Add ADIOS2 sample #14
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Created with PIConGPU / LaserWakefield simulation with parameters:
mpirun -n 2 picongpu -s 550 -d 1 2 1 -g 56 56 28 --openPMD.period 50
--openPMD.file stream --openPMD.infix NULL --openPMD.ext bp
--openPMD.json '{ "adios2": { "engine":
{ "usesteps": true, "type":
"bp4", "parameters": { "InitialBufferSize": "2Gb",
"Profile": "On" } }, "dataset": { "operators": [
] } } } ' --versionOnce --checkpoint.backend openPMD
--checkpoint.period 500 --checkpoint.restart
--checkpoint.restart.backend openPMD
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More blocks is a good idea! You can also make the PIConGPU supercell ( |
Alright, will try that. (I could theoretically use openpmd-pipe to cut the chunks smaller, but I think it's better to use openPMD 0.12.0, so I'll try running it more in parallel first.)
Done |
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Also, ADIOS2 uses aggregation per node, so every block will be on |
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Since we want to use this for read tests, I would say disable node-aggregation so we have more meta-data that we can test |
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Done a further run with parameters: mpirun --oversubscribe -n 16 picongpu -s 550 -d 2 4 2 -g 56 56 28 --openPMD.period 50 --openPMD.file stream --openPMD.infix NULL --openPMD.ext bp --openPMD.json '{ "adios2": { "engine": { "usesteps": true, "type": "bp4", "parameters": { "AggregatorRatio": "1", "InitialBufferSize": "2Gb", "Profile": "On" } }, "dataset": { "operators": [ ] } } } ' --versionOnce --checkpoint.backend openPMD --checkpoint.period 500 --checkpoint.restart.backend openPMD --openPMD.dataPreparationStrategy hdf5 --checkpoint.openPMD.dataPreparationStrategy hdf5 --checkpoint.restarttldr: disable node aggregation, use 16 parallel writers in a 2x4x2 domain decomposition
Commit will follow in a minute. |
Also deactivate node aggregation
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This is cool, awesome! The simulation box size is a bit narrow and thus the LWFA sim looks a bit adventurous (not really an LWFA anymore), but the data is good enough and super nice in size for testing! (We can just rename it here to avoid confusion to Optional for merge here, but general comment for PIConGPU: I think the |
This was referenced Apr 15, 2021
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I thought a bit more about a name that tells what's inside (format and dimension wise), e.g. |
2 tasks
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@franzpoeschel I found a bug in this data set that we need to fix and replace. They should read: just like the non-constant particle record lengths. |
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The bug in PIConGPU is here: https://github.com/ComputationalRadiationPhysics/picongpu/pull/3389/files#r663311000 |
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Good catch! I think we should get back to this once the bug is fixed in PIConGPU? |
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Bug fixed in PIConGPU via ComputationalRadiationPhysics/picongpu#3678 🎉 Yes, ready now to replace :) |
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I'm currently working on new schemas for ADIOS2, so we should add tests to verify that we keep backwards compatibility.
Created with PIConGPU / LaserWakefield simulation, openPMD API 0.12.0 and ADIOS 2.7.0 with parameters:
mpirun -n 2 picongpu -s 550 -d 1 2 1 -g 56 56 28 --openPMD.period 50 --openPMD.file stream --openPMD.infix NULL --openPMD.ext bp --openPMD.json '{ "adios2": { "engine":{ "usesteps": true, "type": "bp4", "parameters": { "InitialBufferSize": "2Gb", "Profile": "On" } }, "dataset": { "operators": [] } } } ' --versionOnce --checkpoint.backend openPMD --checkpoint.period 500 --checkpoint.restart --checkpoint.restart.backend openPMDThis is purposefully executed with two parallel instances in order to create datasets that are composed from multiple blocks. Output of
bpls -D:Todo: