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Paths wrong in CLM's build-namelist after create_clone #2

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billsacks opened this issue Dec 16, 2017 · 2 comments
Closed

Paths wrong in CLM's build-namelist after create_clone #2

billsacks opened this issue Dec 16, 2017 · 2 comments
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closed: wontfix We won't fix this issue, because it would be too difficult and/or isn't important enough to fix priority: low Background task that doesn't need to be done right away.
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future

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@billsacks
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Bill Sacks < sacks@ucar.edu > - 2011-10-20 10:49:00 -0600
Bugzilla Id: 1426
Bugzilla CC: erik@ucar.edu, jedwards@ucar.edu, mvertens@ucar.edu, rfisher@ucar.edu, santos@ucar.edu,

After running create_clone followed by configure -case, the paths used by CLM's build-namelist tool point to the cloned case; they should point to the new case directory.

For example, I cloned a case named test_diags_1014_clm4_0_37, to make a new case test_diags_1017. Here are the paths as documented in clm.buildnml.csh:

#! lnd_in:: Comment:
#! This namelist was created using the following command-line:
#! /glade/proj3/cseg/people/sacks/cesm_code/clm_landice_diagnostics2/models/lnd/clm/bld/build-namelist -config /glade/proj3/cseg/people/sacks/cesm_tests/test_diags_1014_clm4_0_37/Buildconf/clmconf/config_cache.xml -res 1.9x2.5
-mask gx1v6 -ignore_ic_year -use_case 2000_glacierMEC_control -infile cesm_namelist -clm_start_type default -rtm_res R05 -rtm_tstep 10800 -co2_ppmv 367.0 -datm_presaero clim_2000 -glc_grid gland20 -namelist &clm_inparm / -csmdata
$DIN_LOC_ROOT -inputdata /glade/proj3/cseg/people/sacks/cesm_tests/test_diags_1014_clm4_0_37/Buildconf/clm.input_data_list
#! For help on options use: /glade/proj3/cseg/people/sacks/cesm_code/clm_landice_diagnostics2/models/lnd/clm/bld/build-namelist -help

I don't understand the implications of this, but Erik says it's bad.
@billsacks billsacks added this to the future milestone Dec 16, 2017
@billsacks billsacks added the priority: low Background task that doesn't need to be done right away. label Dec 16, 2017
@billsacks
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Sean Santos < santos@ucar.edu > - 2015-07-29 15:32:49 -0600

I suspect that this has been fixed, but if not, it's a CLM rather than a CIME script issue, I think.

@billsacks billsacks mentioned this issue Dec 16, 2017
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billsacks added a commit that referenced this issue Dec 28, 2017
@billsacks
Merge pull request #2 from NCAR/modularize_infiltration
7e1bcd5 
Modularization of Infiltration - first stage

Separate out the first 3 steps of subroutine Infiltration into more modular
homes. The biggest piece of this is to introduce a new
InfiltrationExcessRunoffMod.F90; this will be where alternative
parameterizations of infiltration excess runoff can be put.
@billsacks billsacks mentioned this issue Jan 29, 2018
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I'm not sure if this is still an issue, but if it is, it doesn't seem to have been causing any trouble.

@billsacks billsacks added the closed: wontfix We won't fix this issue, because it would be too difficult and/or isn't important enough to fix label Feb 7, 2018
@slevis-lmwg slevis-lmwg mentioned this issue Feb 19, 2019
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This was referenced Jul 10, 2019
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mariuslam referenced this issue in NordicESMhub/ctsm Aug 26, 2019
Merge pull request #2 from NGEET/master
9577b55 
bring in recent updates in NGEET/fates master
mariuslam referenced this issue in NordicESMhub/ctsm Aug 26, 2019
@ekluzek
Merge pull request #2 from ekluzek/fates_s1.3.0_a1.0.0_nag
4dd7d23 
Shorten lines so can compile with nag compiler on hobart
mariuslam referenced this issue in NordicESMhub/ctsm Aug 26, 2019
@rgknox
Merge pull request #2 from ckoven/rgknox-tools-pftindexswapper
6683715 
added execution permission on pftindexswapper and added silent mode on modify_paramfile.
mariuslam referenced this issue in NordicESMhub/ctsm Aug 26, 2019
@rgknox
Merge pull request #2 from rgknox/jaholm_freezing_stress
1ad0701 
Jaholm freezing stress
mariuslam referenced this issue in NordicESMhub/ctsm Aug 26, 2019
@ckoven
Merge pull request #2 from rgknox/parprof
d55d039 
Syntax updates and merge resolution
mariuslam referenced this issue in NordicESMhub/ctsm Aug 26, 2019
@kovenock
Merge pull request #2 from rgknox/kovenock_slaprofile
6589417 
modularization - variable name updates
mariuslam referenced this issue in NordicESMhub/ctsm Aug 26, 2019
@xuchongang
Merge pull request #2 from rgknox/xuchongang/dense_forest_ready_to_merge
84a50e4 
convert from logical to initial spread options
mariuslam referenced this issue in NordicESMhub/ctsm Aug 26, 2019
@ckoven
Merge pull request #2 from rgknox/cohortfusion_crownareaconserv_offma…
3c01f12 
…ster

integrate minor updates to crown-conservation
mariuslam referenced this issue in NordicESMhub/ctsm Aug 26, 2019
@jkshuman
Merge pull request #2 from rgknox/fire_mortality
898ac97 
conflict resolutions and fixes to canopy layer diagnostics
mariuslam referenced this issue in NordicESMhub/ctsm Aug 26, 2019
@rgknox
Merge pull request #2 from rgknox/xuchongang/HYDRO_UPDATE_v2
ce61db1 
minor fixes to the hydro updates
billsacks referenced this issue in billsacks/ctsm Nov 1, 2019
@pengbinpeluo
Merge pull request #2 from billsacks/agsys
eb2fb5b 
Add agsys_phases_type and accumulated_thermal_time_phases
billsacks referenced this issue in mvertens/ctsm Dec 4, 2019
Merge pull request #2 from jhamman/master
7d57be3 
skeleton architecture of LILAC using ESMF
glemieux referenced this issue in glemieux/ctsm Mar 26, 2020
@JessicaNeedham
Merge pull request #2 from rgknox/JessicaNeedham-IO-sizeagemortality
300c2f2 
fix test length
billsacks referenced this issue in billsacks/ctsm Mar 27, 2020
@billsacks
Merge pull request #2 from lvankampenhout/gh-pages
2de63ad 
Some changes related to snow
billsacks referenced this issue in billsacks/ctsm Apr 15, 2020
@lmbirch89
Merge pull request #2 from lmbirch89/abz_update
ea984f5 
Abz update
billsacks referenced this issue in billsacks/ctsm May 18, 2020
@yanyanchengHydro
Merge pull request #2 from billsacks/bioenergy_ctsm1.0.dev080
05cefc8 
Update to ctsm1.0.dev089
glemieux pushed a commit that referenced this issue Jun 5, 2020
@rosiealice
Merge pull request #2 from glemieux/SP_next_api-deconflict-d525994
57421c9 
Deconflict CTSM PR 985 with fates_next_api (commit d525994)
glemieux pushed a commit that referenced this issue Jul 23, 2020
@slevis-lmwg
Merge pull request #2 from glemieux/lightning_v2_ctsm-externals
4bed6e2 
Updating externals_clm configuration to new tag
glemieux pushed a commit that referenced this issue Jul 29, 2020
@ckoven
Merge pull request #2 from glemieux/fates_landuse-deconflict
70282d8 
Pre-merge deconflict
glemieux added a commit that referenced this issue Aug 25, 2020
@glemieux
Merge pull request #2 from ckoven/timing
e467920 
added timing calls to all subroutines in clmfates_interfaceMod.F90
huitang-earth referenced this issue in huitang-earth/ctsm Sep 2, 2020
Merge pull request #2 from NordicESMhub/fix-ext
f85dc26 
use release 1.0.1 for cime
glemieux pushed a commit that referenced this issue Sep 25, 2020
@rgknox
Merge pull request #2 from glemieux/cnp-emptyif
d2a2ef9 
Cleanup typo and empty logic set
billsacks added a commit that referenced this issue Sep 29, 2020
@billsacks
Merge pull request #2 from Ivanderkelen/dynlakes_master_notools
6ae44c3 
Adjust ice to liquid density in ice mass calculation

Adjust ice to liquid density in ice mass calculation, as lake layer is not adjusted for change in density.
@olyson olyson mentioned this issue Aug 1, 2021
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MiCurry pushed a commit to MiCurry/CTSM that referenced this issue Sep 16, 2021
@dabail10
Merge pull request ESCOMP#2 from jedwards4b/shift_ice_donor
c58d1ef 
bug fix for bfb trcrn
ekluzek added a commit that referenced this issue Nov 19, 2021
@ekluzek
Merge pull request #2 from billsacks/fix_lilac
39062d8 
LILACSMOKE test: point to a still-existing Macros.make
adrifoster pushed a commit to adrifoster/CTSM that referenced this issue Jan 4, 2022
@negin513
Merge pull request ESCOMP#2 from adrifoster/subsetdata_update
782c117 
Subsetdata update
billsacks added a commit that referenced this issue Mar 16, 2022
@billsacks
Change LGRAIN tests to 1850
a9b4286 
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.)
@wwieder wwieder mentioned this issue Apr 4, 2022
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TaranuDev added a commit to TaranuDev/CTSM that referenced this issue Jun 21, 2022
@TaranuDev
Try ESCOMP#2 to fix NaNs: change dom_withd values in water_inst objec…
15cf6e0 
…t to 0.000001 for all gridcells (check if ERROR will still apear for this variable or will shift to next one)
estherbe3 pushed a commit to estherbe3/CTSM that referenced this issue Sep 23, 2022
@mvdebolskiy
Merge pull request ESCOMP#2 from kjetilaas/Exice_wTiles_HackAug2022
254a9cf 
Exice w tiles hack aug2022
samsrabin referenced this issue in samsrabin/CTSM Apr 19, 2024
@jedwards4b
Merge pull request #2 from ESCOMP/add_era5
c0eec95 
add era5 stream source
samsrabin referenced this issue in samsrabin/CTSM Apr 19, 2024
@binli2337
Update CDEPS (#2)
4fd370e 
Update CDEPS to the 20201124 version of the master branch at ESCOMP/CDEPS.
TeaganKing added a commit to wwieder/ctsm that referenced this issue May 1, 2024
@TeaganKing
include plumber in cime_config ESCOMP#2
40701d2
AGonzalezNicolas pushed a commit to HPSCTerrSys/clm5_0 that referenced this issue Jun 27, 2024
@billsacks
Merge pull request ESCOMP#2 from NCAR/modularize_infiltration
fc1b3bb 
Modularization of Infiltration - first stage

Separate out the first 3 steps of subroutine Infiltration into more modular
homes. The biggest piece of this is to introduce a new
InfiltrationExcessRunoffMod.F90; this will be where alternative
parameterizations of infiltration excess runoff can be put.
AGonzalezNicolas pushed a commit to HPSCTerrSys/clm5_0 that referenced this issue Jun 27, 2024
@kvrigor
Added SetBuildOptions.cmake (PR ESCOMP#2)
b61d710 
This module sets compile flags and definitions required for all targets.

Notable changes: 

* Added option to specify build type as 'DEBUG' or 'RELEASE'
* Passed C and Fortran flags to GPTL and MCT Makefiles
* Set default compilers for Ubuntu and JUWELS builds scripts
AGonzalezNicolas added a commit to HPSCTerrSys/clm5_0 that referenced this issue Jun 27, 2024
@AGonzalezNicolas
Merge commit Added SetBuildOptions.cmake (PR ESCOMP#2) 'b61d7108a2f36…
c616438 
…5eb050a094d971c0f0a60a1a6e7' into eclm
AGonzalezNicolas pushed a commit to HPSCTerrSys/clm5_0 that referenced this issue Jul 5, 2024
@billsacks
Merge pull request ESCOMP#2 from NCAR/modularize_infiltration
647a72b 
Modularization of Infiltration - first stage

Separate out the first 3 steps of subroutine Infiltration into more modular
homes. The biggest piece of this is to introduce a new
InfiltrationExcessRunoffMod.F90; this will be where alternative
parameterizations of infiltration excess runoff can be put.
adrifoster pushed a commit to adrifoster/CTSM that referenced this issue Jul 18, 2024
@samsrabin
Merge pull request ESCOMP#2 from glemieux/fates-landuse-v2-harvestmod…
07e811e 
…eseparation

Remove fates dependency on `do_harvest`
TeaganKing added a commit to wwieder/ctsm that referenced this issue Aug 16, 2024
@TeaganKing
include plumber in cime_config ESCOMP#2
d0c6d4c
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