :doc:`atom_modify map <atom_modify>` command. The
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value options for the *atom/map* keyword are identical to the *sort*
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keyword above.
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The *gpu/aware* keyword chooses whether GPU-aware MPI will be used. When
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this keyword is set to *on*, buffers in GPU memory are passed directly
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@ -593,12 +600,13 @@ for OpenMPI 1.8 (or later versions), Mvapich2 1.9 (or later) when the
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Spectrum MPI when the "-gpu" flag is used.
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The *pair/only* keyword can change how the KOKKOS suffix "kk" is applied
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when using an accelerator device. By default device acceleration is
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always used for all available styles. With *pair/only* set to *on* the
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suffix setting will choose device acceleration only for pair styles and
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run all other force computations on the host CPU.
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The *comm* flags will also automatically be changed to *no*\ . This can
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result in better performance for certain configurations and system sizes.
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when using an accelerator device. By default device acceleration is always
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used for all available styles. With *pair/only* set to *on* the suffix
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setting will choose device acceleration only for pair styles and run all
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other force computations on the host CPU. The *comm* flags, along with the
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*sort* and *atom/map* keywords will also automatically be changed to *no*\ .
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This can result in better performance for certain configurations and
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system sizes.
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----------
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@ -684,18 +692,18 @@ Restrictions
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This command cannot be used after the simulation box is defined by a
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:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command.
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The gpu style of this command can only be invoked if LAMMPS was built
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The *gpu* style of this command can only be invoked if LAMMPS was built
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with the GPU package. See the :doc:`Build package <Build_package>` doc
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page for more info.
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The intel style of this command can only be invoked if LAMMPS was
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The *intel* style of this command can only be invoked if LAMMPS was
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built with the INTEL package. See the :doc:`Build package <Build_package>` page for more info.
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The kk style of this command can only be invoked if LAMMPS was built
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The *kokkos* style of this command can only be invoked if LAMMPS was built
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with the KOKKOS package. See the :doc:`Build package <Build_package>`
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doc page for more info.
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The omp style of this command can only be invoked if LAMMPS was built
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The *omp* style of this command can only be invoked if LAMMPS was built
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with the OPENMP package. See the :doc:`Build package <Build_package>`
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doc page for more info.
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@ -704,19 +712,27 @@ Related commands
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:doc:`suffix <suffix>`, :doc:`-pk command-line switch <Run_options>`
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Default
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"""""""
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Defaults
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""""""""
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For the GPU package, the default is Ngpu = 0 and the option defaults are neigh
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= yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0 to Ngpu-1, tpa = 1,
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omp = 0, and platform=-1. These settings are made automatically if the "-sf
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gpu" :doc:`command-line switch <Run_options>` is used. If it is not used, you
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must invoke the package gpu command in your input script or via the "-pk gpu"
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:doc:`command-line switch <Run_options>`.
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For the GPU package, the default parameters and settings are:
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For the INTEL package, the default is Nphi = 1 and the option defaults are omp
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= 0, mode = mixed, lrt = no, balance = -1, tpc = 4, tptask = 240, pppm_table =
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yes. The default ghost option is determined by the pair style being used.
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.. parsed-literal::
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Ngpu = 0, neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0 to Ngpu-1, tpa = 1, omp = 0, platform=-1.
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These settings are made automatically if the "-sf gpu"
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:doc:`command-line switch <Run_options>` is used. If it is not used,
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you must invoke the package gpu command in your input script or via the
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"-pk gpu" :doc:`command-line switch <Run_options>`.
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For the INTEL package, the default parameters and settings are:
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.. parsed-literal::
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Nphi = 1, omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4, tptask = 240, pppm_table = yes
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The default ghost option is determined by the pair style being used.
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This value is output to the screen in the offload report at the end of each
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run. Note that all of these settings, except "omp" and "mode", are ignored if
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LAMMPS was not built with Xeon Phi co-processor support. These settings are
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@ -724,20 +740,35 @@ made automatically if the "-sf intel" :doc:`command-line switch <Run_options>`
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is used. If it is not used, you must invoke the package intel command in your
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input script or via the "-pk intel" :doc:`command-line switch <Run_options>`.
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For the KOKKOS package, the option defaults for GPUs are neigh = full,
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neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default value,
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comm = device, sort = device, neigh/transpose = off, gpu/aware = on. When
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LAMMPS can safely detect that GPU-aware MPI is not available, the default value
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of gpu/aware becomes "off". For CPUs or Xeon Phis, the option defaults are
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neigh = half, neigh/qeq = half, newton = on, binsize = 0.0, comm = no, and sort
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= no. For GPUs, option neigh/thread = on when there are 16k atoms or less on an MPI
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rank, otherwise it is "off". These settings are made automatically by the
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required "-k on" :doc:`command-line switch <Run_options>`. You can change them
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by using the package kokkos command in your input script or via the :doc:`-pk
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kokkos command-line switch <Run_options>`.
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For the KOKKOS package when using GPUs, the option defaults are:
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For the OMP package, the default is Nthreads = 0 and the option defaults are
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neigh = yes. These settings are made automatically if the "-sf omp"
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:doc:`command-line switch <Run_options>` is used. If it is not used, you must
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invoke the package omp command in your input script or via the "-pk omp"
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:doc:`command-line switch <Run_options>`.
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.. parsed-literal::
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neigh = full, neigh/qeq = full, newton = off, binsize = 2x LAMMPS default value, comm = device, sort = device, atom/map = device, neigh/transpose = off, gpu/aware = on
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For GPUs, option neigh/thread = on when there are 16k atoms or less on
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an MPI rank, otherwise it is "off". When LAMMPS can safely detect that
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GPU-aware MPI is not available, the default value of gpu/aware becomes
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"off".
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For the KOKKOS package when using CPUs or Xeon Phis, the option defaults are:
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.. parsed-literal::
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neigh = half, neigh/qeq = half, newton = on, binsize = 0.0, comm = no, sort = no, atom/map = no
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These settings are made automatically by
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the required "-k on" :doc:`command-line switch <Run_options>`. You can
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change them by using the package kokkos command in your input script or
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via the :doc:`-pk kokkos command-line switch <Run_options>`.
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For the OMP package, the defaults are
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.. parsed-literal::
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Nthreads = 0, neigh = yes
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These settings are made automatically if the "-sf omp"
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:doc:`command-line switch <Run_options>` is used. If it is not used,
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you must invoke the package omp command in your input script or via the
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"-pk omp" :doc:`command-line switch <Run_options>`.
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