Add implicit stepping to biogeochemistry#1752
Merged
Merged
Conversation
kmdeck
commented
May 28, 2026
AlexisRenchon
approved these changes
May 29, 2026
kmdeck
force-pushed
the
kd/implicit_co2
branch
3 times, most recently
from
a4c3cd4 to
7d57789
Compare
AlexisRenchon
added a commit
that referenced
this pull request
Jun 2, 2026
…spiration Rebased onto main: brings the soil energy-hydrology Jacobian GPU-codegen fix (hoist float(dtγ) out of the broadcast) that the stale branch was missing. That InvalidIRError crashed every forward-model member at compile time; solve! swallowed it, leaving empty output that observation_map NaN-filled, which read as an "all-NaN" calibration. Also picks up ClimaCore 0.14.52 / GPUCompiler 1.13.3 and the implicit-biogeochemistry update (#1752). Adapted the inversion calibration to main's refactored leaderboard data API (get_sim_var_dict closures -> preprocess_sim_var dispatch): - data_sources.jl: _preprocess_sim_var(::Val{:hr}); get_inversion_obs_var_dict returning full-timeseries OutputVars; merged into get_calibration_obs_var_dict. - observation_map.jl: inv_*->nee/gpp/er/hr sim aliasing + retag after preprocess. Squashed from WIP commits de2971f, ddc2a5c, 8f4071c, 300399e, 0b22d51 (preserved in branch backup/pre-rebase-2026-06-02). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
AlexisRenchon
added a commit
that referenced
this pull request
Jun 12, 2026
Rebased onto main: brings the soil energy-hydrology Jacobian GPU-codegen fix (hoist float(dtγ) out of the broadcast) that the stale branch was missing. That InvalidIRError crashed every forward-model member at compile time; solve! swallowed it, leaving empty output that observation_map NaN-filled, which read as an "all-NaN" calibration. Also picks up ClimaCore 0.14.52 / GPUCompiler 1.13.3 and the implicit-biogeochemistry update (#1752). Adapted the inversion calibration to main's refactored leaderboard data API (get_sim_var_dict closures -> preprocess_sim_var dispatch): - data_sources.jl: _preprocess_sim_var(::Val{:hr}); get_inversion_obs_var_dict returning full-timeseries OutputVars; merged into get_calibration_obs_var_dict. - observation_map.jl: inv_*->nee/gpp/er/hr sim aliasing + retag after preprocess.
Merged
AlexisRenchon
added a commit
that referenced
this pull request
Jun 18, 2026
Rebased onto main: brings the soil energy-hydrology Jacobian GPU-codegen fix (hoist float(dtγ) out of the broadcast) that the stale branch was missing. That InvalidIRError crashed every forward-model member at compile time; solve! swallowed it, leaving empty output that observation_map NaN-filled, which read as an "all-NaN" calibration. Also picks up ClimaCore 0.14.52 / GPUCompiler 1.13.3 and the implicit-biogeochemistry update (#1752). Adapted the inversion calibration to main's refactored leaderboard data API (get_sim_var_dict closures -> preprocess_sim_var dispatch): - data_sources.jl: _preprocess_sim_var(::Val{:hr}); get_inversion_obs_var_dict returning full-timeseries OutputVars; merged into get_calibration_obs_var_dict. - observation_map.jl: inv_*->nee/gpp/er/hr sim aliasing + retag after preprocess.
AlexisRenchon
added a commit
that referenced
this pull request
Jun 24, 2026
Rebased onto main: brings the soil energy-hydrology Jacobian GPU-codegen fix (hoist float(dtγ) out of the broadcast) that the stale branch was missing. That InvalidIRError crashed every forward-model member at compile time; solve! swallowed it, leaving empty output that observation_map NaN-filled, which read as an "all-NaN" calibration. Also picks up ClimaCore 0.14.52 / GPUCompiler 1.13.3 and the implicit-biogeochemistry update (#1752). Adapted the inversion calibration to main's refactored leaderboard data API (get_sim_var_dict closures -> preprocess_sim_var dispatch): - data_sources.jl: _preprocess_sim_var(::Val{:hr}); get_inversion_obs_var_dict returning full-timeseries OutputVars; merged into get_calibration_obs_var_dict. - observation_map.jl: inv_*->nee/gpp/er/hr sim aliasing + retag after preprocess.
AlexisRenchon
added a commit
that referenced
this pull request
Jun 30, 2026
Rebased onto main: brings the soil energy-hydrology Jacobian GPU-codegen fix (hoist float(dtγ) out of the broadcast) that the stale branch was missing. That InvalidIRError crashed every forward-model member at compile time; solve! swallowed it, leaving empty output that observation_map NaN-filled, which read as an "all-NaN" calibration. Also picks up ClimaCore 0.14.52 / GPUCompiler 1.13.3 and the implicit-biogeochemistry update (#1752). Adapted the inversion calibration to main's refactored leaderboard data API (get_sim_var_dict closures -> preprocess_sim_var dispatch): - data_sources.jl: _preprocess_sim_var(::Val{:hr}); get_inversion_obs_var_dict returning full-timeseries OutputVars; merged into get_calibration_obs_var_dict. - observation_map.jl: inv_*->nee/gpp/er/hr sim aliasing + retag after preprocess.
AlexisRenchon
added a commit
that referenced
this pull request
Jul 6, 2026
Rebased onto main: brings the soil energy-hydrology Jacobian GPU-codegen fix (hoist float(dtγ) out of the broadcast) that the stale branch was missing. That InvalidIRError crashed every forward-model member at compile time; solve! swallowed it, leaving empty output that observation_map NaN-filled, which read as an "all-NaN" calibration. Also picks up ClimaCore 0.14.52 / GPUCompiler 1.13.3 and the implicit-biogeochemistry update (#1752). Adapted the inversion calibration to main's refactored leaderboard data API (get_sim_var_dict closures -> preprocess_sim_var dispatch): - data_sources.jl: _preprocess_sim_var(::Val{:hr}); get_inversion_obs_var_dict returning full-timeseries OutputVars; merged into get_calibration_obs_var_dict. - observation_map.jl: inv_*->nee/gpp/er/hr sim aliasing + retag after preprocess.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Purpose
Creates an implicit tendency for the biogeochemistry model with the diffusion terms. This allows us to remove some of the limiters in the model.
Note that source terms are treated explicitly still.
To-do
Content
Current main for US-MOz
This branch: