7.4. Accelerator packages
Accelerated versions of various pair_style, fixes, computes, and other commands have been added to LAMMPS, which will typically run faster than the standard non-accelerated versions. Some require appropriate hardware to be present on your system, e.g. GPUs or Intel Xeon Phi coprocessors.
All of these commands are in packages provided with LAMMPS. An overview of packages is give on the Packages doc pages.
These are the accelerator packages currently in LAMMPS, either as standard or user packages:
|GPU Package||for NVIDIA GPUs as well as OpenCL support|
|USER-INTEL Package||for Intel CPUs and Intel Xeon Phi|
|KOKKOS Package||for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading|
|USER-OMP Package||for OpenMP threading and generic CPU optimizations|
|OPT Package||generic CPU optimizations|
Inverting this list, LAMMPS currently has acceleration support for three kinds of hardware, via the listed packages:
|Many-core CPUs||USER-INTEL, KOKKOS, USER-OMP, OPT packages|
|NVIDIA GPUs||GPU, KOKKOS packages|
|Intel Phi||USER-INTEL, KOKKOS packages|
Which package is fastest for your hardware may depend on the size problem you are running and what commands (accelerated and non-accelerated) are invoked by your input script. While these doc pages include performance guidelines, there is no substitute for trying out the different packages appropriate to your hardware.
Any accelerated style has the same name as the corresponding standard style, except that a suffix is appended. Otherwise, the syntax for the command that uses the style is identical, their functionality is the same, and the numerical results it produces should also be the same, except for precision and round-off effects.
For example, all of these styles are accelerated variants of the Lennard-Jones pair_style lj/cut:
- pair_style lj/cut/gpu
- pair_style lj/cut/intel
- pair_style lj/cut/kk
- pair_style lj/cut/omp
- pair_style lj/cut/opt
To see what accelerate styles are currently available for a particular style, find the style name in the Commands_all style pages (fix,compute,pair,etc) and see what suffixes are listed (g,i,k,o,t) with it. The doc pages for individual commands (e.g. pair lj/cut or fix nve) also list any accelerated variants available for that style.
To use an accelerator package in LAMMPS, and one or more of the styles it provides, follow these general steps. Details vary from package to package and are explained in the individual accelerator doc pages, listed above:
|build the accelerator library||only for GPU package|
|install the accelerator package||make yes-opt, make yes-user-intel, etc|
|add compile/link flags to Makefile.machine in src/MAKE||only for USER-INTEL, KOKKOS, USER-OMP, OPT packages|
|re-build LAMMPS||make machine|
|prepare and test a regular LAMMPS simulation||lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script|
|enable specific accelerator support via ‘-k on’ command-line switch,||only needed for KOKKOS package|
|set any needed options for the package via “-pk” command-line switch or package command,||only if defaults need to be changed|
|use accelerated styles in your input via “-sf” command-line switch or suffix command||lmp_machine -in in.script -sf gpu|
Note that the first 4 steps can be done as a single command with suitable make command invocations. This is discussed on the Packages doc pages, and its use is illustrated in the individual accelerator sections. Typically these steps only need to be done once, to create an executable that uses one or more accelerator packages.
The last 4 steps can all be done from the command-line when LAMMPS is launched, without changing your input script, as illustrated in the individual accelerator sections. Or you can add package and suffix commands to your input script.
With a few exceptions, you can build a single LAMMPS executable with all its accelerator packages installed. Note however that the USER-INTEL and KOKKOS packages require you to choose one of their hardware options when building for a specific platform. I.e. CPU or Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi option for the KOKKOS package.
These are the exceptions. You cannot build a single executable with:
- both the USER-INTEL Phi and KOKKOS Phi options
- the USER-INTEL Phi or Kokkos Phi option, and the GPU package
See the examples/accelerate/README and make.list files for sample Make.py commands that build LAMMPS with any or all of the accelerator packages. As an example, here is a command that builds with all the GPU related packages installed (GPU, KOKKOS with Cuda), including settings to build the needed auxiliary GPU libraries for Kepler GPUs:
Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi
The examples/accelerate directory also has input scripts that can be used with all of the accelerator packages. See its README file for details.
Likewise, the bench directory has FERMI and KEPLER and PHI sub-directories with Make.py commands and input scripts for using all the accelerator packages on various machines. See the README files in those dirs.
As mentioned above, the Benchmark page of the LAMMPS web site gives performance results for the various accelerator packages for several of the standard LAMMPS benchmark problems, as a function of problem size and number of compute nodes, on different hardware platforms.
Here is a brief summary of what the various packages provide. Details are in the individual accelerator sections.
- Styles with a “gpu” suffix are part of the GPU package, and can be run on NVIDIA GPUs. The speed-up on a GPU depends on a variety of factors, discussed in the accelerator sections.
- Styles with an “intel” suffix are part of the USER-INTEL package. These styles support vectorized single and mixed precision calculations, in addition to full double precision. In extreme cases, this can provide speedups over 3.5x on CPUs. The package also supports acceleration in “offload” mode to Intel(R) Xeon Phi(TM) coprocessors. This can result in additional speedup over 2x depending on the hardware configuration.
- Styles with a “kk” suffix are part of the KOKKOS package, and can be run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel Xeon Phi in “native” mode. The speed-up depends on a variety of factors, as discussed on the KOKKOS accelerator page.
- Styles with an “omp” suffix are part of the USER-OMP package and allow a pair-style to be run in multi-threaded mode using OpenMP. This can be useful on nodes with high-core counts when using less MPI processes than cores is advantageous, e.g. when running with PPPM so that FFTs are run on fewer MPI processors or when the many MPI tasks would overload the available bandwidth for communication.
- Styles with an “opt” suffix are part of the OPT package and typically speed-up the pairwise calculations of your simulation by 5-25% on a CPU.
The individual accelerator package doc pages explain:
- what hardware and software the accelerated package requires
- how to build LAMMPS with the accelerated package
- how to run with the accelerated package either via command-line switches or modifying the input script
- speed-ups to expect
- guidelines for best performance