KOKKOS package
==============

Kokkos is a templated C++ library that provides abstractions to allow
a single implementation of an application kernel (e.g. a pair style)
to run efficiently on different kinds of hardware, such as GPUs, Intel
Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto
different back end languages such as CUDA, OpenMP, or Pthreads.  The
Kokkos library also provides data abstractions to adjust (at compile
time) the memory layout of data structures like 2d and 3d arrays to
optimize performance on different hardware. For more information on
Kokkos, see `GitHub <https://github.com/kokkos/kokkos>`_. Kokkos is part
of `Trilinos <http://trilinos.sandia.gov/packages/kokkos>`_. The Kokkos
library was written primarily by Carter Edwards, Christian Trott, and
Dan Sunderland (all Sandia).

The LAMMPS KOKKOS package contains versions of pair, fix, and atom
styles that use data structures and macros provided by the Kokkos
library, which is included with LAMMPS in /lib/kokkos. The KOKKOS
package was developed primarily by Christian Trott (Sandia) and Stan
Moore (Sandia) with contributions of various styles by others,
including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
(Sandia). For more information on developing using Kokkos abstractions
see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos\_PG.pdf.

Kokkos currently provides support for 3 modes of execution (per MPI
task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA
GPUs). You choose the mode at build time to produce an executable
compatible with specific hardware.

.. note::

   Kokkos support within LAMMPS must be built with a C++11 compatible
   compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or
   Clang 3.5.2 or later is required.

.. note::

   To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA
   software version 7.5 or later must be installed on your system. See
   the discussion for the :doc:`GPU package <Speed_gpu>` for details of how
   to check and do this.

.. note::

   Kokkos with CUDA currently implicitly assumes that the MPI library
   is CUDA-aware. This is not always the case, especially when using
   pre-compiled MPI libraries provided by a Linux distribution. This is not
   a problem when using only a single GPU with a single MPI rank. When
   running with multiple MPI ranks, you may see segmentation faults without
   CUDA-aware MPI support. These can be avoided by adding the flags :doc:`-pk kokkos cuda/aware off <Run_options>` to the LAMMPS command line or by
   using the command :doc:`package kokkos cuda/aware off <package>` in the
   input file.

**Building LAMMPS with the KOKKOS package:**

See the :ref:`Build extras <kokkos>` doc page for instructions.

**Running LAMMPS with the KOKKOS package:**

All Kokkos operations occur within the context of an individual MPI
task running on a single node of the machine. The total number of MPI
tasks used by LAMMPS (one or multiple per compute node) is set in the
usual manner via the mpirun or mpiexec commands, and is independent of
Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
-npernode switches. Ditto for MPICH via -np and -ppn.

**Running on a multi-core CPU:**

Here is a quick overview of how to use the KOKKOS package
for CPU acceleration, assuming one or more 16-core nodes.


.. parsed-literal::

   mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj        # 1 node, 16 MPI tasks/node, no multi-threading
   mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj  # 2 nodes, 1 MPI task/node, 16 threads/task
   mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj          # 1 node,  2 MPI tasks/node, 8 threads/task
   mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj  # 8 nodes, 4 MPI tasks/node, 4 threads/task

To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk
kokkos" :doc:`command-line switches <Run_options>` in your mpirun
command.  You must use the "-k on" :doc:`command-line switch <Run_options>` to enable the KOKKOS package. It takes
additional arguments for hardware settings appropriate to your system.
For OpenMP use:


.. parsed-literal::

   -k on t Nt

The "t Nt" option specifies how many OpenMP threads per MPI task to
use with a node. The default is Nt = 1, which is MPI-only mode.  Note
that the product of MPI tasks \* OpenMP threads/task should not exceed
the physical number of cores (on a node), otherwise performance will
suffer. If Hyper-Threading (HT) is enabled, then the product of MPI
tasks \* OpenMP threads/task should not exceed the physical number of
cores \* hardware threads.  The "-k on" switch also issues a
"package kokkos" command (with no additional arguments) which sets
various KOKKOS options to default values, as discussed on the
:doc:`package <package>` command doc page.

The "-sf kk" :doc:`command-line switch <Run_options>` will automatically
append the "/kk" suffix to styles that support it.  In this manner no
modification to the input script is needed. Alternatively, one can run
with the KOKKOS package by editing the input script as described
below.

.. note::

   When using a single OpenMP thread, the Kokkos Serial back end (i.e.
   Makefile.kokkos\_mpi\_only) will give better performance than the OpenMP
   back end (i.e. Makefile.kokkos\_omp) because some of the overhead to make
   the code thread-safe is removed.

.. note::

   Use the "-pk kokkos" :doc:`command-line switch <Run_options>` to
   change the default :doc:`package kokkos <package>` options. See its doc
   page for details and default settings. Experimenting with its options
   can provide a speed-up for specific calculations. For example:


.. parsed-literal::

   mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj       # Newton on, Half neighbor list, non-threaded comm

If the :doc:`newton <newton>` command is used in the input
script, it can also override the Newton flag defaults.

For half neighbor lists and OpenMP, the KOKKOS package uses data
duplication (i.e. thread-private arrays) by default to avoid
thread-level write conflicts in the force arrays (and other data
structures as necessary). Data duplication is typically fastest for
small numbers of threads (i.e. 8 or less) but does increase memory
footprint and is not scalable to large numbers of threads. An
alternative to data duplication is to use thread-level atomic operations
which do not require data duplication. The use of atomic operations can
be enforced by compiling LAMMPS with the "-DLMP\_KOKKOS\_USE\_ATOMICS"
pre-processor flag. Most but not all Kokkos-enabled pair\_styles support
data duplication. Alternatively, full neighbor lists avoid the need for
duplication or atomic operations but require more compute operations per
atom.  When using the Kokkos Serial back end or the OpenMP back end with
a single thread, no duplication or atomic operations are used. For CUDA
and half neighbor lists, the KOKKOS package always uses atomic operations.

**Core and Thread Affinity:**

When using multi-threading, it is important for performance to bind
both MPI tasks to physical cores, and threads to physical cores, so
they do not migrate during a simulation.

If you are not certain MPI tasks are being bound (check the defaults
for your MPI installation), binding can be forced with these flags:


.. parsed-literal::

   OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
   Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ...

For binding threads with KOKKOS OpenMP, use thread affinity
environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
later, intel 12 or later) setting the environment variable
OMP\_PROC\_BIND=true should be sufficient. In general, for best
performance with OpenMP 4.0 or better set OMP\_PROC\_BIND=spread and
OMP\_PLACES=threads.  For binding threads with the KOKKOS pthreads
option, compile LAMMPS the KOKKOS HWLOC=yes option as described below.

**Running on Knight's Landing (KNL) Intel Xeon Phi:**

Here is a quick overview of how to use the KOKKOS package for the
Intel Knight's Landing (KNL) Xeon Phi:

KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are
reserved for the OS, and only 64 or 66 cores are used. Each core has 4
Hyper-Threads,so there are effectively N = 256 (4\*64) or N = 264 (4\*66)
cores to run on. The product of MPI tasks \* OpenMP threads/task should
not exceed this limit, otherwise performance will suffer. Note that
with the KOKKOS package you do not need to specify how many KNLs there
are per node; each KNL is simply treated as running some number of MPI
tasks.

Examples of mpirun commands that follow these rules are shown below.


.. parsed-literal::

   Intel KNL node with 68 cores (272 threads/node via 4x hardware threading):
   mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj      # 1 node, 64 MPI tasks/node, 4 threads/task
   mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj      # 1 node, 66 MPI tasks/node, 4 threads/task
   mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj      # 1 node, 32 MPI tasks/node, 8 threads/task
   mpirun -np 512 -ppn 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj  # 8 nodes, 64 MPI tasks/node, 4 threads/task

The -np setting of the mpirun command sets the number of MPI
tasks/node. The "-k on t Nt" command-line switch sets the number of
threads/task as Nt. The product of these two values should be N, i.e.
256 or 264.

.. note::

   The default for the :doc:`package kokkos <package>` command when
   running on KNL is to use "half" neighbor lists and set the Newton flag
   to "on" for both pairwise and bonded interactions. This will typically
   be best for many-body potentials. For simpler pair-wise potentials, it
   may be faster to use a "full" neighbor list with Newton flag to "off".
   Use the "-pk kokkos" :doc:`command-line switch <Run_options>` to change
   the default :doc:`package kokkos <package>` options. See its doc page for
   details and default settings. Experimenting with its options can provide
   a speed-up for specific calculations. For example:


.. parsed-literal::

   mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax      #  Newton on, half neighbor list, threaded comm
   mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj      # Newton off, full neighbor list, non-threaded comm

.. note::

   MPI tasks and threads should be bound to cores as described
   above for CPUs.

.. note::

   To build with Kokkos support for Intel Xeon Phi co-processors
   such as Knight's Corner (KNC), your system must be configured to use
   them in "native" mode, not "offload" mode like the USER-INTEL package
   supports.

**Running on GPUs:**

Use the "-k" :doc:`command-line switch <Run_options>` to specify the
number of GPUs per node. Typically the -np setting of the mpirun command
should set the number of MPI tasks/node to be equal to the number of
physical GPUs on the node. You can assign multiple MPI tasks to the same
GPU with the KOKKOS package, but this is usually only faster if some
portions of the input script have not been ported to use Kokkos. In this
case, also packing/unpacking communication buffers on the host may give
speedup (see the KOKKOS :doc:`package <package>` command). Using CUDA MPS
is recommended in this scenario.

Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be
avoided by using :doc:`-pk kokkos cuda/aware no <package>`. As above for
multi-core CPUs (and no GPU), if N is the number of physical cores/node,
then the number of MPI tasks/node should not exceed N.


.. parsed-literal::

   -k on g Ng

Here are examples of how to use the KOKKOS package for GPUs, assuming
one or more nodes, each with two GPUs:


.. parsed-literal::

   mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj          # 1 node,   2 MPI tasks/node, 2 GPUs/node
   mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj  # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total)

.. note::

   The default for the :doc:`package kokkos <package>` command when
   running on GPUs is to use "full" neighbor lists and set the Newton flag
   to "off" for both pairwise and bonded interactions, along with threaded
   communication. When running on Maxwell or Kepler GPUs, this will
   typically be best. For Pascal GPUs, using "half" neighbor lists and
   setting the Newton flag to "on" may be faster. For many pair styles,
   setting the neighbor binsize equal to twice the CPU default value will
   give speedup, which is the default when running on GPUs. Use the "-pk
   kokkos" :doc:`command-line switch <Run_options>` to change the default
   :doc:`package kokkos <package>` options. See its doc page for details and
   default settings. Experimenting with its options can provide a speed-up
   for specific calculations. For example:


.. parsed-literal::

   mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff

.. note::

   For good performance of the KOKKOS package on GPUs, you must
   have Kepler generation GPUs (or later). The Kokkos library exploits
   texture cache options not supported by Telsa generation GPUs (or
   older).

.. note::

   When using a GPU, you will achieve the best performance if your
   input script does not use fix or compute styles which are not yet
   Kokkos-enabled. This allows data to stay on the GPU for multiple
   timesteps, without being copied back to the host CPU. Invoking a
   non-Kokkos fix or compute, or performing I/O for
   :doc:`thermo <thermo_style>` or :doc:`dump <dump>` output will cause data
   to be copied back to the CPU incurring a performance penalty.

.. note::

   To get an accurate timing breakdown between time spend in pair,
   kspace, etc., you must set the environment variable CUDA\_LAUNCH\_BLOCKING=1.
   However, this will reduce performance and is not recommended for production runs.

**Run with the KOKKOS package by editing an input script:**

Alternatively the effect of the "-sf" or "-pk" switches can be
duplicated by adding the :doc:`package kokkos <package>` or :doc:`suffix kk <suffix>` commands to your input script.

The discussion above for building LAMMPS with the KOKKOS package, the
mpirun/mpiexec command, and setting appropriate thread are the same.

You must still use the "-k on" :doc:`command-line switch <Run_options>`
to enable the KOKKOS package, and specify its additional arguments for
hardware options appropriate to your system, as documented above.

You can use the :doc:`suffix kk <suffix>` command, or you can explicitly add a
"kk" suffix to individual styles in your input script, e.g.


.. parsed-literal::

   pair_style lj/cut/kk 2.5

You only need to use the :doc:`package kokkos <package>` command if you
wish to change any of its option defaults, as set by the "-k on"
:doc:`command-line switch <Run_options>`.

**Using OpenMP threading and CUDA together (experimental):**

With the KOKKOS package, both OpenMP multi-threading and GPUs can be
used together in a few special cases. In the Makefile, the
KOKKOS\_DEVICES variable must include both "Cuda" and "OpenMP", as is
the case for /src/MAKE/OPTIONS/Makefile.kokkos\_cuda\_mpi


.. parsed-literal::

   KOKKOS_DEVICES=Cuda,OpenMP

The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA,
using the "-sf kk" in the command line gives the default CUDA version
everywhere.  However, if the "/kk/host" suffix is added to a specific
style in the input script, the Kokkos OpenMP (CPU) version of that
specific style will be used instead.  Set the number of OpenMP threads
as "t Nt" and the number of GPUs as "g Ng"


.. parsed-literal::

   -k on t Nt g Ng

For example, the command to run with 1 GPU and 8 OpenMP threads is then:


.. parsed-literal::

   mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk

Conversely, if the "-sf kk/host" is used in the command line and then
the "/kk" or "/kk/device" suffix is added to a specific style in your
input script, then only that specific style will run on the GPU while
everything else will run on the CPU in OpenMP mode. Note that the
execution of the CPU and GPU styles will NOT overlap, except for a
special case:

A kspace style and/or molecular topology (bonds, angles, etc.) running
on the host CPU can overlap with a pair style running on the
GPU. First compile with "--default-stream per-thread" added to CCFLAGS
in the Kokkos CUDA Makefile.  Then explicitly use the "/kk/host"
suffix for kspace and bonds, angles, etc.  in the input file and the
"kk" suffix (equal to "kk/device") on the command line.  Also make
sure the environment variable CUDA\_LAUNCH\_BLOCKING is not set to "1"
so CPU/GPU overlap can occur.

**Speed-ups to expect:**

The performance of KOKKOS running in different modes is a function of
your hardware, which KOKKOS-enable styles are used, and the problem
size.

Generally speaking, the following rules of thumb apply:

* When running on CPUs only, with a single thread per MPI task,
  performance of a KOKKOS style is somewhere between the standard
  (un-accelerated) styles (MPI-only mode), and those provided by the
  USER-OMP package. However the difference between all 3 is small (less
  than 20%).
* When running on CPUs only, with multiple threads per MPI task,
  performance of a KOKKOS style is a bit slower than the USER-OMP
  package.
* When running large number of atoms per GPU, KOKKOS is typically faster
  than the GPU package.
* When running on Intel hardware, KOKKOS is not as fast as
  the USER-INTEL package, which is optimized for that hardware.


See the `Benchmark page <http://lammps.sandia.gov/bench.html>`_ of the
LAMMPS web site for performance of the KOKKOS package on different
hardware.

**Advanced Kokkos options:**

There are other allowed options when building with the KOKKOS package.
As explained on the :ref:`Build extras <kokkos>` doc page,
they can be set either as variables on the make command line or in
Makefile.machine, or they can be specified as CMake variables.  Each
takes a value shown below.  The default value is listed, which is set
in the lib/kokkos/Makefile.kokkos file.

* KOKKOS\_DEBUG, values = *yes*\ , *no*\ , default = *no*
* KOKKOS\_USE\_TPLS, values = *hwloc*\ , *librt*\ , *experimental\_memkind*, default = *none*
* KOKKOS\_CXX\_STANDARD, values = *c++11*\ , *c++1z*\ , default = *c++11*
* KOKKOS\_OPTIONS, values = *aggressive\_vectorization*, *disable\_profiling*, default = *none*
* KOKKOS\_CUDA\_OPTIONS, values = *force\_uvm*, *use\_ldg*, *rdc*\ , *enable\_lambda*, default = *enable\_lambda*

KOKKOS\_USE\_TPLS=hwloc binds threads to hardware cores, so they do not
migrate during a simulation. KOKKOS\_USE\_TPLS=hwloc should always be
used if running with KOKKOS\_DEVICES=Pthreads for pthreads. It is not
necessary for KOKKOS\_DEVICES=OpenMP for OpenMP, because OpenMP
provides alternative methods via environment variables for binding
threads to hardware cores.  More info on binding threads to cores is
given on the :doc:`Speed omp <Speed_omp>` doc page.

KOKKOS\_USE\_TPLS=librt enables use of a more accurate timer mechanism
on most Unix platforms. This library is not available on all
platforms.

KOKKOS\_DEBUG is only useful when developing a Kokkos-enabled style
within LAMMPS. KOKKOS\_DEBUG=yes enables printing of run-time
debugging information that can be useful. It also enables runtime
bounds checking on Kokkos data structures.

KOKKOS\_CXX\_STANDARD and KOKKOS\_OPTIONS are typically not changed when
building LAMMPS.

KOKKOS\_CUDA\_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS
package must be compiled with the *enable\_lambda* option when using
GPUs.

Restrictions
""""""""""""


Currently, there are no precision options with the KOKKOS package. All
compilation and computation is performed in double precision.


.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html
