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add PHYS_CYCLE support & generalize RUN_TYPE=hybrid support #343

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Merged
mnlevy1981 merged 13 commits into from
Sep 5, 2026
Merged

add PHYS_CYCLE support & generalize RUN_TYPE=hybrid support #343

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e9310ac
interim commit of phys_cycle/cplhist updates
klindsay28 Jul 11, 2026
4c89022
continued phys_cycle implementation
Jul 12, 2026
576676d
Merge branch 'main' into phys_cycle
klindsay28 Jul 15, 2026
6115888
updates to phys_cycle implementation
klindsay28 Jul 31, 2026
2b47811
phys_cycle code cleanup
klindsay28 Aug 3, 2026
eb7978e
update phys_cycle_postrun script
klindsay28 Aug 4, 2026
abac576
add DOUT_S=TRUE support to phys_cycle
klindsay28 Aug 4, 2026
68888f2
correct phys_cycle_postrun logging argument
klindsay28 Aug 4, 2026
b67a144
make PHYS_CYCLE cases less error-prone for MARBL init
klindsay28 Aug 5, 2026
5736b09
replace MOM6_PHYS_CYCLE_MARBL_IC_FILE with MOM6_TRACER_IC_FILE_OVERRI…
klindsay28 Aug 21, 2026
a32d8e9
generalize ideal age initialization
klindsay28 Aug 22, 2026
d8f9756
comment JRA PHYS_CYCLE compset, as it doesn't work correctly
klindsay28 Sep 3, 2026
2955556
set REMAP_NON_Z_IC params to true in PHYS_CYCLE cases
klindsay28 Sep 4, 2026
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41 changes: 40 additions & 1 deletion cime_config/config_component.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,10 @@
<entry_id version="3.0">

<description>
<desc ocn="MOM6[%MARBL-BIO][%MARBL-ABIO]">MOM6 OCEAN </desc>
<desc ocn="MOM6[%MARBL-BIO][%MARBL-ABIO][%PHYS-CYCLE]">MOM6 OCEAN </desc>
<desc option="MARBL-BIO">MARBL Biogeochemistry Tracer Library base biotic tracers</desc>
<desc option="MARBL-ABIO">MARBL Biogeochemistry Tracer Library abiotic DIC tracers</desc>
<desc option="PHYS-CYCLE">phys cycle option</desc>
</description>

<entry id="COMP_OCN">
Expand Down Expand Up @@ -206,6 +207,44 @@
</desc>
</entry>

<entry id="MOM6_PHYS_CYCLE_YEARS_IN_CYCLE">
<type>integer</type>
<default_value>0</default_value>
<group>run_component_mom</group>
<file>env_run.xml</file>
<desc>number of years to run before cycling MOM6 physics
MOM6 physics cycling only occurs if MOM6_PHYS_CYCLE_YEARS_IN_CYCLE>0
and pre- and post-run scripts are specified in env vars
PRERUN_SCRIPT and POSTRUN_SCRIPT</desc>
</entry>

<entry id="MOM6_PHYS_CYCLE_MONTHS_RUN_SINCE_CYCLE">
<type>integer</type>
<default_value>0</default_value>
<group>run_component_mom</group>
<file>env_run.xml</file>
<desc>number of months run since most recent cycling of MOM6 physics</desc>
</entry>

<entry id="MOM6_TRACER_IC_FILE_OVERRIDE_POINTER">
<type>char</type>
<default_value></default_value>
<group>run_component_mom</group>
<file>env_run.xml</file>
<desc>File containing tracer IC filenames</desc>
</entry>

<entry id="MARBL_ENFORCE_TRACER_ZINT">
<type>logical</type>
<valid_values>TRUE,FALSE</valid_values>
<default_value>FALSE</default_value>
<group>run_component_mom</group>
<file>env_run.xml</file>
<desc>Rescale MARBL tracers so that their vertical integrals match
their vertical integrals computed from the IC file(s).
</desc>
</entry>

<help>
=========================================
MOM6 naming conventions
Expand Down
41 changes: 41 additions & 0 deletions cime_config/config_compsets.xml
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Expand Up @@ -115,9 +115,50 @@
<lname>1850_DATM%JRA-1p5-2023_SLND_CICE_MOM6%MARBL-BIO_DROF%JRA-1p5-2023_SGLC_WW3</lname>
</compset>

<!-- PHYS_CYCLE configuration requires a cdeps/drof change to work with JRA
<compset>
<alias>GW1850MARBL_JRA_PHYS_CYCLE</alias>
<lname>1850_DATM%JRA-1p5-2023_SLND_CICE_MOM6%MARBL-BIO%PHYS-CYCLE_DROF%JRA-1p5-2023_SGLC_WW3</lname>
</compset>
-->

<compset>
<alias>GW1850MARBL_CPLHIST</alias>
<lname>1850_DATM%CPLHIST_SLND_CICE_MOM6%MARBL-BIO_DROF%CPLHIST_SGLC_WW3</lname>
</compset>

<compset>
<alias>GW1850MARBL_CPLHIST_PHYS_CYCLE</alias>
<lname>1850_DATM%CPLHIST_SLND_CICE_MOM6%MARBL-BIO%PHYS-CYCLE_DROF%CPLHIST_SGLC_WW3</lname>
</compset>

<compset>
<alias>GW1850ABIOMARBL_JRA</alias>
<lname>1850_DATM%JRA-1p5-2023_SLND_CICE_MOM6%MARBL-ABIO_DROF%JRA-1p5-2023_SGLC_WW3</lname>
</compset>

<!-- ENTRIES -->

<entries>

<entry id="PRERUN_SCRIPT">
<values>
<value compset="MOM6%[^_]*PHYS-CYCLE">$SRCROOT/components/mom/cime_config/phys_cycle_prerun</value>
</values>
</entry>

<entry id="POSTRUN_SCRIPT">
<values>
<value compset="MOM6%[^_]*PHYS-CYCLE">$SRCROOT/components/mom/cime_config/phys_cycle_postrun</value>
</values>
</entry>

<entry id="RESUBMIT_SETS_CONTINUE_RUN">
<values>
<value compset="MOM6%[^_]*PHYS-CYCLE">FALSE</value>
</values>
</entry>

</entries>

</compsets>
71 changes: 38 additions & 33 deletions cime_config/config_pes.xml
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Expand Up @@ -210,39 +210,6 @@
<rootpe_glc>0</rootpe_glc>
</rootpe>
</pes>
<pes pesize="any" compset="_DATM.+_CICE.*_MOM6%[^_]*MARBL-BIO.+_WW3">
<comment>none</comment>
<ntasks>
<ntasks_atm>384</ntasks_atm>
<ntasks_rof>384</ntasks_rof>
<ntasks_cpl>384</ntasks_cpl>
<ntasks_ice>384</ntasks_ice>
<ntasks_ocn>2560</ntasks_ocn>
<ntasks_lnd>1</ntasks_lnd>
<ntasks_wav>128</ntasks_wav>
<ntasks_glc>1</ntasks_glc>
</ntasks>
<nthrds>
<nthrds_atm>1</nthrds_atm>
<nthrds_lnd>1</nthrds_lnd>
<nthrds_rof>1</nthrds_rof>
<nthrds_ice>1</nthrds_ice>
<nthrds_ocn>1</nthrds_ocn>
<nthrds_glc>1</nthrds_glc>
<nthrds_wav>1</nthrds_wav>
<nthrds_cpl>1</nthrds_cpl>
</nthrds>
<rootpe>
<rootpe_atm>0</rootpe_atm>
<rootpe_rof>0</rootpe_rof>
<rootpe_cpl>0</rootpe_cpl>
<rootpe_ice>0</rootpe_ice>
<rootpe_ocn>512</rootpe_ocn>
<rootpe_lnd>0</rootpe_lnd>
<rootpe_wav>384</rootpe_wav>
<rootpe_glc>0</rootpe_glc>
</rootpe>
</pes>
<pes pesize="any" compset="_DATM.+_DICE.*_MOM6(?!.*%MARBL-BIO).+_SWAV">
<comment>none</comment>
<ntasks>
Expand Down Expand Up @@ -413,6 +380,44 @@
</mach>
</grid>

<grid name="oi%tx2_3v[23]">
<mach name="derecho">
<pes pesize="any" compset="_DATM.+_CICE.*_MOM6%[^_]*MARBL-BIO.+_WW3">
<comment>MARBL 2/3, any DATM forcing, including CPLHIST</comment>
<ntasks>
<ntasks_atm>384</ntasks_atm>
<ntasks_rof>384</ntasks_rof>
<ntasks_cpl>384</ntasks_cpl>
<ntasks_ice>384</ntasks_ice>
<ntasks_ocn>2560</ntasks_ocn>
<ntasks_lnd>1</ntasks_lnd>
<ntasks_wav>128</ntasks_wav>
<ntasks_glc>1</ntasks_glc>
</ntasks>
<nthrds>
<nthrds_atm>1</nthrds_atm>
<nthrds_lnd>1</nthrds_lnd>
<nthrds_rof>1</nthrds_rof>
<nthrds_ice>1</nthrds_ice>
<nthrds_ocn>1</nthrds_ocn>
<nthrds_glc>1</nthrds_glc>
<nthrds_wav>1</nthrds_wav>
<nthrds_cpl>1</nthrds_cpl>
</nthrds>
<rootpe>
<rootpe_atm>0</rootpe_atm>
<rootpe_rof>0</rootpe_rof>
<rootpe_cpl>0</rootpe_cpl>
<rootpe_ice>0</rootpe_ice>
<rootpe_ocn>512</rootpe_ocn>
<rootpe_lnd>0</rootpe_lnd>
<rootpe_wav>384</rootpe_wav>
<rootpe_glc>0</rootpe_glc>
</rootpe>
</pes>
</mach>
</grid>

<grid name="a%(TL319|T62).+oi%tx2_0v1">
<mach name="derecho">
<pes pesize="any" compset="any">
Expand Down
121 changes: 121 additions & 0 deletions cime_config/phys_cycle_postrun
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@@ -0,0 +1,121 @@
#!/usr/bin/env python

"""mom6 physics cycle postrun script
"""

import logging
import os
import sys

_CIMEROOT = os.environ.get("CIMEROOT")
if _CIMEROOT is None:
raise SystemExit("ERROR: must set CIMEROOT environment variable")
sys.path.append(os.path.join(_CIMEROOT, "CIME", "Tools"))

from standard_script_setup import *
from CIME.case import Case
from CIME.utils import expect

logger = logging.getLogger(__name__)

###############################################################################
def phys_cycle_postrun(caseroot):
###############################################################################

ch = logging.StreamHandler(stream=sys.stdout)
ch.setLevel(logging.INFO)
logger.addHandler(ch)

with Case(caseroot, read_only=False) as case:
mom6_phys_cycle_years_in_cycle = case.get_value("MOM6_PHYS_CYCLE_YEARS_IN_CYCLE")
expect(mom6_phys_cycle_years_in_cycle is not None,
f"MOM6_PHYS_CYCLE_YEARS_IN_CYCLE should be defined when {sys.argv[0]} is called")
if mom6_phys_cycle_years_in_cycle <= 0:
return

# -------------------------------------------------------------------------
# Determine if model has run the length of MOM6 physics run cycle length
# this assumes that STOP_ options have not been changed during the submission
# -------------------------------------------------------------------------

stop_option = case.get_value("STOP_OPTION")
stop_n = case.get_value("STOP_N")

mom6_phys_cycle_months_run_since_cycle = case.get_value(
"MOM6_PHYS_CYCLE_MONTHS_RUN_SINCE_CYCLE"
)

# we know from phys_cycle_prerun that stop_option is either "nmonth*" or "nyear*"

if stop_option.find("nmonth") == 0:
mom6_phys_cycle_months_run_since_cycle_new = (
mom6_phys_cycle_months_run_since_cycle + stop_n
)
if stop_option.find("nyear") == 0:
mom6_phys_cycle_months_run_since_cycle_new = (
mom6_phys_cycle_months_run_since_cycle + stop_n * 12
)

case.set_value("MOM6_PHYS_CYCLE_MONTHS_RUN_SINCE_CYCLE",
mom6_phys_cycle_months_run_since_cycle_new)
logger.info("MOM6_PHYS_CYCLE_MONTHS_RUN_SINCE_CYCLE incremented to %d",
mom6_phys_cycle_months_run_since_cycle_new)

if mom6_phys_cycle_months_run_since_cycle_new < mom6_phys_cycle_years_in_cycle * 12:
case.set_value("CONTINUE_RUN", "TRUE")
case.set_value("MOM6_TRACER_IC_FILE_OVERRIDE_POINTER", "")
case.set_value("MARBL_ENFORCE_TRACER_ZINT", "FALSE")
case.flush()
return

# -------------------------------------------------------------------------
# Model has run the length of MOM6 physics run cycle length, reset model physics
# -------------------------------------------------------------------------

logger.info("resetting model physics")
case.set_value("CONTINUE_RUN", "FALSE")
case.set_value("MOM6_PHYS_CYCLE_MONTHS_RUN_SINCE_CYCLE", 0)

# -------------------------------------------------------------------------
# Compute new RUN_STARTDATE
# -------------------------------------------------------------------------

run_startdate = case.get_value("RUN_STARTDATE")
yyyy = int(run_startdate[:4])
yyyy = yyyy + mom6_phys_cycle_years_in_cycle
run_startdate = f"{yyyy:04d}{run_startdate[4:]}"
case.set_value("RUN_STARTDATE", run_startdate)
logger.info("RUN_STARTDATE incremented to %s", run_startdate)

# -------------------------------------------------------------------------
# Configure tracer module initialization for new PHYS_CYCLE cycle
# -------------------------------------------------------------------------

case.set_value("MOM6_TRACER_IC_FILE_OVERRIDE_POINTER",
f"./rpointer.ocn.{run_startdate}-00000")
case.set_value("MARBL_ENFORCE_TRACER_ZINT", "TRUE")

# -------------------------------------------------------------------------
# Update CPLHIST ALIGN variables
# -------------------------------------------------------------------------

varnames_dict = {
'DATM_MODE': 'DATM_YR_ALIGN',
'DROF_MODE': 'DROF_CPLHIST_YR_ALIGN'
}
for mode_varname, align_varname in varnames_dict.items():
if case.get_value(mode_varname) == "CPLHIST":
align_val = case.get_value(align_varname)
if align_val is not None:
align_val = align_val + mom6_phys_cycle_years_in_cycle
case.set_value(align_varname, align_val)
logger.info("%s incremented to %d", align_varname, align_val)

case.flush()

###############################################################################

if __name__ == "__main__":
expect(len(sys.argv) == 2, "caseroot is a required input argument")
caseroot = sys.argv[1]
phys_cycle_postrun(caseroot)
80 changes: 80 additions & 0 deletions cime_config/phys_cycle_prerun
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#!/usr/bin/env python

"""mom6 physics cycle prerun script
"""

import logging
import os
import sys

_CIMEROOT = os.environ.get("CIMEROOT")
if _CIMEROOT is None:
raise SystemExit("ERROR: must set CIMEROOT environment variable")
sys.path.append(os.path.join(_CIMEROOT, "CIME", "Tools"))

from standard_script_setup import *
from CIME.case import Case
from CIME.utils import expect

logger = logging.getLogger(__name__)

###############################################################################
def phys_cycle_prerun(caseroot):
###############################################################################

ch = logging.StreamHandler(stream=sys.stdout)
ch.setLevel(logging.INFO)
logger.addHandler(ch)

with Case(caseroot, read_only=False) as case:
mom6_phys_cycle_years_in_cycle = case.get_value("MOM6_PHYS_CYCLE_YEARS_IN_CYCLE")
expect(mom6_phys_cycle_years_in_cycle is not None,
f"MOM6_PHYS_CYCLE_YEARS_IN_CYCLE should be defined when {sys.argv[0]} is called")
logger.info("mom6_phys_cycle_years_in_cycle = %d", mom6_phys_cycle_years_in_cycle)
if mom6_phys_cycle_years_in_cycle <= 0:
return

# RUN_TYPE cannot be branch
expect(case.get_value("RUN_TYPE") != "branch",
"RUN_TYPE set to branch not implemented for MOM6 physics cycling"
" because RUN_STARTDATE cannot be incremented")

# stop_option must be nmonth, nmonths, nyear or nyears
stop_option = case.get_value("STOP_OPTION")
expect((stop_option.find("nmonth") == 0) or (stop_option.find("nyear") == 0),
f"STOP_OPTION={stop_option} not implemented for MOM6 physics cycling")

# -------------------------------------------------------------------------
# Ensure that phys_cycle scripts are in charge of setting CONTINUE_RUN
# -------------------------------------------------------------------------
case.set_value("RESUBMIT_SETS_CONTINUE_RUN", "FALSE")
case.flush()

# -------------------------------------------------------------------------
# Ensure that the current run length will not overshoot the phys_cycle run length
# -------------------------------------------------------------------------

mom6_phys_cycle_months_run_since_cycle = case.get_value(
"MOM6_PHYS_CYCLE_MONTHS_RUN_SINCE_CYCLE"
)
mom6_phys_cycle_years_in_cycle = case.get_value("MOM6_PHYS_CYCLE_YEARS_IN_CYCLE")

stop_n = case.get_value("STOP_N")
if stop_option.find("nmonth") == 0:
mom6_phys_cycle_months_run_since_cycle_new = (
mom6_phys_cycle_months_run_since_cycle + stop_n
)
elif stop_option.find("nyear") == 0:
mom6_phys_cycle_months_run_since_cycle_new = (
mom6_phys_cycle_months_run_since_cycle + stop_n * 12
)

expect(mom6_phys_cycle_months_run_since_cycle_new <= mom6_phys_cycle_years_in_cycle * 12,
"run will overshoot phys_cycle run length")

###############################################################################

if __name__ == "__main__":
expect(len(sys.argv) == 2, "caseroot is a required input argument")
caseroot = sys.argv[1]
phys_cycle_prerun(caseroot)
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