From c316b7fe8506e3c897b62afec690367bb86978ee Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 25 Mar 2024 09:54:00 -0700 Subject: [PATCH 01/11] update default fates parameter file --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 5c86d230fd..b82fc9ee03 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -494,7 +494,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/fates_params_api.32.0.0_12pft_c231215.nc +lnd/clm2/paramdata/fates_params_api.35.0.0_12pft_c240326.nc From 618a083840b65ac16a5027b31b5928066d47505a Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 25 Mar 2024 09:58:03 -0700 Subject: [PATCH 02/11] update fates externals --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 69d13ca73b..866b9ac5b2 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/rgknox/fates -tag = sci.1.72.2_api.34.0.0 +repo_url = https://github.com/NGEET/fates +tag = sci.1.73.0_api.35.0.0 required = True [externals_description] From 5c98773fbc39f2b60690c3f9d62e854c02392645 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 25 Mar 2024 10:01:12 -0700 Subject: [PATCH 03/11] remove out-of-date cheyenne expected failures These failures are already tracked with derecho versions --- cime_config/testdefs/ExpectedTestFails.xml | 28 ---------------------- 1 file changed, 28 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 8a18fc2901..ced31d4cd2 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -38,13 +38,6 @@ - - - FAIL - #1733 - - - FAIL @@ -130,13 +123,6 @@ - - - FAIL - FATES#701 - - - FAIL @@ -144,13 +130,6 @@ - - - PEND - #1045 - - - PEND @@ -166,13 +145,6 @@ - - - FAIL - FATES#1089 - - - FAIL From 7481a5a684e87fccdf5add0cee6482c987b14572 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 25 Mar 2024 10:08:04 -0700 Subject: [PATCH 04/11] add failing 5x5_amazon test to aux_clm and known failures to track --- cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++ cime_config/testdefs/testlist_clm.xml | 9 +++++++++ 2 files changed, 16 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index ced31d4cd2..ab453382f8 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -152,6 +152,13 @@ + + + FAIL + #2423 + + + FAIL diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 0e1424fd7c..9e90309492 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -3444,6 +3444,15 @@ + + + + + + + + + From e9fb075891f90f97159071d03b376ed44c451bfc Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 25 Mar 2024 10:14:37 -0700 Subject: [PATCH 05/11] temporarily convert fates seed dispersal test to use f10 This will be reverted once issue #2423 has been addressed --- cime_config/testdefs/testlist_clm.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 9e90309492..24153d15c9 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2467,7 +2467,7 @@ - + @@ -2477,7 +2477,7 @@ - + From 3c73756250187aae0a1ccc5a22c6bf560562f18a Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 9 Apr 2024 12:22:35 -0600 Subject: [PATCH 06/11] add graceful failure for fates hydro + sp mode This also adds a corresponding namelist build unit test and similar test to check that sp mode + spitfire fails --- bld/CLMBuildNamelist.pm | 4 ++++ bld/unit_testers/build-namelist_test.pl | 12 +++++++++++- 2 files changed, 15 insertions(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index b4eefd984c..f1a1e5b2ce 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4469,6 +4469,10 @@ sub setup_logic_fates { if ( $nl->get_value('fates_spitfire_mode') > 0 ) { $log->fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true'); } + # hydro isn't currently supported to work when FATES SP mode is active + if (&value_is_true( $nl->get_value('use_fates_planthydro') )) { + $log->fatal_error('fates sp mode is currently not supported to work with fates hydro'); + } } } my $var = "use_fates_inventory_init"; diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 6224acc815..9f7891b386 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1549; +my $ntests = 1551; if ( defined($opts{'compare'}) ) { $ntests += 907; @@ -1024,6 +1024,16 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, + "usespitfireusefatessp" =>{ options=>"-envxml_dir . --bgc fates", + namelst=>"fates_spitfire_mode=1,use_fates_sp=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "usefatesspusefateshydro" =>{ options=>"-envxml_dir . --bgc fates", + namelst=>"use_fates_sp=.true.,use_fates_planthydro=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, "useloggingButNOTFATES" =>{ options=>"-envxml_dir . -no-megan", namelst=>"use_fates_logging=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", From 810272b0cda8d2443027b116dcc96a40c3ece565 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 22 Apr 2024 17:01:23 -0700 Subject: [PATCH 07/11] remove fates sp mode expected fail per sci.1.72.7_api.34.0.0 tag fix --- cime_config/testdefs/ExpectedTestFails.xml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 1673804c16..0d01428ba7 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -254,13 +254,6 @@ - - - FAIL - #2478 - - - FAIL From 3425304c04ecb9774eca267d2053d92d88372ca4 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 23 Apr 2024 00:04:31 -0600 Subject: [PATCH 08/11] update compset for 5x5_amazon failing test --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 66aa18403d..bf4d23a500 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -3665,7 +3665,7 @@ - + From 9b1355fd5dbce1a7c32a9081c4660f0883a3e32b Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 23 Apr 2024 12:51:41 -0700 Subject: [PATCH 09/11] Update ChangeLog and ChangeSum --- doc/ChangeLog | 117 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 118 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 671f5020de..91fe800b4a 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,121 @@ =============================================================== +Tag name: ctsm5.2.002 +Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov) +Date: Tue Apr 23 10:30:00 MDT 2024 +One-line Summary: FATES default allometry parameter file update + +Purpose and description of changes +---------------------------------- + +This updates the default FATES parameter file which includes a number +of changes: + + - Default global tree pft allometry update + - New allometric mode options + - New scaling coefficients for alternative leaf maintenance respiration + - New switch to control the use of host land model day length scaling factor + +This also incorporates some testing additions and clean up, including: + + - Removes cheyenne expected failure tests that have been converted to derecho + - Adds a 5x5_amazon test to aux_clm and the expected failures list + - Temporarilry converts a fates 5x5_amazon test to f10 test + - Adds namelist check and corresponding unit test to make sure fates hydro + and fates satellite phenology mode can not be used together + +The FATES externals tag is also updated which includes a number of bug fixes +and the addition of new history output. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm6_0 + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + NOTE: FATES hydro mode and FATES satellite phenology mode can not + be used in conjunction as of this API update + +Changes made to namelist defaults (e.g., changed parameter values): + FATES parameter file default updated to fates_params_api.35.0.0_12pft_c240326.nc + + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: + A 5x5_amazon smoke test, not using MPI-serial has been added to the test list + and list of expected failures to track issue #2423. + Out-of-date cheyenne tests on the expected failure list have been removed. + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + derecho - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- OK + izumi ------- OK + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + + derecho ----- OK + izumi ------- OK + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes, only for FATES configurations + + Summarize any changes to answers, i.e., + - what code configurations: FATES + - what platforms/compilers: ALL + - nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff + + The FATES externals update incorporates a number of bug fixes and the new allometry default + paramters result in a new scientific baseline. + + +Other details +------------- + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + FATES: sci.1.72.2_api.34.0.0 -> sci.1.73.0_api.35.0.0 + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + +#2436 -- FATES API35 parameter file update +NGEET#1093 -- Update default allometry parameters for tree PFTs +NGEET#1128 -- New allometric modes +NGEET#1149 -- Alternative vertical scaling of leaf maintenance respiration +NGEET#1161 -- Adding day length factor switch + +=============================================================== +=============================================================== Tag name: ctsm5.2.001 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) Date: Mon 22 Apr 2024 02:10:55 PM MDT diff --git a/doc/ChangeSum b/doc/ChangeSum index 2451783ec2..bc7b4379f1 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.2.002 glemieux 04/23/2024 FATES default allometry parameter file update ctsm5.2.001 erik 04/22/2024 Merge b4b-dev ctsm5.2.0 many 04/20/2024 New mksurfdata_esmf tool to create new surface datasets that are in place ctsm5.1.dev176 afoster 04/04/2024 Merge b4b-dev From f72e9cf2e4015578aca642dee8243cf84b02bf96 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 26 Apr 2024 11:13:36 -0600 Subject: [PATCH 10/11] A few changes based on my review as author is out --- cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++ cime_config/testdefs/testlist_clm.xml | 5 +++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 0d01428ba7..3365565a5e 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -219,6 +219,13 @@ + + + FAIL + FATES#1089 + + + FAIL diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index bf4d23a500..c2a90507ba 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2661,7 +2661,7 @@ - + @@ -2671,7 +2671,7 @@ - + @@ -3671,6 +3671,7 @@ + From e0e6f116c7bc051a41b93748be4666830a066c78 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 26 Apr 2024 11:14:14 -0600 Subject: [PATCH 11/11] Update date --- doc/ChangeLog | 2 +- doc/ChangeSum | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 91fe800b4a..e5c2466085 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.2.002 Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov) -Date: Tue Apr 23 10:30:00 MDT 2024 +Date: Fri 26 Apr 2024 11:13:46 AM MDT One-line Summary: FATES default allometry parameter file update Purpose and description of changes diff --git a/doc/ChangeSum b/doc/ChangeSum index bc7b4379f1..40033a7d6f 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.2.002 glemieux 04/23/2024 FATES default allometry parameter file update + ctsm5.2.002 glemieux 04/26/2024 FATES default allometry parameter file update ctsm5.2.001 erik 04/22/2024 Merge b4b-dev ctsm5.2.0 many 04/20/2024 New mksurfdata_esmf tool to create new surface datasets that are in place ctsm5.1.dev176 afoster 04/04/2024 Merge b4b-dev