Marine B-matrix refactor companion PR#1346
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DavidNew-NOAA
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This PR is a companion to Global Workflow PR [#2992](NOAA-EMC/global-workflow#2992) and GDASApp PR [#1346](NOAA-EMC/GDASApp#1346). It adds JCB templates for the input YAMLS of JEDI applications used in the marine B-matrix task in the Global Workflow. --------- Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Co-authored-by: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
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@guillaumevernieres @AndrewEichmann-NOAA @danholdaway @CoryMartin-NOAA Can I get a final review on this PR, so we can merge and hopefully move forward on GW PR #2992 next week? |
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Looks good to me, merge once @guillaumevernieres is happy
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This PR will break marine testing until GW PR #2992 is merged, so I might as well wait until I meet with Rahul and Walter next week to hash out the issues with that PR before I merge this one. The companion jcb-gdas PR that just got merged shouldn't break anything though, so that's good. |
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develop is broken anyways, the default state ... But yes, lets hold on! |
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I'm going to go ahead and merge this PR since GW PR #2992 should be ready for review soon after discussing with the GW team yesterday. Let me know if anyone objects. |
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Go for it. We'll have bugfixes coming in after yours (#1359), but what you have in this PR should still be OK with the low-res test cases. |
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…efactoring (#2992) This PR is a companion to GDASApp PR NOAA-EMC/GDASApp#1312 (merged) and NOAA-EMC/jcb-gdas#31 (merged). This PR does three things: 1. It changes the observation and bias staging for the atmospheric analysis tasks to use JCB templates instead of reading the full JEDI input configuration dictionary in order to construct a list of files to stage. This is cleaner and places fewer constraints on how to initialize the analysis. 2. The ```Jedi``` constructor now takes as input a dictionary that is essentially subset of the ```task_config``` dictionary. This makes the code clearer and less opaque and makes debugging easier. Each dictionary is constructed from a YAML file with configuration parameters for each JEDI application that is run. 3. All JEDI applications and their input YAMLs are now initialized in the initialize job of the ```AtmAnalysis``` and ```AtmEnsAnalysis```. Before, in the ```atmensanl*``` jobs for example, the LETKF solver was initialized in the ```atmensanlinit```cjob, but the LETKF solver and FV3 increment converter were both initialized and executed in the ```atmensanlobs``` and ```atmensanlfv3inc``` jobs respectively. This makes more sense in terms of resource allocation. Addendum: I'm now rolling in the refactoring of the marine B-matrix task into this PR. That makes it also a companion of NOAA-EMC/GDASApp#1346 and NOAA-EMC/jcb-gdas#36. These new changes introduce the ```Jedi``` class and JCB into the marine B-matrix job. Partially resolvesNOAA-EMC/GDASApp#1296 --------- Co-authored-by: RussTreadon-NOAA <Russ.Treadon@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
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…efactoring (NOAA-EMC#2992) This PR is a companion to GDASApp PR NOAA-EMC/GDASApp#1312 (merged) and NOAA-EMC/jcb-gdas#31 (merged). This PR does three things: 1. It changes the observation and bias staging for the atmospheric analysis tasks to use JCB templates instead of reading the full JEDI input configuration dictionary in order to construct a list of files to stage. This is cleaner and places fewer constraints on how to initialize the analysis. 2. The ```Jedi``` constructor now takes as input a dictionary that is essentially subset of the ```task_config``` dictionary. This makes the code clearer and less opaque and makes debugging easier. Each dictionary is constructed from a YAML file with configuration parameters for each JEDI application that is run. 3. All JEDI applications and their input YAMLs are now initialized in the initialize job of the ```AtmAnalysis``` and ```AtmEnsAnalysis```. Before, in the ```atmensanl*``` jobs for example, the LETKF solver was initialized in the ```atmensanlinit```cjob, but the LETKF solver and FV3 increment converter were both initialized and executed in the ```atmensanlobs``` and ```atmensanlfv3inc``` jobs respectively. This makes more sense in terms of resource allocation. Addendum: I'm now rolling in the refactoring of the marine B-matrix task into this PR. That makes it also a companion of NOAA-EMC/GDASApp#1346 and NOAA-EMC/jcb-gdas#36. These new changes introduce the ```Jedi``` class and JCB into the marine B-matrix job. Partially resolvesNOAA-EMC/GDASApp#1296 --------- Co-authored-by: RussTreadon-NOAA <Russ.Treadon@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
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…efactoring (#2992) This PR is a companion to GDASApp PR #1312 (merged) and NOAA-EMC/jcb-gdas#31 (merged). This PR does three things: 1. It changes the observation and bias staging for the atmospheric analysis tasks to use JCB templates instead of reading the full JEDI input configuration dictionary in order to construct a list of files to stage. This is cleaner and places fewer constraints on how to initialize the analysis. 2. The ```Jedi``` constructor now takes as input a dictionary that is essentially subset of the ```task_config``` dictionary. This makes the code clearer and less opaque and makes debugging easier. Each dictionary is constructed from a YAML file with configuration parameters for each JEDI application that is run. 3. All JEDI applications and their input YAMLs are now initialized in the initialize job of the ```AtmAnalysis``` and ```AtmEnsAnalysis```. Before, in the ```atmensanl*``` jobs for example, the LETKF solver was initialized in the ```atmensanlinit```cjob, but the LETKF solver and FV3 increment converter were both initialized and executed in the ```atmensanlobs``` and ```atmensanlfv3inc``` jobs respectively. This makes more sense in terms of resource allocation. Addendum: I'm now rolling in the refactoring of the marine B-matrix task into this PR. That makes it also a companion of #1346 and NOAA-EMC/jcb-gdas#36. These new changes introduce the ```Jedi``` class and JCB into the marine B-matrix job. Partially resolvesNOAA-EMC/GDASApp#1296 --------- Co-authored-by: RussTreadon-NOAA <Russ.Treadon@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
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This PR is a companion to Global Workflow PR [#2992](NOAA-EMC/global-workflow#2992) and GDASApp PR [#1346](#1346). It adds JCB templates for the input YAMLS of JEDI applications used in the marine B-matrix task in the Global Workflow. --------- Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Co-authored-by: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
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This PR is a companion to Global Workflow PR [#2992](NOAA-EMC/global-workflow#2992) and JCB-GDAS PR [#36](NOAA-EMC/jcb-gdas#36). It makes a few necessary changes to the marine JCB base YAML required to have JCB working in the B-matrix task in the Global Workflow.
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This PR is a companion to Global Workflow PR #2992 and JCB-GDAS PR #36.
It makes a few necessary changes to the marine JCB base YAML required to have JCB working in the B-matrix task in the Global Workflow.