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Merge pull request #695 from ekluzek/relfatesndepmiscupdate
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Add more ndep files, fix some bugs, point to new SSP CO2 files
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ekluzek authored May 3, 2019
2 parents aa0d0ff + 5a72bb9 commit 5267673
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Showing 47 changed files with 664 additions and 243 deletions.
2 changes: 1 addition & 1 deletion Externals.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ required = True
local_path = cime
protocol = git
repo_url = https://github.com/ESMCI/cime
tag = cime5.6.12
tag = cime5.6.14
required = True

[externals_description]
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4 changes: 2 additions & 2 deletions Externals_CLM.cfg
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
[fates]
local_path = src/fates
protocol = git
repo_url = https://github.com/NCAR/fates-release
tag = fates_s1.8.1_a3.0.0
repo_url = https://github.com/ncar/fates-release
tag = fates_s1.21.0_a7.0.0_br_rev2
required = True

[PTCLM]
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9 changes: 5 additions & 4 deletions bld/CLMBuildNamelist.pm
Original file line number Diff line number Diff line change
Expand Up @@ -775,7 +775,7 @@ sub setup_cmdl_fates_mode {
} else {
# dis-allow fates specific namelist items with non-fates runs
my @list = ( "use_fates_spitfire", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
"use_fates_inventory_init", "fates_inventory_ctrl_filename","use_fates_logging" );
"use_fates_inventory_init", "fates_inventory_ctrl_filename","use_fates_logging","fates_parteh_mode" );
foreach my $var ( @list ) {
if ( defined($nl->get_value($var)) ) {
$log->fatal_error("$var is being set, but can ONLY be set when -bgc fates option is used.\n");
Expand Down Expand Up @@ -3824,18 +3824,19 @@ sub setup_logic_fates {
if ($physv->as_long() >= $physv->as_long("clm4_5") && &value_is_true( $nl_flags->{'use_fates'}) ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
my @list = ( "use_fates_spitfire", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
"use_fates_inventory_init", "use_fates_logging" );
"use_fates_inventory_init", "use_fates_logging","fates_parteh_mode" );
foreach my $var ( @list ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'} );
}
my $var = "use_fates_inventory_init";
if ( defined($nl->get_value($var)) ) {
if ( &value_is_true($nl->get_value($var)) ) {
$var = "fates_inventory_ctrl_filename";
my $fname = substr $nl->get_value($var), 1, -1; # ignore first and last positions of string because those are quote characters
if ( ! defined($nl->get_value($var)) ) {
$log->fatal_error("$var is required when use_fates_inventory_init is set" );
} elsif ( ! -f "$nl->get_value($var)" ) {
$log->fatal_error("$var does NOT point to a valid filename" );
} elsif ( ! -f "$fname" ) {
$log->fatal_error("$fname does NOT point to a valid filename" );
}
}
}
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1 change: 1 addition & 0 deletions bld/configure
Original file line number Diff line number Diff line change
Expand Up @@ -670,6 +670,7 @@ sub write_filepath_cesmbld
"fates/biogeophys",
"fates/biogeochem",
"fates/fire",
"fates/parteh",
"utils",
"cpl" );

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96 changes: 34 additions & 62 deletions bld/namelist_files/namelist_defaults_clm4_5.xml

Large diffs are not rendered by default.

36 changes: 28 additions & 8 deletions bld/namelist_files/namelist_defaults_clm4_5_tools.xml
Original file line number Diff line number Diff line change
Expand Up @@ -78,9 +78,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
>lnd/clm2/mappingdata/grids/SCRIPgrid_10x10min_IGBPmergeICESatGIS_c110818.nc</scripgriddata>
<scripgriddata hgrid="3x3min" lmask="MODIS"
>lnd/clm2/mappingdata/grids/SCRIPgrid_3minx3min_MODIS_c110915.nc</scripgriddata>
<scripgriddata hgrid="3x3min" lmask="MODISv2"
>lnd/clm2/mappingdata/grids/SCRIPgrid_3minx3min_MODISv2_c190503.nc</scripgriddata>
<scripgriddata hgrid="3x3min" lmask="MODIS-wCsp"
>lnd/clm2/mappingdata/grids/SCRIPgrid_3minx3min_MODISwcspsea_c151020.nc</scripgriddata>
<scripgriddata_lrgfile_needed hgrid="3x3min" lmask="MODIS" >64bit_offset</scripgriddata_lrgfile_needed>
<scripgriddata_lrgfile_needed hgrid="3x3min" lmask="MODISv2" >64bit_offset</scripgriddata_lrgfile_needed>
<scripgriddata_lrgfile_needed hgrid="3x3min" lmask="MODIS-wCsp">64bit_offset</scripgriddata_lrgfile_needed>
<scripgriddata hgrid="3x3min" lmask="USGS"
>lnd/clm2/mappingdata/grids/SCRIPgrid_3x3_USGS_c120912.nc</scripgriddata>
Expand Down Expand Up @@ -133,13 +136,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<lmask type="wet" >AVHRR</lmask>
<lmask type="voc" >AVHRR</lmask>
<lmask type="lai" >MODIS</lmask>
<lmask type="lai" hirespft="on">MODIS</lmask>
<lmask type="lai" hirespft="on">MODISv2</lmask>
<lmask type="veg" >MODIS</lmask>
<lmask type="veg" hirespft="on">MODIS</lmask>
<lmask type="veg" hirespft="on">MODISv2</lmask>
<lmask type="hrv" >MODIS</lmask>
<lmask type="urb" >LandScan2004</lmask>
<lmask type="col" >MODIS</lmask>
<lmask type="col" hirespft="on">MODIS</lmask>
<lmask type="col" hirespft="on">MODISv2</lmask>
<lmask type="org" >ISRIC-WISE</lmask>
<lmask type="glc" >GLOBE-Gardner</lmask>
<lmask type="glc" mergeGIS="on">GLOBE-Gardner-mergeGIS</lmask>
Expand Down Expand Up @@ -211,7 +214,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).

<!-- mksrf_lai -->

<mksrf_flai hgrid="3x3min" lmask="MODIS"
<mksrf_flai hgrid="3x3min" lmask="MODISv2"
>lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190119/mksrf_lai_histclm52deg005_earthstatmirca_2005.c190119.nc
</mksrf_flai>

Expand All @@ -226,7 +229,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<mksrf_fsoitex hgrid="5x5min" lmask="IGBP-GSDP"
>lnd/clm2/rawdata/mksrf_soitex.10level.c010119.nc</mksrf_fsoitex>

<mksrf_fsoicol hgrid="3x3min" lmask="MODIS"
<mksrf_fsoicol hgrid="3x3min" lmask="MODISv2"
>lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190119/mksrf_soilcolor_histclm52deg005_earthstatmirca_2005.c190116.nc
</mksrf_fsoicol>

Expand Down Expand Up @@ -305,8 +308,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<!-- mksrf_fvegtyp -->

<!-- High resolution -->
<mksrf_fvegtyp hgrid="3x3min" ssp_rcp="hist" sim_year="1850" crop="on"
>lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190119/mksrf_landuse_clm52deg005_histLUH2_1850.c190119.nc
</mksrf_fvegtyp>
<mksrf_fvegtyp hgrid="3x3min" ssp_rcp="hist" sim_year="2005" crop="on"
>lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190119/mksrf_lai_histclm52deg005_earthstatmirca_2005.c190119.nc
>lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190119/mksrf_landuse_clm52deg005_histLUH2_2005.c190119.nc
</mksrf_fvegtyp>


Expand Down Expand Up @@ -7392,7 +7398,21 @@ attributes from the config_cache.xml file (with keys converted to upper-case).


<!-- Historical Greenhouse gas concentrations from CAM -->
<mkghg_bndtvghg hgrid="lat-bands" >atm/waccm/lb/LBC_17500116-20150116_CMIP6_0p5degLat_c180905.nc</mkghg_bndtvghg>
<mkghg_bndtvghg hgrid="global" >/gpfs/fs1/p/acom/acom-climate/cesm2/inputdata/atm/waccm/lb/LBC_1750-2015_CMIP6_GlobAnnAvg_c180905.nc</mkghg_bndtvghg>
<mkghg_bndtvghg hgrid="lat-bands" >atm/waccm/lb/LBC_17500116-20150116_CMIP6_0p5degLat_c180905.nc</mkghg_bndtvghg>
<mkghg_bndtvghg hgrid="global" >atm/waccm/lb/LBC_1750-2015_CMIP6_GlobAnnAvg_c180926.nc</mkghg_bndtvghg>

<mkghg_bndtvghg hgrid="lat-bands" ssp_rcp="SSP1-2.6" >atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP126_0p5degLat_c180905.nc</mkghg_bndtvghg>
<mkghg_bndtvghg hgrid="lat-bands" ssp_rcp="SSP2-4.5" >atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP245_0p5degLat_c180905.nc</mkghg_bndtvghg>
<mkghg_bndtvghg hgrid="lat-bands" ssp_rcp="SSP3-7.0" >atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP370_0p5degLat_c180905.nc</mkghg_bndtvghg>
<mkghg_bndtvghg hgrid="lat-bands" ssp_rcp="SSP4-6.0" >atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP460_0p5degLat_c180905.nc</mkghg_bndtvghg>
<mkghg_bndtvghg hgrid="lat-bands" ssp_rcp="SSP5-3.4" >atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP534os_0p5degLat_c180905.nc</mkghg_bndtvghg>
<mkghg_bndtvghg hgrid="lat-bands" ssp_rcp="SSP5-8.5" >atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP585_0p5degLat_c180905.nc</mkghg_bndtvghg>

<mkghg_bndtvghg hgrid="global" ssp_rcp="SSP1-2.6" >atm/waccm/lb/LBC_2014-2500_CMIP6_SSP126_0p5degLat_GlobAnnAvg_c190301.nc</mkghg_bndtvghg>
<mkghg_bndtvghg hgrid="global" ssp_rcp="SSP2-4.5" >atm/waccm/lb/LBC_2014-2500_CMIP6_SSP245_0p5degLat_GlobAnnAvg_c190301.nc</mkghg_bndtvghg>
<mkghg_bndtvghg hgrid="global" ssp_rcp="SSP3-7.0" >atm/waccm/lb/LBC_2014-2500_CMIP6_SSP370_0p5degLat_GlobAnnAvg_c190301.nc</mkghg_bndtvghg>
<mkghg_bndtvghg hgrid="global" ssp_rcp="SSP4-6.0" >atm/waccm/lb/LBC_2014-2500_CMIP6_SSP460_0p5degLat_GlobAnnAvg_c190301.nc</mkghg_bndtvghg>
<mkghg_bndtvghg hgrid="global" ssp_rcp="SSP5-3.4" >atm/waccm/lb/LBC_2014-2500_CMIP6_SSP534os_0p5degLat_GlobAnnAvg_c190301.nc</mkghg_bndtvghg>
<mkghg_bndtvghg hgrid="global" ssp_rcp="SSP5-8.5" >atm/waccm/lb/LBC_2014-2500_CMIP6_SSP585_0p5degLat_GlobAnnAvg_c190301.nc</mkghg_bndtvghg>

</namelist_defaults>
2 changes: 1 addition & 1 deletion bld/namelist_files/namelist_definition_clm4_0.xml
Original file line number Diff line number Diff line change
Expand Up @@ -685,7 +685,7 @@ Note: 0.1x0.1, 0.5x0.5, 5x5min, 10x10min, 3x3min and 0.33x0.33 are only used for

<entry id="mask" type="char*10" category="default_settings"
group="default_settings"
valid_values="USGS,gx3v7,gx1v6,gz1v7,navy,test,tx0.1v2,tx1v1,T62,cruncep">
valid_values="USGS,gx3v7,gx1v6,gx1v7,navy,test,tx0.1v2,tx1v1,T62,cruncep">
Land mask description
</entry>

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7 changes: 6 additions & 1 deletion bld/namelist_files/namelist_definition_clm4_5.xml
Original file line number Diff line number Diff line change
Expand Up @@ -613,6 +613,11 @@ Toggle to turn on the FATES model
(use_fates= '.true.' is EXPERIMENTAL NOT SUPPORTED!)
</entry>

<entry id="fates_parteh_mode" type="integer" category="physics"
group="clm_inparm" valid_values="1">
Switch deciding which nutrient model to use in FATES.
</entry>

<entry id="use_fates_spitfire" type="logical" category="physics"
group="clm_inparm" valid_values="" value=".false.">
Toggle to turn on spitfire module for modeling fire (only relevant if FATES is being used).
Expand Down Expand Up @@ -1724,7 +1729,7 @@ Mapping file to go from one resolution/land-mask to another resolution/land-mask

<entry id="lmask" type="char*10" category="mksurfdata"
group="default_settings"
valid_values="nomask,navy,AVHRR,MODIS,USGS,IGBPmergeICESatGIS,IGBP-GSDP,ISRIC-WISE,LandScan2004,GLOBE-Gardner,GLOBE-Gardner-mergeGIS,GRDC,HYDRO1K-merge-nomask,ORNL-Soil">
valid_values="nomask,navy,AVHRR,MODIS,MODISv2,USGS,IGBPmergeICESatGIS,IGBP-GSDP,ISRIC-WISE,LandScan2004,GLOBE-Gardner,GLOBE-Gardner-mergeGIS,GRDC,HYDRO1K-merge-nomask,ORNL-Soil">
Land mask description for mksurfdata input files
</entry>

Expand Down
6 changes: 3 additions & 3 deletions bld/unit_testers/build-namelist_test.pl
Original file line number Diff line number Diff line change
Expand Up @@ -123,9 +123,9 @@ sub make_env_run {
#
# Figure out number of tests that will run
#
my $ntests = 860;
my $ntests = 872;
if ( defined($opts{'compare'}) ) {
$ntests += 531;
$ntests += 540;
}
plan( tests=>$ntests );

Expand Down Expand Up @@ -1292,7 +1292,7 @@ sub make_env_run {
system( "../configure -s $mode" );
my @tran_res = ( "0.9x1.25", "1.9x2.5", "10x15" );
foreach my $usecase ( "1850_control", "1850-2100_SSP5-8.5_transient", "1850-2100_SSP1-2.6_transient", "1850-2100_SSP3-7.0_transient",
"1850-2100_SSP5-3.4_transient", "1850-2100_SSP2-4.5_transient", "1850-2100_SSP1-1.9_transient",
"1850-2100_SSP4-3.4_transient", "1850-2100_SSP5-3.4_transient", "1850-2100_SSP2-4.5_transient", "1850-2100_SSP1-1.9_transient",
"1850-2100_SSP4-6.0_transient" ) {
foreach my $res ( @tran_res ) {
$options = "-res $res -bgc bgc -crop -use_case $usecase -envxml_dir . ";
Expand Down
37 changes: 37 additions & 0 deletions cime_config/SystemTests/lciso.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
"""
Implementation of the CIME LCISO (Land Carbon Isotope) test.
This is a CTSM specific test:
Verifies turning on carbon isotopes doesn't change answers
(1) do a run with Carbon isotopes off (suffix base)
(2) add C13 and C14 carbon isotopes on with their time-series (suffix cisoallon)
"""

from CIME.SystemTests.system_tests_compare_two import SystemTestsCompareTwo
from CIME.XML.standard_module_setup import *
from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files

logger = logging.getLogger(__name__)

class LCISO(SystemTestsCompareTwo):

def __init__(self, case):
SystemTestsCompareTwo.__init__(self, case,
separate_builds = False,
run_two_suffix = 'cisoallon',
run_one_description = 'carbon isotopes off',
run_two_description = 'c13 and c14 isotopes on as well as C isotope time series')

def _case_one_setup(self):
append_to_user_nl_files(caseroot = self._get_caseroot(),
component = "clm",
contents = "use_c13=F, use_c14=F")

def _case_two_setup(self):
append_to_user_nl_files(caseroot = self._get_caseroot(),
component = "clm",
contents = "use_c13=.true.,use_c14=.true.,use_c13_timeseries=.true.,use_c14_bombspike=.true.," + \
"hist_fexcl1='C13_AR','C13_GPP','C13_HR','C13_NBP','C13_SOILC_vr','C13_TOTECOSYSC'," + \
"'C13_TOTLITC','C13_TOTSOMC','C13_TOTVEGC','C14_AR','C14_GPP','C14_HR','C14_NBP'," + \
"'C14_SOILC_vr','C14_TOTECOSYSC','C14_TOTLITC','C14_TOTSOMC','C14_TOTVEGC'")


1 change: 1 addition & 0 deletions cime_config/buildlib
Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,7 @@ def _main_func():
os.path.join(lnd_root,"src","fates","biogeophys"),
os.path.join(lnd_root,"src","fates","biogeochem"),
os.path.join(lnd_root,"src","fates","fire"),
os.path.join(lnd_root,"src","fates","parteh"),
os.path.join(lnd_root,"src","utils"),
os.path.join(lnd_root,"src","cpl")]
with open(filepath_file, "w") as filepath:
Expand Down
5 changes: 3 additions & 2 deletions cime_config/config_component.xml
Original file line number Diff line number Diff line change
Expand Up @@ -242,8 +242,9 @@
<valid_values></valid_values>
<default_value></default_value>
<values match="last">
<value compset="_CLM50%[^_]*CMIP6DECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
<value compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
<value compset="_CLM50%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
<value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
<value compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
</values>
<group>run_component_clm</group>
<file>env_case.xml</file>
Expand Down
10 changes: 10 additions & 0 deletions cime_config/config_tests.xml
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,16 @@ SSP smoke CLM spinup test (only valid for CLM compsets with CLM45)
<HIST_OPTION>never</HIST_OPTION>
</test>

<test NAME="LCISO">
<DESC>CTSM Land model test to ensure Carbon isotopes on or off does NOT change answers</DESC>
<INFO_DBUG>1</INFO_DBUG>
<DOUT_S>FALSE</DOUT_S>
<CONTINUE_RUN>FALSE</CONTINUE_RUN>
<REST_OPTION>never</REST_OPTION>
<HIST_OPTION>$STOP_OPTION</HIST_OPTION>
<HIST_N>$STOP_N</HIST_N>
</test>

<test NAME="SSP">
<DESC>smoke CLM spinup test (only valid for CLM45 or CLM50 compsets)</DESC>
<INFO_DBUG>1</INFO_DBUG>
Expand Down
13 changes: 4 additions & 9 deletions cime_config/testdefs/ExpectedTestFails.xml
Original file line number Diff line number Diff line change
Expand Up @@ -8,16 +8,11 @@
<entry issue="#384" >FAIL ERP_D_Ld5.f09_g17.I2000Clm50Vic.cheyenne_intel.clm-vrtlay RUN</entry>
<entry issue="#442" >FAIL SMS.f10_f10_musgs.I2000Clm50BgcCrop.hobart_pgi.clm-crop RUN</entry>
<entry issue="#442" >FAIL SMS_D.f10_f10_musgs.I2000Clm50BgcCrop.hobart_pgi.clm-crop RUN</entry>
<entry issue="#675" >FAIL LCISO_Lm13.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-ciso_monthly COMPARE_base_cisoallon</entry>
</category>
<category name="fates">
<entry issue="NGEET/fates#315">FAIL ERS_Ld60.f45_f45_mg37.I2000Clm45Fates.hobart_nag.clm-Fates COMPARE_base_rest</entry>
<entry issue="NGEET/fates#315">FAIL ERP_Ld9.f45_f45_mg37.I2000Clm45Fates.hobart_nag.clm-FatesAllVars COMPARE_base_rest</entry>
<entry issue="NGEET/fates#315">FAIL ERS_Ld60.f45_f45_mg37.I2000Clm45Fates.cheyenne_intel.clm-FatesLogging COMPARE_base_rest</entry>
<entry issue="NGEET/fates#315">FAIL ERS_Ld60.f45_f45_mg37.I2000Clm45Fates.cheyenne_intel.clm-Fates COMPARE_base_rest</entry>
<entry issue="NGEET/fates#315">FAIL ERS_Ld60.f45_f45_mg37.I2000Clm45Fates.cheyenne_intel.clm-FatesNoFire COMPARE_base_rest</entry>
<entry issue="NGEET/fates#315">FAIL ERS_Ld60.f45_f45_mg37.I2000Clm45Fates.cheyenne_intel.clm-FatesPPhys COMPARE_base_rest</entry>
<entry issue="NGEET/fates#315">FAIL ERS_Ld60.f45_f45_mg37.I2000Clm45Fates.cheyenne_intel.clm-FatesST3 COMPARE_base_rest</entry>
<entry issue="NGEET/fates#315">FAIL ERP_Ld9.f45_f45_mg37.I2000Clm45Fates.cheyenne_intel.clm-FatesAllVars COMPARE_base_rest</entry>
<entry issue="NGEET/fates#315">FAIL ERS_Ld60.f45_f45_mg37.I2000Clm45Fates.cheyenne_gnu.clm-Fates COMPARE_base_rest</entry>
<entry issue="667" >FAIL ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruGs.cheyenne_intel.clm-FatesHydro COMPARE_base_rest</entry>
<entry issue="667" >FAIL ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruGs.hobart_nag.clm-FatesHydro RUN</entry>
<entry issue="NGEET/fates/#510" >FAIL SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruGs.hobart_nag.clm-FatesHydro MEMLEAK</entry>
</category>
</expectedFails>
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