use span to allocate mesh data by default #6123
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this makes it possible to aggregate data for later flush
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guj
changed the title
ax3l
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Performance optimization
component: openPMD
| * if isBTD=true, advice to use ADIOS Put() instead of PDW for better performance. | ||
| * in ADIOS, the action will be PerformDataWrite | ||
| * if isBTD=true, in ADIOS, the action will be PerformPut | ||
| * because no action is taken for the span tasks. |
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Is this generally true? You only add spans for fields right now, what if particles are involved?
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You are right BTD particles will be calling PerformPut. Right now particles is not the I/O performance bottleneck for BTD. It will happen when you have enormous amount of particles. I will definitely revisit this issue with another pull request.
| }); | ||
| auto span = dynamicMemoryView.currentBuffer(); | ||
| amrex::Gpu::dtoh_memcpy_async(span.data(), fab.dataPtr(icomp), local_box.numPts()*sizeof(amrex::Real)); | ||
| } else |
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Do we need this else branch for D2H? I thought openPMD-api has a fallback implementation for HDF5...?
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Turns out no. We do need it.
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That might be an issue, can you please open an issue in https://github.com/openPMD/openPMD-api/ ?
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@franzpoeschel do you understand why this is needed?
| auto span = dynamicMemoryView.currentBuffer(); | ||
| std::memcpy(span.data(), fab.dataPtr(icomp), local_box.numPts()*sizeof(amrex::Real)); | ||
| } | ||
| else |
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Same as above: I thought openPMD-api has a fallback implementation for Span for backends that do not support it?
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I added this because the first round of CPU span failed pull request (it uses HDF5) so the fallback does not work with collecting a few buffers (during a snapshot) and then flush out. The fallback works if flushes out immediately.
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@guj thank you! As follow-ups, can you please
Thank you! 🙏 |
| if (hasADIOS) | ||
| { | ||
| WARPX_PROFILE("WarpXOpenPMDPlot::WriteOpenPMDFields::D2H_Span()"); | ||
| auto dynamicMemoryView = mesh_comp.storeChunk<amrex::Real>( |
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Oh no, when we have an un-equal number of blocks over all MPI ranks, this will not work because storeChunk is collective :-o openPMD/openPMD-api#1794
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To double check: is Iteration::open() called before these blocks, so the ADIOS engine is definitely open? -- Yes
https://github.com/guj/WarpX/blob/d0bbf79e64beed82b64d29f85ec0a56ed0f5f087/Source/Diagnostics/WarpXOpenPMD.cpp#L1426-L1430
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Oh no, when we have an un-equal number of blocks over all MPI ranks, this will not work because
storeChunkis collective :-o openPMD/openPMD-api#1794
Only one rank is writing when using BTD. Other ranks have no data.
2 participants
So we can aggregate (mainly for BTD) data for a later flush.
introduced an optional but related entry in the input file:
<diag>.buffer_flush_limit_btdby default it is 5.New implementation of #3200 but so far only for fields/meshes. Particles will be a follow-up PR.