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5.3.2 GPU package

The GPU package was developed by Mike Brown at ORNL and his collaborators, particularly Trung Nguyen (ORNL). It provides GPU versions of many pair styles, including the 3-body Stillinger-Weber pair style, and for kspace_style pppm for long-range Coulombics. It has the following general features:

• It is designed to exploit common GPU hardware configurations where one or more GPUs are coupled to many cores of one or more multi-core CPUs, e.g. within a node of a parallel machine.
• Atom-based data (e.g. coordinates, forces) moves back-and-forth between the CPU(s) and GPU every timestep.
• Neighbor lists can be built on the CPU or on the GPU
• 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.
• Asynchronous force computations can be performed simultaneously on the CPU(s) and GPU.
• It allows for GPU computations to be performed in single or double precision, or in mixed-mode precision, where pairwise forces are computed in single precision, but accumulated into double-precision force vectors.
• 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.

Here is a quick overview of how to use the GPU package:

• build the library in lib/gpu for your GPU hardware wity desired precision
• include the GPU package and build LAMMPS
• use the mpirun command to set the number of MPI tasks/node which determines the number of MPI tasks/GPU
• specify the # of GPUs per node
• use GPU styles in your input script

The latter two steps can be done using the "-pk gpu" and "-sf gpu" command-line switches respectively. Or the effect of the "-pk" or "-sf" switches can be duplicated by adding the package gpu or suffix gpu commands respectively to your input script.

Required hardware/software:

To use this package, you currently need to have an NVIDIA GPU and install the NVIDIA Cuda software on your system:

• Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/0/information
• Go to http://www.nvidia.com/object/cuda_get.html
• Install a driver and toolkit appropriate for your system (SDK is not necessary)
• Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to list supported devices and properties

Building LAMMPS with the GPU package:

This requires two steps (a,b): build the GPU library, then build LAMMPS with the GPU package.

You can do both these steps in one line, using the src/Make.py script, described in Section 2.4 of the manual. Type "Make.py -h" for help. If run from the src directory, this command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the starting Makefile.machine:

Make.py -p gpu -gpu mode=single arch=31 -o gpu lib-gpu file mpi 

Or you can follow these two (a,b) steps:

(a) Build the GPU library

The GPU library is in lammps/lib/gpu. Select a Makefile.machine (in lib/gpu) appropriate for your system. You should pay special attention to 3 settings in this makefile.

• CUDA_HOME = needs to be where NVIDIA Cuda software is installed on your system
• CUDA_ARCH = needs to be appropriate to your GPUs
• CUDA_PREC = precision (double, mixed, single) you desire

See lib/gpu/Makefile.linux.double for examples of the ARCH settings for different GPU choices, e.g. Fermi vs Kepler. It also lists the possible precision settings:

CUDA_PREC = -D_SINGLE_SINGLE  # single precision for all calculations
CUDA_PREC = -D_DOUBLE_DOUBLE  # double precision for all calculations
CUDA_PREC = -D_SINGLE_DOUBLE  # accumulation of forces, etc, in double 

The last setting is the mixed mode referred to above. Note that your GPU must support double precision to use either the 2nd or 3rd of these settings.

To build the library, type:

make -f Makefile.machine 

If successful, it will produce the files libgpu.a and Makefile.lammps.

The latter file has 3 settings that need to be appropriate for the paths and settings for the CUDA system software on your machine. Makefile.lammps is a copy of the file specified by the EXTRAMAKE setting in Makefile.machine. You can change EXTRAMAKE or create your own Makefile.lammps.machine if needed.

Note that to change the precision of the GPU library, you need to re-build the entire library. Do a "clean" first, e.g. "make -f Makefile.linux clean", followed by the make command above.

(b) Build LAMMPS with the GPU package

cd lammps/src
make yes-gpu
make machine 

No additional compile/link flags are needed in Makefile.machine.

Note that if you change the GPU library precision (discussed above) and rebuild the GPU library, then you also need to re-install the GPU package and re-build LAMMPS, so that all affected files are re-compiled and linked to the new GPU library.

Run with the GPU package from the command line:

The mpirun or mpiexec command sets the total number of MPI tasks used by LAMMPS (one or multiple per compute node) and the number of MPI tasks used per node. E.g. the mpirun command in MPICH does this via its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.

When using the GPU package, you cannot assign more than one GPU to a single MPI task. However multiple MPI tasks can share the same GPU, and in many cases it will be more efficient to run this way. Likewise it may be more efficient to use less MPI tasks/node than the available # of CPU cores. Assignment of multiple MPI tasks to a GPU will happen automatically if you create more MPI tasks/node than there are GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be shared by 4 MPI tasks.

Use the "-sf gpu" command-line switch, which will automatically append "gpu" to styles that support it. Use the "-pk gpu Ng" command-line switch to set Ng = # of GPUs/node to use.

lmp_machine -sf gpu -pk gpu 1 -in in.script                         # 1 MPI task uses 1 GPU
mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script           # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script   # ditto on 4 16-core nodes 

Note that if the "-sf gpu" switch is used, it also issues a default package gpu 1 command, which sets the number of GPUs/node to 1.

Using the "-pk" switch explicitly allows for setting of the number of GPUs/node to use and additional options. Its syntax is the same as same as the "package gpu" command. See the package command doc page for details, including the default values used for all its options if it is not specified.

Note that the default for the package gpu command is to set the Newton flag to "off" pairwise interactions. It does not affect the setting for bonded interactions (LAMMPS default is "on"). The "off" setting for pairwise interaction is currently required for GPU package pair styles.

Or run with the GPU package by editing an input script:

The discussion above for the mpirun/mpiexec command, MPI tasks/node, and use of multiple MPI tasks/GPU is the same.

Use the suffix gpu command, or you can explicitly add an "gpu" suffix to individual styles in your input script, e.g.

pair_style lj/cut/gpu 2.5 

You must also use the package gpu command to enable the GPU package, unless the "-sf gpu" or "-pk gpu" command-line switches were used. It specifies the number of GPUs/node to use, as well as other options.

Speed-ups to expect:

The performance of a GPU versus a multi-core CPU is a function of your hardware, which pair style is used, the number of atoms/GPU, and the precision used on the GPU (double, single, mixed).

See the Benchmark page of the LAMMPS web site for performance of the GPU package on various hardware, including the Titan HPC platform at ORNL.

You should also experiment with how many MPI tasks per GPU to use to give the best performance for your problem and machine. This is also a function of the problem size and the pair style being using. Likewise, you should experiment with the precision setting for the GPU library to see if single or mixed precision will give accurate results, since they will typically be faster.

Guidelines for best performance:

• Using multiple MPI tasks per GPU will often give the best performance, as allowed my most multi-core CPU/GPU configurations.
• If the number of particles per MPI task is small (e.g. 100s of particles), it can be more efficient to run with fewer MPI tasks per GPU, even if you do not use all the cores on the compute node.
• The package gpu command has several options for tuning performance. Neighbor lists can be built on the GPU or CPU. Force calculations can be dynamically balanced across the CPU cores and GPUs. GPU-specific settings can be made which can be optimized for different hardware. See the packakge command doc page for details.
• As described by the package gpu 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, angle, dihedral, improper, and long-range 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.
• The output section "GPU Time Info (average)" reports "Max Mem / Proc". This is the maximum memory used at one time on the GPU for data storage by a single MPI process.

Restrictions:

None.