Read IO plugin configuration (openPMD plugin) from reading applications (TOML) #3720
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franzpoeschel
commented
Aug 12, 2021
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Just did a little test run with this thing: First TOML file: [period]
200 = ["E", "B"]
400 = "fields_all"Second one: [period]
500 = "species_all"Resulting dataset: |
franzpoeschel
commented
Aug 13, 2021
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The latest commit fixes waiting for late files and adds logging for that: Next up: parallel reading (i.e. non-parallel reading) |
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(PR stalled for now until René is back from holiday to review this approach.) |
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Discussed offline with René: [openPMD]
"file" = "simOutput"
"ext" = "bp"
"backend_config" = "@./adios2_config.json"
[sink.analysis_code_name.period]
200 = ["E", "B"]
400 = "fields_all"
[sink.other_analysis_code_name.period]
500 = "species_all"Under the # this will not be part of this PR
# just demonstrating that this schema is extensible
[sink.analysis_code_name]
"logging" = trueOther points discussed: Allow time slicing syntax, Do not activate this in every step, but instead tell the plugin controller about the periods @psychocoderHPC Any additions? |
franzpoeschel
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Time slice syntax and reading of normal plugin parameters from TOML now implemented: file = "output"
infix = ""
[sink.1.period]
"100:300:200" = ["E", "B"]
"300:10000:200" = "fields_all"
[sink.2.period]
500 = "species_all"Result: |
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Alright, command line parameter handling should now work. Still need to test that checkpoint/restarting is handled correctly, and I might need some help so that this PR does not also add a parameter |
franzpoeschel
commented
Oct 19, 2021
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Did some thorough cleanup, including commit history |
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@franzpoeschel What is the status of this pul request? |
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@PrometheusPi I meet with René next week to discuss the current status. If we agree that the approach taken by this is ok, I expect it can be merged soon. Note that this PR is not about TOML configuration for the openPMD-api, but for PIConGPU's openPMD plugin. |
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I added the things we talked about yesterday @psychocoderHPC:
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psychocoderHPC
added
component: plugin
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I tested that multi-plugin usage with command line parameters still works. |
psychocoderHPC
previously requested changes
Nov 25, 2021
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PR can be rebased |
done |
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@franzpoeschel What do you mean by |
In our intended workflows, the TOML file is created asynchronously by the reading codes. So, as long as the file is not there yet, these lines here will sleep until the file is found. Should I keep that part? If yes, I think I should add a timeout. @psychocoderHPC |
Ohh yes, a timeout makes sense. IMO set as default 5min. |
Done and tested |
Move collective file reading to a common header Add TOML header and implementation Without using it yet though Use TOML stuff in openPMD plugin Use stateless DataSources class Accept empty string as unspecified parameter for toml option Timeout 5min: If toml file is not there, throw an error
steindev
approved these changes
Jan 28, 2022
steindev
dismissed
psychocoderHPC’s stale review
All comments adressed. Offline discussed to merge now.
This was referenced Feb 9, 2022
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Close #3717, see there for a detailed description
TODO:
selfRegister==trueis handled correctly (checkpoint writing)keep the
.tomloption out of--checkpoint.openPMDsomehow?--openPMD.period dynamicthing, it's easy to implement for now) Update:--openPMD.periodand--openPMD.tomlare now mutually exclusive. If using TOML, then the parameter must be the only parameter.