2011-05-27 07:45:30 +08:00
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<HTML>
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<CENTER><A HREF = "Section_python.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> - <A HREF = "Section_errors.html">Next Section</A>
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<HR>
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<H3>10. Using accelerated CPU and GPU styles
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</H3>
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2011-06-01 08:11:58 +08:00
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<P>NOTE: These doc pages are still incomplete as of 1Jun11.
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</P>
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<P>NOTE: The USER-CUDA package discussed below has not yet been
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officially released in LAMMPS.
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</P>
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2011-05-27 07:45:30 +08:00
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<P>Accelerated versions of various <A HREF = "pair_style.html">pair_style</A>,
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2011-06-09 04:56:17 +08:00
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<A HREF = "fix.html">fixes</A>, <A HREF = "compute.html">computes</A>, and other commands have
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been added to LAMMPS, which will typically run faster than the
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standard non-accelerated versions, if you have the appropriate
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hardware on your system.
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2011-05-27 07:45:30 +08:00
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</P>
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2011-06-09 04:56:17 +08:00
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<P>The accelerated styles have the same name as the standard styles,
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except that a suffix is appended. Otherwise, the syntax for the
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command is identical, their functionality is the same, and the
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numerical results it produces should also be identical, except for
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precision and round-off issues.
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2011-05-27 07:45:30 +08:00
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</P>
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<P>For example, all of these variants of the basic Lennard-Jones pair
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style exist in LAMMPS:
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</P>
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<UL><LI><A HREF = "pair_lj.html">pair_style lj/cut</A>
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<LI><A HREF = "pair_lj.html">pair_style lj/cut/opt</A>
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<LI><A HREF = "pair_lj.html">pair_style lj/cut/gpu</A>
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<LI><A HREF = "pair_lj.html">pair_style lj/cut/cuda</A>
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</UL>
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<P>Assuming you have built LAMMPS with the appropriate package, these
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styles can be invoked by specifying them explicitly in your input
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2011-06-01 07:08:32 +08:00
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script. Or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
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2011-05-27 07:45:30 +08:00
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switch</A> to invoke the accelerated versions
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2011-06-09 04:56:17 +08:00
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automatically, without changing your input script. The
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<A HREF = "suffix.html">suffix</A> command also allows you to set a suffix and to
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turn off/on the comand-line switch setting within your input script.
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2011-05-27 07:45:30 +08:00
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</P>
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<P>Styles with an "opt" suffix are part of the OPT package and typically
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2011-06-09 04:56:17 +08:00
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speed-up the pairwise calculations of your simulation by 5-25%.
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2011-05-27 07:45:30 +08:00
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</P>
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<P>Styles with a "gpu" or "cuda" suffix are part of the GPU or USER-CUDA
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packages, and can be run on NVIDIA GPUs associated with your CPUs.
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The speed-up due to GPU usage depends on a variety of factors, as
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discussed below.
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</P>
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<P>To see what styles are currently available in each of the accelerated
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packages, see <A HREF = "Section_commands.html#3_5">this section</A> of the manual.
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A list of accelerated styles is included in the pair, fix, compute,
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and kspace sections.
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</P>
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<P>The following sections explain:
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</P>
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2011-06-09 04:56:17 +08:00
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<UL><LI>what hardware and software the accelerated styles require
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<LI>how to install the accelerated packages
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2011-05-27 07:45:30 +08:00
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<LI>what kind of problems they run best on
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2011-06-09 04:56:17 +08:00
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<LI>guidelines for how to use them to best advantage
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2011-05-27 07:45:30 +08:00
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<LI>the kinds of speed-ups you can expect
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</UL>
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<P>The final section compares and contrasts the GPU and USER-CUDA
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packages, since they are both designed to use NVIDIA GPU hardware.
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</P>
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10.1 <A HREF = "#10_1">OPT package</A><BR>
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10.2 <A HREF = "#10_2">GPU package</A><BR>
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10.3 <A HREF = "#10_3">USER-CUDA package</A><BR>
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10.4 <A HREF = "#10_4">Comparison of GPU and USER-CUDA packages</A> <BR>
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<HR>
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2011-06-09 04:56:17 +08:00
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<HR>
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2011-05-27 07:45:30 +08:00
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<H4><A NAME = "10_1"></A>10.1 OPT package
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</H4>
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2011-05-28 01:59:03 +08:00
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<P>The OPT package was developed by James Fischer (High Performance
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Technologies), David Richie and Vincent Natoli (Stone Ridge
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2011-06-09 04:56:17 +08:00
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Technologies). It contains a handful of pair styles whose compute()
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methods were rewritten in C++ templated form to reduce the overhead
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due to if tests and other conditional code.
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</P>
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<P>The procedure for building LAMMPS with the OPT package is simple. It
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is the same as for any other package which has no additional library
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dependencies:
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</P>
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<PRE>make yes-opt
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make machine
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</PRE>
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<P>If your input script uses one of the OPT pair styles,
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you can run it as follows:
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</P>
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<PRE>lmp_machine -sf opt < in.script
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mpirun -np 4 lmp_machine -sf opt < in.script
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</PRE>
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<P>You should see a reduction in the "Pair time" printed out at the end
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of the run. On most machines and problems, this will typically be a 5
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to 20% savings.
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2011-05-28 01:59:03 +08:00
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</P>
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2011-05-27 07:45:30 +08:00
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<HR>
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<H4><A NAME = "10_2"></A>10.2 GPU package
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</H4>
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2011-06-09 05:26:06 +08:00
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<P>Additional requirements in your input script to run the styles with a
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<I>gpu</I> suffix are as follows:
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</P>
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<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
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gpu</A> command must be used. The fix controls the GPU
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selection and initialization steps.
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</P>
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2011-05-28 01:59:03 +08:00
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<P>The GPU package was developed by Mike Brown at ORNL.
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</P>
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2011-05-27 07:45:30 +08:00
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<P>A few LAMMPS <A HREF = "pair_style.html">pair styles</A> can be run on graphical
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processing units (GPUs). We plan to add more over time. Currently,
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they only support NVIDIA GPU cards. To use them you need to install
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certain NVIDIA CUDA software on your system:
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</P>
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2011-05-28 01:59:03 +08:00
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<UL><LI>Check if you have an NVIDIA card: cat /proc/driver/nvidia/cards/0 Go
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<LI>to http://www.nvidia.com/object/cuda_get.html Install a driver and
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<LI>toolkit appropriate for your system (SDK is not necessary) Follow the
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<LI>instructions in README in lammps/lib/gpu to build the library Run
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<LI>lammps/lib/gpu/nvc_get_devices to list supported devices and
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<LI>properties
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2011-05-27 07:45:30 +08:00
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</UL>
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<H4>GPU configuration
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</H4>
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<P>When using GPUs, you are restricted to one physical GPU per LAMMPS
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process. Multiple processes can share a single GPU and in many cases
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it will be more efficient to run with multiple processes per GPU. Any
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GPU accelerated style requires that <A HREF = "fix_gpu.html">fix gpu</A> be used in
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the input script to select and initialize the GPUs. The format for the
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fix is:
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</P>
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<PRE>fix <I>name</I> all gpu <I>mode</I> <I>first</I> <I>last</I> <I>split</I>
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</PRE>
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<P>where <I>name</I> is the name for the fix. The gpu fix must be the first
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fix specified for a given run, otherwise the program will exit with an
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error. The gpu fix will not have any effect on runs that do not use
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GPU acceleration; there should be no problem with specifying the fix
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first in any input script.
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</P>
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<P><I>mode</I> can be either "force" or "force/neigh". In the former, neighbor
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list calculation is performed on the CPU using the standard LAMMPS
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routines. In the latter, the neighbor list calculation is performed on
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the GPU. The GPU neighbor list can be used for better performance,
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however, it cannot not be used with a triclinic box or with
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<A HREF = "pair_hybrid.html">hybrid</A> pair styles.
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</P>
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<P>There are cases when it might be more efficient to select the CPU for
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neighbor list builds. If a non-GPU enabled style requires a neighbor
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list, it will also be built using CPU routines. Redundant CPU and GPU
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neighbor list calculations will typically be less efficient.
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</P>
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<P><I>first</I> is the ID (as reported by lammps/lib/gpu/nvc_get_devices) of
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the first GPU that will be used on each node. <I>last</I> is the ID of the
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last GPU that will be used on each node. If you have only one GPU per
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node, <I>first</I> and <I>last</I> will typically both be 0. Selecting a
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non-sequential set of GPU IDs (e.g. 0,1,3) is not currently supported.
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</P>
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<P><I>split</I> is the fraction of particles whose forces, torques, energies,
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and/or virials will be calculated on the GPU. This can be used to
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perform CPU and GPU force calculations simultaneously. If <I>split</I> is
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negative, the software will attempt to calculate the optimal fraction
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automatically every 25 timesteps based on CPU and GPU timings. Because
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the GPU speedups are dependent on the number of particles, automatic
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calculation of the split can be less efficient, but typically results
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in loop times within 20% of an optimal fixed split.
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</P>
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<P>If you have two GPUs per node, 8 CPU cores per node, and would like to
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run on 4 nodes with dynamic balancing of force calculation across CPU
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and GPU cores, the fix might be
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</P>
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<PRE>fix 0 all gpu force/neigh 0 1 -1
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</PRE>
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<P>with LAMMPS run on 32 processes. In this case, all CPU cores and GPU
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devices on the nodes would be utilized. Each GPU device would be
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shared by 4 CPU cores. The CPU cores would perform force calculations
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for some fraction of the particles at the same time the GPUs performed
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force calculation for the other particles.
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</P>
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<P>Because of the large number of cores on each GPU device, it might be
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more efficient to run on fewer processes per GPU when the number of
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particles per process is small (100's of particles); this can be
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necessary to keep the GPU cores busy.
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</P>
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<H4>GPU input script
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</H4>
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<P>In order to use GPU acceleration in LAMMPS, <A HREF = "fix_gpu.html">fix_gpu</A>
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should be used in order to initialize and configure the GPUs for
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use. Additionally, GPU enabled styles must be selected in the input
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script. Currently, this is limited to a few <A HREF = "pair_style.html">pair
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styles</A> and PPPM. Some GPU-enabled styles have
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additional restrictions listed in their documentation.
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</P>
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<H4>GPU asynchronous pair computation
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</H4>
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<P>The GPU accelerated pair styles can be used to perform pair style
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force calculation on the GPU while other calculations are performed on
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the CPU. One method to do this is to specify a <I>split</I> in the gpu fix
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as described above. In this case, force calculation for the pair
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style will also be performed on the CPU.
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</P>
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<P>When the CPU work in a GPU pair style has finished, the next force
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computation will begin, possibly before the GPU has finished. If
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<I>split</I> is 1.0 in the gpu fix, the next force computation will begin
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almost immediately. This can be used to run a
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<A HREF = "pair_hybrid.html">hybrid</A> GPU pair style at the same time as a hybrid
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CPU pair style. In this case, the GPU pair style should be first in
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the hybrid command in order to perform simultaneous calculations. This
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also allows <A HREF = "bond_style.html">bond</A>, <A HREF = "angle_style.html">angle</A>,
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<A HREF = "dihedral_style.html">dihedral</A>, <A HREF = "improper_style.html">improper</A>, and
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<A HREF = "kspace_style.html">long-range</A> force computations to be run
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simultaneously with the GPU pair style. Once all CPU force
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computations have completed, the gpu fix will block until the GPU has
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finished all work before continuing the run.
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</P>
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<H4>GPU timing
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</H4>
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<P>GPU accelerated pair styles can perform computations asynchronously
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with CPU computations. The "Pair" time reported by LAMMPS will be the
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maximum of the time required to complete the CPU pair style
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computations and the time required to complete the GPU pair style
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computations. Any time spent for GPU-enabled pair styles for
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computations that run simultaneously with <A HREF = "bond_style.html">bond</A>,
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<A HREF = "angle_style.html">angle</A>, <A HREF = "dihedral_style.html">dihedral</A>,
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<A HREF = "improper_style.html">improper</A>, and <A HREF = "kspace_style.html">long-range</A>
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calculations will not be included in the "Pair" time.
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</P>
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<P>When <I>mode</I> for the gpu fix is force/neigh, the time for neighbor list
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calculations on the GPU will be added into the "Pair" time, not the
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"Neigh" time. A breakdown of the times required for various tasks on
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the GPU (data copy, neighbor calculations, force computations, etc.)
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are output only with the LAMMPS screen output at the end of each
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run. These timings represent total time spent on the GPU for each
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routine, regardless of asynchronous CPU calculations.
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</P>
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<H4>GPU single vs double precision
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</H4>
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<P>See the lammps/lib/gpu/README file for instructions on how to build
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the LAMMPS gpu library for single, mixed, and double precision. The
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latter requires that your GPU card supports double precision.
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</P>
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<HR>
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<H4><A NAME = "10_3"></A>10.3 USER-CUDA package
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</H4>
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2011-05-28 01:59:03 +08:00
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<P>The USER-CUDA package was developed by Christian Trott at U Technology
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Ilmenau in Germany.
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</P>
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2011-05-27 07:45:30 +08:00
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<HR>
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<H4><A NAME = "10_4"></A>10.4 Comparison of GPU and USER-CUDA packages
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</H4>
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</HTML>
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