Some Very Slow CPU Plugins

[ax3l]

Some of our regularly used plugins seem to be really, really slow with our omp2b backend.

a few that stand out, especially with the very low particle number in my setup:

• PhaseSpace (extremely slow)
• EnergyHistogram (very slow)

OK, although just 1 core per device seems to do the work (maybe I observed on a node with only few particles):

• CountParticles: count macro particles of a species
  (probably same routines used as prep for HDF5/ADIOS output?)
• ADIOS (1 file per device default; --adios.compression blosc:threshold=2048,shuffle=bit,lvl=1,threads=20,compressor=zstd)

OK:

• PNG (40% size, ~100 KByte per Image)
• sumEnergy (fields & particles)
• HDF5 (as usual a bit slow)

Environment

• Hemera (HZDR) CPUs in defq (24 devices)
• PIConGPU 0.4.1
• default defq_picongpu.profile & defq.tpl
• default supercell 8x8x4
• box is 1536x2880x1536; cubic cells (dx=dy=dz)
• 3 ion species and 1 electron species (total of ~1.e9 particles; simulation is field dominated)

[psychocoderHPC]

Both slow plugins are written in logstep paralism schema else they will not provide correct results. In both cases the reason why it is slow is IMO the global reduce within one device.
It could be that it is faster if we update to the latest alpaka because I implemented native openmp atomic. Atomics between alpaka blocks are in alpaka 0.3.X OpenMP barriers which are very slow.

[ax3l]

Yep, might be. Interesting though, the global reduces such as "count" (0D reduce) are still ok. Just the phase-space (2D map-reduce) and energy histogram (1D map-reduce) are really slow.

Atomics between alpaka blocks are [...] very slow

That's weird, because the blocks of those are reduced just once in the end and most time is spend doing the map to bins inside a collaborating block (which of course is also atomic). Unless "between" meant "within a block" in your comment.

Both plugins are not too different from what we do in current deposition.

So just to be sure, what is slow in Alpaka 0.3.4: an atomic within a collaborating block (aka "shared mem") or an atomic across blocks (aka "global mem")?

[psychocoderHPC]

Across blocks within a grid.
But please do not associate global memory with across block atomics because you can use atomics those are only save between threads in a alpaka block on global memory. This means alpaka atomics are memory hierarchy independent.

[ax3l]

Yes, that makes sense. I just wanted to put in brackets what we are doing in those two plugins currently on GPU.

[ax3l]

After about 9hrs with no initial output, I can't say for sure if it's not also deadlocking (with high CPU load) in some cases for those plugins or if the barriers are just extraordinary slow currently. Nevertheless, it does not seem (multiple) energy histograms and phase space can be used in CPU production yet due to it.

[ax3l]

cc @sbastrakov @tdd11235813 this is the Alpaka 3.4 OpenMP 2.0 (blocks) map-reduce performance issue we currently face in PIConGPU.

Help wanted, @psychocoderHPC just recently implemented proper atomics in https://github.com/ComputationalRadiationPhysics/alpaka/pull/664 :)

We could update PIConGPU dev to alpaka dev and upgrade all upcoming Alpaka 0.4.0 API-changes.

[ax3l]

@psychocoderHPC I update my local alpaka on PIConGPU 0.4.1 to https://github.com/ComputationalRadiationPhysics/alpaka/pull/698 and it improved the situation significantly. (Using GCC 7.30 on Hemera with OpenMP 2 blocks backend but OpenMP 4.5 available.)

Thanks a ton, this is awesome! ✨ 💖

[ax3l]

This issue will receive a two-fold fix: for the current stable PIConGPU 0.4.* release line, the 0.4.2 release will ship Alpaka 0.3.5 to improve performance: #2810

For the upcoming next stable PIConGPU 0.5/1.0 release and current PIConGPU dev, #2807 will update to Alpaka dev/upcoming-0.4.0 to fix performance.