Couple pflotran biogeochemistry to alm #1649

wanggangsheng · 2017-07-18T21:46:42Z

Migrate NGEE-Arctic CLM-PFLOTRAN to ACME Land Model through a generic clm_interface.

clm_interface_dataType consists of biogeochemistry (bgcType) & thermal-hydrology (thType).
Rename namelist ‘use_bgc_interface’ to ‘use_clm_interface’ to include bgc & th interfaces.
Data passing between ALM & clm_interface is implemented in clm_interface_funcsMod.F90.
Data passing between clm_interface & PFLOTRAN is implemented in clm_interface_pflotranMod.F90.
Global-scale ALM-PFLOTRAN-bgc coupled run is tested.
The clm_interface is extended to incorporate PLFOTRAN thermal-hydrology in next step.
Add configuration for mach "cades" for alm-pflotran coupled run.
makefile: update "PETSC_LIB"-"variables" dir for petsc-git-version 1a9d3c3

[BFB]

…NLY BGC coupling).

…ent edits in regarding to soil column indexing and filtering in clm-pflotran-interface subroutines. These edits are for column-mode and tested for at global-scale.

… It's because the coupling not yet includes P bgc.

…iables.

…iables: (2) rename namelist ‘use_bgc_interface’ to ‘use_clm_interface’, so that it includes thermal-hydrology and biogeochemical interfaces.

…thermal-hydrology (TH) modules in interface. (1) Separate original ’clm_bgc_data’ into ‘th’ and ‘bgc’ data types, which included in a general interface data type, ‘clm_interface_data_type’; (2) Rename ‘clm_bgc_interfaceMod’ to ‘clm_interface_funcsMod’; (3) Rename ‘clm_pflotran_interfaceMod’ to ‘clm_interface_pflotranMod’.

…. By this commit, BGC coupling runs correctly with hyrolog-coupled codes.

… not coupled.

…uxes

…9d3c3

rljacob · 2017-07-26T22:24:46Z

What are these "test names" you guys are talking about? The trailing characters in a test entry like "ERP_Ln9.ne30_ne30.FC5", "cam-outfrq9s")" refer to a directory called "cam-outfrq9s" which has commands to modify the test. You can't just append arbitrary strings to the end of a test name in update_acme_tests.py.

bishtgautam · 2017-07-26T22:30:24Z

I understand that trailing characters refer to a directory e.g. a test name ending in .clm-bgcinterface implies that the testing infrastructure will look for files present in cime/cime_config/acme/testmods_dirs/allactive/clm/bgcinterface.

[BFB]

jqyin · 2017-07-28T14:11:50Z

@bishtgautam : Gangsheng and I have added the new test for clm-bgcinterface, and we tested that it's BFB.

bishtgautam · 2017-07-28T14:47:44Z

Thanks for adding the test.

#1649) Migrate NGEE-Arctic CLM-PFLOTRAN to ACME Land Model through a generic clm_interface 1. clm_interface_dataType consists of biogeochemistry (bgcType) and thermal-hydrology (thType). 2. Rename namelist use_bgc_interface to use_clm_interface to include bgc & th interfaces. 3. Data passing between ALM & clm_interface is implemented in clm_interface_funcsMod.F90. 4. Data passing between clm_interface & PFLOTRAN is implemented in clm_interface_pflotranMod.F90. 5. Global-scale ALM-PFLOTRAN-bgc coupled run is tested. 6. The clm_interface is extended to incorporate PLFOTRAN thermal-hydrology in next step. 7. Add configuration for mach "cades" for alm-pflotran coupled run. 8. makefile: update "PETSC_LIB"-"variables" dir for petsc-git-version 1a9d3c3. [BFB] Conflicts: components/clm/src/biogeochem/CNNStateUpdate1Mod.F90 components/clm/src/biogeochem/CNNitrogenFluxType.F90 components/clm/src/biogeochem/PStateUpdate1Mod.F90 components/clm/src/biogeochem/PStateUpdate2Mod.F90 components/clm/src/biogeochem/PStateUpdate3Mod.F90 components/clm/src/biogeophys/HydrologyNoDrainageMod.F90 components/clm/src/main/clm_initializeMod.F90 components/clm/src/main/controlMod.F90

jqyin · 2017-08-09T19:19:12Z

Merged to next.

…o next (PR #1649)" This reverts commit eae0ffd, reversing changes made to 572b281.

jqyin · 2017-08-14T17:08:30Z

@rljacob, can I re-merge (revert the revert) this PR ? The tests passed on ornl Cades cluster, nersc Edison (with same version gnu) and Skybridge (with intel), but it failed on Melvin due to that uninitialized local variables are not set to zero by default on Melvin (it passed with adding -finit-local-zero flag).

rljacob · 2017-08-14T17:10:59Z

I thought PR #1468 was the one that had different results on mevlin.

rljacob · 2017-08-14T17:13:19Z

failed or had a diff with baselines?

jqyin · 2017-08-14T17:13:21Z

I think they both are since they both touched the BGC code region, and we confirmed the -finit-local-zero fix for this PR. I haven't done that for PR #1468 yet.

rljacob · 2017-08-14T17:15:23Z

Well I'd like to get 1468 done first since its so old.

jqyin · 2017-08-14T17:18:16Z

OK. I'll request the same test be done on Melvin to confirm -finit-local-zero is also the fix for PR #1468. BTW, this PR is high priority.

…se3' into next (PR #1649)"" This reverts commit 8e11d46.

Migrate NGEE-Arctic CLM-PFLOTRAN to ACME Land Model through a generic clm_interface 1. clm_interface_dataType consists of biogeochemistry (bgcType) and thermal-hydrology (thType). 2. Rename namelist use_bgc_interface to use_clm_interface to include bgc & th interfaces. 3. Data passing between ALM & clm_interface is implemented in clm_interface_funcsMod.F90. 4. Data passing between clm_interface & PFLOTRAN is implemented in clm_interface_pflotranMod.F90. 5. Global-scale ALM-PFLOTRAN-bgc coupled run is tested. 6. The clm_interface is extended to incorporate PLFOTRAN thermal-hydrology in next step. 7. Add configuration for mach "cades" for alm-pflotran coupled run. 8. makefile: update "PETSC_LIB"-"variables" dir for petsc-git-version 1a9d3c3. [BFB] Conflicts: components/clm/src/biogeochem/CNNStateUpdate1Mod.F90 components/clm/src/biogeochem/CNNitrogenFluxType.F90 components/clm/src/biogeochem/PStateUpdate1Mod.F90 components/clm/src/biogeochem/PStateUpdate2Mod.F90 components/clm/src/biogeochem/PStateUpdate3Mod.F90 components/clm/src/biogeophys/HydrologyNoDrainageMod.F90 components/clm/src/main/clm_initializeMod.F90 components/clm/src/main/controlMod.F90

amametjanov · 2017-08-18T15:42:24Z

Can you take a look at the ERS.f09_g16.I1850CLM45CN.cetus_ibm.clm-bgcinterface test on CDash?

jqyin · 2017-08-18T16:20:36Z

@amametjanov Since threading was used for the test, I think the error was caused by similar issues as reported in issue #1379, which should be fixed by PR #1468. It seems the test was run with a next version before PR #1468 was merge. I think it should clear out with current next.

Updates modules for cori-knl in cesm Test suite: Test baseline: Test namelist changes: Test status: roundoff Fixes User interface changes?: Code review:

Migrate NGEE-Arctic CLM-PFLOTRAN to ACME Land Model through a generic clm_interface 1. clm_interface_dataType consists of biogeochemistry (bgcType) and thermal-hydrology (thType). 2. Rename namelist use_bgc_interface to use_clm_interface to include bgc & th interfaces. 3. Data passing between ALM & clm_interface is implemented in clm_interface_funcsMod.F90. 4. Data passing between clm_interface & PFLOTRAN is implemented in clm_interface_pflotranMod.F90. 5. Global-scale ALM-PFLOTRAN-bgc coupled run is tested. 6. The clm_interface is extended to incorporate PLFOTRAN thermal-hydrology in next step. 7. Add configuration for mach "cades" for alm-pflotran coupled run. 8. makefile: update "PETSC_LIB"-"variables" dir for petsc-git-version 1a9d3c3. [BFB] Conflicts: components/clm/src/biogeochem/CNNStateUpdate1Mod.F90 components/clm/src/biogeochem/CNNitrogenFluxType.F90 components/clm/src/biogeochem/PStateUpdate1Mod.F90 components/clm/src/biogeochem/PStateUpdate2Mod.F90 components/clm/src/biogeochem/PStateUpdate3Mod.F90 components/clm/src/biogeophys/HydrologyNoDrainageMod.F90 components/clm/src/main/clm_initializeMod.F90 components/clm/src/main/controlMod.F90

fmyuan and others added 30 commits July 18, 2017 12:49

Migrating NGEE-Arctic CLM-PFLOTRAN codes - STEP 1: coding.

73c87f3

Migrating NGEE-Arctic CLM-PFLOTRAN codes - STEP 3: clean codes (now O…

4303af3

…NLY BGC coupling).

Migrating NGEE-Arctic CLM-PFLOTRAN codes - STEP 4: manually merge rec…

f20cdb3

…ent edits in regarding to soil column indexing and filtering in clm-pflotran-interface subroutines. These edits are for column-mode and tested for at global-scale.

fix a P cycle nc variable writing error, when coupling with PFLOTRAN.…

bcc4e97

… It's because the coupling not yet includes P bgc.

Migrating CLM-PFLOTRAN TH-MODE - Step 1. Interface data types and var…

f48954e

…iables.

Migrating CLM-PFLOTRAN TH-MODE - Step 1. Interface data types and var…

b2a0738

…iables: (2) rename namelist ‘use_bgc_interface’ to ‘use_clm_interface’, so that it includes thermal-hydrology and biogeochemical interfaces.

Migrating CLM-PFLOTRAN TH-MODE - Step 3. Hydrology coupling.

52dfa86

Migrating CLM-PFLOTRAN TH-MODE - Step 4. Manually edit/clean-up codes…

f3ec343

…. By this commit, BGC coupling runs correctly with hyrolog-coupled codes.

Migrating CLM-PFLOTRAN TH-MODE - Step 4. Manually edit/clean-up codes…

81af67e

…. By this commit, BGC coupling runs correctly with hyrolog-coupled codes.

enable clm_pf_finalize() call.

c29135f

missing one 'use_pflotran' exclusion in 'clm_driver.F90'.

6d3dad4

add an if...endif block to pass BFB lnd-developer tests when pflotran…

1c17503

… not coupled.

edit comments on clm_interface

5f37372

ensure that plant N/P uptake rate <= mineral N/P pool size

6bfc077

ensure plant N/P uptake rate <= mineral N/P pool size

eb004d0

add pflotran balance check

57f0a5c

correct errors in pflotran mass balance check

e85a705

alm-pflotran: clean comments & unused variables

30826a1

use array in pflotran mass balance check

babbe1a

improve pflotran mass balance check

d3a4e3f

edit output for "err_found" in plfotran mass balance check

83d7274

comment out "initialization to 0" for net and gross mineralization fl…

8c83152

…uxes

change pflotran mass balance check functions from public to private

0a08490

move private functions (mass balance) into #ifdef CLM_PFLOTRAN

260a7ff

initialize local variables to 0: smin_nh4/no3_to_plant_vr_loc

d497bae

change col to col_pp

b3a0fde

change grc/lun/col to grc_pp/lun_pp/col_pp

e14ed7a

configure machines/compilers for ALM-PFLOTRAN coupling

0ef1518

Makefile: update "PETSC_LIB"-"variables" dir for petsc-git-version 1a…

7ce7171

…9d3c3

jqyin added 2 commits July 28, 2017 10:00

Add a new test for ALM-PFLOTRAN's bgc interface

ff93994

[BFB]

Change clm-interface's zi dimension to be consistent with ALM

2adbce1

[BFB]

bishtgautam approved these changes Jul 28, 2017

View reviewed changes

jqyin added a commit that referenced this pull request Aug 10, 2017

Revert "Merge branch 'wanggangsheng/lnd/alm-pflotran-bgc-rebase3' int…

8e11d46

…o next (PR #1649)" This reverts commit eae0ffd, reversing changes made to 572b281.

jqyin mentioned this pull request Aug 15, 2017

Uninitialized local variables in land code #1717

Closed

jqyin added a commit that referenced this pull request Aug 15, 2017

Revert "Revert "Merge branch 'wanggangsheng/lnd/alm-pflotran-bgc-reba…

d320acf

…se3' into next (PR #1649)"" This reverts commit 8e11d46.

jqyin mentioned this pull request Aug 17, 2017

Fixes land BGC computation for a threaded simulation #1468

Merged

jqyin merged commit 2adbce1 into master Aug 17, 2017

bishtgautam mentioned this pull request Aug 30, 2017

Attempt to use pointer EP_BETR when it is not associated with a target. Intel #1745

Closed

rljacob added the enhancement label Sep 6, 2017

jgfouca pushed a commit that referenced this pull request Oct 3, 2017

Merge pull request #1649 from jedwards4b/cori_update

19a4641

Updates modules for cori-knl in cesm Test suite: Test baseline: Test namelist changes: Test status: roundoff Fixes User interface changes?: Code review:

wanggangsheng deleted the wanggangsheng/lnd/alm-pflotran-bgc-rebase3 branch February 5, 2018 20:53

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Couple pflotran biogeochemistry to alm #1649

Couple pflotran biogeochemistry to alm #1649

wanggangsheng commented Jul 18, 2017 •

edited by rljacob

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Couple pflotran biogeochemistry to alm #1649

Couple pflotran biogeochemistry to alm #1649

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