e3sm-skill

"What do I need?"
│
├─ First time. What is E3SM and how do I get the code on a supported machine?
│  └─ Read: reference/getting-started.md
│     (clone with git-fleximod externals, supported DOE machines, CIME)
│
├─ I want to understand which components live where in the source tree
│  └─ Read: reference/architecture.md
│     (EAM, EAMxx, ELM, MPAS-Ocean, MPAS-Seaice, MOSART, driver-mct vs driver-moab)
│
├─ I want to run a coupled or single-component case
│  └─ Read: reference/running-cases.md
│     (create_newcase, compsets WCYCL/F/I, ne30/ne120/ne256, build, submit)
│
├─ I am working on the atmosphere physics (ZM, P3, CLUBB, RRTMGP, MAM)
│  └─ Read: reference/eam-atmosphere.md
│     (EAM physics suite vs EAMxx/SCREAM, namelists, COSP)
│
├─ I am working on the ocean or sea ice
│  └─ Read: reference/mpas-ocean-seaice.md
│     (unstructured Voronoi mesh, time stepping, MARBL BGC, Icepack column physics)
│
├─ I want to inspect or post-process output
│  └─ Read: reference/output-and-postprocess.md
│     (h0/h1/h2/h3 history streams, e3sm_diags, mpas_analysis, zppy)
│
├─ I need to tune PE layout, threading, or run on GPU
│  └─ Read: reference/performance-and-scaling.md
│     (PELAYOUT, threading, Kokkos GPU, Frontier/Perlmutter notes)
│
├─ My case crashed at build or run time, or restart is not bit-for-bit
│  └─ Read: reference/debugging.md
│     (build failures, e3sm.log/cesm.log, conservation, BFB testing)
│
└─ I want to submit a pull request to E3SM-Project/E3SM
   └─ Read: reference/contributing-pr.md
      (fork, feature branch naming, integration tests, NextGen vs maintenance)

E3SM/
├── README.md · AGENTS.md · CONTRIBUTING.md · CITATION.cff · LICENSE
├── mkdocs.yaml                          ← top-level MkDocs config (docs.e3sm.org)
├── run_e3sm.template.sh                 ← example coupled run script
│
├── cime/                                ← CIME submodule (case control system)
├── cime_config/                         ← E3SM-specific CIME configuration
│   ├── allactive/config_compsets.xml    ← coupled compsets (WCYCL*, CRYO*)
│   ├── machines/config_machines.xml     ← supported DOE machines
│   ├── machines/config_batch.xml        ← batch system configs
│   ├── machines/cmake_macros/           ← per-machine build flags
│   ├── config_grids.xml                 ← grid aliases (ne30pg2_r05_*, ...)
│   ├── tests.py                         ← e3sm_*_developer test suites
│   └── usermods_dirs/                   ← reusable case modifications
│
├── components/
│   ├── eam/                             ← E3SM Atmosphere Model (Fortran, EAMv3)
│   │   ├── src/{dynamics,physics,...}
│   │   ├── docs/{tech-guide,user-guide,dev-guide}
│   │   └── cime_config/
│   ├── eamxx/                           ← Next-gen atmosphere (C++/Kokkos, SCREAM)
│   │   ├── src/{dynamics,physics,share,...}
│   │   ├── scripts/test-all-eamxx
│   │   └── AGENTS.md                    ← standalone testing guide
│   ├── elm/                             ← E3SM Land Model (Fortran, fork of CLM)
│   │   └── src/external_models/{fates,mpp,sbetr}
│   ├── mosart/                          ← River routing
│   ├── mpas-ocean/                      ← Ocean (unstructured Voronoi)
│   │   └── src/{MARBL, cvmix, BGC, gotm, SHTNS, FFTW}
│   ├── mpas-seaice/                     ← Sea ice (MPAS + Icepack column physics)
│   │   └── src/icepack
│   ├── mpas-albany-landice/             ← MALI land-ice / SeaLevelModel
│   ├── mpas-framework/                  ← Shared MPAS infrastructure
│   ├── homme/                           ← Spectral element dycore (used by EAM)
│   ├── cice/                            ← Legacy CICE (rarely used in modern compsets)
│   ├── ww3/                             ← WaveWatch III (optional)
│   ├── data_comps/                      ← Data atmosphere/ocean/ice (D{ATM,OCN,ICE,...})
│   ├── stub_comps/                      ← Stub components (S{ATM,LND,OCN,...})
│   └── xcpl_comps/                      ← Test exchange components
│
├── driver-mct/                          ← MCT-based coupler driver (default)
├── driver-moab/                         ← MOAB-based coupler driver (newer)
├── share/                               ← Shared utilities (timing, RNG, streams)
├── externals/                           ← Submodules: ekat, scorpio, mam4xx,
│                                          haero, YAKL, mct, cub, ninja
├── docs/                                ← MkDocs source for docs.e3sm.org
└── tools/                               ← Diagnostic and grid generation tools

# 1. Get the code (recursive picks up CIME, MCT, scorpio, MARBL, Icepack, ...)
git clone --recursive https://github.com/E3SM-Project/E3SM.git
cd E3SM

# 2. Create a case (replace MACHINE; query_config --machines lists supported)
cd cime/scripts
./create_newcase \
    --case ../../cases/test_wcycl \
    --compset WCYCL1850 \
    --res ne30pg2_r05_IcoswISC30E3r5 \
    --mach pm-cpu \
    --pecount M \
    --project <your_DOE_allocation>

# 3. Setup, build, submit
cd ../../cases/test_wcycl
./case.setup
./case.build                   # ~30-90 min depending on machine and compset
./xmlchange STOP_OPTION=ndays,STOP_N=5
./case.submit

# 4. Inspect output
./xmlquery RUNDIR              # path to history files
ls $(./xmlquery --value RUNDIR)/*.eam.h0.*.nc