forked from lijiext/lammps
277 lines
12 KiB
Plaintext
277 lines
12 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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package command :h3
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[Syntax:]
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package style args :pre
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style = {gpu} or {cuda} or {omp} :ulb,l
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args = arguments specific to the style :l
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{gpu} args = mode first last split keyword value ...
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mode = force or force/neigh
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first = ID of first GPU to be used on each node
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last = ID of last GPU to be used on each node
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split = fraction of particles assigned to the GPU
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zero or more keyword/value pairs may be appended
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keywords = {threads_per_atom} or {cellsize}
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{threads_per_atom} value = Nthreads
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Nthreads = # of GPU threads used per atom
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{cellsize} value = dist
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dist = length (distance units) in each dimension for neighbor bins
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{cuda} args = keyword value ...
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one or more keyword/value pairs may be appended
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keywords = {gpu/node} or {gpu/node/special} or {timing} or {test} or {override/bpa}
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{gpu/node} value = N
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N = number of GPUs to be used per node
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{gpu/node/special} values = N gpu1 .. gpuN
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N = number of GPUs to be used per node
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gpu1 .. gpuN = N IDs of the GPUs to use
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{timing} values = none
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{test} values = id
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id = atom-ID of a test particle
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{override/bpa} values = flag
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flag = 0 for TpA algorithm, 1 for BpA algorithm
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{omp} args = Nthreads mode
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Nthreads = # of OpenMP threads to associate with each MPI process
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mode = force or force/neigh (optional) :pre
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:ule
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[Examples:]
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package gpu force 0 0 1.0
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package gpu force 0 0 0.75
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package gpu force/neigh 0 0 1.0
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package gpu force/neigh 0 1 -1.0
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package cuda gpu/node/special 2 0 2
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package cuda test 3948
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package omp * force/neigh
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package omp 4 force :pre
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[Description:]
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This command invokes package-specific settings. Currently the
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following packages use it: GPU, USER-CUDA, and USER-OMP.
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To use the accelerated GPU and USER-OMP styles, the use of the package
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command is required. However, as described in the "Defaults" section
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below, if you use the "-sf gpu" or "-sf omp" "command-line
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options"_Section_start.html#start_7 to enable use of these styles,
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then default package settings are enabled. In that case you only need
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to use the package command if you want to change the defaults.
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To use the accelerate USER-CUDA styles, the package command is not
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required as defaults are assigned internally. You only need to use
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the package command if you want to change the defaults.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more details about using these various packages for accelerating
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LAMMPS calculations.
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:line
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The {gpu} style invokes options associated with the use of the GPU
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package.
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The {mode} setting specifies where neighbor list calculations will be
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performed. If {mode} is force, neighbor list calculation is performed
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on the CPU. If {mode} is force/neigh, neighbor list calculation is
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performed on the GPU. GPU neighbor list calculation currently cannot
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be used with a triclinic box. GPU neighbor list calculation currently
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cannot be used with "hybrid"_pair_hybrid.html pair styles. GPU
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neighbor lists are not compatible with styles that are not
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GPU-enabled. When a non-GPU enabled style requires a neighbor list,
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it will also be built using CPU routines. In these cases, it will
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typically be more efficient to only use CPU neighbor list builds.
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The {first} and {last} settings specify the GPUs that will be used for
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simulation. On each node, the GPU IDs in the inclusive range from
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{first} to {last} will be used.
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The {split} setting can be used for load balancing force calculation
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work between CPU and GPU cores in GPU-enabled pair styles. If 0 <
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{split} < 1.0, a fixed fraction of particles is offloaded to the GPU
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while force calculation for the other particles occurs simulataneously
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on the CPU. If {split}<0, the optimal fraction (based on CPU and GPU
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timings) is calculated every 25 timesteps. If {split} = 1.0, all force
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calculations for GPU accelerated pair styles are performed on the
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GPU. In this case, "hybrid"_pair_hybrid.html, "bond"_bond_style.html,
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"angle"_angle_style.html, "dihedral"_dihedral_style.html,
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"improper"_improper_style.html, and "long-range"_kspace_style.html
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calculations can be performed on the CPU while the GPU is performing
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force calculations for the GPU-enabled pair style. If all CPU force
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computations complete before the GPU, LAMMPS will block until the GPU
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has finished before continuing the timestep.
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As an example, if you have two GPUs per node and 8 CPU cores per node,
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and would like to run on 4 nodes (32 cores) with dynamic balancing of
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force calculation across CPU and GPU cores, you could specify
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package gpu force/neigh 0 1 -1 :pre
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In this case, all CPU cores and GPU devices on the nodes would be
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utilized. Each GPU device would be shared by 4 CPU cores. The CPU
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cores would perform force calculations for some fraction of the
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particles at the same time the GPUs performed force calculation for
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the other particles.
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The {threads_per_atom} keyword allows control of the number of GPU
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threads used per-atom to perform the short range force calculation.
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By default, the value will be chosen based on the pair style, however,
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the value can be set with this keyword to fine-tune performance. For
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large cutoffs or with a small number of particles per GPU, increasing
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the value can improve performance. The number of threads per atom must
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be a power of 2 and currently cannot be greater than 32.
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The {cellsize} keyword can be used to control the size of the cells used
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for binning atoms in neighbor list calculations. Setting this value is
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normally not needed; the optimal value is close to the default
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(equal to the cutoff distance for the short range interactions
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plus the neighbor skin). GPUs can perform efficiently with much larger cutoffs
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than CPUs and this can be used to reduce the time required for long-range
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calculations or in some cases to eliminate them with models such as
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"coul/wolf"_pair_coul.html or "coul/dsf"_pair_coul.html. For very large cutoffs,
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it can be more efficient to use smaller values for cellsize in parallel
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simulations. For example, with a cutoff of 20*sigma and a neighbor skin of
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sigma, a cellsize of 5.25*sigma can be efficient for parallel simulations.
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:line
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The {cuda} style invokes options associated with the use of the
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USER-CUDA package.
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The {gpu/node} keyword specifies the number {N} of GPUs to be used on
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each node. An MPI process with rank {K} will use the GPU (K mod N).
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This implies that processes should be assigned with successive ranks
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on each node, which is the default with most (or even all) MPI
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implementations. The default value for {N} is 2.
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The {gpu/node/special} keyword also specifies the number (N) of GPUs
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to be used on each node, but allows more control over their
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specification. An MPI process with rank {K} will use the GPU {gpuI}
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with l = (K mod N) + 1. This implies that processes should be assigned
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with successive ranks on each node, which is the default with most (or
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even all) MPI implementations. For example if you have three GPUs on
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a machine, one of which is used for the X-Server (the GPU with the ID
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1) while the others (with IDs 0 and 2) are used for computations you
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would specify:
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package cuda gpu/node/special 2 0 2 :pre
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A main purpose of the {gpu/node/special} optoin is to allow two (or
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more) simulations to be run on one workstation. In that case one
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would set the first simulation to use GPU 0 and the second to use GPU
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1. This is not necessary though, if the GPUs are in what is called
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{compute exclusive} mode. Using that setting, every process will get
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its own GPU automatically. This {compute exclusive} mode can be set
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as root using the {nvidia-smi} tool which is part of the CUDA
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installation.
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Note that if the {gpu/node/special} keyword is not used, the USER-CUDA
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package sorts existing GPUs on each node according to their number of
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multiprocessors. This way, compute GPUs will be priorized over
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X-Server GPUs.
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Use of the {timing} keyword will output detailed timing information
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for various subroutines.
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The {test} keyword will output info for the the specified atom at
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several points during each time step. This is mainly usefull for
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debugging purposes. Note that the simulation will be severly slowed
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down if this option is used.
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The {override/bpa} keyword can be used to specify which mode is used
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for pair-force evaluation. TpA = one thread per atom; BpA = one block
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per atom. If this keyword is not used, a short test at the begin of
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each run will determine which method is more effective (the result of
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this test is part of the LAMMPS output). Therefore it is usually not
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necessary to use this keyword.
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:line
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The {omp} style invokes options associated with the use of the
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USER-OMP package.
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The first argument allows to explicitly set the number of OpenMP
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threads to be allocated for each MPI process. For example, if your
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system has nodes with dual quad-core processors, it has a total of 8
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cores per node. You could run MPI on 2 cores on each node (e.g. using
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options for the mpirun command), and set the {Nthreads} setting to 4.
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This would effectively use all 8 cores on each node. Since each MPI
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process would spawn 4 threads (one of which runs as part of the MPI
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process itself).
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For performance reasons, you should not set {Nthreads} to more threads
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than there are physical cores (per MPI task), but LAMMPS cannot check
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for this.
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An {Nthreads} value of '*' instructs LAMMPS to use whatever is the
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default for the given OpenMP environment. This is usually determined
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via the {OMP_NUM_THREADS} environment variable or the compiler
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runtime. Please note that in most cases the default for OpenMP
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capable compilers is to use one thread for each available CPU core
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when {OMP_NUM_THREADS} is not set, which can lead to extremely bad
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performance.
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Which combination of threads and MPI tasks gives the best performance
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is difficult to predict and can depend on many components of your input.
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Not all features of LAMMPS support OpenMP and the parallel efficiency
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can be very different, too.
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The {mode} setting specifies where neighbor list calculations will be
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multi-threaded as well. If {mode} is force, neighbor list calculation
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is performed in serial. If {mode} is force/neigh, a multi-threaded
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neighbor list build is used. Using the force/neigh setting is almost
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always faster and should produce idential neighbor lists at the
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expense of using some more memory (neighbor list pages are always
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allocated for all threads at the same time and each thread works on
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its own pages).
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:line
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[Restrictions:]
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This command cannot be used after the simulation box is defined by a
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"read_data"_read_data.html or "create_box"_create_box.html command.
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The cuda style of this command can only be invoked if LAMMPS was built
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with the USER-CUDA package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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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 "Making
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LAMMPS"_Section_start.html#start_3 section 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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with the USER-OMP package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"suffix"_suffix.html
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[Default:]
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If the "-sf gpu" "command-line switch"_Section_start.html#start_7 is
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used then it is as if the command "package gpu force/neigh 0 0 1" were
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invoked, to specify default settings for the GPU package. If the
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command-line switch is not used, then no defaults are set, and you
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must specify the appropriate package command in your input script.
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The default settings for the USER CUDA package are "package cuda gpu
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2". This is the case whether the "-sf cuda" "command-line
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switch"_Section_start.html#start_7 is used or not.
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If the "-sf omp" "command-line switch"_Section_start.html#start_7 is
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used then it is as if the command "package omp *" were invoked, to
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specify default settings for the USER-OMP package. If the
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command-line switch is not used, then no defaults are set, and you
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must specify the appropriate package command in your input script.
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