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Refactor UFS-DA ATM var component to use python g-w #1372

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merged 51 commits into from
Apr 18, 2023
Merged

Refactor UFS-DA ATM var component to use python g-w #1372

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e90ef97
refactor UFS-DA atm var to use python g-w (#1313)
RussTreadon-NOAA Mar 4, 2023
4417877
remove UFS-DA ATM ens changes in env files, fix pynorms violation (#1…
RussTreadon-NOAA Mar 4, 2023
6efd7ea
convert UFS-DA ATM increment to UFS model readable format (#1313)
RussTreadon-NOAA Mar 6, 2023
d068288
replace bump with gisbec as UFS-DA ATM var staticb option (#1313)
RussTreadon-NOAA Mar 6, 2023
84d4b40
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 7, 2023
67c025b
add bias correction file processing to UFS-DA ATM var finalize (#1313)
RussTreadon-NOAA Mar 7, 2023
5659a45
update UFS-DA ATM var sfcanl and analcalc job dependencies (#1313)
RussTreadon-NOAA Mar 7, 2023
bca9ea4
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 8, 2023
3d31aa4
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 10, 2023
083153c
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 13, 2023
31ef48c
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 15, 2023
01d54e3
remove DATA from var diagnostic file tarball path (#1313)
RussTreadon-NOAA Mar 17, 2023
22e622e
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 17, 2023
12e7cb0
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 21, 2023
00a3d88
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 22, 2023
9b4c510
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 22, 2023
60fd3f9
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 23, 2023
fa35b09
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 24, 2023
0d40801
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 27, 2023
bb3e89d
update UFS-DA ATM var crtm and fix stage (#1313)
RussTreadon-NOAA Mar 27, 2023
909276c
update atm_analysis.py to handle bump and gsibec static-b (#1313)
RussTreadon-NOAA Mar 27, 2023
42e6b0e
fix python coding norm errors in atm_analysis.py (#1313)
RussTreadon-NOAA Mar 27, 2023
a79facc
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 28, 2023
7ae652a
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 28, 2023
0a7856f
update UFS-DA atm parm/parm_gdas yaml to new g-w format (#1313)
RussTreadon-NOAA Mar 28, 2023
8615eb0
replace curly brackets with parentheses in atm_crtm_coeff.yaml (#1313)
RussTreadon-NOAA Mar 28, 2023
ddbbbf5
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 29, 2023
4c747e1
sync UFS-DA ATM var jobs and atm_analysis task with g-w python (#1313)
RussTreadon-NOAA Mar 30, 2023
551d55c
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 31, 2023
390d065
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Mar 31, 2023
c0537a1
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Apr 4, 2023
4efe032
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Apr 4, 2023
1fc94d2
Merge branch 'develop' into feature/refactor_jedivar
RussTreadon-NOAA Apr 12, 2023
c27618b
updates based on reviewer input (#1313)
RussTreadon-NOAA Apr 12, 2023
ab6d43f
add jediinc2fv3.py link to HOMEgfs/ush, consistently reference dictio…
RussTreadon-NOAA Apr 12, 2023
68a7f61
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Apr 12, 2023
b8fd6a5
use python script for atm_analysis_run (#1313)
RussTreadon-NOAA Apr 13, 2023
af3e0d6
add method jedi2fv3inc to atm_analysis.py (#1313)
RussTreadon-NOAA Apr 13, 2023
86e63f0
add methods for bump and gsibec background error file lists (#1313)
RussTreadon-NOAA Apr 13, 2023
4b4ca4d
change berror method output from list to dictionary (#1313)
RussTreadon-NOAA Apr 13, 2023
3501d59
modify get_berror methods (#1313)
RussTreadon-NOAA Apr 13, 2023
8492ccf
fold patch update and other updates into atm_analysis.py (#1313)
RussTreadon-NOAA Apr 15, 2023
4d353e5
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Apr 15, 2023
8f2c8e6
add linked file ush/jediinc2fv3.py to .gitignore (#1313)
RussTreadon-NOAA Apr 17, 2023
ca5d325
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Apr 17, 2023
1ca8a2a
correct comment and runtime message in get_berror_dict_identity (#1313)
RussTreadon-NOAA Apr 17, 2023
9d3d147
return empty dictionary for get_berror_dict_identity (#1313)
RussTreadon-NOAA Apr 17, 2023
e6fbc44
add doc block for identity BE
aerorahul Apr 17, 2023
62c3ad2
Merge branch 'NOAA-EMC:develop' into feature/refactor_jedivar
RussTreadon-NOAA Apr 17, 2023
c7d2a8d
Merge branch 'develop' into feature/refactor_jedivar
RussTreadon-NOAA Apr 18, 2023
d80b646
remove CFP variables in atmanlrun section of machine env files (#1313)
RussTreadon-NOAA Apr 18, 2023
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -129,6 +129,7 @@ ush/global_chgres.sh
ush/global_chgres_driver.sh
ush/global_cycle.sh
ush/global_cycle_driver.sh
ush/jediinc2fv3.py
ush/mkwfsgbl.sh
ush/ufsda
ush/wafs_blending.sh
Expand Down
3 changes: 1 addition & 2 deletions env/CONTAINER.env
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,7 @@ if [[ $# -ne 1 ]]; then

echo "Must specify an input argument to set runtime environment variables!"
echo "argument can be any one of the following:"
echo "atmanalrun atmensanalrun"
echo "aeroanlrun"
echo "atmanlrun atmensanalrun aeroanlrun"
echo "anal sfcanl fcst post vrfy metp"
echo "eobs eupd ecen efcs epos"
echo "postsnd awips gempak"
Expand Down
17 changes: 6 additions & 11 deletions env/HERA.env
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,7 @@ if [[ $# -ne 1 ]]; then

echo "Must specify an input argument to set runtime environment variables!"
echo "argument can be any one of the following:"
echo "atmanalrun atmensanalrun"
echo "aeroanlrun"
echo "atmanlrun atmensanalrun aeroanlrun"
echo "anal sfcanl fcst post vrfy metp"
echo "eobs eupd ecen efcs epos"
echo "postsnd awips gempak"
Expand Down Expand Up @@ -49,22 +48,18 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
export wavempexec=${launcher}
export wave_mpmd=${mpmd_opt}

elif [[ "${step}" = "atmanalrun" ]]; then
elif [[ "${step}" = "atmanlrun" ]]; then

export CFP_MP=${CFP_MP:-"YES"}
export USE_CFP=${USE_CFP:-"YES"}
export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

nth_max=$((npe_node_max / npe_node_atmanalrun))
nth_max=$((npe_node_max / npe_node_atmanlrun))

export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
[[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
[[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"

elif [[ "${step}" = "atmensanalrun" ]]; then

export CFP_MP=${CFP_MP:-"YES"}
export USE_CFP=${USE_CFP:-"YES"}
export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

nth_max=$((npe_node_max / npe_node_atmensanalrun))
Expand Down
12 changes: 6 additions & 6 deletions env/JET.env
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ if [[ $# -ne 1 ]]; then

echo "Must specify an input argument to set runtime environment variables!"
echo "argument can be any one of the following:"
echo "atmanalrun atmensanalrun aeroanlrun"
echo "atmanlrun atmensanalrun aeroanlrun"
echo "anal sfcanl fcst post vrfy metp"
echo "eobs eupd ecen efcs epos"
echo "postsnd awips gempak"
Expand Down Expand Up @@ -43,13 +43,13 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
export wavempexec=${launcher}
export wave_mpmd=${mpmd_opt}

elif [[ "${step}" = "atmanalrun" ]]; then
elif [[ "${step}" = "atmanlrun" ]]; then

nth_max=$((npe_node_max / npe_node_atmanalrun))
nth_max=$((npe_node_max / npe_node_atmanlrun))

export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
[[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
export APRUN_ATMANAL="${launcher} ${npe_atmanalrun}"
export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
[[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
export APRUN_ATMANL="${launcher} ${npe_atmanlrun}"

elif [[ "${step}" = "atmensanalrun" ]]; then

Expand Down
13 changes: 6 additions & 7 deletions env/ORION.env
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,7 @@ if [[ $# -ne 1 ]]; then

echo "Must specify an input argument to set runtime environment variables!"
echo "argument can be any one of the following:"
echo "atmanalrun atmensanalrun"
echo "aeroanlrun"
echo "atmanlrun atmensanalrun aeroanlrun"
echo "anal sfcanl fcst post vrfy metp"
echo "eobs eupd ecen efcs epos"
echo "postsnd awips gempak"
Expand Down Expand Up @@ -49,17 +48,17 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
export wavempexec=${launcher}
export wave_mpmd=${mpmd_opt}

elif [[ "${step}" = "atmanalrun" ]]; then
elif [[ "${step}" = "atmanlrun" ]]; then

export CFP_MP=${CFP_MP:-"YES"}
export USE_CFP=${USE_CFP:-"YES"}
export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

nth_max=$((npe_node_max / npe_node_atmanalrun))
nth_max=$((npe_node_max / npe_node_atmanlrun))

export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
[[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
[[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"

elif [[ "${step}" = "atmensanalrun" ]]; then

Expand Down
13 changes: 6 additions & 7 deletions env/S4.env
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,7 @@ if [[ $# -ne 1 ]]; then

echo "Must specify an input argument to set runtime environment variables!"
echo "argument can be any one of the following:"
echo "atmanalrun atmensanalrun"
echo "aeroanlrun"
echo "atmanlrun atmensanalrun aeroanlrun"
echo "anal sfcanl fcst post vrfy metp"
echo "eobs eupd ecen efcs epos"
echo "postsnd awips gempak"
Expand Down Expand Up @@ -47,17 +46,17 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
export wavempexec=${launcher}
export wave_mpmd=${mpmd_opt}

elif [[ "${step}" = "atmanalrun" ]]; then
elif [[ "${step}" = "atmanlrun" ]]; then

export CFP_MP=${CFP_MP:-"YES"}
export USE_CFP=${USE_CFP:-"YES"}
export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

nth_max=$((npe_node_max / npe_node_atmanalrun))
nth_max=$((npe_node_max / npe_node_atmanlrun))

export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
[[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
[[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"

elif [[ "${step}" = "atmensanalrun" ]]; then

Expand Down
13 changes: 6 additions & 7 deletions env/WCOSS2.env
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,7 @@ if [[ $# -ne 1 ]]; then

echo "Must specify an input argument to set runtime environment variables!"
echo "argument can be any one of the following:"
echo "atmanalrun atmensanalrun"
echo "aeroanlrun"
echo "atmanlrun atmensanalrun aeroanlrun"
echo "anal sfcanl fcst post vrfy metp"
echo "eobs eupd ecen esfc efcs epos"
echo "postsnd awips gempak"
Expand Down Expand Up @@ -36,17 +35,17 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
export wavempexec="${launcher} -np"
export wave_mpmd=${mpmd_opt}

elif [[ "${step}" = "atmanalrun" ]]; then
elif [[ "${step}" = "atmanlrun" ]]; then

export CFP_MP=${CFP_MP:-"YES"}
export USE_CFP=${USE_CFP:-"YES"}
export APRUNCFP="${launcher} -np \$ncmd ${mpmd_opt}"

nth_max=$((npe_node_max / npe_node_atmanalrun))
nth_max=$((npe_node_max / npe_node_atmanlrun))

export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
[[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
[[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"

elif [[ "${step}" = "atmensanalrun" ]]; then

Expand Down
63 changes: 0 additions & 63 deletions jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST
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62 changes: 0 additions & 62 deletions jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP
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63 changes: 0 additions & 63 deletions jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN
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