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5. Accelerating LAMMPS performance :h3

This section describes various methods for improving LAMMPS
performance for different classes of problems running
on different kinds of machines.

5.1 "OPT package"_#acc_1
5.2 "USER-OMP package"_#acc_2
5.3 "GPU package"_#acc_3
5.4 "USER-CUDA package"_#acc_4
5.5 "Comparison of GPU and USER-CUDA packages"_#acc_5 :all(b)

Accelerated versions of various "pair_style"_pair_style.html,
"fixes"_fix.html, "computes"_compute.html, and other commands have
been added to LAMMPS, which will typically run faster than the
standard non-accelerated versions, if you have the appropriate
hardware on your system.

The accelerated styles have the same name as the standard styles,
except that a suffix is appended.  Otherwise, the syntax for the
command is identical, their functionality is the same, and the
numerical results it produces should also be identical, except for
precision and round-off issues.

For example, all of these variants of the basic Lennard-Jones pair
style exist in LAMMPS:

"pair_style lj/cut"_pair_lj.html
"pair_style lj/cut/opt"_pair_lj.html
"pair_style lj/cut/omp"_pair_lj.html
"pair_style lj/cut/gpu"_pair_lj.html
"pair_style lj/cut/cuda"_pair_lj.html :ul

Assuming you have built LAMMPS with the appropriate package, these
styles can be invoked by specifying them explicitly in your input
script.  Or you can use the "-suffix command-line
switch"_Section_start.html#start_7 to invoke the accelerated versions
automatically, without changing your input script.  The
"suffix"_suffix.html command allows you to set a suffix explicitly and
to turn off/on the comand-line switch setting, both from within your
input script.

Styles with an "opt" suffix are part of the OPT package and typically
speed-up the pairwise calculations of your simulation by 5-25%.

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 a "gpu" or "cuda" suffix are part of the GPU or USER-CUDA
packages, and can be run on NVIDIA GPUs associated with your CPUs.
The speed-up due to GPU usage depends on a variety of factors, as
discussed below.

To see what styles are currently available in each of the accelerated
packages, see "Section_commands 5"_Section_commands.html#cmd_5 of the
manual.  A list of accelerated styles is included in the pair, fix,
compute, and kspace sections.

The following sections explain:

what hardware and software the accelerated styles require
how to build LAMMPS with the accelerated packages in place
what changes (if any) are needed in your input scripts
guidelines for best performance
speed-ups you can expect :ul

The final section compares and contrasts the GPU and USER-CUDA
packages, since they are both designed to use NVIDIA GPU hardware.

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5.1 OPT package :h4,link(acc_1)

The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technologies).  It contains a handful of pair styles whose compute()
methods were rewritten in C++ templated form to reduce the overhead
due to if tests and other conditional code.

The procedure for building LAMMPS with the OPT package is simple.  It
is the same as for any other package which has no additional library
dependencies:

make yes-opt
make machine :pre

If your input script uses one of the OPT pair styles,
you can run it as follows:

lmp_machine -sf opt < in.script
mpirun -np 4 lmp_machine -sf opt < in.script :pre

You should see a reduction in the "Pair time" printed out at the end
of the run.  On most machines and problems, this will typically be a 5
to 20% savings.

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5.2 USER-OMP package :h4,link(acc_2)

The USER-OMP package was developed by Axel Kohlmeyer at Temple University.
It provides multi-threaded versions of most pair styles, all dihedral
styles and a few fixes in LAMMPS. The package currently uses the OpenMP
interface which requires using a specific compiler flag in the makefile
to enable multiple threads; without this flag the corresponding pair
styles will still be compiled and work, but do not support multi-threading.

[Building LAMMPS with the USER-OMP package:]

The procedure for building LAMMPS with the USER-OMP package is simple.
You have to edit your machine specific makefile to add the flag to
enable OpenMP support to the CCFLAGS and LINKFLAGS variables. For the
GNU compilers for example this flag is called {-fopenmp}. Check your
compiler documentation to find out which flag you need to add.
The rest of the compilation is the same as for any other package which
has no additional library dependencies:

make yes-user-omp
make machine :pre

Please note that this will only install accelerated versions
of styles that are already installed, so you want to install
this package as the last package, or else you may be missing
some accelerated styles. If you plan to uninstall some package,
you should first uninstall the USER-OMP package then the other
package and then re-install USER-OMP, to make sure that there
are no orphaned {omp} style files present, which would lead to
compilation errors.

If your input script uses one of regular styles that are also
exist as an OpenMP version in the USER-OMP package you can run
it as follows:

env OMP_NUM_THREADS=4 lmp_serial -sf omp -in in.script
env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script :pre

The value of the environment variable OMP_NUM_THREADS determines how
many threads per MPI task are launched. All three examples above use
a total of 4 CPU cores.  For different MPI implementations the method
to pass the OMP_NUM_THREADS environment variable to all processes is
different.  Two different variants, one for MPICH and OpenMPI, respectively
are shown above.  Please check the documentation of your MPI installation
for additional details.  Alternatively, the value provided by OMP_NUM_THREADS
can be overridded with the "package omp"_package.html command.
Depending on which styles are accelerated in your input, you should
see a reduction in the "Pair time" and/or "Bond time" and "Loop time"
printed out at the end of the run. The optimal ratio of MPI to OpenMP
can vary a lot and should always be confirmed through some benchmark
runs for the current system and on the current machine.

[Restrictions:]

None of the pair styles in the USER-OMP package support the "inner",
"middle", "outer" options for r-RESPA integration, only the "pair"
option is supported.

[Parallel efficiency and performance tips:]

In most simple cases the MPI parallelization in LAMMPS is more
efficient than multi-threading implemented in the USER-OMP package.
Also the parallel efficiency varies between individual styles.
On the other hand, in many cases you still want to use the {omp} version
- even when compiling or running without OpenMP support - since they
all contain optimizations similar to those in the OPT package, which
can result in serial speedup.

Using multi-threading is most effective under the following circumstances:

Individual compute nodes have a significant number of CPU cores
but the CPU itself has limited memory bandwidth, e.g. Intel Xeon 53xx
(Clovertown) and 54xx (Harpertown) quad core processors. Running
one MPI task per CPU core will result in significant performance
degradation, so that running with 4 or even only 2 MPI tasks per
nodes is faster. Running in hybrid MPI+OpenMP mode will reduce the
inter-node communication bandwidth contention in the same way,
but offers and additional speedup from utilizing the otherwise
idle CPU cores. :ulb,l

The interconnect used for MPI communication is not able to provide
sufficient bandwidth for a large number of MPI tasks per node.
This applies for example to running over gigabit ethernet or
on Cray XT4 or XT5 series supercomputers. Same as in the aforementioned
case this effect worsens with using an increasing number of nodes. :l

The input is a system that has an inhomogeneous particle density
which cannot be mapped well to the domain decomposition scheme
that LAMMPS employs. While this can be to some degree alleviated
through using the "processors"_processors.html keyword, multi-threading
provides a parallelism that parallelizes over the number of particles
not their distribution in space. :l

Finally, multi-threaded styles can improve performance when running
LAMMPS in "capability mode", i.e. near the point where the MPI
parallelism scales out. This can happen in particular when using
as kspace style for long-range electrostatics. Here the scaling
of the kspace style is the performance limiting factor and using
multi-threaded styles allows to operate the kspace style at the
limit of scaling and then increase performance parallelizing
the real space calculations with hybrid MPI+OpenMP. Sometimes
additional speedup can be achived by increasing the real-space
coulomb cutoff and thus reducing the work in the kspace part. :l,ule

The best parallel efficiency from {omp} styles is typically 
achieved when there is at least one MPI task per physical 
processor, i.e. socket or die.

Using threads on hyper-threading enabled cores is usually
counterproductive, as the cost in additional memory bandwidth
requirements is not offset by the gain in CPU utilization
through hyper-threading.

A description of the multi-threading strategy and some performance
examples are "presented here"_http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1

:line
:line

5.3 GPU package :h4,link(acc_3)

The GPU package was developed by Mike Brown at ORNL.  It provides GPU
versions of several pair styles and for long-range Coulombics via the
PPPM command.  It has the following features:

The package is designed to exploit common GPU hardware configurations
where one or more GPUs are coupled with many cores of a multi-core
CPUs, e.g. within a node of a parallel machine. :ulb,l

Atom-based data (e.g. coordinates, forces) moves back-and-forth
between the CPU(s) and GPU every timestep. :l

Neighbor lists can be constructed on the CPU or on the GPU :l

The charge assignement and force interpolation portions of PPPM can be
run on the GPU.  The FFT portion, which requires MPI communication
between processors, runs on the CPU. :l

Asynchronous force computations can be performed simultaneously on the
CPU(s) and GPU. :l

LAMMPS-specific code is in the GPU package.  It makes calls to a
generic GPU library in the lib/gpu directory.  This library provides
NVIDIA support as well as more general OpenCL support, so that the
same functionality can eventually be supported on a variety of GPU
hardware. :l,ule

[Hardware and software requirements:]

To use this package, you currently need to have specific NVIDIA
hardware and install specific NVIDIA CUDA software on your system:

Check if you have an NVIDIA card: cat /proc/driver/nvidia/cards/0
Go to http://www.nvidia.com/object/cuda_get.html
Install a driver and toolkit appropriate for your system (SDK is not necessary)
Follow the instructions in lammps/lib/gpu/README to build the library (see below)
Run lammps/lib/gpu/nvc_get_devices to list supported devices and properties :ul

[Building LAMMPS with the GPU package:]

As with other packages that include a separately compiled library, you
need to first build the GPU library, before building LAMMPS itself.
General instructions for doing this are in "this
section"_doc/Section_start.html#start_3 of the manual.  For this
package, do the following, using a Makefile in lib/gpu appropriate for
your system:

cd lammps/lib/gpu
make -f Makefile.linux
(see further instructions in lammps/lib/gpu/README) :pre

If you are successful, you will produce the file lib/libgpu.a.

Now you are ready to build LAMMPS with the GPU package installed:

cd lammps/src
make yes-gpu
make machine :pre

Note that the lo-level Makefile (e.g. src/MAKE/Makefile.linux) has
these settings: gpu_SYSINC, gpu_SYSLIB, gpu_SYSPATH.  These need to be
set appropriately to include the paths and settings for the CUDA
system software on your machine.  See src/MAKE/Makefile.g++ for an
example.

[GPU configuration]

When using GPUs, you are restricted to one physical GPU per LAMMPS
process, which is an MPI process running on a single core or
processor.  Multiple MPI processes (CPU cores) can share a single GPU,
and in many cases it will be more efficient to run this way.

[Input script requirements:]

Additional input script requirements to run pair or PPPM styles with a
{gpu} suffix are as follows:

To invoke specific styles from the GPU package, you can either append
"gpu" to the style name (e.g. pair_style lj/cut/gpu), or use the
"-suffix command-line switch"_Section_start.html#start_7, or use the
"suffix"_suffix.html command. :ulb,l

The "newton pair"_newton.html setting must be {off}. :l

The "package gpu"_package.html command must be used near the beginning
of your script to control the GPU selection and initialization
settings.  It also has an option to enable asynchronous splitting of
force computations between the CPUs and GPUs. :l,ule

As an example, if you have two GPUs per node and 8 CPU cores per node,
and would like to run on 4 nodes (32 cores) with dynamic balancing of
force calculation across CPU and GPU cores, you could specify

package gpu force/neigh 0 1 -1 :pre

In this case, all CPU cores and GPU devices on the nodes would be
utilized.  Each GPU device would be shared by 4 CPU cores. The CPU
cores would perform force calculations for some fraction of the
particles at the same time the GPUs performed force calculation for
the other particles.

[Timing output:]

As described by the "package gpu"_package.html command, GPU
accelerated pair styles can perform computations asynchronously with
CPU computations. The "Pair" time reported by LAMMPS will be the
maximum of the time required to complete the CPU pair style
computations and the time required to complete the GPU pair style
computations. Any time spent for GPU-enabled pair styles for
computations that run simultaneously with "bond"_bond_style.html,
"angle"_angle_style.html, "dihedral"_dihedral_style.html,
"improper"_improper_style.html, and "long-range"_kspace_style.html
calculations will not be included in the "Pair" time.

When the {mode} setting for the package gpu command is force/neigh,
the time for neighbor list calculations on the GPU will be added into
the "Pair" time, not the "Neigh" time.  An additional breakdown of the
times required for various tasks on the GPU (data copy, neighbor
calculations, force computations, etc) are output only with the LAMMPS
screen output (not in the log file) at the end of each run.  These
timings represent total time spent on the GPU for each routine,
regardless of asynchronous CPU calculations.

[Performance tips:]

Generally speaking, for best performance, you should use multiple CPUs
per GPU, as provided my most multi-core CPU/GPU configurations.

Because of the large number of cores within each GPU device, it may be
more efficient to run on fewer processes per GPU when the number of
particles per MPI process is small (100's of particles); this can be
necessary to keep the GPU cores busy.

See the lammps/lib/gpu/README file for instructions on how to build
the GPU library for single, mixed, or double precision.  The latter
requires that your GPU card support double precision.

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:line

5.4 USER-CUDA package :h4,link(acc_4)

The USER-CUDA package was developed by Christian Trott at U Technology
Ilmenau in Germany.  It provides NVIDIA GPU versions of many pair
styles, many fixes, a few computes, and for long-range Coulombics via
the PPPM command.  It has the following features:

The package is designed to allow an entire LAMMPS calculation, for
many timesteps, to run entirely on the GPU (except for inter-processor
MPI communication), so that atom-based data (e.g. coordinates, forces)
do not have to move back-and-forth between the CPU and GPU. :ulb,l

The speed-up advantage of this approach is typically better when the
number of atoms per GPU is large :l

Data will stay on the GPU until a timestep where a non-GPU-ized fix or
compute is invoked.  Whenever a non-GPU operation occurs (fix,
compute, output), data automatically moves back to the CPU as needed.
This may incur a performance penalty, but should otherwise work
transparently. :l

Neighbor lists for GPU-ized pair styles are constructed on the
GPU. :l

The package only supports use of a single CPU (core) with each
GPU. :l,ule

[Hardware and software requirements:]

To use this package, you need to have specific NVIDIA hardware and
install specific NVIDIA CUDA software on your system.

Your NVIDIA GPU needs to support Compute Capability 1.3. This list may
help you to find out the Compute Capability of your card:

http://en.wikipedia.org/wiki/Comparison_of_Nvidia_graphics_processing_units

Install the Nvidia Cuda Toolkit in version 3.2 or higher and the
corresponding GPU drivers. The Nvidia Cuda SDK is not required for
LAMMPSCUDA but we recommend it be installed.  You can then make sure
that its sample projects can be compiled without problems.

[Building LAMMPS with the USER-CUDA package:]

As with other packages that include a separately compiled library, you
need to first build the USER-CUDA library, before building LAMMPS
itself.  General instructions for doing this are in "this
section"_doc/Section_start.html#start_3 of the manual.  For this
package, do the following, using settings in the lib/cuda Makefiles
appropriate for your system:

Go to the lammps/lib/cuda directory :ulb,l

If your {CUDA} toolkit is not installed in the default system directoy
{/usr/local/cuda} edit the file {lib/cuda/Makefile.common}
accordingly. :l

Type "make OPTIONS", where {OPTIONS} are one or more of the following
options. The settings will be written to the
{lib/cuda/Makefile.defaults} and used in the next step. :l

{precision=N} to set the precision level
  N = 1 for single precision (default)
  N = 2 for double precision
  N = 3 for positions in double precision
  N = 4 for positions and velocities in double precision
{arch=M} to set GPU compute capability
  M = 20 for CC2.0 (GF100/110, e.g. C2050,GTX580,GTX470) (default)
  M = 21 for CC2.1 (GF104/114,  e.g. GTX560, GTX460, GTX450)
  M = 13 for CC1.3 (GF200, e.g. C1060, GTX285)
{prec_timer=0/1} to use hi-precision timers
  0 = do not use them (default)
  1 = use these timers
  this is usually only useful for Mac machines 
{dbg=0/1} to activate debug mode
  0 = no debug mode (default)
  1 = yes debug mode
  this is only useful for developers
{cufft=1} to determine usage of CUDA FFT library
  0 = no CUFFT support (default)
  in the future other CUDA-enabled FFT libraries might be supported :pre

Type "make" to build the library.  If you are successful, you will
produce the file lib/libcuda.a. :l,ule

Now you are ready to build LAMMPS with the USER-CUDA package installed:

cd lammps/src
make yes-user-cuda
make machine :pre

Note that the LAMMPS build references the lib/cuda/Makefile.common
file to extract setting specific CUDA settings.  So it is important
that you have first built the cuda library (in lib/cuda) using
settings appropriate to your system.

[Input script requirements:]

Additional input script requirements to run styles with a {cuda}
suffix are as follows:

To invoke specific styles from the USER-CUDA package, you can either
append "cuda" to the style name (e.g. pair_style lj/cut/cuda), or use
the "-suffix command-line switch"_Section_start.html#start_7, or use
the "suffix"_suffix.html command.  One exception is that the
"kspace_style pppm/cuda"_kspace_style.html command has to be requested
explicitly. :ulb,l

To use the USER-CUDA package with its default settings, no additional
command is needed in your input script.  This is because when LAMMPS
starts up, it detects if it has been built with the USER-CUDA package.
See the "-cuda command-line switch"_Section_start.html#start_7 for
more details. :l

To change settings for the USER-CUDA package at run-time, the "package
cuda"_package.html command can be used near the beginning of your
input script.  See the "package"_package.html command doc page for
details. :l,ule

[Performance tips:]

The USER-CUDA package offers more speed-up relative to CPU performance
when the number of atoms per GPU is large, e.g. on the order of tens
or hundreds of 1000s.

As noted above, this package will continue to run a simulation
entirely on the GPU(s) (except for inter-processor MPI communication),
for multiple timesteps, until a CPU calculation is required, either by
a fix or compute that is non-GPU-ized, or until output is performed
(thermo or dump snapshot or restart file).  The less often this
occurs, the faster your simulation will run.

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:line

5.5 Comparison of GPU and USER-CUDA packages :h4,link(acc_5)

Both the GPU and USER-CUDA packages accelerate a LAMMPS calculation
using NVIDIA hardware, but they do it in different ways.

As a consequence, for a particular simulation on specific hardware,
one package may be faster than the other.  We give guidelines below,
but the best way to determine which package is faster for your input
script is to try both of them on your machine.  See the benchmarking
section below for examples where this has been done.

[Guidelines for using each package optimally:]

The GPU package allows you to assign multiple CPUs (cores) to a single
GPU (a common configuration for "hybrid" nodes that contain multicore
CPU(s) and GPU(s)) and works effectively in this mode.  The USER-CUDA
package does not allow this; you can only use one CPU per GPU. :ulb,l

The GPU package moves per-atom data (coordinates, forces)
back-and-forth between the CPU and GPU every timestep.  The USER-CUDA
package only does this on timesteps when a CPU calculation is required
(e.g. to invoke a fix or compute that is non-GPU-ized).  Hence, if you
can formulate your input script to only use GPU-ized fixes and
computes, and avoid doing I/O too often (thermo output, dump file
snapshots, restart files), then the data transfer cost of the
USER-CUDA package can be very low, causing it to run faster than the
GPU package. :l

The GPU package is often faster than the USER-CUDA package, if the
number of atoms per GPU is "small".  The crossover point, in terms of
atoms/GPU at which the USER-CUDA package becomes faster depends
strongly on the pair style.  For example, for a simple Lennard Jones
system the crossover (in single precision) is often about 50K-100K
atoms per GPU.  When performing double precision calculations the
crossover point can be significantly smaller. :l

Both packages compute bonded interactions (bonds, angles, etc) on the
CPU.  This means a model with bonds will force the USER-CUDA package
to transfer per-atom data back-and-forth between the CPU and GPU every
timestep.  If the GPU package is running with several MPI processes
assigned to one GPU, the cost of computing the bonded interactions is
spread across more CPUs and hence the GPU package can run faster. :l

When using the GPU package with multiple CPUs assigned to one GPU, its
performance depends to some extent on high bandwidth between the CPUs
and the GPU.  Hence its performance is affected if full 16 PCIe lanes
are not available for each GPU.  In HPC environments this can be the
case if S2050/70 servers are used, where two devices generally share
one PCIe 2.0 16x slot.  Also many multi-GPU mainboards do not provide
full 16 lanes to each of the PCIe 2.0 16x slots. :l,ule

[Differences between the two packages:]

The GPU package accelerates only pair force, neighbor list, and PPPM
calculations.  The USER-CUDA package currently supports a wider range
of pair styles and can also accelerate many fix styles and some
compute styles, as well as neighbor list and PPPM calculations. :ulb,l

The USER-CUDA package does not support acceleration for minimization. :l

The USER-CUDA package does not support hybrid pair styles. :l

The USER-CUDA package can order atoms in the neighbor list differently
from run to run resulting in a different order for force accumulation. :l

The USER-CUDA package has a limit on the number of atom types that can be
used in a simulation. :l

The GPU package requires neighbor lists to be built on the CPU when using
exclusion lists or a triclinic simulation box. :l

The GPU package uses more GPU memory than the USER-CUDA package.  This
is generally not a problem since typical runs are computation-limited
rather than memory-limited. :l,ule

[Examples:]

The LAMMPS distribution has two directories with sample input scripts
for the GPU and USER-CUDA packages.

lammps/examples/gpu = GPU package files
lammps/examples/USER/cuda = USER-CUDA package files :ul

These contain input scripts for identical systems, so they can be used
to benchmark the performance of both packages on your system.

:line

[Benchmark data:]

NOTE: We plan to add some benchmark results and plots here for the
examples described in the previous section.

Simulations:

1. Lennard Jones

256,000 atoms
2.5 A cutoff
0.844 density :ul

2. Lennard Jones

256,000 atoms
5.0 A cutoff
0.844 density :ul

3. Rhodopsin model

256,000 atoms
10A cutoff
Coulomb via PPPM :ul

4. Lihtium-Phosphate

295650 atoms
15A cutoff
Coulomb via PPPM :ul

Hardware:

Workstation:

2x GTX470
i7 950@3GHz
24Gb DDR3 @ 1066Mhz
CentOS 5.5
CUDA 3.2
Driver 260.19.12 :ul

eStella:

6 Nodes
2xC2050
2xQDR Infiniband interconnect(aggregate bandwidth 80GBps)
Intel X5650 HexCore @ 2.67GHz
SL 5.5
CUDA 3.2
Driver 260.19.26 :ul

Keeneland:

HP SL-390 (Ariston) cluster
120 nodes
2x Intel Westmere hex-core CPUs
3xC2070s
QDR InfiniBand interconnect :ul