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722 lines
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<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
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<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_howto.html">Next
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Section</A>
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</CENTER>
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<HR>
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<H3>5. Accelerating LAMMPS performance
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</H3>
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<P>This section describes various methods for improving LAMMPS
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performance for different classes of problems running on different
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kinds of machines.
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</P>
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5.1 <A HREF = "#acc_1">Measuring performance</A><BR>
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5.2 <A HREF = "#acc_2">General strategies</A><BR>
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5.3 <A HREF = "#acc_3">Packages with optimized styles</A><BR>
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5.4 <A HREF = "#acc_4">OPT package</A><BR>
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5.5 <A HREF = "#acc_5">USER-OMP package</A><BR>
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5.6 <A HREF = "#acc_6">GPU package</A><BR>
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5.7 <A HREF = "#acc_7">USER-CUDA package</A><BR>
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5.8 <A HREF = "#acc_8">Comparison of GPU and USER-CUDA packages</A> <BR>
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<HR>
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<HR>
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<H4><A NAME = "acc_1"></A>5.1 Measuring performance
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</H4>
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<P>Before trying to make your simulation run faster, you should
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understand how it currently performs and where the bottlenecks are.
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</P>
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<P>The best way to do this is run the your system (actual number of
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atoms) for a modest number of timesteps (say 100, or a few 100 at
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most) on several different processor counts, including a single
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processor if possible. Do this for an equilibrium version of your
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system, so that the 100-step timings are representative of a much
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longer run. There is typically no need to run for 1000s or timesteps
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to get accurate timings; you can simply extrapolate from short runs.
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</P>
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<P>For the set of runs, look at the timing data printed to the screen and
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log file at the end of each LAMMPS run. <A HREF = "Section_start.html#start_8">This
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section</A> of the manual has an overview.
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</P>
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<P>Running on one (or a few processors) should give a good estimate of
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the serial performance and what portions of the timestep are taking
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the most time. Running the same problem on a few different processor
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counts should give an estimate of parallel scalability. I.e. if the
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simulation runs 16x faster on 16 processors, its 100% parallel
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efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
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</P>
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<P>The most important data to look at in the timing info is the timing
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breakdown and relative percentages. For example, trying different
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options for speeding up the long-range solvers will have little impact
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if they only consume 10% of the run time. If the pairwise time is
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dominating, you may want to look at GPU or OMP versions of the pair
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style, as discussed below. Comparing how the percentages change as
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you increase the processor count gives you a sense of how different
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operations within the timestep are scaling. Note that if you are
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running with a Kspace solver, there is additional output on the
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breakdown of the Kspace time. For PPPM, this includes the fraction
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spent on FFTs, which can be communication intensive.
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</P>
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<P>Another important detail in the timing info are the histograms of
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atoms counts and neighbor counts. If these vary widely across
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processors, you have a load-imbalance issue. This often results in
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inaccurate relative timing data, because processors have to wait when
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communication occurs for other processors to catch up. Thus the
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reported times for "Communication" or "Other" may be higher than they
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really are, due to load-imbalance. If this is an issue, you can
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uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
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LAMMPS, to obtain synchronized timings.
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</P>
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<HR>
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<H4><A NAME = "acc_2"></A>5.2 General strategies
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</H4>
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<P>NOTE: this sub-section is still a work in progress
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</P>
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<P>Here is a list of general ideas for improving simulation performance.
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Most of them are only applicable to certain models and certain
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bottlenecks in the current performance, so let the timing data you
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intially generate be your guide. It is hard, if not impossible, to
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predict how much difference these options will make, since it is a
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function of your problem and your machine. There is no substitute for
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simply trying them out.
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</P>
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<UL><LI>rRESPA
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<LI>2-FFT PPPM
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<LI>Staggered PPPM
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<LI>single vs double PPPM
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<LI>partial charge PPPM
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<LI>verlet/split
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<LI>processor mapping via processors numa command
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<LI>load-balancing: balance and fix balance
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<LI>processor command for layout
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<LI>OMP when lots of cores
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</UL>
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<P>2-FFT PPPM, also called <I>analytic differentiation</I> or <I>ad</I> PPPM, uses
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2 FFTs instead of the 4 FFTs used by the default <I>ik differentiation</I>
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PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
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achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
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cost is the performance bottleneck (typically large problems running
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on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
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</P>
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<P>Staggered PPPM performs calculations using two different meshes, one
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shifted slightly with respect to the other. This can reduce force
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aliasing errors and increase the accuracy of the method, but also
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doubles the amount of work required. For high relative accuracy, using
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staggered PPPM allows one to half the mesh size in each dimension as
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compared to regular PPPM, which can give around a 4x speedup in the
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kspace time. However, for low relative accuracy, using staggered PPPM
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gives little benefit and can be up to 2x slower in the kspace
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time. For example, the rhodopsin benchmark was run on a single
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processor, and results for kspace time vs. relative accuracy for the
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different methods are shown in the figure below. For this system,
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staggered PPPM (using ik differentiation) becomes useful when using a
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relative accuracy of slightly greater than 1e-5 and above.
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</P>
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<CENTER><IMG SRC = "JPG/rhodo_staggered.jpg">
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</CENTER>
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<P>IMPORTANT NOTE: Using staggered PPPM may not give the same increase in
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accuracy of energy and pressure as it does in forces, so some caution
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must be used if energy and/or pressure are quantities of interest,
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such as when using a barostat.
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</P>
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<HR>
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<H4><A NAME = "acc_3"></A>5.3 Packages with optimized styles
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</H4>
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<P>Accelerated versions of various <A HREF = "pair_style.html">pair_style</A>,
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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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</P>
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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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</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/omp</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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script. Or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
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switch</A> to invoke the accelerated versions
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automatically, without changing your input script. The
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<A HREF = "suffix.html">suffix</A> command allows you to set a suffix explicitly and
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to turn off/on the comand-line switch setting, both from within your
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input script.
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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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speed-up the pairwise calculations of your simulation by 5-25%.
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</P>
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<P>Styles with an "omp" suffix are part of the USER-OMP package and allow
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a pair-style to be run in multi-threaded mode using OpenMP. This can
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be useful on nodes with high-core counts when using less MPI processes
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than cores is advantageous, e.g. when running with PPPM so that FFTs
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are run on fewer MPI processors or when the many MPI tasks would
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overload the available bandwidth for communication.
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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#cmd_5">Section_commands 5</A> of the
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manual. A list of accelerated styles is included in the pair, fix,
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compute, 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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<UL><LI>what hardware and software the accelerated styles require
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<LI>how to build LAMMPS with the accelerated packages in place
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<LI>what changes (if any) are needed in your input scripts
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<LI>guidelines for best performance
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<LI>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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<HR>
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<H4><A NAME = "acc_4"></A>5.4 OPT package
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</H4>
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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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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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</P>
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<HR>
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<H4><A NAME = "acc_5"></A>5.5 USER-OMP package
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</H4>
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<P>The USER-OMP package was developed by Axel Kohlmeyer at Temple University.
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It provides multi-threaded versions of most pair styles, all dihedral
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styles and a few fixes in LAMMPS. The package currently uses the OpenMP
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interface which requires using a specific compiler flag in the makefile
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to enable multiple threads; without this flag the corresponding pair
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styles will still be compiled and work, but do not support multi-threading.
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</P>
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<P><B>Building LAMMPS with the USER-OMP package:</B>
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</P>
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<P>The procedure for building LAMMPS with the USER-OMP package is simple.
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You have to edit your machine specific makefile to add the flag to
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enable OpenMP support to the CCFLAGS and LINKFLAGS variables. For the
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GNU compilers for example this flag is called <I>-fopenmp</I>. Check your
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compiler documentation to find out which flag you need to add.
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The rest of the compilation is the same as for any other package which
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has no additional library dependencies:
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</P>
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<PRE>make yes-user-omp
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make machine
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</PRE>
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<P>Please note that this will only install accelerated versions
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of styles that are already installed, so you want to install
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this package as the last package, or else you may be missing
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some accelerated styles. If you plan to uninstall some package,
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you should first uninstall the USER-OMP package then the other
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package and then re-install USER-OMP, to make sure that there
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are no orphaned <I>omp</I> style files present, which would lead to
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compilation errors.
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</P>
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<P>If your input script uses one of regular styles that are also
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exist as an OpenMP version in the USER-OMP package you can run
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it as follows:
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</P>
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<PRE>env OMP_NUM_THREADS=4 lmp_serial -sf omp -in in.script
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env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
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mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script
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</PRE>
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<P>The value of the environment variable OMP_NUM_THREADS determines how
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many threads per MPI task are launched. All three examples above use
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a total of 4 CPU cores. For different MPI implementations the method
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to pass the OMP_NUM_THREADS environment variable to all processes is
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different. Two different variants, one for MPICH and OpenMPI, respectively
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are shown above. Please check the documentation of your MPI installation
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for additional details. Alternatively, the value provided by OMP_NUM_THREADS
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can be overridded with the <A HREF = "package.html">package omp</A> command.
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Depending on which styles are accelerated in your input, you should
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see a reduction in the "Pair time" and/or "Bond time" and "Loop time"
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printed out at the end of the run. The optimal ratio of MPI to OpenMP
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can vary a lot and should always be confirmed through some benchmark
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runs for the current system and on the current machine.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>None of the pair styles in the USER-OMP package support the "inner",
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"middle", "outer" options for r-RESPA integration, only the "pair"
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option is supported.
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</P>
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<P><B>Parallel efficiency and performance tips:</B>
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</P>
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<P>In most simple cases the MPI parallelization in LAMMPS is more
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efficient than multi-threading implemented in the USER-OMP package.
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Also the parallel efficiency varies between individual styles.
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On the other hand, in many cases you still want to use the <I>omp</I> version
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- even when compiling or running without OpenMP support - since they
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all contain optimizations similar to those in the OPT package, which
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can result in serial speedup.
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</P>
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<P>Using multi-threading is most effective under the following circumstances:
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</P>
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<UL><LI>Individual compute nodes have a significant number of CPU cores
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but the CPU itself has limited memory bandwidth, e.g. Intel Xeon 53xx
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(Clovertown) and 54xx (Harpertown) quad core processors. Running
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one MPI task per CPU core will result in significant performance
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degradation, so that running with 4 or even only 2 MPI tasks per
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nodes is faster. Running in hybrid MPI+OpenMP mode will reduce the
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inter-node communication bandwidth contention in the same way,
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but offers and additional speedup from utilizing the otherwise
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idle CPU cores.
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<LI>The interconnect used for MPI communication is not able to provide
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sufficient bandwidth for a large number of MPI tasks per node.
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This applies for example to running over gigabit ethernet or
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on Cray XT4 or XT5 series supercomputers. Same as in the aforementioned
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case this effect worsens with using an increasing number of nodes.
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<LI>The input is a system that has an inhomogeneous particle density
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which cannot be mapped well to the domain decomposition scheme
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that LAMMPS employs. While this can be to some degree alleviated
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through using the <A HREF = "processors.html">processors</A> keyword, multi-threading
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provides a parallelism that parallelizes over the number of particles
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not their distribution in space.
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<LI>Finally, multi-threaded styles can improve performance when running
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LAMMPS in "capability mode", i.e. near the point where the MPI
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parallelism scales out. This can happen in particular when using
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as kspace style for long-range electrostatics. Here the scaling
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of the kspace style is the performance limiting factor and using
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multi-threaded styles allows to operate the kspace style at the
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limit of scaling and then increase performance parallelizing
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the real space calculations with hybrid MPI+OpenMP. Sometimes
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additional speedup can be achived by increasing the real-space
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coulomb cutoff and thus reducing the work in the kspace part.
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</UL>
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<P>The best parallel efficiency from <I>omp</I> styles is typically
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achieved when there is at least one MPI task per physical
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processor, i.e. socket or die.
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</P>
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<P>Using threads on hyper-threading enabled cores is usually
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counterproductive, as the cost in additional memory bandwidth
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requirements is not offset by the gain in CPU utilization
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through hyper-threading.
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</P>
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<P>A description of the multi-threading strategy and some performance
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examples are <A HREF = "http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1">presented here</A>
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</P>
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<HR>
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<H4><A NAME = "acc_6"></A>5.6 GPU package
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</H4>
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<P>The GPU package was developed by Mike Brown at ORNL. It provides GPU
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versions of several pair styles and for long-range Coulombics via the
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PPPM command. It has the following features:
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</P>
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<UL><LI>The package is designed to exploit common GPU hardware configurations
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where one or more GPUs are coupled with many cores of a multi-core
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CPUs, e.g. within a node of a parallel machine.
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<LI>Atom-based data (e.g. coordinates, forces) moves back-and-forth
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between the CPU(s) and GPU every timestep.
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<LI>Neighbor lists can be constructed on the CPU or on the GPU
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<LI>The charge assignement and force interpolation portions of PPPM can be
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run on the GPU. The FFT portion, which requires MPI communication
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between processors, runs on the CPU.
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<LI>Asynchronous force computations can be performed simultaneously on the
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CPU(s) and GPU.
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<LI>LAMMPS-specific code is in the GPU package. It makes calls to a
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generic GPU library in the lib/gpu directory. This library provides
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NVIDIA support as well as more general OpenCL support, so that the
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same functionality can eventually be supported on a variety of GPU
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hardware.
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</UL>
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<P>NOTE:
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discuss 3 precisions
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if change, also have to re-link with LAMMPS
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always use newton off
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expt with differing numbers of CPUs vs GPU - can't tell what is fastest
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give command line switches in examples
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</P>
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<P>I am not very clear to the meaning of "Max Mem / Proc"
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in the "GPU Time Info (average)".
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Is it the maximal of GPU memory used by one CPU core?
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</P>
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<P>It is the maximum memory used at one time on the GPU for data storage by
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a single MPI process. - Mike
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</P>
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<P><B>Hardware and software requirements:</B>
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</P>
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<P>To use this package, you currently need to have specific NVIDIA
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hardware and install specific NVIDIA CUDA software on your system:
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</P>
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<UL><LI>Check if you have an NVIDIA card: cat /proc/driver/nvidia/cards/0
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<LI>Go to http://www.nvidia.com/object/cuda_get.html
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<LI>Install a driver and toolkit appropriate for your system (SDK is not necessary)
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<LI>Follow the instructions in lammps/lib/gpu/README to build the library (see below)
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<LI>Run lammps/lib/gpu/nvc_get_devices to list supported devices and properties
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</UL>
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<P><B>Building LAMMPS with the GPU package:</B>
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</P>
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<P>As with other packages that include a separately compiled library, you
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need to first build the GPU library, before building LAMMPS itself.
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General instructions for doing this are in <A HREF = "Section_start.html#start_3">this
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section</A> of the manual. For this package,
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do the following, using a Makefile in lib/gpu appropriate for your
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system:
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</P>
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<PRE>cd lammps/lib/gpu
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make -f Makefile.linux
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(see further instructions in lammps/lib/gpu/README)
|
|
</PRE>
|
|
<P>If you are successful, you will produce the file lib/libgpu.a.
|
|
</P>
|
|
<P>Now you are ready to build LAMMPS with the GPU package installed:
|
|
</P>
|
|
<PRE>cd lammps/src
|
|
make yes-gpu
|
|
make machine
|
|
</PRE>
|
|
<P>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.
|
|
</P>
|
|
<P><B>GPU configuration</B>
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P><B>Input script requirements:</B>
|
|
</P>
|
|
<P>Additional input script requirements to run pair or PPPM styles with a
|
|
<I>gpu</I> suffix are as follows:
|
|
</P>
|
|
<UL><LI>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
|
|
<A HREF = "Section_start.html#start_7">-suffix command-line switch</A>, or use the
|
|
<A HREF = "suffix.html">suffix</A> command.
|
|
|
|
<LI>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I>.
|
|
|
|
<LI>The <A HREF = "package.html">package gpu</A> 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.
|
|
</UL>
|
|
<P>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
|
|
</P>
|
|
<PRE>package gpu force/neigh 0 1 -1
|
|
</PRE>
|
|
<P>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.
|
|
</P>
|
|
<P><B>Timing output:</B>
|
|
</P>
|
|
<P>As described by the <A HREF = "package.html">package gpu</A> 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 <A HREF = "bond_style.html">bond</A>,
|
|
<A HREF = "angle_style.html">angle</A>, <A HREF = "dihedral_style.html">dihedral</A>,
|
|
<A HREF = "improper_style.html">improper</A>, and <A HREF = "kspace_style.html">long-range</A>
|
|
calculations will not be included in the "Pair" time.
|
|
</P>
|
|
<P>When the <I>mode</I> 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.
|
|
</P>
|
|
<P><B>Performance tips:</B>
|
|
</P>
|
|
<P>Generally speaking, for best performance, you should use multiple CPUs
|
|
per GPU, as provided my most multi-core CPU/GPU configurations.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<HR>
|
|
|
|
<H4><A NAME = "acc_7"></A>5.7 USER-CUDA package
|
|
</H4>
|
|
<P>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:
|
|
</P>
|
|
<UL><LI>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.
|
|
|
|
<LI>The speed-up advantage of this approach is typically better when the
|
|
number of atoms per GPU is large
|
|
|
|
<LI>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.
|
|
|
|
<LI>Neighbor lists for GPU-ized pair styles are constructed on the
|
|
GPU.
|
|
|
|
<LI>The package only supports use of a single CPU (core) with each
|
|
GPU.
|
|
</UL>
|
|
<P><B>Hardware and software requirements:</B>
|
|
</P>
|
|
<P>To use this package, you need to have specific NVIDIA hardware and
|
|
install specific NVIDIA CUDA software on your system.
|
|
</P>
|
|
<P>Your NVIDIA GPU needs to support Compute Capability 1.3. This list may
|
|
help you to find out the Compute Capability of your card:
|
|
</P>
|
|
<P>http://en.wikipedia.org/wiki/Comparison_of_Nvidia_graphics_processing_units
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P><B>Building LAMMPS with the USER-CUDA package:</B>
|
|
</P>
|
|
<P>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 <A HREF = "Section_start.html#start_3">this
|
|
section</A> of the manual. For this package,
|
|
do the following, using settings in the lib/cuda Makefiles appropriate
|
|
for your system:
|
|
</P>
|
|
<UL><LI>Go to the lammps/lib/cuda directory
|
|
|
|
<LI>If your <I>CUDA</I> toolkit is not installed in the default system directoy
|
|
<I>/usr/local/cuda</I> edit the file <I>lib/cuda/Makefile.common</I>
|
|
accordingly.
|
|
|
|
<LI>Type "make OPTIONS", where <I>OPTIONS</I> are one or more of the following
|
|
options. The settings will be written to the
|
|
<I>lib/cuda/Makefile.defaults</I> and used in the next step.
|
|
|
|
<PRE><I>precision=N</I> 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
|
|
<I>arch=M</I> 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)
|
|
<I>prec_timer=0/1</I> to use hi-precision timers
|
|
0 = do not use them (default)
|
|
1 = use these timers
|
|
this is usually only useful for Mac machines
|
|
<I>dbg=0/1</I> to activate debug mode
|
|
0 = no debug mode (default)
|
|
1 = yes debug mode
|
|
this is only useful for developers
|
|
<I>cufft=1</I> to determine usage of CUDA FFT library
|
|
0 = no CUFFT support (default)
|
|
in the future other CUDA-enabled FFT libraries might be supported
|
|
</PRE>
|
|
<LI>Type "make" to build the library. If you are successful, you will
|
|
produce the file lib/libcuda.a.
|
|
</UL>
|
|
<P>Now you are ready to build LAMMPS with the USER-CUDA package installed:
|
|
</P>
|
|
<PRE>cd lammps/src
|
|
make yes-user-cuda
|
|
make machine
|
|
</PRE>
|
|
<P>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.
|
|
</P>
|
|
<P><B>Input script requirements:</B>
|
|
</P>
|
|
<P>Additional input script requirements to run styles with a <I>cuda</I>
|
|
suffix are as follows:
|
|
</P>
|
|
<UL><LI>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 <A HREF = "Section_start.html#start_7">-suffix command-line switch</A>, or use
|
|
the <A HREF = "suffix.html">suffix</A> command. One exception is that the
|
|
<A HREF = "kspace_style.html">kspace_style pppm/cuda</A> command has to be requested
|
|
explicitly.
|
|
|
|
<LI>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 <A HREF = "Section_start.html#start_7">-cuda command-line switch</A> for
|
|
more details.
|
|
|
|
<LI>To change settings for the USER-CUDA package at run-time, the <A HREF = "package.html">package
|
|
cuda</A> command can be used near the beginning of your
|
|
input script. See the <A HREF = "package.html">package</A> command doc page for
|
|
details.
|
|
</UL>
|
|
<P><B>Performance tips:</B>
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<HR>
|
|
|
|
<HR>
|
|
|
|
<H4><A NAME = "acc_8"></A>5.8 Comparison of GPU and USER-CUDA packages
|
|
</H4>
|
|
<P>Both the GPU and USER-CUDA packages accelerate a LAMMPS calculation
|
|
using NVIDIA hardware, but they do it in different ways.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P><B>Guidelines for using each package optimally:</B>
|
|
</P>
|
|
<UL><LI>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.
|
|
|
|
<LI>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.
|
|
|
|
<LI>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.
|
|
|
|
<LI>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.
|
|
|
|
<LI>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.
|
|
</UL>
|
|
<P><B>Differences between the two packages:</B>
|
|
</P>
|
|
<UL><LI>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.
|
|
|
|
<LI>The USER-CUDA package does not support acceleration for minimization.
|
|
|
|
<LI>The USER-CUDA package does not support hybrid pair styles.
|
|
|
|
<LI>The USER-CUDA package can order atoms in the neighbor list differently
|
|
from run to run resulting in a different order for force accumulation.
|
|
|
|
<LI>The USER-CUDA package has a limit on the number of atom types that can be
|
|
used in a simulation.
|
|
|
|
<LI>The GPU package requires neighbor lists to be built on the CPU when using
|
|
exclusion lists or a triclinic simulation box.
|
|
|
|
<LI>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.
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<P>The LAMMPS distribution has two directories with sample input scripts
|
|
for the GPU and USER-CUDA packages.
|
|
</P>
|
|
<UL><LI>lammps/examples/gpu = GPU package files
|
|
<LI>lammps/examples/USER/cuda = USER-CUDA package files
|
|
</UL>
|
|
<P>These contain input scripts for identical systems, so they can be used
|
|
to benchmark the performance of both packages on your system.
|
|
</P>
|
|
</HTML>
|