CLM5 Fruit Tree v1.1 #97
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Patching strategy#
# 1. Create working directories
#
PATCH_WORKDIR=$HOME/CLM_FruitTree
PATCHFILES_DIR=$PATCH_WORKDIR/patch_files
eCLM_DIR=$PATCH_WORKDIR/eCLM
CLM5_DIR=$PATCH_WORKDIR/CLM5
mkdir -vp ${PATCHFILES_DIR}
#
# 2. Clone repos
#
cd ${PATCH_WORKDIR}
git clone -b master https://github.com/HPSCTerrSys/eCLM.git
git clone -b release-clm5.0_FruitTree https://github.com/odombro/CTSM CLM5
#
# 3. Get a grasp of changed files
#
# Show last 20 commits leading to the official release (CLM5_FruitTree_v1.1)
cd $CLM5_DIR
git log --pretty=format:"%h %as %<(15,trunc)%an %<(30,trunc)%s %d" -20 CLM5_FruitTree_v1.1 | cat
#
# 59b6a3009 2023-07-17 OlgaDom Corrected flux assignment fr.. (tag: CLM5_FruitTree_v1.1)
# 7edde0ba8 2022-11-15 OlgaDom cleaned up some scripts, add..
# a6bd8ded3 2022-11-15 OlgaDom added new subroutine for orc..
# 2a21cb018 2022-11-04 OlgaDom Fix orchard rotation carbon ..
# 17f3e8ae6 2022-10-18 OlgaDom debug planting of fruit tree..
# 7c9a3bbc8 2022-08-17 OlgaDom Included harvest trigger whe..
# ad3d25b07 2022-05-30 OlgaDom Bug fix in CNPhenology and C..
# 57586d70e 2022-05-22 OlgaDom added references to CLM-Palm..
# 2a6d95e08 2022-05-05 OlgaDom Update parameter file with t..
# 093c985b9 2022-05-05 OlgaDom Make taper and nstem PFT par..
# 87b35bed2 2022-03-14 OlgaDom Correct orchard rotation/rep..
# 64c874934 2022-02-09 OlgaDom Update README (tag: CLM5_FruitTree)
# 7b823206d 2022-02-09 OlgaDom Update README
# 2a1f5b91d 2022-02-09 odombro Update README
# c4f164e92 2022-02-08 odombro Update README
# 9fa4d0dfe 2022-02-08 Olga Dombrowski Implement CLM-FruitTree sub-..
# d2b270654 2021-11-30 Bill Sacks Merge pull request #1568 fro.. (origin/release-clm5.0)
# d035667e3 2021-11-30 Keith Oleson Fix errors in technical note..
# 4d9bb14b9 2021-09-08 Bill Sacks Merge pull request #1480 fro..
# 3c00edf2b 2021-09-07 Samuel Levis Bringing a copy of master_li..
#
# List modified files under src/ folder starting from the commit after release-clm5.0 (9fa4d0dfe) to CLM5_FruitTree_v1.1 (59b6a3009)
git diff origin/release-clm5.0..CLM5_FruitTree_v1.1 --numstat -- src | cat
# +++ ---
# 3 3 src/biogeochem/CNBalanceCheckMod.F90
# 13 3 src/biogeochem/CNCIsoFluxMod.F90
# 97 38 src/biogeochem/CNCStateUpdate1Mod.F90
# 0 2 src/biogeochem/CNCStateUpdate2Mod.F90
# 6 3 src/biogeochem/CNDriverMod.F90
# 5 3 src/biogeochem/CNFUNMod.F90
# 21 9 src/biogeochem/CNGRespMod.F90
# 3 2 src/biogeochem/CNGapMortalityMod.F90
# 4 1 src/biogeochem/CNMRespMod.F90
# 73 27 src/biogeochem/CNNStateUpdate1Mod.F90
# 1875 581 src/biogeochem/CNPhenologyMod.F90
# 65 5 src/biogeochem/CNVegCarbonFluxType.F90
# 51 13 src/biogeochem/CNVegCarbonStateType.F90
# 2 2 src/biogeochem/CNVegComputeSeedMod.F90
# 39 2 src/biogeochem/CNVegNitrogenFluxType.F90
# 38 2 src/biogeochem/CNVegNitrogenStateType.F90
# 157 5 src/biogeochem/CNVegStateType.F90
# 31 27 src/biogeochem/CNVegStructUpdateMod.F90
# 9 2 src/biogeochem/CropType.F90
# 383 120 src/biogeochem/NutrientCompetitionFlexibleCNMod.F90
# 6 6 src/biogeochem/dynHarvestMod.F90
# 31 1 src/biogeophys/TemperatureType.F90
# 91 2 src/main/pftconMod.F90
#
#
# 4. Generate FruitTree patchset
#
git -C ${CLM5_DIR} format-patch --output-directory ${PATCHFILES_DIR} origin/release-clm5.0..CLM5_FruitTree_v1.1
#
# /home/user/CLM_FruitTree/patch_files/0001-Implement-CLM-FruitTree-sub-model-for-deciduous-frui.patch
# /home/user/CLM_FruitTree/patch_files/0002-Update-README.patch
# /home/user/CLM_FruitTree/patch_files/0003-Update-README.patch
# /home/user/CLM_FruitTree/patch_files/0004-Update-README.patch
# /home/user/CLM_FruitTree/patch_files/0005-Update-README.patch
# /home/user/CLM_FruitTree/patch_files/0006-Correct-orchard-rotation-replanting-trigger.patch
# /home/user/CLM_FruitTree/patch_files/0007-Make-taper-and-nstem-PFT-parameters-to-be-set-in-par.patch
# /home/user/CLM_FruitTree/patch_files/0008-Update-parameter-file-with-taper-and-nstem-parameter.patch
# /home/user/CLM_FruitTree/patch_files/0009-added-references-to-CLM-Palm-Fan-et-al.-2015.patch
# /home/user/CLM_FruitTree/patch_files/0010-Bug-fix-in-CNPhenology-and-CNVegStructUpdateMod-and-.patch
# /home/user/CLM_FruitTree/patch_files/0011-Included-harvest-trigger-when-leaf-offset-starts.patch
# /home/user/CLM_FruitTree/patch_files/0012-debug-planting-of-fruit-trees-make-two-more-CFTs-act.patch
# /home/user/CLM_FruitTree/patch_files/0013-Fix-orchard-rotation-carbon-balance-error.patch
# /home/user/CLM_FruitTree/patch_files/0014-added-new-subroutine-for-orchard-rotation.patch
# /home/user/CLM_FruitTree/patch_files/0015-cleaned-up-some-scripts-added-some-crop-types-to-act.patch
# /home/user/CLM_FruitTree/patch_files/0016-Corrected-flux-assignment-from-column-to-patch-level.patch
# /home/user/CLM_FruitTree/patch_files/0017-Update-README.patch
# /home/user/CLM_FruitTree/patch_files/0018-Update-README.patch
#
#
# 5. Transform CLM5 paths in patchfiles into their equivalent eCLM paths
#
# Show instances of CLM5 paths
grep -RE "src/(biogeochem|biogeophys|main)" $PATCHFILES_DIR
# src/* -> src/clm5/*
sed -i 's#src/biogeochem#src/clm5/biogeochem#g' ${PATCHFILES_DIR}/*.patch
sed -i 's#src/biogeophys#src/clm5/biogeophys#g' ${PATCHFILES_DIR}/*.patch
sed -i 's#src/main#src/clm5/main#g' $PATCHFILES_DIR/*.patch
# Check if sed worked
grep -RE "src/(biogeochem|biogeophys|main)" $PATCHFILES_DIR # should show no results
grep -RE "src/clm5/(biogeochem|biogeophys|main)" $PATCHFILES_DIR # show transformed paths
#
# 6. Apply FruitTree patchset to eCLM
#
cd ${eCLM_DIR}
git checkout -b CLM5_FruitTree_v1.1
# Start interactive patching
git am --ignore-whitespace $PATCHFILES_DIR/*
# The ff. patches include README updates which isn't in eCLM and thus skipped:
#
# /home/user/CLM_FruitTree/patch_files/0002-Update-README.patch
# /home/user/CLM_FruitTree/patch_files/0003-Update-README.patch
# /home/user/CLM_FruitTree/patch_files/0004-Update-README.patch
# /home/user/CLM_FruitTree/patch_files/0005-Update-README.patch
git am --show-current-patch=diff
git am --skip
# Show diff summary after patching
git log --pretty=format:"%h %as %<(15,trunc)%an %<(30,trunc)%s %d" -20 | cat
#
# acf0b4cbc 2023-07-17 OlgaDom Corrected flux assignment fr.. (HEAD -> CLM5_FruitTree_v1.1, origin/CLM5_FruitTree_v1.1)
# 1d07087dc 2022-11-15 OlgaDom cleaned up some scripts, add..
# be24b9368 2022-11-15 OlgaDom added new subroutine for orc..
# 1dbab6aeb 2022-11-04 OlgaDom Fix orchard rotation carbon ..
# cbf5e76d5 2022-10-18 OlgaDom debug planting of fruit tree..
# 288c754ca 2022-08-17 OlgaDom Included harvest trigger whe..
# 27db3e604 2022-05-30 OlgaDom Bug fix in CNPhenology and C..
# 9e8401d62 2022-05-22 OlgaDom added references to CLM-Palm..
# 3eef0a65b 2022-05-05 OlgaDom Update parameter file with t..
# 99dca29bc 2022-05-05 OlgaDom Make taper and nstem PFT par..
# 50fddc120 2022-03-14 OlgaDom Correct orchard rotation/rep..
# 3fe2de2d8 2022-02-09 OlgaDom Update README
# 1bcfffbd5 2022-02-08 Olga Dombrowski Implement CLM-FruitTree sub-..
# e1781edc1 2025-12-02 Johannes Keller PDAF-related: GRACE-DA chang.. (origin/master, origin/dev-merge-eclm_with_FT_WC, origin/HEAD, master)
# cece7aa74 2025-12-02 Johannes Keller Set cpl_inst_tag from pdaf_i..
# 91d5f7b40 2025-11-25 Johannes Keller Soil Hydraulic Parameter fro..
# 7877e5cc2 2025-11-21 Johannes Keller Soil Hydraulic Parameter Per..
# 860a68c49 2025-11-20 Johannes Keller PDAF-related perturbation ro..
# 7853ec4db 2025-11-04 Johannes Keller docs: secure jupyter-book v1..
# 923b0fcd1 2025-10-02 Paul Rigor Fixed wrong working director..
# Show eCLM files modified by the FruitTree patchset
git diff master..acf0b4cbc --numstat | cat
# +++ ---
# - - clm5_params.c171117__FruitTree.nc
# 3 3 src/clm5/biogeochem/CNBalanceCheckMod.F90
# 13 3 src/clm5/biogeochem/CNCIsoFluxMod.F90
# 97 38 src/clm5/biogeochem/CNCStateUpdate1Mod.F90
# 0 2 src/clm5/biogeochem/CNCStateUpdate2Mod.F90
# 6 3 src/clm5/biogeochem/CNDriverMod.F90
# 5 3 src/clm5/biogeochem/CNFUNMod.F90
# 21 9 src/clm5/biogeochem/CNGRespMod.F90
# 3 2 src/clm5/biogeochem/CNGapMortalityMod.F90
# 4 1 src/clm5/biogeochem/CNMRespMod.F90
# 73 27 src/clm5/biogeochem/CNNStateUpdate1Mod.F90
# 1875 581 src/clm5/biogeochem/CNPhenologyMod.F90
# 65 5 src/clm5/biogeochem/CNVegCarbonFluxType.F90
# 51 13 src/clm5/biogeochem/CNVegCarbonStateType.F90
# 2 2 src/clm5/biogeochem/CNVegComputeSeedMod.F90
# 39 2 src/clm5/biogeochem/CNVegNitrogenFluxType.F90
# 38 2 src/clm5/biogeochem/CNVegNitrogenStateType.F90
# 157 5 src/clm5/biogeochem/CNVegStateType.F90
# 31 27 src/clm5/biogeochem/CNVegStructUpdateMod.F90
# 9 2 src/clm5/biogeochem/CropType.F90
# 383 120 src/clm5/biogeochem/NutrientCompetitionFlexibleCNMod.F90
# 6 6 src/clm5/biogeochem/dynHarvestMod.F90
# 31 1 src/clm5/biogeophys/TemperatureType.F90
# 91 2 src/clm5/main/pftconMod.F90
|
kvrigor
commented
Jan 21, 2026
| call ncd_io('season_decid', this%season_decid, 'read', ncid, readvar=readv, posNOTonfile=.true.) | ||
| if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) | ||
|
|
||
| call ncd_io('perennial', this%perennial, 'read', ncid, readvar=readv, posNOTonfile=.true.) |
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Requiring perennial and mulch_pruning in the PFT file is causing the CI failure. Some adjustments are necessary to make this parameters optional.
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Equivalent to CLM5_FruitTree_v1.1 by @odombro.