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Assign machine- and RUN-specific resources #2672

Merged
merged 59 commits into from
Jun 25, 2024
Merged

Assign machine- and RUN-specific resources #2672

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8f0185a
Add run-specific resource variables
DavidHuber-NOAA Jun 10, 2024
420edf8
Add machine-specific resource files
DavidHuber-NOAA Jun 10, 2024
8376ee6
Force npe_node_eobs to be set properly #2092
DavidHuber-NOAA Jun 10, 2024
aacecb0
Use run-specific variables
DavidHuber-NOAA Jun 10, 2024
cf0e397
Fix tabbing
DavidHuber-NOAA Jun 10, 2024
463c931
Make nth_anal independent of run
DavidHuber-NOAA Jun 10, 2024
a9ebe3b
Fix gdas FHMAX/OUT variable
DavidHuber-NOAA Jun 10, 2024
e5084f9
Correct enkf task variable name
DavidHuber-NOAA Jun 10, 2024
6bed0d1
Fixed shellcheck issues
DavidHuber-NOAA Jun 10, 2024
b716671
Fix more shellcheck issues
DavidHuber-NOAA Jun 10, 2024
e2e2421
Remove unused case
DavidHuber-NOAA Jun 10, 2024
7fd5f0e
Make additional fcst, efcs, anal variables RUN-specific
DavidHuber-NOAA Jun 11, 2024
ffec316
Strip enkf from RUN when reading config.anal
DavidHuber-NOAA Jun 11, 2024
b80814b
Add double quotes
DavidHuber-NOAA Jun 11, 2024
63b97dc
Fix fcst/efcs RUNs in variable declarations
DavidHuber-NOAA Jun 11, 2024
552ddda
Fix C768 analysis case in config.resources
DavidHuber-NOAA Jun 11, 2024
27cdab4
Corrected machine-specific resource config names
DavidHuber-NOAA Jun 12, 2024
12b880b
Add memory requirement for WCOSS2 prep job
DavidHuber-NOAA Jun 12, 2024
41134d5
Adjust epos and analcalc high res time limits/memory upward
DavidHuber-NOAA Jun 12, 2024
7271bfe
Increase memory for UPP @C384 on WCOSS2.
DavidHuber-NOAA Jun 13, 2024
4e28b2c
Make wtime for waveprep RUN-agnostic
DavidHuber-NOAA Jun 13, 2024
9166934
Declare runtime job resource variables based on RUN
DavidHuber-NOAA Jun 13, 2024
10a75b9
Clean up env files
DavidHuber-NOAA Jun 13, 2024
d9e2f32
Add {} around EXPDIR
DavidHuber-NOAA Jun 13, 2024
824c16f
Add double quotes to nth_
DavidHuber-NOAA Jun 13, 2024
b21f736
Fix resource tests
DavidHuber-NOAA Jun 13, 2024
e14a0e1
Merge remote-tracking branch 'emc/develop' into feature/machine_res
Jun 13, 2024
24946a6
Use -n instead of ! -z
DavidHuber-NOAA Jun 13, 2024
803add5
Declare one variable per line
DavidHuber-NOAA Jun 14, 2024
dae27f0
Use the environment bash for new config files
DavidHuber-NOAA Jun 14, 2024
3204824
Declare one variable per line; unset dynamic variables
DavidHuber-NOAA Jun 14, 2024
7c4e095
Add comment on sourcing machine resources file
DavidHuber-NOAA Jun 14, 2024
a80e008
Merge remote-tracking branch 'emc/develop' into feature/machine_res
DavidHuber-NOAA Jun 14, 2024
93248b3
Merge remote-tracking branch 'emc/develop' into feature/machine_res
DavidHuber-NOAA Jun 17, 2024
0286dd0
Rename mem/node variable, move to config.resources.
DavidHuber-NOAA Jun 17, 2024
238ae98
Ignore unused shellcheck warnings
DavidHuber-NOAA Jun 17, 2024
e5680e8
Apply suggestions from Walter's code review
DavidHuber-NOAA Jun 18, 2024
c499a96
Merge branch 'feature/machine_res' of github.com:DavidHuber-NOAA/glob…
DavidHuber-NOAA Jun 18, 2024
ac0778d
Increase memory requirement on S4 for ediag
DavidHuber-NOAA Jun 18, 2024
c5659e3
Adjusted available memory on kjet to what is accepted by the job sche…
InnocentSouopgui-NOAA Jun 19, 2024
0562ef0
Merge branch 'feature/machine_res' of github.com:DavidHuber-NOAA/glob…
DavidHuber-NOAA Jun 20, 2024
03496d5
Merge remote-tracking branch 'emc/develop' into feature/machine_res
DavidHuber-NOAA Jun 20, 2024
71704d3
Merge branch 'feature/machine_res' of github.com:InnocentSouopgui-NOA…
InnocentSouopgui-NOAA Jun 20, 2024
1caf612
Prevent OpenMP over-allocation of resources on S4
InnocentSouopgui-NOAA Jun 20, 2024
7cc2753
Add array length check for older bash versions.
DavidHuber-NOAA Jun 20, 2024
895d018
Recalculate analysis npe_node when redefining threads for machines
DavidHuber-NOAA Jun 20, 2024
b901c47
Correct rocoto version in hercules setup module.
DavidHuber-NOAA Jun 20, 2024
fdd0850
Only run analyses @ 8 threads at C768 on WCOSS2.
DavidHuber-NOAA Jun 20, 2024
7ba6006
Merge branch 'feature/machine_res' of https://github.com/DavidHuber-N…
InnocentSouopgui-NOAA Jun 20, 2024
859da0a
fix typo preventing a S4 to check array size
InnocentSouopgui-NOAA Jun 21, 2024
f34bdd6
High res wallclock/memory adjustments
DavidHuber-NOAA Jun 21, 2024
4b21dbc
Correct max mem requestable on WCOSS2
DavidHuber-NOAA Jun 21, 2024
88e7f50
Merge branch 'feature/machine_res' of https://github.com/DavidHuber-N…
InnocentSouopgui-NOAA Jun 21, 2024
11556d0
Merge pull request #13 from InnocentSouopgui-NOAA/feature/machine_res
DavidHuber-NOAA Jun 21, 2024
68063b0
Merge remote-tracking branch 'emc/develop' into feature/machine_res
DavidHuber-NOAA Jun 21, 2024
cb03a52
Merge branch 'feature/machine_res' of github.com:DavidHuber-noaa/glob…
DavidHuber-NOAA Jun 21, 2024
184d235
Fix atmensanlfv3inc resource declarations
DavidHuber-NOAA Jun 23, 2024
9917143
Remove reference to non-existent RUN-specific gempak variables
DavidHuber-NOAA Jun 24, 2024
fe85950
Merge branch 'develop' into feature/machine_res
DavidHuber-NOAA Jun 24, 2024
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32 changes: 5 additions & 27 deletions env/AWSPW.env
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,6 @@
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 "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
echo "anal sfcanl fcst post metp"
echo "eobs eupd ecen efcs epos"
echo "postsnd awips gempak"
exit 1

fi
Expand All @@ -26,13 +21,11 @@ ulimit -a

if [[ "${step}" = "fcst" ]] || [[ "${step}" = "efcs" ]]; then

if [[ "${CDUMP}" =~ "gfs" ]]; then
nprocs="npe_${step}_gfs"
ppn="npe_node_${step}_gfs" || ppn="npe_node_${step}"
else
nprocs="npe_${step}"
ppn="npe_node_${step}"
fi
ppn="npe_node_${step}_${RUN}"
[[ -z "${!ppn+0}" ]] && ppn="npe_node_${step}"
nprocs="npe_${step}_${RUN}"
[[ -z ${!nprocs+0} ]] && nprocs="npe_${step}"

(( nnodes = (${!nprocs}+${!ppn}-1)/${!ppn} ))
(( ntasks = nnodes*${!ppn} ))
# With ESMF threading, the model wants to use the full node
Expand Down Expand Up @@ -109,21 +102,6 @@ elif [[ "${step}" = "awips" ]]; then
[[ ${NTHREADS_AWIPS} -gt ${nth_max} ]] && export NTHREADS_AWIPS=${nth_max}
export APRUN_AWIPSCFP="${launcher} -n ${npe_awips} ${mpmd_opt}"

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

export CFP_MP="YES"

if [[ ${CDUMP} == "gfs" ]]; then
npe_gempak=${npe_gempak_gfs}
npe_node_gempak=${npe_node_gempak_gfs}
fi

nth_max=$((npe_node_max / npe_node_gempak))

export NTHREADS_GEMPAK=${nth_gempak:-1}
[[ ${NTHREADS_GEMPAK} -gt ${nth_max} ]] && export NTHREADS_GEMPAK=${nth_max}
export APRUN="${launcher} -n ${npe_gempak} ${mpmd_opt}"


elif [[ "${step}" = "fit2obs" ]]; then

Expand Down
5 changes: 0 additions & 5 deletions env/CONTAINER.env
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Expand Up @@ -3,11 +3,6 @@
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 "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
echo "anal sfcanl fcst post metp"
echo "eobs eupd ecen efcs epos"
echo "postsnd awips gempak"
exit 1

fi
Expand Down
14 changes: 5 additions & 9 deletions env/GAEA.env
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Expand Up @@ -3,8 +3,6 @@
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 "fcst atmos_products"
exit 1

fi
Expand All @@ -19,13 +17,11 @@ ulimit -a

if [[ "${step}" = "fcst" ]]; then

if [[ "${CDUMP}" =~ "gfs" ]]; then
nprocs="npe_${step}_gfs"
ppn="npe_node_${step}_gfs" || ppn="npe_node_${step}"
else
nprocs="npe_${step}"
ppn="npe_node_${step}"
fi
ppn="npe_node_${step}_${RUN}"
[[ -z "${!ppn+0}" ]] && ppn="npe_node_${step}"
nprocs="npe_${step}_${RUN}"
[[ -z ${!nprocs+0} ]] && nprocs="npe_${step}"

(( nnodes = (${!nprocs}+${!ppn}-1)/${!ppn} ))
(( ntasks = nnodes*${!ppn} ))
# With ESMF threading, the model wants to use the full node
Expand Down
21 changes: 5 additions & 16 deletions env/HERA.env
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Expand Up @@ -3,11 +3,6 @@
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 "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
echo "anal sfcanl fcst post metp"
echo "eobs eupd ecen efcs epos"
echo "postsnd awips gempak"
WalterKolczynski-NOAA marked this conversation as resolved.
Show resolved Hide resolved
exit 1

fi
Expand Down Expand Up @@ -219,13 +214,11 @@ elif [[ "${step}" = "eupd" ]]; then

elif [[ "${step}" = "fcst" ]] || [[ "${step}" = "efcs" ]]; then

if [[ "${CDUMP}" =~ "gfs" ]]; then
nprocs="npe_${step}_gfs"
ppn="npe_node_${step}_gfs" || ppn="npe_node_${step}"
else
nprocs="npe_${step}"
ppn="npe_node_${step}"
fi
ppn="npe_node_${step}_${RUN}"
[[ -z "${!ppn+0}" ]] && ppn="npe_node_${step}"
nprocs="npe_${step}_${RUN}"
[[ -z ${!nprocs+0} ]] && nprocs="npe_${step}"

(( nnodes = (${!nprocs}+${!ppn}-1)/${!ppn} ))
(( ntasks = nnodes*${!ppn} ))
# With ESMF threading, the model wants to use the full node
Expand Down Expand Up @@ -314,10 +307,6 @@ elif [[ "${step}" = "gempak" ]]; then

export CFP_MP="YES"

if [[ ${CDUMP} == "gfs" ]]; then
npe_node_gempak=${npe_node_gempak_gfs}
fi

nth_max=$((npe_node_max / npe_node_gempak))

export NTHREADS_GEMPAK=${nth_gempak:-1}
Expand Down
29 changes: 7 additions & 22 deletions env/HERCULES.env
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,6 @@
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 "fcst post"
echo "Note: Hercules is only set up to run in forecast-only mode"
exit 1

fi
Expand Down Expand Up @@ -211,13 +208,12 @@ case ${step} in
"fcst" | "efcs")

export OMP_STACKSIZE=512M
if [[ "${CDUMP}" =~ "gfs" ]]; then
nprocs="npe_${step}_gfs"
ppn="npe_node_${step}_gfs" || ppn="npe_node_${step}"
else
nprocs="npe_${step}"
ppn="npe_node_${step}"
fi

ppn="npe_node_${step}_${RUN}"
[[ -z "${!ppn+0}" ]] && ppn="npe_node_${step}"
nprocs="npe_${step}_${RUN}"
[[ -z ${!nprocs+0} ]] && nprocs="npe_${step}"

(( nnodes = (${!nprocs}+${!ppn}-1)/${!ppn} ))
(( ntasks = nnodes*${!ppn} ))
# With ESMF threading, the model wants to use the full node
Expand Down Expand Up @@ -312,18 +308,7 @@ case ${step} in
;;
"gempak")

export CFP_MP="YES"

if [[ ${CDUMP} == "gfs" ]]; then
npe_gempak=${npe_gempak_gfs}
npe_node_gempak=${npe_node_gempak_gfs}
fi

nth_max=$((npe_node_max / npe_node_gempak))

export NTHREADS_GEMPAK=${nth_gempak:-1}
[[ ${NTHREADS_GEMPAK} -gt ${nth_max} ]] && export NTHREADS_GEMPAK=${nth_max}
export APRUN="${launcher} -n ${npe_gempak} ${mpmd_opt}"
echo "WARNING: ${step} is not enabled on ${machine}!"

;;
"fit2obs")
Expand Down
17 changes: 5 additions & 12 deletions env/JET.env
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,6 @@
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 "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
echo "anal sfcanl fcst post metp"
echo "eobs eupd ecen efcs epos"
echo "postsnd awips gempak"
exit 1

fi
Expand Down Expand Up @@ -192,13 +187,11 @@ elif [[ "${step}" = "eupd" ]]; then

elif [[ "${step}" = "fcst" ]] || [[ "${step}" = "efcs" ]]; then

if [[ "${CDUMP}" =~ "gfs" ]]; then
nprocs="npe_${step}_gfs"
ppn="npe_node_${step}_gfs" || ppn="npe_node_${step}"
else
nprocs="npe_${step}"
ppn="npe_node_${step}"
fi
ppn="npe_node_${step}_${RUN}"
[[ -z "${!ppn+0}" ]] && ppn="npe_node_${step}"
nprocs="npe_${step}_${RUN}"
[[ -z ${!nprocs+0} ]] && nprocs="npe_${step}"

(( nnodes = (${!nprocs}+${!ppn}-1)/${!ppn} ))
(( ntasks = nnodes*${!ppn} ))
# With ESMF threading, the model wants to use the full node
Expand Down
31 changes: 6 additions & 25 deletions env/ORION.env
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,6 @@
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 "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
echo "anal sfcanl fcst post metp"
echo "eobs eupd ecen efcs epos"
echo "postsnd awips gempak"
exit 1

fi
Expand Down Expand Up @@ -226,14 +221,11 @@ elif [[ "${step}" = "eupd" ]]; then

elif [[ "${step}" = "fcst" ]] || [[ "${step}" = "efcs" ]]; then

export OMP_STACKSIZE=512M
if [[ "${CDUMP}" =~ "gfs" ]]; then
nprocs="npe_${step}_gfs"
ppn="npe_node_${step}_gfs" || ppn="npe_node_${step}"
else
nprocs="npe_${step}"
ppn="npe_node_${step}"
fi
ppn="npe_node_${step}_${RUN}"
[[ -z "${!ppn+0}" ]] && ppn="npe_node_${step}"
nprocs="npe_${step}_${RUN}"
[[ -z ${!nprocs+0} ]] && nprocs="npe_${step}"

(( nnodes = (${!nprocs}+${!ppn}-1)/${!ppn} ))
(( ntasks = nnodes*${!ppn} ))
# With ESMF threading, the model wants to use the full node
Expand Down Expand Up @@ -319,18 +311,7 @@ elif [[ "${step}" = "awips" ]]; then

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

export CFP_MP="YES"

if [[ ${CDUMP} == "gfs" ]]; then
npe_gempak=${npe_gempak_gfs}
npe_node_gempak=${npe_node_gempak_gfs}
fi

nth_max=$((npe_node_max / npe_node_gempak))

export NTHREADS_GEMPAK=${nth_gempak:-1}
[[ ${NTHREADS_GEMPAK} -gt ${nth_max} ]] && export NTHREADS_GEMPAK=${nth_max}
export APRUN="${launcher} -n ${npe_gempak} ${mpmd_opt}"
echo "WARNING: ${step} is not enabled on ${machine}!"

elif [[ "${step}" = "fit2obs" ]]; then

Expand Down
18 changes: 6 additions & 12 deletions env/S4.env
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,6 @@
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 "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
echo "anal sfcanl fcst post metp"
echo "eobs eupd ecen efcs epos"
echo "postsnd awips gempak"
exit 1

fi
Expand Down Expand Up @@ -179,13 +174,11 @@ elif [[ "${step}" = "eupd" ]]; then

elif [[ "${step}" = "fcst" ]] || [[ "${step}" = "efcs" ]]; then

if [[ "${CDUMP}" =~ "gfs" ]]; then
nprocs="npe_${step}_gfs"
ppn="npe_node_${step}_gfs" || ppn="npe_node_${step}"
else
nprocs="npe_${step}"
ppn="npe_node_${step}"
fi
ppn="npe_node_${step}_${RUN}"
[[ -z "${!ppn+0}" ]] && ppn="npe_node_${step}"
nprocs="npe_${step}_${RUN}"
[[ -z ${!nprocs+0} ]] && nprocs="npe_${step}"

(( nnodes = (${!nprocs}+${!ppn}-1)/${!ppn} ))
(( ntasks = nnodes*${!ppn} ))
# With ESMF threading, the model wants to use the full node
Expand All @@ -198,6 +191,7 @@ elif [[ "${step}" = "upp" ]]; then

export NTHREADS_UPP=${nth_upp:-1}
[[ ${NTHREADS_UPP} -gt ${nth_max} ]] && export NTHREADS_UPP=${nth_max}
export OMP_NUM_THREADS="${NTHREADS_UPP}"
export APRUN_UPP="${launcher} -n ${npe_upp}"

elif [[ "${step}" = "atmos_products" ]]; then
Expand Down
23 changes: 5 additions & 18 deletions env/WCOSS2.env
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,6 @@
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 "atmanlvar atmanlfv3inc atmensanlletkf atmensanlfv3inc aeroanlrun snowanl"
echo "anal sfcanl fcst post metp"
echo "eobs eupd ecen esfc efcs epos"
echo "postsnd awips gempak"
exit 1

fi
Expand Down Expand Up @@ -38,7 +33,6 @@ elif [[ "${step}" = "prep_emissions" ]]; then
elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostbndpntbll" ]] || [[ "${step}" = "wavepostpnt" ]]; then

export USE_CFP="YES"
if [[ "${step}" = "waveprep" ]] && [[ "${CDUMP}" = "gfs" ]]; then export NTASKS=${NTASKS_gfs} ; fi
export wavempexec="${launcher} -np"
export wave_mpmd=${mpmd_opt}

Expand Down Expand Up @@ -182,13 +176,11 @@ elif [[ "${step}" = "eupd" ]]; then

elif [[ "${step}" = "fcst" ]] || [[ "${step}" = "efcs" ]]; then

if [[ "${CDUMP}" =~ "gfs" ]]; then
nprocs="npe_${step}_gfs"
ppn="npe_node_${step}_gfs" || ppn="npe_node_${step}"
else
nprocs="npe_${step}"
ppn="npe_node_${step}"
fi
ppn="npe_node_${step}_${RUN}"
[[ -z "${!ppn+0}" ]] && ppn="npe_node_${step}"
nprocs="npe_${step}_${RUN}"
[[ -z ${!nprocs+0} ]] && nprocs="npe_${step}"

(( nnodes = (${!nprocs}+${!ppn}-1)/${!ppn} ))
(( ntasks = nnodes*${!ppn} ))
# With ESMF threading, the model wants to use the full node
Expand Down Expand Up @@ -291,11 +283,6 @@ elif [[ "${step}" = "awips" ]]; then

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

if [[ ${CDUMP} == "gfs" ]]; then
npe_gempak=${npe_gempak_gfs}
npe_node_gempak=${npe_node_gempak_gfs}
fi

nth_max=$((npe_node_max / npe_node_gempak))

export NTHREADS_GEMPAK=${nth_gempak:-1}
Expand Down
2 changes: 1 addition & 1 deletion modulefiles/module_gwsetup.hercules.lua
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ Load environment to run GFS workflow ci scripts on Hercules
]])

load(pathJoin("contrib","0.1"))
load(pathJoin("rocoto","1.3.5"))
load(pathJoin("rocoto","1.3.7"))

prepend_path("MODULEPATH", "/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.6.0/envs/gsi-addon-env/install/modulefiles/Core")

Expand Down
2 changes: 1 addition & 1 deletion parm/config/gefs/config.resources
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Original file line number Diff line number Diff line change
Expand Up @@ -202,7 +202,7 @@ case ${step} in
declare -x "wtime_${step}_gfs"="06:00:00"
;;
*)
echo "FATAL ERROR: Resources not defined for job ${job} at resolution ${CASE}"
echo "FATAL ERROR: Resources not defined for job ${step} at resolution ${CASE}"
exit 4
;;
esac
Expand Down
8 changes: 2 additions & 6 deletions parm/config/gfs/config.anal
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Expand Up @@ -19,12 +19,8 @@ if [[ "${CDUMP}" = "gfs" ]] ; then
export DIAG_TARBALL="YES"
fi

export npe_gsi=${npe_anal}

if [[ "${CDUMP}" == "gfs" ]] ; then
export npe_gsi=${npe_anal_gfs}
export nth_anal=${nth_anal_gfs}
fi
npe_var="npe_anal_${RUN/enkf}"
export npe_gsi="${!npe_var}"
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# Set parameters specific to L127
if [[ ${LEVS} = "128" ]]; then
Expand Down
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