Some clm test namelists have empty field lists for 1-d history output #3

billsacks · 2017-12-16T20:06:09Z

Bill Sacks < [email protected] > - 2012-01-21 19:38:36 -0700
Bugzilla Id: 1454
Bugzilla Depends: 1455,
Bugzilla CC: [email protected],

Some of the namelists in test/system/nl_files have hist_dov2xy for a history file, but do not add any fields to this file, so there aren't actually any 1-d comparisons done.

For example, nl_crop and nl_cn_conly. These namelists could be changed according to the following diffs; note that these field lists are basically the same as what's currently used in nl_urb, which correctly includes 1-d output:

Index: nl_crop
===================================================================
--- nl_crop     (revision 31723)
+++ nl_crop     (working copy)
@@ -9,6 +9,24 @@
  hist_fincl1    = 'GDD0', 'GDD8', 'GDD10', 
                   'GDD020', 'GDD820', 'GDD1020',
                   'GDDPLANT', 'GDDTSOI', 'A5TMIN', 'A10TMIN'
+ hist_fincl2    = 'TG','TBOT','FIRE','FIRA','FLDS','FSDS',
+                  'FSR','FSA','FGEV','FSH','FGR','TSOI',
+                  'ERRSOI','BUILDHEAT','SABV','SABG',
+                  'FSDSVD','FSDSND','FSDSVI','FSDSNI',
+                  'FSRVD','FSRND','FSRVI','FSRNI',
+                  'TSA','FCTR','FCEV','QBOT','RH2M','H2OSOI',
+                  'H2OSNO','SOILLIQ','SOILICE', 
+                  'TSA_U', 'TSA_R',
+                  'TREFMNAV_U', 'TREFMNAV_R',
+                  'TREFMXAV_U', 'TREFMXAV_R',
+                  'TG_U', 'TG_R',
+                  'RH2M_U', 'RH2M_R',
+                  'QRUNOFF_U', 'QRUNOFF_R',
+                  'SoilAlpha_U',
+                  'Qanth', 'SWup', 'LWup', 'URBAN_AC', 'URBAN_HEAT',
+                  'GDD0', 'GDD8', 'GDD10', 
+                  'GDD020', 'GDD820', 'GDD1020',
+                  'GDDPLANT', 'GDDTSOI', 'A5TMIN', 'A10TMIN'
  /
  ! Adding the following variable causes the model to abort in debug mode
  ! with multiplying by a NaN, bugzilla bug 1325. EBK Apr/28/2011

Index: nl_cn_conly
===================================================================
--- nl_cn_conly (revision 31723)
+++ nl_cn_conly (working copy)
@@ -8,4 +8,19 @@
  hist_dov2xy    = .true.,.false.
  hist_ndens     = 1,1
  hist_fincl1    = 'TRAFFICFLUX', 'SNOWLIQ:A','SNOWICE:A'
+ hist_fincl2    = 'TG','TBOT','FIRE','FIRA','FLDS','FSDS',
+                  'FSR','FSA','FGEV','FSH','FGR','TSOI',
+                  'ERRSOI','BUILDHEAT','SABV','SABG',
+                  'FSDSVD','FSDSND','FSDSVI','FSDSNI',
+                  'FSRVD','FSRND','FSRVI','FSRNI',
+                  'TSA','FCTR','FCEV','QBOT','RH2M','H2OSOI',
+                  'H2OSNO','SOILLIQ','SOILICE', 
+                  'TSA_U', 'TSA_R',
+                  'TREFMNAV_U', 'TREFMNAV_R',
+                  'TREFMXAV_U', 'TREFMXAV_R',
+                  'TG_U', 'TG_R',
+                  'RH2M_U', 'RH2M_R',
+                  'QRUNOFF_U', 'QRUNOFF_R',
+                  'SoilAlpha_U',
+                  'Qanth', 'SWup', 'LWup', 'URBAN_AC', 'URBAN_HEAT'
  /

billsacks · 2017-12-16T20:06:15Z

Bill Sacks < [email protected] > - 2012-01-21 19:54:30 -0700

I have not put these changes in place, because when I tried to do so, I got the unexpected error noted in bug 1455.

I think that, for these changes to be put in place, either bug 1455 will have to be fixed, or else the history frequency of these auxiliary files will have to be changed (e.g., to daily???).

Rename things related to saturated surface runoff Renames the module, derived type, variables and methods related to saturated surface runoff. The rename qflx_sat_surf -> qflx_sat_excess_surf was suggested at a ctsm meeting. The other renames are to be consistent with that and consistent with InfiltrationExcessRunoffMod. Also, remove a long yellowstone test, change PE count for cheyenne: Removing this long test that sometimes exceeds the 2-hour limit I give it (other times it takes just slightly less than 2 hours): ERS_Ly5_P60x1.f10_f10_musgs.IHistClm50BgcCrop.yellowstone_intel.clm-cropMonthOutput. We still have an identical test on cheyenne. Also, increase the PE count on cheyenne to use two full nodes, rather than a partial node.

billsacks · 2018-11-07T17:19:17Z

Since we have moved to using the CESM test system, this issue is no longer relevant as written. And it seems like it has been fixed, at least for the two testmods mentioned above (crop and cn_conly): they include default, which does add some vector output.

logging parameters and refactors

To be consistent with the master branch

fates_s1.3.0_a2.0.0

added link to developer repo policy and fixed a couple typos

Bchristo planthydro longlived

merge master

make slamax a PFT profile

…rged restarts

Updated termination diagnostic arrays to fill over canopy layer

forward loop for same height sorting

fix CWD issue, indexing and parameter file

fixed units of prescribed npp terms in prescribed physiology mode

Rename files

…-clean PR882 manage externals update and clean

update branch

Adding fix for pft indexing bounds

Dynlakes: fix some subtle issues ### Description of changes Fix a variety of subtle issues with dynamic lakes - particularly the accounting of total water and energy. ### Specific notes This branch contains the following commits: - a9fa875: This is needed to avoid counting lake water in the begwb and endwb terms, which is needed because these are used to calculate gridcell total water store (TWS), which in turn influences the methane code. Because the methane code was tuned around old values of TWS, changing TWS would lead to unintentional – and potentially large – changes in methane terms. Eventually we'd like to remove methane's dependence on TWS, but for now this workaround is needed to avoid changing behavior too much. See #659 (comment) for more details. - 52105c4: This minor fix is needed for the sake of water tracers / water isotopes. It shouldn't have any impact outside of that (because the tracer_ratio of bulk water is 1) - de3e12c and acf0984: This one is especially subtle; it is needed for backwards compatibility with old restart files. The main changes are in de3e12c; acf0984 is just a minor tweak on top of that. The problem is that, on existing initial conditions files, there can be already-existing DYNBAL_BASELINE variables (for LIQUID, ICE & HEAT). But these pre-existing variables will have baseline values of 0 for lake. Before this commit, when you started up from an old initial conditions file, the code would use these 0 values for lake baselines (because baselines are only reset if the user explicitly asks them to be reset with a namelist flag). This commit adds some code to detect if the initial conditions file is old, and if so, recomputes dynbal baselines for lake using the new definition. Note that some even older initial conditions files didn't have the DYNBAL_BASELINE variables at all; those would have been okay before this change: the problem is with initial conditions files that are somewhat but not very old - so have DYNBAL_BASELINE variables on them that use the old definition (where lake baseline values were 0). - 8088c3c: Minor fix for a pre-existing issue - a31875d: I'm not sure if this is actually needed, but I thought it would be good to group together the lake water content and the roughly equal-but-opposite baselines, so that these can cancel to near zero before adding the smaller terms. In principle, this should help maintain precision in these smaller terms. I thought this might help resolve some of the larger-than-expected answer changes I was seeing in testing, but I don't think it actually does... but I still thought this would be good to keep in place. **I have double and triple checked these changes, but it would be good to have an extra set of eyes on them to make sure I did this reordering correctly. In particular, I think there were some subtleties about when a term should accumulate on top of an existing value vs. setting the initial value of a variable.**

Snow occlusion updates fates

Run fsurdat_modifier via an appropriate python version on cheyenne

Updating flags wording to avoid confusions

Ideally we would do year-2000 tests to have more crop cover and thus potentially be more useful tests. However, there are problems running a year-2000 ciso test with crop. These problems exist even with an SMS test on master: I tried tests like SMS_Ly1_P72x1.f10_f10_mg37.I2000Clm45BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput, but both debug & non-debug, intel & gnu versions. Debug tests fail like this (from SMS_D_Ly1_P72x1.f10_f10_mg37.I2000Clm45BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput): 30:Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation. 30: 30:Backtrace for this error: 13: 13:Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation. 13: 13:Backtrace for this error: 13:#0 0x2b9d1acc4aff in ??? 30:#0 0x2b9d1acc4aff in ??? 13:#1 0xf63fff in cisofluxcalc 13: at /glade/work/sacks/ctsm_code/ctsm/src/biogeochem/CNCIsoFluxMod.F90:1555 30:#1 0xf63fff in cisofluxcalc 30: at /glade/work/sacks/ctsm_code/ctsm/src/biogeochem/CNCIsoFluxMod.F90:1555 30:#2 0xf6b489 in __cncisofluxmod_MOD_cisoflux1 30: at /glade/work/sacks/ctsm_code/ctsm/src/biogeochem/CNCIsoFluxMod.F90:153 13:#2 0xf6b489 in __cncisofluxmod_MOD_cisoflux1 13: at /glade/work/sacks/ctsm_code/ctsm/src/biogeochem/CNCIsoFluxMod.F90:153 13:#3 0xe45657 in __cndrivermod_MOD_cndrivernoleaching 13: at /glade/work/sacks/ctsm_code/ctsm/src/biogeochem/CNDriverMod.F90:559 30:#3 0xe45657 in __cndrivermod_MOD_cndrivernoleaching 30: at /glade/work/sacks/ctsm_code/ctsm/src/biogeochem/CNDriverMod.F90:559 An intel test dies in the same place. Non-debug versions die like this (both for gnu and intel): 30: set_curr_delta ERROR: found unexpected non-zero delta mid-year 30: Dribbler name: hrv_xsmrpool_to_atm_c_13 30: i, delta = 2 NaN 30: Start of time step date (yr, mon, day, tod) = 2000 1 15 57600 30: This indicates that some non-zero flux was generated at a time step 30: other than the first time step of the year, which this dribbler was told not to expect. 30: If this non-zero mid-year delta is expected, then you can suppress this error 30: by setting allows_non_annual_delta to .true. when constructing this dribbler. 30:iam = 30: local gridcell index = 2 30:iam = 30: global gridcell index = 103 30:iam = 30: gridcell longitude = 285.0000000 30:iam = 30: gridcell latitude = -10.0000000 30: ENDRUN: 30: ERROR: set_curr_delta: found unexpected non-zero delta mid-year: ERROR in /glade/work/sacks/ctsm_code/ctsm/src/utils/AnnualFluxDr ibbler.F90 at line 276 So there is some issue with year-2000 ciso tests with crop. This issue exists on master, for clm45 and clm50 tests. (e.g., for clm50, I tried SMS_D_Ly1_P72x1.f10_f10_mg37.I2000Clm50BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput.)

Excess ice docs review changes

added missing compset from featureCESM2.1.0-OsloDevelopment

Update the PPE with externals from the release-cesm2.2 branch so that it will work on Derecho

updating input data file paths

Sync HAFS for with recent work in NOAA/EMC

Rename things related to saturated surface runoff Renames the module, derived type, variables and methods related to saturated surface runoff. The rename qflx_sat_surf -> qflx_sat_excess_surf was suggested at a ctsm meeting. The other renames are to be consistent with that and consistent with InfiltrationExcessRunoffMod. Also, remove a long yellowstone test, change PE count for cheyenne: Removing this long test that sometimes exceeds the 2-hour limit I give it (other times it takes just slightly less than 2 hours): ERS_Ly5_P60x1.f10_f10_musgs.IHistClm50BgcCrop.yellowstone_intel.clm-cropMonthOutput. We still have an identical test on cheyenne. Also, increase the PE count on cheyenne to use two full nodes, rather than a partial node.

* Imported CLM5 namelist generator scripts * Made namelist generator installable with pip * Used PEP517 approach to packaging, with setuptools as build backend. More info: https://setuptools.readthedocs.io/en/latest/userguide/quickstart.html * Renamed 'build-clm5nl' to 'clm5nl-gen'. 'clm5nl-gen' sounds more unique which makes it easier to be "tab-completed" by the shell.

…d0e7e3b77f2cc3401f3f097e444ef28ff827f549' into eclm

Rename things related to saturated surface runoff Renames the module, derived type, variables and methods related to saturated surface runoff. The rename qflx_sat_surf -> qflx_sat_excess_surf was suggested at a ctsm meeting. The other renames are to be consistent with that and consistent with InfiltrationExcessRunoffMod. Also, remove a long yellowstone test, change PE count for cheyenne: Removing this long test that sometimes exceeds the 2-hour limit I give it (other times it takes just slightly less than 2 hours): ERS_Ly5_P60x1.f10_f10_musgs.IHistClm50BgcCrop.yellowstone_intel.clm-cropMonthOutput. We still have an identical test on cheyenne. Also, increase the PE count on cheyenne to use two full nodes, rather than a partial node.

Update `fates_harvest_mode` to use characters for namelist option select

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Run fsurdat_modifier via an appropriate python version on cheyenne

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Update `fates_harvest_mode` to use characters for namelist option select

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Some clm test namelists have empty field lists for 1-d history output #3

Some clm test namelists have empty field lists for 1-d history output #3

billsacks commented Dec 16, 2017 •

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billsacks commented Nov 7, 2018

Some clm test namelists have empty field lists for 1-d history output #3

Some clm test namelists have empty field lists for 1-d history output #3

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