NAME

SYNOPSIS

gmx nonbonded-benchmark [-o [<.csv>]] [-size <int>] [-nt <int>]
             [-simd <enum>] [-coulomb <enum>] [-[no]table]
             [-combrule <enum>] [-[no]halflj] [-[no]energy]
             [-[no]all] [-cutoff <real>] [-iter <int>]
             [-warmup <int>] [-[no]cycles] [-[no]time]

DESCRIPTION

OpenMP parallelization is used to utilize multiple hardware threads within a compute node. In these benchmarks there is no interaction between threads, apart from starting and closing a single OpenMP parallel region per iteration. Additionally, threads interact through sharing and evicting data from shared caches. The number of threads to use is set with the -nt option. Thread affinity is important, especially with SMT and shared caches. Affinities can be set through the OpenMP library using the GOMP_CPU_AFFINITY environment variable.

The benchmark tool times one or more kernels by running them repeatedly for a number of iterations set by the -iter option. An initial kernel call is done to avoid additional initial cache misses. Times are recording in cycles read from efficient, high accuracy counters in the CPU. Note that these often do not correspond to actual clock cycles. For each kernel, the tool reports the total number of cycles, cycles per iteration, and (total and useful) pair interactions per cycle. Because a cluster pair list is used instead of an atom pair list, interactions are also computed for some atom pairs that are beyond the cut-off distance. These pairs are not useful (except for additional buffering, but that is not of interest here), only a side effect of the cluster-pair setup. The SIMD 2xMM kernel has a higher useful pair ratio then the 4xM kernel due to a smaller cluster size, but a lower total pair throughput. It is best to run this, or for that matter any, benchmark with locked CPU clocks, as thermal throttling can significantly affect performance. If that is not an option, the -warmup option can be used to run initial, untimed iterations to warm up the processor.

The most relevant regime is between 0.1 to 1 millisecond per iteration. Thus it is useful to run with system sizes that cover both ends of this regime.

The -simd and -table options select different implementations to compute the same physics. The choice of these options should ideally be optimized for the target hardware. Historically, we only found tabulated Ewald correction to be useful on 2-wide SIMD or 4-wide SIMD without FMA support. As all modern architectures are wider and support FMA, we do not use tables by default. The only exceptions are kernels without SIMD, which only support tables. Options -coulomb, -combrule and -halflj depend on the force field and composition of the simulated system. The optimization of computing Lennard-Jones interactions for only half of the atoms in a cluster is useful for water, which does not use Lennard-Jones on hydrogen atoms in most water models. In the MD engine, any clusters where at most half of the atoms have LJ interactions will automatically use this kernel. And finally, the -energy option selects the computation of energies, which are usually only needed infrequently.

OPTIONS

Other options:

SEE ALSO

More information about GROMACS is available at <http://www.gromacs.org/>.

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