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Fix problems encountered with running PLUMBER2 sites #4092

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Fix problems encountered with running PLUMBER2 sites #4092

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af5001e
Get wetland sites to run
olyson Jun 11, 2026
952eea4
Fix some pylint errors
olyson Jun 13, 2026
1dd9a01
Fix too many positional arguments errors
olyson Jun 13, 2026
b425d8a
Fix testing error
olyson Jun 13, 2026
2d2418d
Another attempt to fix test
olyson Jun 13, 2026
dbb736b
Another test fix
olyson Jun 13, 2026
dd3082b
Add check to subprocess
olyson Jun 15, 2026
0ae1e01
Fix line lengths
olyson Jun 15, 2026
c89b251
Make black happy
olyson Jun 16, 2026
d7e2085
Update ncl script to add spinup variables to csv file
olyson Jun 25, 2026
21cf30a
Changes to generate new shell commands for spinup
olyson Jun 25, 2026
58b2285
Make black happy
olyson Jun 25, 2026
53ce662
Only set RUN_STARTDATE for NEON sites
olyson Jun 25, 2026
130ea64
Make black happy
olyson Jun 25, 2026
5fb47fe
Remove calendar setting
olyson Jun 25, 2026
479de7f
Turn off HumanIndexMod
olyson Jun 25, 2026
70d10e1
shell_commands for spinup
olyson Jun 25, 2026
d4a8625
Change dtlimit from 30 to 50 for spinup
olyson Jun 25, 2026
ff5cde9
Fix some typos and ask a question
olyson Jun 29, 2026
129a96c
Make black happy
olyson Jun 29, 2026
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6 changes: 5 additions & 1 deletion cime_config/usermods_dirs/clm/PLUMBER2/AR-SLu/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-33.464802
./xmlchange DATM_YR_END=2010
./xmlchange DATM_YR_START_FILENAME=2010
./xmlchange DATM_YR_END_FILENAME=2010
./xmlchange START_TOD=10800
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -35,8 +36,11 @@ if [[ $compset =~ ^HIST ]]; then
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange CALENDAR=NO_LEAP
./xmlchange DATM_YR_START=2010
./xmlchange DATM_YR_END=2010
./xmlchange DATM_YR_ALIGN=1
./xmlchange START_TOD=10800
fi

# Turn on LAI streams for a SP case
Expand Down
10 changes: 7 additions & 3 deletions cime_config/usermods_dirs/clm/PLUMBER2/AT-Neu/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=47.116669
./xmlchange DATM_YR_END=2012
./xmlchange DATM_YR_START_FILENAME=2002
./xmlchange DATM_YR_END_FILENAME=2012
./xmlchange START_TOD=82800
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -34,9 +35,12 @@ if [[ $compset =~ ^HIST ]]; then
./xmlchange DATM_YR_START=2001
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange DATM_YR_START=2002
./xmlchange RUN_STARTDATE=2003-01-01
./xmlchange CALENDAR=GREGORIAN
./xmlchange DATM_YR_START=2003
./xmlchange DATM_YR_END=2010
./xmlchange DATM_YR_ALIGN=2003
./xmlchange START_TOD=82800
fi

# Turn on LAI streams for a SP case
Expand Down
10 changes: 7 additions & 3 deletions cime_config/usermods_dirs/clm/PLUMBER2/AU-ASM/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-22.283001
./xmlchange DATM_YR_END=2017
./xmlchange DATM_YR_START_FILENAME=2011
./xmlchange DATM_YR_END_FILENAME=2017
./xmlchange START_TOD=54000
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -34,9 +35,12 @@ if [[ $compset =~ ^HIST ]]; then
./xmlchange DATM_YR_START=2010
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange DATM_YR_START=2011
./xmlchange RUN_STARTDATE=2012-01-01
./xmlchange CALENDAR=GREGORIAN
./xmlchange DATM_YR_START=2012
./xmlchange DATM_YR_END=2015
./xmlchange DATM_YR_ALIGN=2012
./xmlchange START_TOD=54000
fi

# Turn on LAI streams for a SP case
Expand Down
10 changes: 7 additions & 3 deletions cime_config/usermods_dirs/clm/PLUMBER2/AU-Cow/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-16.23819
./xmlchange DATM_YR_END=2015
./xmlchange DATM_YR_START_FILENAME=2010
./xmlchange DATM_YR_END_FILENAME=2015
./xmlchange START_TOD=50400
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -34,9 +35,12 @@ if [[ $compset =~ ^HIST ]]; then
./xmlchange DATM_YR_START=2009
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange DATM_YR_START=2010
./xmlchange RUN_STARTDATE=2011-01-01
./xmlchange CALENDAR=GREGORIAN
./xmlchange DATM_YR_START=2011
./xmlchange DATM_YR_END=2014
./xmlchange DATM_YR_ALIGN=2011
./xmlchange START_TOD=50400
fi

# Turn on LAI streams for a SP case
Expand Down
10 changes: 7 additions & 3 deletions cime_config/usermods_dirs/clm/PLUMBER2/AU-Cpr/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-34.00206
./xmlchange DATM_YR_END=2017
./xmlchange DATM_YR_START_FILENAME=2011
./xmlchange DATM_YR_END_FILENAME=2017
./xmlchange START_TOD=46800
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -34,9 +35,12 @@ if [[ $compset =~ ^HIST ]]; then
./xmlchange DATM_YR_START=2010
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange DATM_YR_START=2011
./xmlchange RUN_STARTDATE=2012-01-01
./xmlchange CALENDAR=GREGORIAN
./xmlchange DATM_YR_START=2012
./xmlchange DATM_YR_END=2015
./xmlchange DATM_YR_ALIGN=2012
./xmlchange START_TOD=46800
fi

# Turn on LAI streams for a SP case
Expand Down
10 changes: 7 additions & 3 deletions cime_config/usermods_dirs/clm/PLUMBER2/AU-Ctr/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-16.103279
./xmlchange DATM_YR_END=2017
./xmlchange DATM_YR_START_FILENAME=2010
./xmlchange DATM_YR_END_FILENAME=2017
./xmlchange START_TOD=50400
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -34,9 +35,12 @@ if [[ $compset =~ ^HIST ]]; then
./xmlchange DATM_YR_START=2009
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange DATM_YR_START=2010
./xmlchange RUN_STARTDATE=2011-01-01
./xmlchange CALENDAR=GREGORIAN
./xmlchange DATM_YR_START=2011
./xmlchange DATM_YR_END=2014
./xmlchange DATM_YR_ALIGN=2011
./xmlchange START_TOD=50400
fi

# Turn on LAI streams for a SP case
Expand Down
10 changes: 7 additions & 3 deletions cime_config/usermods_dirs/clm/PLUMBER2/AU-Cum/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-33.613297
./xmlchange DATM_YR_END=2018
./xmlchange DATM_YR_START_FILENAME=2013
./xmlchange DATM_YR_END_FILENAME=2018
./xmlchange START_TOD=46800
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -34,9 +35,12 @@ if [[ $compset =~ ^HIST ]]; then
./xmlchange DATM_YR_START=2012
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange DATM_YR_START=2013
./xmlchange RUN_STARTDATE=2014-01-01
./xmlchange CALENDAR=GREGORIAN
./xmlchange DATM_YR_START=2014
./xmlchange DATM_YR_END=2017
./xmlchange DATM_YR_ALIGN=2014
./xmlchange START_TOD=46800
fi

# Turn on LAI streams for a SP case
Expand Down
6 changes: 5 additions & 1 deletion cime_config/usermods_dirs/clm/PLUMBER2/AU-DaP/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-14.0633
./xmlchange DATM_YR_END=2012
./xmlchange DATM_YR_START_FILENAME=2009
./xmlchange DATM_YR_END_FILENAME=2012
./xmlchange START_TOD=54000
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -35,8 +36,11 @@ if [[ $compset =~ ^HIST ]]; then
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange CALENDAR=NO_LEAP
./xmlchange DATM_YR_START=2009
./xmlchange DATM_YR_END=2009
./xmlchange DATM_YR_ALIGN=1
./xmlchange START_TOD=0
fi

# Turn on LAI streams for a SP case
Expand Down
10 changes: 7 additions & 3 deletions cime_config/usermods_dirs/clm/PLUMBER2/AU-DaS/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-14.159283
./xmlchange DATM_YR_END=2017
./xmlchange DATM_YR_START_FILENAME=2010
./xmlchange DATM_YR_END_FILENAME=2017
./xmlchange START_TOD=54000
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -34,9 +35,12 @@ if [[ $compset =~ ^HIST ]]; then
./xmlchange DATM_YR_START=2009
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange DATM_YR_START=2010
./xmlchange RUN_STARTDATE=2011-01-01
./xmlchange CALENDAR=GREGORIAN
./xmlchange DATM_YR_START=2011
./xmlchange DATM_YR_END=2014
./xmlchange DATM_YR_ALIGN=2011
./xmlchange START_TOD=54000
fi

# Turn on LAI streams for a SP case
Expand Down
6 changes: 5 additions & 1 deletion cime_config/usermods_dirs/clm/PLUMBER2/AU-Dry/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-15.2588
./xmlchange DATM_YR_END=2015
./xmlchange DATM_YR_START_FILENAME=2011
./xmlchange DATM_YR_END_FILENAME=2015
./xmlchange START_TOD=54000
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -35,8 +36,11 @@ if [[ $compset =~ ^HIST ]]; then
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange CALENDAR=NO_LEAP
./xmlchange DATM_YR_START=2011
./xmlchange DATM_YR_END=2011
./xmlchange DATM_YR_ALIGN=1
./xmlchange START_TOD=0
fi

# Turn on LAI streams for a SP case
Expand Down
6 changes: 5 additions & 1 deletion cime_config/usermods_dirs/clm/PLUMBER2/AU-Emr/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-23.8587
./xmlchange DATM_YR_END=2013
./xmlchange DATM_YR_START_FILENAME=2012
./xmlchange DATM_YR_END_FILENAME=2013
./xmlchange START_TOD=50400
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -35,8 +36,11 @@ if [[ $compset =~ ^HIST ]]; then
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange CALENDAR=NO_LEAP
./xmlchange DATM_YR_START=2012
./xmlchange DATM_YR_END=2012
./xmlchange DATM_YR_ALIGN=1
./xmlchange START_TOD=0
fi

# Turn on LAI streams for a SP case
Expand Down
6 changes: 5 additions & 1 deletion cime_config/usermods_dirs/clm/PLUMBER2/AU-GWW/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-30.191299
./xmlchange DATM_YR_END=2017
./xmlchange DATM_YR_START_FILENAME=2013
./xmlchange DATM_YR_END_FILENAME=2017
./xmlchange START_TOD=57600
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -35,8 +36,11 @@ if [[ $compset =~ ^HIST ]]; then
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange CALENDAR=NO_LEAP
./xmlchange DATM_YR_START=2013
./xmlchange DATM_YR_END=2013
./xmlchange DATM_YR_ALIGN=1
./xmlchange START_TOD=0
fi

# Turn on LAI streams for a SP case
Expand Down
10 changes: 7 additions & 3 deletions cime_config/usermods_dirs/clm/PLUMBER2/AU-Gin/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-31.375
./xmlchange DATM_YR_END=2017
./xmlchange DATM_YR_START_FILENAME=2012
./xmlchange DATM_YR_END_FILENAME=2017
./xmlchange START_TOD=57600
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -34,9 +35,12 @@ if [[ $compset =~ ^HIST ]]; then
./xmlchange DATM_YR_START=2011
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange DATM_YR_START=2012
./xmlchange RUN_STARTDATE=2013-01-01
./xmlchange CALENDAR=GREGORIAN
./xmlchange DATM_YR_START=2013
./xmlchange DATM_YR_END=2016
./xmlchange DATM_YR_ALIGN=2013
./xmlchange START_TOD=57600
fi

# Turn on LAI streams for a SP case
Expand Down
10 changes: 7 additions & 3 deletions cime_config/usermods_dirs/clm/PLUMBER2/AU-How/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-12.4952
./xmlchange DATM_YR_END=2017
./xmlchange DATM_YR_START_FILENAME=2003
./xmlchange DATM_YR_END_FILENAME=2017
./xmlchange START_TOD=54000
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -34,9 +35,12 @@ if [[ $compset =~ ^HIST ]]; then
./xmlchange DATM_YR_START=2002
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange DATM_YR_START=2003
./xmlchange RUN_STARTDATE=2004-01-01
./xmlchange CALENDAR=GREGORIAN
./xmlchange DATM_YR_START=2004
./xmlchange DATM_YR_END=2015
./xmlchange DATM_YR_ALIGN=2004
./xmlchange START_TOD=54000
fi

# Turn on LAI streams for a SP case
Expand Down
6 changes: 5 additions & 1 deletion cime_config/usermods_dirs/clm/PLUMBER2/AU-Lit/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-13.17904
./xmlchange DATM_YR_END=2017
./xmlchange DATM_YR_START_FILENAME=2016
./xmlchange DATM_YR_END_FILENAME=2017
./xmlchange START_TOD=54000
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -35,8 +36,11 @@ if [[ $compset =~ ^HIST ]]; then
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange CALENDAR=NO_LEAP
./xmlchange DATM_YR_START=2016
./xmlchange DATM_YR_END=2016
./xmlchange DATM_YR_ALIGN=1
./xmlchange START_TOD=0
fi

# Turn on LAI streams for a SP case
Expand Down
6 changes: 5 additions & 1 deletion cime_config/usermods_dirs/clm/PLUMBER2/AU-Otw/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-38.532341
./xmlchange DATM_YR_END=2010
./xmlchange DATM_YR_START_FILENAME=2009
./xmlchange DATM_YR_END_FILENAME=2010
./xmlchange START_TOD=46800
./xmlchange ATM_NCPL=24

Expand Down Expand Up @@ -35,8 +36,11 @@ if [[ $compset =~ ^HIST ]]; then
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange CALENDAR=NO_LEAP
./xmlchange DATM_YR_START=2009
./xmlchange DATM_YR_END=2009
./xmlchange DATM_YR_ALIGN=1
./xmlchange START_TOD=0
fi

# Turn on LAI streams for a SP case
Expand Down
10 changes: 7 additions & 3 deletions cime_config/usermods_dirs/clm/PLUMBER2/AU-Rig/shell_commands
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
./xmlchange PTS_LAT=-36.649899
./xmlchange DATM_YR_END=2016
./xmlchange DATM_YR_START_FILENAME=2011
./xmlchange DATM_YR_END_FILENAME=2016
./xmlchange START_TOD=46800
./xmlchange ATM_NCPL=48

Expand Down Expand Up @@ -34,9 +35,12 @@ if [[ $compset =~ ^HIST ]]; then
./xmlchange DATM_YR_START=2010
else
# for spinup case with I2000 compset
./xmlchange RUN_STARTDATE=0001-01-01
./xmlchange DATM_YR_ALIGN=1
./xmlchange DATM_YR_START=2011
./xmlchange RUN_STARTDATE=2012-01-01
./xmlchange CALENDAR=GREGORIAN
./xmlchange DATM_YR_START=2012
./xmlchange DATM_YR_END=2015
./xmlchange DATM_YR_ALIGN=2012
./xmlchange START_TOD=46800
fi

# Turn on LAI streams for a SP case
Expand Down
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