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Jgfouca/eamxx downstream merge 2024 06 26 #6489

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merged 548 commits into from
Jul 1, 2024

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@jgfouca jgfouca commented Jun 26, 2024

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mam4xx/aero_model.hpp
/// Identifiers for aerosol species that inhabit MAM4 modes.
enum class AeroId {
  SOA = 2,  // secondary organic aerosol
  SO4 = 0,  // sulphate
  POM = 1,  // primary organic matter
  BC = 3,   // black carbon
  NaCl = 5, // sodium chloride
  DST = 4,  // dust
  MOM = 6,  // marine organic matter,
  None = 7  // invalid aerosol species
};
…et prog index

Changes for formatting and species reordering are reverted back
in mam_coupling. Adds a new function in mam_couplingto map
indexing to the prognostic array index.

I changed the following mam4xx/aero_modes.cpp
function (this is the only change in this file) to change species
ordering:
KOKKOS_INLINE_FUNCTION AeroId mode_aero_species(const int modeNo,
                                                const int speciesNo) {
  // A list of species within each mode for MAM4.
    static constexpr AeroId mode_aero_species[4][7] = {
      {// accumulation mode
       AeroId::SO4, AeroId::POM, AeroId::SOA, AeroId::BC, AeroId::DST,
       AeroId::NaCl, AeroId::MOM},
      {
          // aitken mode
          AeroId::SO4,
          AeroId::SOA,
          AeroId::NaCl,
          AeroId::MOM,
          AeroId::None,
          AeroId::None,
          AeroId::None,
      },
      {// coarse mode
       AeroId::DST, AeroId::NaCl, AeroId::SO4, AeroId::BC, AeroId::POM,
       AeroId::SOA, AeroId::MOM},
      {// primary carbon mode
       AeroId::POM, AeroId::BC, AeroId::MOM, AeroId::None, AeroId::None,
       AeroId::None, AeroId::None}};
  return mode_aero_species[modeNo][speciesNo];
}
bartgol and others added 9 commits June 24, 2024 11:31
…-io-timers-per-yaml-file

Automatically Merged using E3SM Pull Request AutoTester
PR Title: Add timers on a per-yaml-file-basis
PR Author: bartgol
PR LABELS: I/O, AT: AUTOMERGE
…tive-ml/20240611_fix

Automatically Merged using E3SM Pull Request AutoTester
PR Title: Aarondonahue/corrective ml/20240611 fix
PR Author: AaronDonahue
PR LABELS: AT: AUTOMERGE, bugfix, AT: Skip Stand-Alone Testing, AT: Skip v1 Testing, machine learning
Automatically Merged using E3SM Pull Request AutoTester
PR Title: Initial implementation of pyscream module(s) for running eamxx from python
PR Author: bartgol
PR LABELS: AT: AUTOMERGE, python
…_2858

Automatically Merged using E3SM Pull Request AutoTester
PR Title: Addresses some suggestions in issue #2858.
PR Author: overfelt
PR LABELS: BFB, AT: AUTOMERGE, code cleanup, EAGLES, MAM
…io-v1.6.4

Automatically Merged using E3SM Pull Request AutoTester
PR Title: Updating to SCORPIO v1.6.4
PR Author: jayeshkrishna
PR LABELS: BFB, I/O, AT: AUTOMERGE
…ownstream_merge_2024_06_26

* downstream/master: (473 commits)
  remove redundant operation, fix the python library path in ruby cmake
  EAMxx: bump micro version of pyeamxx
  EAMxx: add timers to output manager on a per-yaml-file basis
  EAMxx: fix compiler warning
  Revert "EAMxx: add buildnml-time check for IC file and cmake option compatibility"
  Reduces buffer size by 1 for shoc small kernels
  Updating to SCORPIO v1.6.4
  EAMxx: remove empty if statement in jenkins bash script
  Addresses some suggestions in issue #2858.
  EAMxx: fix typo in dummy XML selector for scripts unit tests
  EAMxx: fix sneaky error when parsing string in buildnml
  EAMxx: use special selector for cime scripts test
  EAMxx: fix invocation of cime-nml-tests in jenkins script
  Fix baselines_to_be_generated
  Remove unnecessary upstream master merge
  test-all-scream: Simplify the baseline model
  EAMxx: add buildnml-time check for IC file and cmake option compatibility
  Update EKAT submodule
  EAMxx: fix relative humidity unit test
  EAMxx: fix usage of code deprecated in Kokkos 4
  ...
@jgfouca jgfouca added the EAMxx PRs focused on capabilities for EAMxx label Jun 26, 2024
@jgfouca jgfouca self-assigned this Jun 26, 2024
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github-actions bot commented Jun 26, 2024

PR Preview Action v1.4.7
🚀 Deployed preview to https://E3SM-Project.github.io/E3SM/pr-preview/pr-6489/
on branch gh-pages at 2024-06-28 23:06 UTC

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I'm not going through 300 files. Since all eamxx code was already reviewed in the scream repo, I'm fine with merging.

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jgfouca commented Jun 26, 2024

I'm not going through 300 files. Since all eamxx code was already reviewed in the scream repo, I'm fine with merging.

Jeez, what a slacker!! 😆 In seriousness, I of course do not expect any reviewers to look at the entirety of this PR. I assigned reviewers just to let you guys know that the downstream merge is happening and to see if any you had any general thoughts.

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I skimmed through and didn't see any concerning

jgfouca added a commit that referenced this pull request Jun 27, 2024
…#6489)

* jgfouca/eamxx_downstream_merge_2024_06_26: (475 commits)
  Fixes for rrtmgp updates
  let's not lint files in components/eamxx for now
  remove redundant operation, fix the python library path in ruby cmake
  EAMxx: bump micro version of pyeamxx
  EAMxx: add timers to output manager on a per-yaml-file basis
  EAMxx: fix compiler warning
  Revert "EAMxx: add buildnml-time check for IC file and cmake option compatibility"
  Reduces buffer size by 1 for shoc small kernels
  Updating to SCORPIO v1.6.4
  EAMxx: remove empty if statement in jenkins bash script
  Addresses some suggestions in issue #2858.
  EAMxx: fix typo in dummy XML selector for scripts unit tests
  EAMxx: fix sneaky error when parsing string in buildnml
  EAMxx: use special selector for cime scripts test
  EAMxx: fix invocation of cime-nml-tests in jenkins script
  Fix baselines_to_be_generated
  Remove unnecessary upstream master merge
  test-all-scream: Simplify the baseline model
  EAMxx: add buildnml-time check for IC file and cmake option compatibility
  Update EKAT submodule
  ...
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jgfouca commented Jun 27, 2024

Merged to next.

@rljacob rljacob mentioned this pull request Jun 27, 2024
jgfouca added a commit that referenced this pull request Jun 28, 2024
@jgfouca jgfouca merged commit c7d7998 into master Jul 1, 2024
22 checks passed
@jgfouca jgfouca deleted the jgfouca/eamxx_downstream_merge_2024_06_26 branch July 1, 2024 20:42
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rljacob commented Jul 2, 2024

ERP_Ln9.ne4pg2_ne4pg2.F2010-SCREAMv1.pm-gpu_gnugpu still has a build fail.

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