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First attempt at using containerized MOM6SIS2 for NWA12 and NEP10 RT (#…
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…115)

* First attempt at using containerized MOM6SIS2 for NWA12 RT

* fixed gha workflow

* update NEP RT driver, parameter_doc, and gha workflow

* fix workflow

* Modifty NEP10 RT driver
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@yichengt900
yichengt900 authored Nov 16, 2024
1 parent f330c32 commit 0ac7670
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16 changes: 8 additions & 8 deletions .github/workflows/CEFI_MOM6-ci.yaml
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Expand Up @@ -15,7 +15,7 @@ env:
jobs:
checkout-build:
if: ${{ github.event.label.name == 'CEFI_MOM6_RT_container' }}
runs-on: [self-hosted, container]
runs-on: [self-hosted]
timeout-minutes: 600
strategy:
max-parallel: 1
Expand All @@ -31,7 +31,7 @@ jobs:
- name: Build MOM6SIS2 using container
run: |
cd ${{ env.TEST_DIR }}/CEFI_MOM6_CHECK/builds
pwd
#pwd
#img=/gpfs/f6/ira-cefi/world-shared/container/ubuntu22.04-intel-ufs-env-v1.8.0-llvm.img
#apptainer exec -B /gpfs -B /ncrc/home2/Yi-cheng.Teng:/ncrc/home2/Yi-cheng.Teng $img bash linux-build.bash -m docker -p linux-intel -t repro -f mom6sis2
jobid=$(sbatch --parsable ci_build_driver.sh | awk -F';' '{print $1}' | cut -f1)
Expand Down Expand Up @@ -59,16 +59,16 @@ jobs:
run-CEFI_MOM6-ci:
needs: checkout-build
runs-on: [self-hosted, container]
runs-on: [self-hosted]
strategy:
max-parallel: 1
matrix:
case: ["NEP10.COBALT"]
case: ["NWA12.COBALT", "NEP10.COBALT"]
steps:
- name: Run Experiment ${{ matrix.case }}
run: |
cd ${{ env.TEST_DIR }}/CEFI_MOM6_CHECK/exps/${{ matrix.case }}
jobid=$(sbatch --parsable run_container.sh | awk -F';' '{print $1}' | cut -f1)
jobid=$(sbatch --parsable driver.sh | awk -F';' '{print $1}' | cut -f1)
#
sleep 1
while :; do
Expand All @@ -83,7 +83,7 @@ jobs:
sleep 60 # Adjust the sleep duration as needed
done
#
expected_string="ocean.stats is identical to ref, PASS"
expected_string="All restart files are identical, PASS"
check_file="${{ env.TEST_DIR }}/CEFI_MOM6_CHECK/exps/${{ matrix.case }}/${{ matrix.case }}_o.$jobid"
if [ -f "$check_file" ]; then
if grep -qF "$expected_string" $check_file; then
Expand All @@ -99,7 +99,7 @@ jobs:
add-pass-label:
needs: run-CEFI_MOM6-ci
runs-on: [self-hosted, container]
runs-on: [self-hosted]
if: ${{ needs.run-CEFI_MOM6-ci.result == 'success' }}
steps:
- name: Add "pass_CEFI_MOM6_RT_container" label on success
Expand All @@ -123,7 +123,7 @@ jobs:
clean-up:
needs: add-pass-label
runs-on: [self-hosted, container]
runs-on: [self-hosted]
strategy:
max-parallel: 1
steps:
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212 changes: 115 additions & 97 deletions exps/NEP10.COBALT/COBALT_parameter_doc.all
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Expand Up @@ -285,15 +285,15 @@ bresp_bact = 0.0075 ! [day-1] default = 0.0075
! basal respiration rate for bacteria at 0 deg. C
q_p_2_n_bact = 0.0625 ! [mol P mol N-1] default = 0.0625
! Bacteria P:N
frac_mu_stress_Sm = 0.25 ! [none] default = 0.25
frac_mu_stress_Sm = 0.4 ! [none] default = 0.4
! fraction of max growth when stress-dependent losses initiate for small
! phytoplankton
frac_mu_stress_Di = 0.25 ! [none] default = 0.25
frac_mu_stress_Di = 0.4 ! [none] default = 0.4
! fraction of max growth when stress-dependent losses initiate for diazotrophs
frac_mu_stress_Lg = 0.25 ! [none] default = 0.25
frac_mu_stress_Lg = 0.4 ! [none] default = 0.4
! fraction of max growth when stress-dependent losses initiate for large
! phytoplankton
frac_mu_stress_Md = 0.25 ! [none] default = 0.25
frac_mu_stress_Md = 0.4 ! [none] default = 0.4
! fraction of max growth when stress-dependent losses initiate for medium
! phytoplankton
agg_Sm = 0.05 ! [day-1 (micromol N kg-1)-1] default = 0.05
Expand Down Expand Up @@ -429,104 +429,122 @@ mswitch_mdz = 2.0 ! [none] default = 2.0
! prey switching parameter 2 for medium zooplankton
mswitch_lgz = 2.0 ! [none] default = 2.0
! prey switching parameter 2 for large zooplankton
gge_max_smz = 0.4 ! [unitless] default = 0.4
! gge_max_smz
gge_max_mdz = 0.4 ! [unitless] default = 0.4
! gge_max_mdz
gge_max_lgz = 0.4 ! [unitless] default = 0.4
! gge_max_lgz
gge_max_smz = 0.4 ! [none] default = 0.4
! maximum gross growth efficiency for small zooplankton
gge_max_mdz = 0.4 ! [none] default = 0.4
! maximum gross growth efficiency for medium zooplankton
gge_max_lgz = 0.4 ! [none] default = 0.4
! maximum gross growth efficiency for large zooplankton
bresp_smz = 0.016 ! [day-1] default = 0.016
! bresp_smz
! basal respiration rate for small zooplankton
bresp_mdz = 0.008 ! [day-1] default = 0.008
! bresp_mdz
! basal respiration rate for medium zooplankton
bresp_lgz = 0.0032 ! [day-1] default = 0.0032
! bresp_lgz
phi_det_smz = 0.0 ! [unitless] default = 0.0
! phi_det_smz
phi_det_mdz = 0.15 ! [unitless] default = 0.15
! phi_det_mdz
phi_det_lgz = 0.3 ! [unitless] default = 0.3
! phi_det_lgz
phi_ldon_smz = 0.1875 ! [unitless] default = 0.1875
! phi_ldon_smz
phi_ldon_mdz = 0.09375 ! [unitless] default = 0.09375
! phi_ldon_mdz
phi_ldon_lgz = 0.0 ! [unitless] default = 0.0
! phi_ldon_lgz
phi_ldop_smz = 0.1725 ! [unitless] default = 0.1725
! phi_ldop_smz
phi_ldop_mdz = 0.08625 ! [unitless] default = 0.08625
! phi_ldop_mdz
phi_ldop_lgz = 0.0 ! [unitless] default = 0.0
! phi_ldop_lgz
phi_srdon_smz = 0.0225 ! [unitless] default = 0.0225
! phi_srdon_smz
phi_srdon_mdz = 0.01125 ! [unitless] default = 0.01125
! phi_srdon_mdz
phi_srdon_lgz = 0.0 ! [unitless] default = 0.0
! phi_srdon_lgz
phi_srdop_smz = 0.0375 ! [unitless] default = 0.0375
! phi_srdop_smz
phi_srdop_mdz = 0.01875 ! [unitless] default = 0.01875
! phi_srdop_mdz
phi_srdop_lgz = 0.0 ! [unitless] default = 0.0
! phi_srdop_lgz
phi_sldon_smz = 0.09 ! [unitless] default = 0.09
! phi_sldon_smz
phi_sldon_mdz = 0.045 ! [unitless] default = 0.045
! phi_sldon_mdz
phi_sldon_lgz = 0.0 ! [unitless] default = 0.0
! phi_sldon_lgz
phi_sldop_smz = 0.09 ! [unitless] default = 0.09
! phi_sldop_smz
phi_sldop_mdz = 0.045 ! [unitless] default = 0.045
! phi_sldop_mdz
phi_sldop_lgz = 0.0 ! [unitless] default = 0.0
! phi_sldop_lgz
phi_ldon_vir = 0.625 ! [unitless] default = 0.625
! phi_ldon_vir
phi_srdon_vir = 0.075 ! [unitless] default = 0.075
! phi_srdon_vir
phi_sldon_vir = 0.3 ! [unitless] default = 0.3
! phi_sldon_vir
phi_ldop_vir = 0.575 ! [unitless] default = 0.575
! phi_ldop_vir
phi_srdop_vir = 0.125 ! [unitless] default = 0.125
! phi_srdop_vir
phi_sldop_vir = 0.3 ! [unitless] default = 0.3
! phi_sldop_vir
! basal respiration rate for large zooplankton
phi_det_smz = 0.0 ! [none] default = 0.0
! fraction of ingestion by small zooplankton to detritus
phi_det_mdz = 0.15 ! [none] default = 0.15
! fraction of ingestion by medium zooplankton to detritus
phi_det_lgz = 0.3 ! [none] default = 0.3
! fraction of ingestion by large zooplankton to detritus
phi_ldon_smz = 0.1875 ! [none] default = 0.1875
! fraction of N ingestion by small zooplankton to labile dissolved organic
! nitrogen
phi_ldon_mdz = 0.09375 ! [none] default = 0.09375
! fraction of N ingestion by medium zooplankton to labile dissolved organic
! nitrogen
phi_ldon_lgz = 0.0 ! [none] default = 0.0
! fraction of N ingestion by large zooplankton to labile dissolved organic
! nitrogen
phi_ldop_smz = 0.1725 ! [none] default = 0.1725
! fraction of P ingestion by small zooplankton to labile dissolved organic
! phosphorus
phi_ldop_mdz = 0.08625 ! [none] default = 0.08625
! fraction of P ingestion by medium zooplankton to labile dissolved organic
! phosphorus
phi_ldop_lgz = 0.0 ! [none] default = 0.0
! fraction of P ingestion by large zooplankton to labile dissolved organic
! phosphorus
phi_srdon_smz = 0.0225 ! [none] default = 0.0225
! fraction of N ingestion by small zooplankton to semi-refractory dissolved
! organic nitrogen
phi_srdon_mdz = 0.01125 ! [none] default = 0.01125
! fraction of N ingestion by medium zooplankton to semi-refractory dissolved
! organic nitrogen
phi_srdon_lgz = 0.0 ! [none] default = 0.0
! fraction of N ingestion by large zooplankton to semi-refractory dissolved
! organic nitrogen
phi_srdop_smz = 0.0375 ! [none] default = 0.0375
! fraction of P ingestion by small zooplankton to semi-refractory dissolved
! organic phosphorus
phi_srdop_mdz = 0.01875 ! [none] default = 0.01875
! fraction of P ingestion by medium zooplankton to semi-refractory dissolved
! organic phosphorus
phi_srdop_lgz = 0.0 ! [none] default = 0.0
! fraction of P ingestion by large zooplankton to semi-refractory dissolved
! organic phosphorus
phi_sldon_smz = 0.09 ! [none] default = 0.09
! fraction of N ingestion by small zooplankton to semi-labile dissolved organic
! nitrogen
phi_sldon_mdz = 0.045 ! [none] default = 0.045
! fraction of N ingestion by medium zooplankton to semi-labile dissolved organic
! nitrogen
phi_sldon_lgz = 0.0 ! [none] default = 0.0
! fraction of N ingestion by large zooplankton to semi-labile dissolved organic
! nitrogen
phi_sldop_smz = 0.09 ! [none] default = 0.09
! fraction of P ingestion by small zooplankton to semi-labile dissolved organic
! phosphorus
phi_sldop_mdz = 0.045 ! [none] default = 0.045
! fraction of P ingestion by medium zooplankton to semi-labile dissolved organic
! phosphorus
phi_sldop_lgz = 0.0 ! [none] default = 0.0
! fraction of P ingestion by large zooplankton to semi-labile dissolved organic
! phosphorus
phi_ldon_vir = 0.625 ! [none] default = 0.625
! fraction of viral lysis of N to labile dissolved organic nitrogen
phi_srdon_vir = 0.075 ! [none] default = 0.075
! fraction of viral lysis of N to semi-refractory dissolved organic nitrogen
phi_sldon_vir = 0.3 ! [none] default = 0.3
! fraction of viral lysis of N to semi-labile dissolved organic nitrogen
phi_ldop_vir = 0.575 ! [none] default = 0.575
! fraction of viral lysis of P to labile dissolved organic phosphorus
phi_srdop_vir = 0.125 ! [none] default = 0.125
! fraction of viral lysis of P to semi-refractory dissolved organic phosphorus
phi_sldop_vir = 0.3 ! [none] default = 0.3
! fraction of viral lysis of P to semi-labile dissolved organic phosphorus
imax_hp = 0.09 ! [day-1] default = 0.09
! imax_hp
! max ingestion rate for higher predators @ 0 deg. C
ki_hp = 1.25E-06 ! [mol N kg-1] default = 1.25E-06
! ki_hp
coef_hp = 2.0 ! [unitless] default = 2.0
! coef_hp
ktemp_hp = 0.063 ! [C-1] default = 0.063
! ktemp_hp
nswitch_hp = 2.0 ! [unitless] default = 2.0
! nswitch_hp
mswitch_hp = 2.0 ! [unitless] default = 2.0
! mswitch_hp
hp_ipa_smp = 0.0 ! [unitless] default = 0.0
! hp_ipa_smp
hp_ipa_mdp = 0.0 ! [unitless] default = 0.0
! hp_ipa_mdp
hp_ipa_lgp = 0.0 ! [unitless] default = 0.0
! hp_ipa_lgp
hp_ipa_diaz = 0.0 ! [unitless] default = 0.0
! hp_ipa_diaz
hp_ipa_smz = 0.0 ! [unitless] default = 0.0
! hp_ipa_smz
hp_ipa_mdz = 1.0 ! [unitless] default = 1.0
! hp_ipa_mdz
hp_ipa_lgz = 1.0 ! [unitless] default = 1.0
! hp_ipa_lgz
hp_ipa_bact = 0.0 ! [unitless] default = 0.0
! hp_ipa_bact
hp_ipa_det = 0.0 ! [unitless] default = 0.0
! hp_ipa_det
hp_phi_det = 0.35 ! [unitless] default = 0.35
! hp_phi_det
! half-sat for ingestion by higher predators
coef_hp = 2.0 ! [none] default = 2.0
! coefficient for higher predator losses (2=quadratic)
ktemp_hp = 0.063 ! [deg. C-1] default = 0.063
! exponential temperature dependence of higher predator rates
nswitch_hp = 2.0 ! [none] default = 2.0
! prey switching parameter 1 for higher predators
mswitch_hp = 2.0 ! [none] default = 2.0
! prey switching parameter 2 for higher predators
hp_ipa_smp = 0.0 ! [none] default = 0.0
! innate availability of small phytoplankton to higher predator feeding (0-1)
hp_ipa_mdp = 0.0 ! [none] default = 0.0
! innate availability of medium phytoplankton to higher predator feeding (0-1)
hp_ipa_lgp = 0.0 ! [none] default = 0.0
! innate availability of large phytoplankton to higher predator feeding (0-1)
hp_ipa_diaz = 0.0 ! [none] default = 0.0
! innate availability of diazotrophs to higher predator feeding (0-1)
hp_ipa_smz = 0.0 ! [none] default = 0.0
! innate availability of small zooplankton to higher predator feeding (0-1)
hp_ipa_mdz = 1.0 ! [none] default = 1.0
! innate availability of medium zooplankton to higher predator feeding (0-1)
hp_ipa_lgz = 1.0 ! [none] default = 1.0
! innate availability of large zooplankton to higher predator feeding (0-1)
hp_ipa_bact = 0.0 ! [none] default = 0.0
! innate availability of bacteria to higher predator feeding (0-1)
hp_ipa_det = 0.0 ! [none] default = 0.0
! innate availability of detritus to higher predator feeding (0-1)
hp_phi_det = 0.35 ! [none] default = 0.35
! fraction of ingestion by higher predators to detritus
ffe_sed_max = 170.0 ! [micromoles Fe m-2 day-1] default = 170.0
! maximum iron release from the sediment
ffe_geotherm_ratio = 2.0E-12 ! [mol Fe m-2 s-1 (W m-2)-1] default = 2.0E-12
Expand Down
5 changes: 0 additions & 5 deletions exps/NEP10.COBALT/INPUT/MOM_override
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Expand Up @@ -21,10 +21,5 @@
#override PHA_MLD_DRHO = 0.03
#override HREF_FOR_MLD = 5.0
#override DIAG_MLD_DENSITY_DIFF = 0.03
#override OBC_REMAPPING_USE_OM4_SUBCELLS = True
#override REMAPPING_USE_OM4_SUBCELLS = True
#override DIAG_REMAPPING_USE_OM4_SUBCELLS = True
#override VISC_REM_BUG = True
#override FRICTWORK_BUG = True
#override INTWAVE_REMAPPING_USE_OM4_SUBCELLS = True
#override GENERIC_TRACER_IC_FILE = "NEP_COBALT_spinup_2003.nc"
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