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Replay Mover Updates #15

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merged 5 commits into from
Mar 20, 2024
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Merged

Replay Mover Updates #15

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1c01f74
just re-move the whole dataset
timothyas Mar 8, 2024
82b4c77
done moving 1/4 degree dataset ... finally
timothyas Mar 18, 2024
e842519
actually revert this change to the source code
timothyas Mar 18, 2024
e40c3b0
this flag is dangerous, remove it to reduce accidents
timothyas Mar 19, 2024
3b381f0
add 1 degree config with all variables
timothyas Mar 20, 2024
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205 changes: 162 additions & 43 deletions examples/replay/config-0.25-degree.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,16 +7,9 @@ FV3Dataset:
coords_path_out: "gcs://noaa-ufs-gefsv13replay/ufs-hr1/0.25-degree/coordinates/zarr/"
forecast_hours : [0, 3]

chunks_in:
# estimated 37MB per chunk (the full 3D field)
time : 1
pfull : 127
grid_yt : 768
grid_xt : 1536

chunks_out:
time : 1
pfull : 127
pfull : 1
grid_yt : 768
grid_xt : 1536

Expand All @@ -29,56 +22,182 @@ FV3Dataset:
- bk

data_vars:
# 3D atmospheric vars
- tmp
- ugrd
- vgrd
- delz
- dzdt
- dpres
- spfh
- o3mr
# 3D land vars
- soilt1
- soilt2
- soilt3
- soilt4
- acond
- albdo_ave
- alnsf
- alnwf
- alvsf
- alvwf
- c0
- cd
- cduvb_ave
- cldfra
- cnvprcp
- cnwat
- cpofp
- cprat_ave
- cpratb_ave
- crain
- csdlf
- csdsf
- csulf
- csulftoa
- csusf
- csusftoa
- cwork_aveclm
- dconv
- dlwrf
- dlwrf_ave
- dswrf
- dswrf_ave
- dswrf_avetoa
- dtcool
- duvb_ave
- ecan_acc
- edir_acc
- etran_acc
- evbs_ave
- evcw_ave
- f10m
- facsf
- facwf
- ffhh
- ffmm
- fldcp
- fricv
- frozr
- frozrb
- frzr
- frzrb
- gflux
- gflux_ave
- hgt_hyblev1
- hpbl
- icec
- icetk
- land
- lfrac
- lhtfl
- lhtfl_ave
- nbdsf_ave
- nddsf_ave
- orog
- pah_ave
- pahi
- pevpr
- pevpr_ave
- prate_ave
- prateb_ave
- pres_avehcb
- pres_avehct
- pres_avelcb
- pres_avelct
- pres_avemcb
- pres_avemct
- prescnvclb
- prescnvclt
- pressfc
- pwat
- qrain
- rhonewsn
- sbsno_ave
- sfcr
- sfexc
- shdmax
- shdmin
- shtfl
- shtfl_ave
- sltyp
- snoalb
- snod
- snohf
- snowc_ave
- soill1
- soill2
- soill3
- soill4
- soilm
- soilt1
- soilt2
- soilt3
- soilt4
- soilw1
- soilw2
- soilw3
- soilw4
# 2D vars
- snod
- prateb_ave
- pressfc
- weasd
- f10m
- sfcr
# Surface forcing vars
- land
- vtype
- sotyp
- veg
- icec
- spfh2m
- spfh_hyblev1
- spfhmax_max2m
- spfhmin_min2m
- ssrun_acc
- sunsd_acc
- tcdc_avebndcl
- tcdc_aveclm
- tcdc_avehcl
- tcdc_avelcl
- tcdc_avemcl
- tcdccnvcl
- tg3
- tisfc
- tmax_max2m
- tmin_min2m
- tmp2m
- tmp_avehct
- tmp_avelct
- tmp_avemct
- tmp_hyblev1
- tmpsfc
# For TOA solar radiation
- dswrf_avetoa
- tprcp
- trans_ave
- tref
- tsnowp
- tsnowpb
- u-gwd_ave
- uflx_ave
- ugrd10m
- ugrd_hyblev1
- ulwrf
- ulwrf_ave
- ulwrf_avetoa
- uswrf
- uswrf_ave
- uswrf_avetoa
# Ease comparison
- tmp2m
- ugrd10m
- v-gwd_ave
- vbdsf_ave
- vddsf_ave
- veg
- vflx_ave
- vgrd10m
# For cloudy assimilation
- vgrd_hyblev1
- vtype
- w0
- wa_acc
- watr_acc
- wd
- weasd
- wilt
- xs
- xt
- xtts
- xu
- xv
- xz
- xzts
- zc
- clwmr
- delz
- dpres
- dzdt
- grle
- hgtsfc
- icmr
- nicp
- ntrnc
- o3mr
- rwmr
- snmr
# For future operational implementation
- ntrnc
- nicp
- spfh
- tmp
- ugrd
- vgrd
4 changes: 1 addition & 3 deletions examples/replay/fill_quarter_degree.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,6 @@ def submit_slurm_filler(job_id, mover):
f"from replay_filler import ReplayFiller\n"+\
f"mover = ReplayMoverQuarterDegree(\n"+\
f" n_jobs={mover.n_jobs},\n"+\
f" n_cycles={mover.n_cycles},\n"+\
f" config_filename='{mover.config_filename}',\n"+\
f" storage_options={mover.storage_options},\n"+\
f" main_cache_path='{mover.main_cache_path}',\n"+\
Expand Down Expand Up @@ -56,8 +55,7 @@ def submit_slurm_filler(job_id, mover):

# Recreated from what we used to put up quarter degree in the first place
mover = ReplayMoverQuarterDegree(
n_jobs=15
n_cycles=1,
n_jobs=1,
config_filename="config-0.25-degree.yaml",
storage_options={"token": "/contrib/Tim.Smith/.gcs/replay-service-account.json"},
main_cache_path="/lustre/Tim.Smith/tmp-replay/0.25-degree",
Expand Down
11 changes: 11 additions & 0 deletions examples/replay/find_nans.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
#! /bin/bash

echo " --- 0.25 Degree ---"
awk '!/ 0 NaN/ && (/NaN/) {print FILENAME, $1, $2, $3, $4}' slurm/verify-0.25-degree/march15/*.out
echo ""
echo ""

echo " --- 1.00 Degree ---"
awk '!/ 0 NaN/ && (/NaN/) {print FILENAME, $1, $2, $3, $4}' slurm/verify-1.00-degree/*.out
echo ""
echo ""
24 changes: 14 additions & 10 deletions examples/replay/replay_mover.py
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yep these were the exact same bugs I found!

  • import logging was needed
  • in def(run) when you called move_single_dataset it would say replay doesn't exist so had to be fixed.

I did not make the updates to region on my end, but I see why that was needed. I think one time I got an error that "pfull" didnt exist because none of the variables in that specific run had that dimension so I think I just commented out pfull and it worked fine. But anyways -- this is an actual fix!

Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from os.path import join, isdir
from datetime import datetime, timedelta
import logging
import yaml
from shutil import rmtree
import itertools
Expand Down Expand Up @@ -136,15 +137,14 @@ def run(self, job_id):

walltime = Timer()
localtime = Timer()
replay = FV3Dataset(path_in=self.cached_path, config_filename=self.config_filename)

store_coords = False # we don't need a separate coords dataset for FV3
for cycle in self.my_cycles(job_id):

localtime.start(f"Reading {str(cycle)}")

try:
self.move_single_dataset(cycle)
self.move_single_dataset(job_id, cycle)
except Exception as e:
logging.exception(e)
print(f"ReplayMover.run({job_id}): Failed to store {str(cycle)}")
Expand All @@ -153,22 +153,26 @@ def run(self, job_id):

walltime.stop("Total Walltime")

def move_single_dataset(self, cycle):
def move_single_dataset(self, job_id, cycle):
"""Store a single cycle to zarr"""

replay = FV3Dataset(path_in=self.cached_path, config_filename=self.config_filename)
xds = replay.open_dataset(cycle, **self.ods_kwargs(job_id))

index = list(self.xtime.values).index(xds.time.values[0])
tslice = slice(index, index+2)

region = {
"time": tslice,
"pfull": slice(None, None),
"grid_yt": slice(None, None),
"grid_xt": slice(None, None),
}
region = {k : v for k,v in region.items() if k in xds.dims}

replay.store_dataset(
xds,
region={
"time": tslice,
"pfull": slice(None, None),
"grid_yt": slice(None, None),
"grid_xt": slice(None, None),
},
region=region,
storage_options=self.storage_options,
)
# This is a hacky way to clear the cache, since we don't create a filesystem object
Expand Down Expand Up @@ -226,7 +230,7 @@ def store_container(self):

localtime.start("Storing to zarr")
store = NestedDirectoryStore(path=replay.data_path) if replay.is_nested else replay.data_path
dds.to_zarr(store, compute=False, storage_options=self.storage_options)
dds.to_zarr(store, compute=False, storage_options=self.storage_options, mode="w")
localtime.stop()

# This is a hacky way to clear the cache, since we don't create a filesystem object
Expand Down
14 changes: 14 additions & 0 deletions examples/replay/submit_move_quarter.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
#!/bin/bash

#SBATCH -J quarter_container
#SBATCH -o slurm/quarter_container.%j.out
#SBATCH -e slurm/quarter_container.%j.err
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=30
#SBATCH --partition=compute
#SBATCH -t 120:00:00

source /contrib/Tim.Smith/miniconda3/etc/profile.d/conda.sh
conda activate ufs2arco
python move_quarter_degree.py
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