jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
lammps/doc/accelerate_kokkos.html

427 lines
19 KiB
HTML
Raw Normal View History

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12464 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-09-10 23:32:24 +08:00
<HTML>
<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
</P>
<H4>5.3.4 KOKKOS package
</H4>
<P>The KOKKOS package was developed primaritly by Christian Trott
(Sandia) with contributions of various styles by others, including
Sikandar Mashayak (UIUC). The underlying Kokkos library was written
primarily by Carter Edwards, Christian Trott, and Dan Sunderland (all
Sandia).
</P>
<P>The 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.
</P>
<P>The Kokkos library is part of
<A HREF = "http://trilinos.sandia.gov/packages/kokkos">Trilinos</A> and is a
templated C++ library that provides two key abstractions for an
application like LAMMPS. First, it allows a single implementation of
an application kernel (e.g. a pair style) to run efficiently on
different kinds of hardware, such as a GPU, Intel Phi, or many-core
chip.
</P>
<P>The Kokkos library also provides data abstractions to adjust (at
compile time) the memory layout of basic data structures like 2d and
3d arrays and allow the transparent utilization of special hardware
load and store operations. Such data structures are used in LAMMPS to
store atom coordinates or forces or neighbor lists. The layout is
chosen to optimize performance on different platforms. Again this
functionality is hidden from the developer, and does not affect how
the kernel is coded.
</P>
<P>These abstractions are set at build time, when LAMMPS is compiled with
the KOKKOS package installed. This is done by selecting a "host" and
"device" to build for, compatible with the compute nodes in your
machine (one on a desktop machine or 1000s on a supercomputer).
</P>
<P>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.
</P>
<P>Kokkos provides support for two different modes of execution per MPI
task. This means that computational tasks (pairwise interactions,
neighbor list builds, time integration, etc) can be parallelized for
one or the other of the two modes. The first mode is called the
"host" and is one or more threads running on one or more physical CPUs
(within the node). Currently, both multi-core CPUs and an Intel Phi
processor (running in native mode, not offload mode like the
USER-INTEL package) are supported. The second mode is called the
"device" and is an accelerator chip of some kind. Currently only an
NVIDIA GPU is supported. If your compute node does not have a GPU,
then there is only one mode of execution, i.e. the host and device are
the same.
</P>
<P>Here is a quick overview of how to use the KOKKOS package
for GPU acceleration:
</P>
<UL><LI>specify variables and settings in your Makefile.machine that enable GPU, Phi, or OpenMP support
<LI>include the KOKKOS package and build LAMMPS
<LI>enable the KOKKOS package and its hardware options via the "-k on" command-line switch
<LI>use KOKKOS styles in your input script
</UL>
<P>The latter two steps can be done using the "-k on", "-pk kokkos" and
"-sf kk" <A HREF = "Section_start.html#start_7">command-line switches</A>
respectively. Or the effect of the "-pk" or "-sf" switches can be
duplicated by adding the <A HREF = "package.html">package kokkos</A> or <A HREF = "suffix.html">suffix
kk</A> commands respectively to your input script.
</P>
<P><B>Required hardware/software:</B>
</P>
<P>The KOKKOS package can be used to build and run LAMMPS on the
following kinds of hardware:
</P>
<UL><LI>CPU-only: one MPI task per CPU core (MPI-only, but using KOKKOS styles)
<LI>CPU-only: one or a few MPI tasks per node with additional threading via OpenMP
<LI>Phi: on one or more Intel Phi coprocessors (per node)
<LI>GPU: on the GPUs of a node with additional OpenMP threading on the CPUs
</UL>
<P>Note that Intel Xeon Phi coprocessors are supported in "native" mode,
not "offload" mode like the USER-INTEL package supports.
</P>
<P>Only NVIDIA GPUs are currently supported.
</P>
<P>IMPORTANT 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).
</P>
<P>To build the KOKKOS package for GPUs, NVIDIA Cuda software must be
installed on your system. See the discussion above for the USER-CUDA
and GPU packages for details of how to check and do this.
</P>
<P><B>Building LAMMPS with the KOKKOS package:</B>
</P>
<P>Unlike other acceleration packages discussed in this section, the
Kokkos library in lib/kokkos does not have to be pre-built before
building LAMMPS itself. Instead, options for the Kokkos library are
specified at compile time, when LAMMPS itself is built. This can be
done in one of two ways, as discussed below.
</P>
<P>Here are examples of how to build LAMMPS for the different compute-node
configurations listed above.
</P>
<P>CPU-only (run all-MPI or with OpenMP threading):
</P>
<PRE>cd lammps/src
make yes-kokkos
make g++ OMP=yes
</PRE>
<P>Intel Xeon Phi:
</P>
<PRE>cd lammps/src
make yes-kokkos
make g++ OMP=yes MIC=yes
</PRE>
<P>CPUs and GPUs:
</P>
<PRE>cd lammps/src
make yes-kokkos
make cuda CUDA=yes
</PRE>
<P>These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
make command line which requires a GNU-compatible make command. Try
"gmake" if your system's standard make complains.
</P>
<P>IMPORTANT NOTE: If you build using make line variables and re-build
LAMMPS twice with different KOKKOS options and the *same* target,
e.g. g++ in the first two examples above, then you *must* perform a
"make clean-all" or "make clean-machine" before each build. This is
to force all the KOKKOS-dependent files to be re-compiled with the new
options.
</P>
<P>You can also hardwire these make variables in the specified machine
makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
with a line like:
</P>
<PRE>MIC = yes
</PRE>
<P>Note that if you build LAMMPS multiple times in this manner, using
different KOKKOS options (defined in different machine makefiles), you
do not have to worry about doing a "clean" in between. This is
because the targets will be different.
</P>
<P>IMPORTANT NOTE: The 3rd example above for a GPU, uses a different
machine makefile, in this case src/MAKE/Makefile.cuda, which is
included in the LAMMPS distribution. To build the KOKKOS package for
a GPU, this makefile must use the NVIDA "nvcc" compiler. And it must
have a CCFLAGS -arch setting that is appropriate for your NVIDIA
hardware and installed software. Typical values for -arch are given
in <A HREF = "Section_start.html#start_3_4">Section 2.3.4</A> of the manual, as well
as other settings that must be included in the machine makefile, if
you create your own.
</P>
<P>There are other allowed options when building with the KOKKOS package.
As above, They can be set either as variables on the make command line
or in the machine makefile in the src/MAKE directory. See <A HREF = "Section_start.html#start_3_4">Section
2.3.4</A> of the manual for details.
</P>
<P>IMPORTANT NOTE: Currently, there are no precision options with the
KOKKOS package. All compilation and computation is performed in
double precision.
</P>
<P><B>Run with the KOKKOS package from the command line:</B>
</P>
<P>The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command does this via its -np
and -ppn switches.
</P>
<P>When using KOKKOS built with host=OMP, you need to choose how many
OpenMP threads per MPI task will be used (via the "-k" command-line
switch discussed below). 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.
</P>
<P>When using the KOKKOS package built with device=CUDA, you must use
exactly one MPI task per physical GPU.
</P>
<P>When using the KOKKOS package built with host=MIC for Intel Xeon Phi
coprocessor support you need to insure there are one or more MPI tasks
per coprocessor, and choose the number of coprocessor threads to use
per MPI task (via the "-k" command-line switch discussed below). The
product of MPI tasks * coprocessor threads/task should not exceed the
maximum number of threads the coproprocessor is designed to run,
otherwise performance will suffer. This value is 240 for current
generation Xeon Phi(TM) chips, which is 60 physical cores * 4
threads/core. Note that with the KOKKOS package you do not need to
specify how many Phi coprocessors there are per node; each
coprocessors is simply treated as running some number of MPI tasks.
</P>
<P>You must use the "-k on" <A HREF = "Section_start.html#start_7">command-line
switch</A> to enable the KOKKOS package. It
takes additional arguments for hardware settings appropriate to your
system. Those arguments are <A HREF = "Section_start.html#start_7">documented
here</A>. The two most commonly used arguments
are:
</P>
<PRE>-k on t Nt
-k on g Ng
</PRE>
<P>The "t Nt" option applies to host=OMP (even if device=CUDA) and
host=MIC. For host=OMP, it specifies how many OpenMP threads per MPI
task to use with a node. For host=MIC, it specifies how many Xeon Phi
threads per MPI task to use within a node. The default is Nt = 1.
Note that for host=OMP this is effectively MPI-only mode which may be
fine. But for host=MIC you will typically end up using far less than
all the 240 available threads, which could give very poor performance.
</P>
<P>The "g Ng" option applies to device=CUDA. It specifies how many GPUs
per compute node to use. The default is 1, so this only needs to be
specified is you have 2 or more GPUs per compute node.
</P>
<P>The "-k on" switch also issues a default <A HREF = "package.html">package kokkos neigh full
comm host</A> command which sets various KOKKOS options to
default values, as discussed on the <A HREF = "package.html">package</A> command doc
page.
</P>
<P>Use the "-sf kk" <A HREF = "Section_start.html#start_7">command-line switch</A>,
which will automatically append "kk" to styles that support it. Use
the "-pk kokkos" <A HREF = "Section_start.html#start_7">command-line switch</A> if
you wish to override any of the default values set by the <A HREF = "package.html">package
kokkos</A> command invoked by the "-k on" switch.
</P>
<PRE>host=OMP, dual hex-core nodes (12 threads/node):
mpirun -np 12 lmp_g++ -in in.lj # MPI-only mode with no Kokkos
mpirun -np 12 lmp_g++ -k on -sf kk -in in.lj # MPI-only mode with Kokkos
mpirun -np 1 lmp_g++ -k on t 12 -sf kk -in in.lj # one MPI task, 12 threads
mpirun -np 2 lmp_g++ -k on t 6 -sf kk -in in.lj # two MPI tasks, 6 threads/task
mpirun -np 32 -ppn 2 lmp_g++ -k on t 6 -sf kk -in in.lj # ditto on 16 nodes
</PRE>
<P>host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240
mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240
mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240
mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis
</P>
<PRE>host=OMP, device=CUDA, node = dual hex-core CPUs and a single GPU:
mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU
mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes
</PRE>
<PRE>host=OMP, device=CUDA, node = dual 8-core CPUs and 2 GPUs:
mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # two MPI tasks, 8 threads per CPU
mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # ditto on 16 nodes
</PRE>
<P><B>Or run with the KOKKOS package by editing an input script:</B>
</P>
<P>The discussion above for the mpirun/mpiexec command and setting
appropriate thread and GPU values for host=OMP or host=MIC or
device=CUDA are the same.
</P>
<P>You must still use the "-k on" <A HREF = "Section_start.html#start_7">command-line
switch</A> to enable the KOKKOS package, and
specify its additional arguments for hardware options appopriate to
your system, as documented above.
</P>
<P>Use the <A HREF = "suffix.html">suffix kk</A> command, or you can explicitly add a
"kk" suffix to individual styles in your input script, e.g.
</P>
<PRE>pair_style lj/cut/kk 2.5
</PRE>
<P>You only need to use the <A HREF = "package.html">package kokkos</A> command if you
wish to change any of its option defaults.
</P>
<P><B>Speed-ups to expect:</B>
</P>
<P>The performance of KOKKOS running in different modes is a function of
your hardware, which KOKKOS-enable styles are used, and the problem
size.
</P>
<P>Generally speaking, the following rules of thumb apply:
</P>
<UL><LI>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%).
<LI>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.
<LI>When running on GPUs, KOKKOS is typically faster than the USER-CUDA
and GPU packages.
<LI>When running on Intel Xeon Phi, KOKKOS is not as fast as
the USER-INTEL package, which is optimized for that hardware.
</UL>
<P>See the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the
LAMMPS web site for performance of the KOKKOS package on different
hardware.
</P>
<P><B>Guidelines for best performance:</B>
</P>
<P>Here are guidline for using the KOKKOS package on the different
hardware configurations listed above.
</P>
<P>Many of the guidelines use the <A HREF = "package.html">package kokkos</A> command
See its doc page for details and default settings. Experimenting with
its options can provide a speed-up for specific calculations.
</P>
<P><B>Running on a multi-core CPU:</B>
</P>
<P>If N is the number of physical cores/node, then the number of MPI
tasks/node * number of threads/task should not exceed N, and should
typically equal N. Note that the default threads/task is 1, as set by
the "t" keyword of the "-k" <A HREF = "Section_start.html#start_7">command-line
switch</A>. If you do not change this, no
additional parallelism (beyond MPI) will be invoked on the host
CPU(s).
</P>
<P>You can compare the performance running in different modes:
</P>
<UL><LI>run with 1 MPI task/node and N threads/task
<LI>run with N MPI tasks/node and 1 thread/task
<LI>run with settings in between these extremes
</UL>
<P>Examples of mpirun commands in these modes are shown above.
</P>
<P>When using KOKKOS to perform 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.
</P>
<P>If you are not certain MPI tasks are being bound (check the defaults
for your MPI installation), binding can be forced with these flags:
</P>
<PRE>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 ...
</PRE>
<P>For binding threads with the KOKKOS OMP option, 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. For binding threads with the
KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option, as
discussed in <A HREF = "Sections_start.html#start_3_4">Section 2.3.4</A> of the
manual.
</P>
<P><B>Running on GPUs:</B>
</P>
<P>Insure the -arch setting in the machine makefile you are using,
e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software
(see <A HREF = "Section_start.html#start_3_4">this section</A> of the manual for
details).
</P>
<P>The -np setting of the mpirun command should set the number of MPI
tasks/node to be equal to the # of physical GPUs on the node.
</P>
<P>Use the "-k" <A HREF = "Section_commands.html#start_7">command-line switch</A> to
specify the number of GPUs per node, and the number of threads per MPI
task. 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 * number of
threads/task should not exceed N. With one GPU (and one MPI task) it
may be faster to use less than all the available cores, by setting
threads/task to a smaller value. This is because using all the cores
on a dual-socket node will incur extra cost to copy memory from the
2nd socket to the GPU.
</P>
<P>Examples of mpirun commands that follow these rules are shown above.
</P>
<P>IMPORTANT NOTE: When using a GPU, you will achieve the best
performance if your input script does not use any 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
<A HREF = "thermo_style.html">thermo</A> or <A HREF = "dump.html">dump</A> output will cause data
to be copied back to the CPU.
</P>
<P>You cannot yet assign multiple MPI tasks to the same GPU with the
KOKKOS package. We plan to support this in the future, similar to the
GPU package in LAMMPS.
</P>
<P>You cannot yet use both the host (multi-threaded) and device (GPU)
together to compute pairwise interactions with the KOKKOS package. We
hope to support this in the future, similar to the GPU package in
LAMMPS.
</P>
<P><B>Running on an Intel Phi:</B>
</P>
<P>Kokkos only uses Intel Phi processors in their "native" mode, i.e.
not hosted by a CPU.
</P>
<P>As illustrated above, build LAMMPS with OMP=yes (the default) and
MIC=yes. The latter insures code is correctly compiled for the Intel
Phi. The OMP setting means OpenMP will be used for parallelization on
the Phi, which is currently the best option within Kokkos. In the
future, other options may be added.
</P>
<P>Current-generation Intel Phi chips have either 61 or 57 cores. One
core should be excluded for running the OS, leaving 60 or 56 cores.
Each core is hyperthreaded, so there are effectively N = 240 (4*60) or
N = 224 (4*56) cores to run on.
</P>
<P>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 2 values should be N, i.e.
240 or 224. Also, the number of threads/task should be a multiple of
4 so that logical threads from more than one MPI task do not run on
the same physical core.
</P>
<P>Examples of mpirun commands that follow these rules are shown above.
</P>
<P><B>Restrictions:</B>
</P>
<P>As noted above, if using GPUs, the number of MPI tasks per compute
node should equal to the number of GPUs per compute node. In the
future Kokkos will support assigning multiple MPI tasks to a single
GPU.
</P>
<P>Currently Kokkos does not support AMD GPUs due to limits in the
available backend programming models. Specifically, Kokkos requires
extensive C++ support from the Kernel language. This is expected to
change in the future.
</P>
</HTML>