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Modify workflow to access files from obs component #1202

Merged
merged 19 commits into from
Jan 30, 2023
Merged

Modify workflow to access files from obs component #1202

merged 19 commits into from
Jan 30, 2023

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lgannoaa
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@lgannoaa lgannoaa commented Jan 3, 2023 •
edited by WalterKolczynski-NOAA
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Description
Observations in the current cycled system are linked/copied or created into the atmos/ subdirectory under ROTDIR
There are three files linked from emc dump to atmos subdirectory:
syndata.tcvitals.tm00
snogrb_t1534.3072.1536
seaice.5min.blend.grb
The nsstbufr, prepbufr will be created in obs subdirectory.

There should be only prep jobs need to access GDA location to link files to the obs component. All other jobs should be using obsproc files under the obs component.
Modify the following scripts to use COMIN_OBS in access files under obs component.
JGDAS_ATMOS_ANALYSIS_DIAG
JGDAS_ATMOS_CHGRES_FORENKF
JGDAS_ENKF_DIAG
JGDAS_ENKF_ECEN
JGDAS_ENKF_SELECT_OBS
JGDAS_ENKF_SFC
JGLOBAL_ATMOS_ANALYSIS
JGLOBAL_ATMOS_ANALYSIS_CALC
JGLOBAL_ATMOS_SFCANL
config.anal
config.base.emc.dyn
exglobal_atmos_sfcanl.sh

Fixes #1198

How Has This Been Tested?

Cycled tests on WCOSS
HOMEgfs:/lfs/h2/emc/global/noscrub/lin.gan/git/PR/issue-1184
EXPDIR:/lfs/h2/emc/global/noscrub/lin.gan/expdir/obsproc_da
KEEPDATA=YES

The following log file show a cycle with MAKE_NSSTBUFR="NO"
/lfs/h2/emc/ptmp/lin.gan/com/obsproc_da/gfs/v16.3/logs/2022062006

The following log file show a cycle with MAKE_NSSTBUFR="YES"
/lfs/h2/emc/ptmp/lin.gan/com/obsproc_da/gfs/v16.3/logs/2022062012
You may execute the following CMD to exam the log:
(In gdas/gfs prep step, the linking of the obsproc files is in the correct target /lfs/h2/emc/ptmp/lin.gan/com/obsproc_da/gfs/v16.3/gfs.20220620/12/obs/)
grep "ln " prep |grep -v "20220620/12/obs/"
(The bufr files located in new directory have been used in gdas prep, gfs prep, gdas anal, gfs anal, gdassfcanl, gfssfcanl, eobs, )
grep "ln " * |grep "20220620/12/obs/"
(No reference to emc dump archive other then the prep step. I.e. all other step used files from the new location under obs component)
grep "ln " * |grep bufr|grep "emc.global/dump"|grep -v "prep.log"|wc -l
(Exam the creation of the nsstbufr file when MAKE_NSSTBUFR="YES")
grep nsst *prep.log
Forecast-only tested on Hera

Checklist

  • My code follows the style guidelines of this project
  • I have performed a self-review of my own code
  • I have commented my code, particularly in hard-to-understand areas

@lgannoaa
Modify workflow to access files from obs component.
af35fd9 
Modify config and archive list scripts to access file from obs component.

GitHub: 1198
github-advanced-security[bot]
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shellcheck found more than 10 potential problems in the proposed changes. Check the Files changed tab for more details.

@lgannoaa lgannoaa changed the title Modify workflow to access files from obs component in supporting issue 1198 Modify workflow to access files from obs component Jan 4, 2023
github-advanced-security[bot]
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jobs/rocoto/prep.sh Outdated
fi

# exception handling to ensure no dead link
[[ $(find ${COMOBS} -xtype l | wc -l) -ge 1 ]] && exit 9

Check notice

Code scanning / shellcheck

Consider invoking this command separately to avoid masking its return value (or use '|| true' to ignore).

Consider invoking this command separately to avoid masking its return value (or use '|| true' to ignore).
jobs/rocoto/prep.sh Fixed Show fixed Hide fixed
jobs/rocoto/prep.sh

# exception handling to ensure no dead link
[[ $(find ${COMOBS} -xtype l | wc -l) -ge 1 ]] && exit 9
[[ $(find ${gCOMOBS} -xtype l | wc -l) -ge 1 ]] && exit 9

Check notice

Code scanning / shellcheck

Consider invoking this command separately to avoid masking its return value (or use '|| true' to ignore).

Consider invoking this command separately to avoid masking its return value (or use '|| true' to ignore).
jobs/rocoto/prep.sh

# exception handling to ensure no dead link
[[ $(find ${COMOBS} -xtype l | wc -l) -ge 1 ]] && exit 9
[[ $(find ${gCOMOBS} -xtype l | wc -l) -ge 1 ]] && exit 9

Check notice

Code scanning / shellcheck

Consider invoking this command separately to avoid masking its return value (or use '|| true' to ignore).

Consider invoking this command separately to avoid masking its return value (or use '|| true' to ignore).
jobs/rocoto/prep.sh Fixed Show fixed Hide fixed
@lgannoaa lgannoaa self-assigned this Jan 4, 2023
@lgannoaa lgannoaa mentioned this pull request Jan 6, 2023
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@lgannoaa lgannoaa marked this pull request as ready for review January 11, 2023 19:27
WalterKolczynski-NOAA
WalterKolczynski-NOAA requested changes Jan 12, 2023
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jobs/JGDAS_ATMOS_ANALYSIS_DIAG Outdated Show resolved Hide resolved
jobs/JGDAS_ATMOS_CHGRES_FORENKF Outdated Show resolved Hide resolved
jobs/JGDAS_ENKF_DIAG Outdated Show resolved Hide resolved
jobs/JGDAS_ENKF_DIAG Outdated Show resolved Hide resolved
jobs/JGDAS_ENKF_SELECT_OBS Outdated Show resolved Hide resolved
jobs/JGLOBAL_ATMOS_ANALYSIS Outdated
export COMOUT="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
export COMIN_OBS="${DMPDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
export COMIN_GES_OBS="${DMPDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
export COMOUT="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}"
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Same as above

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Same as above

jobs/JGLOBAL_ATMOS_ANALYSIS_CALC Outdated Show resolved Hide resolved
jobs/JGLOBAL_ATMOS_SFCANL Outdated Show resolved Hide resolved
jobs/rocoto/prep.sh Outdated Show resolved Hide resolved
ush/forecast_det.sh Outdated Show resolved Hide resolved
github-advanced-security[bot]
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jobs/rocoto/prep.sh
fi

# exception handling to ensure no dead link
[[ $(find ${COMIN_OBS} -xtype l | wc -l) -ge 1 ]] && exit 9

Check notice

Code scanning / shellcheck

Consider invoking this command separately to avoid masking its return value (or use '|| true' to ignore).

Consider invoking this command separately to avoid masking its return value (or use '|| true' to ignore).
aerorahul
aerorahul requested changes Jan 12, 2023
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For file specific changes, please see the inline comments.
A number of files have changed their permissions from 100755 -> 100644.
Please revert those permission changes.

jobs/JGDAS_ATMOS_ANALYSIS_DIAG Outdated Show resolved Hide resolved
jobs/JGDAS_ATMOS_CHGRES_FORENKF Outdated Show resolved Hide resolved
jobs/JGDAS_ENKF_DIAG Outdated Show resolved Hide resolved
jobs/JGDAS_ENKF_DIAG Outdated Show resolved Hide resolved
jobs/JGDAS_ENKF_SELECT_OBS Outdated Show resolved Hide resolved
parm/config/config.anal
if [[ "$CDATE" -ge "2019042300" ]]; then
export AHIBF="$DMPDIR/${CDUMP}x.${PDY}/${cyc}/atmos/${CDUMP}.t${cyc}z.ahicsr.tm00.bufr_d"
if [[ "${CDATE}" -ge "2019042300" ]]; then
export AHIBF="${COMIN_OBS}/${CDUMP}.t${cyc}z.ahicsr.tm00.bufr_d"
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The changes are consistent w/ the PR, but I am not sure this is entirely correct.
This is going to be true, if script that gets the obs copies them into the COMIN_OBS. But if it doesn't, we have to go to the DMPDIR.
May be @RussTreadon-NOAA might know the details of these conditionals

scripts/exglobal_atmos_sfcanl.sh Outdated
export FNACNA=${FNACNA:-${COMIN}/${OPREFIX}seaice.5min.blend.grb}
export FNSNOA=${FNSNOA:-${COMIN}/${OPREFIX}snogrb_t${JCAP_CASE}.${LONB_CASE}.${LATB_CASE}}
[[ ! -f ${FNSNOA} ]] && export FNSNOA="${COMIN_OBS}/${OPREFIX}snogrb_t1534.3072.1536"
FNSNOG=${FNSNOG:-${COMIN_GES_OBS}/${GPREFIX}snogrb_t${JCAP_CASE}.${LONB_CASE}.${LATB_CASE}}
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Shouldn't this be looking in COMIN_GES since we are retaining this file in the atmos component directory?

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It looks like the logic is to access these files in COMIN. Maybe there is no need to config the COMIN_GES.

ush/forecast_det.sh Outdated Show resolved Hide resolved
ush/hpssarch_gen.sh
Comment on lines +102 to +104
echo "${obs_dirname}${head}nsstbufr " >>gfsa.txt
echo "${obs_dirname}${head}prepbufr " >>gfsa.txt
echo "${obs_dirname}${head}prepbufr.acft_profiles " >>gfsa.txt
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fix indentation.

ush/hpssarch_gen.sh
Comment on lines +366 to +368
echo "${obs_dirname}${head}nsstbufr " >>gdas_restarta.txt
echo "${obs_dirname}${head}prepbufr " >>gdas_restarta.txt
echo "${obs_dirname}${head}prepbufr.acft_profiles " >>gdas_restarta.txt
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fix indentation.

aerorahul
aerorahul reviewed Jan 13, 2023
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a couple of if-blocks and an indentation fix.
we can worry about the leftover $COMPONENT in the files in a later PR.

Please fix the if-blocks at the very least and we can merge this PR.

jobs/JGDAS_ENKF_DIAG Outdated Show resolved Hide resolved
jobs/JGDAS_ENKF_SELECT_OBS Outdated Show resolved Hide resolved
WalterKolczynski-NOAA
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There are still permissions issues with execute being removed from several scripts.

@lgannoaa
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There are still permissions issues with execute being removed from several scripts.

Please provide more detail. Which one?

@WalterKolczynski-NOAA
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There are still permissions issues with execute being removed from several scripts.

Please provide more detail. Which one?

image

@lgannoaa
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755 permission restored to 9 scripts.

aerorahul
aerorahul requested changes Jan 18, 2023
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This branch at its current state fails in the gdasanal and gdaseobs jobs.
This branch needs to merge develop into it.

@lgannoaa
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This branch at its current state fails in the gdasanal and gdaseobs jobs.
At the time this PR created, It was tested against the develop. Develop has multiple commits after that without this PR been merged.

@lgannoaa
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@aerorahul Conflicting resolved.

WalterKolczynski-NOAA
WalterKolczynski-NOAA requested changes Jan 23, 2023
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Several of the scripts have had their permissions changed again. Please correct.

@lgannoaa
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755 permission updated.

WalterKolczynski-NOAA
WalterKolczynski-NOAA approved these changes Jan 23, 2023
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Seems okay now.

aerorahul
aerorahul approved these changes Jan 23, 2023
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Some suggestions as they won't break anything (ROTDIR_DUMP=NO does not work), but other than those changes look ok.
I have not tested and assume that @lgannoaa tested these changes for a few cycles for both GDAS and GFS.

parm/config/config.base.emc.dyn
Comment on lines +124 to +125
export COMIN_OBS=${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}
export COMIN_GES_OBS=${COMIN_GES_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}
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Is there a reason this needs to have a variable? This is a configuration file and nothing is set before calling config.base

Suggested change
export COMIN_OBS=${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}
export COMIN_GES_OBS=${COMIN_GES_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}
export COMIN_OBS="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs"
export COMIN_GES_OBS="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs"

jobs/JGDAS_ATMOS_CHGRES_FORENKF
@@ -38,8 +38,8 @@ if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
else
export COMOUT="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
export COMOUT_ENS="${ROTDIR}/enkfgdas.${PDY}/${cyc}"
export COMIN_OBS="${DMPDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
export COMIN_GES_OBS="${DMPDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
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Suggested change
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
export COMIN_OBS="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs"

jobs/JGDAS_ATMOS_ANALYSIS_DIAG
@@ -35,8 +35,8 @@ if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
export COMIN_GES_OBS=${COMIN_GES_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${GDUMP}.${gPDY}/${gcyc}/atmos}
else
export COMOUT="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
export COMIN_OBS="${DMPDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
export COMIN_GES_OBS="${DMPDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
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Suggested change
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
export COMIN_OBS="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs"

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ROTDIR_DUMP=NO does not work, so this change is untested.

jobs/JGDAS_ENKF_ECEN
@@ -42,8 +42,8 @@ if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${RUN}.${PDY}/${cyc}/atmos}
export COMIN_GES_OBS=${COMIN_GES_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${GDUMP}.${gPDY}/${gcyc}/atmos}
else
export COMIN_OBS="${DMPDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
export COMIN_GES_OBS="${DMPDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
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Suggested change
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
export COMIN_OBS="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs"

jobs/JGDAS_ENKF_SELECT_OBS
@@ -36,8 +36,8 @@ if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${RUN}.${PDY}/${cyc}/${COMPONENT}}
export COMIN_GES_OBS=${COMIN_GES_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${GDUMP}.${gPDY}/${gcyc}/${COMPONENT}}
else
export COMIN_OBS="${DMPDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}"
export COMIN_GES_OBS="${DMPDIR}/${GDUMP}.${gPDY}/${gcyc}/${COMPONENT}"
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
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Suggested change
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
export COMIN_OBS="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs"

jobs/JGLOBAL_ATMOS_ANALYSIS Outdated
@@ -38,8 +38,8 @@ if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
export COMIN_GES_OBS=${COMIN_GES_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${GDUMP}.${gPDY}/${gcyc}/atmos}
else
export COMOUT="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
export COMIN_OBS="${DMPDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
export COMIN_GES_OBS="${DMPDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
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Suggested change
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
export COMIN_OBS="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs"

jobs/JGLOBAL_ATMOS_SFCANL
@@ -38,8 +38,8 @@ if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
export COMIN_GES_OBS=${COMIN_GES_OBS:-${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos}
else
export COMOUT="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
export COMIN_OBS="${DMPDIR}/${CDATE}/${CDUMP}"
export COMIN_GES_OBS="${DMPDIR}/${GDATE}/${GDUMP}"
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
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Suggested change
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
export COMIN_OBS="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs"

jobs/JGDAS_ENKF_SFC
@@ -42,8 +42,8 @@ if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${RUN}.${PDY}/${cyc}/atmos}
export COMIN_GES_OBS=${COMIN_GES_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${GDUMP}.${gPDY}/${gcyc}/atmos}
else
export COMIN_OBS="${DMPDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
export COMIN_GES_OBS="${DMPDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
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Suggested change
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
export COMIN_OBS="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs"

jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
@@ -36,8 +36,8 @@ if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
export COMIN_GES_OBS=${COMIN_GES_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${GDUMP}.${gPDY}/${gcyc}/atmos}
else
export COMOUT="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
export COMIN_OBS="${DMPDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
export COMIN_GES_OBS="${DMPDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
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Suggested change
export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
export COMIN_OBS="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs"

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@lgannoaa I noticed some files changed permissions again. You might want to look at what is making this change.

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@RussTreadon-NOAA
Will you be reviewing this PR at all or should we merge it?

@RussTreadon-NOAA
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Has a cycled test been run from the feature branch for sufficient duration to confirm that the proposed changes do not alter cycled results from a control run using develop? If so, approval from @WalterKolczynski-NOAA and @aerorahul is sufficient.

@lgannoaa
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@lgannoaa I noticed some files changed permissions again. You might want to look at what is making this change.

The permission change is to fix the config file permission issue from the develop branch. There issues are not introduced from this PR.

@lgannoaa
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I discovered the Global Workflow develop #f98433f (Jan 23, 2023) has an internal silent failure "unary operator expected" in gdassfcanl and gfssfcanl.
This error caused SNOW_NUDGE_COEFF=-2 and CYCLVARS=FSNOL=-2., been used in cycled run. This is a result changing error.

File exglobal_atmos_sfcanl.sh contain incorrect application logic in FNSNOG assignment.
I fixed this issue in file exglobal_atmos_sfcanl.sh (PR 1212). The correct value is presented after the bug fix.

@RussTreadon-NOAA
C96C48 ATM cycled test has been run on Orion. The gdas/gfs/enkfgdas netcdf and master files are bit identical between PR 1212 and GW develop with the above bug fixed.

@WalterKolczynski-NOAA WalterKolczynski-NOAA merged commit 659b462 into NOAA-EMC:develop Jan 30, 2023
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When the conflicts were resolved in this PR, the permission on some of the parm/config/config.... files were reset to 755.
Please make sure next time the developers check if there are files that are not inadvertently changing permissions.

@DavidHuber-NOAA DavidHuber-NOAA mentioned this pull request Feb 10, 2023
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@WalterKolczynski-NOAA WalterKolczynski-NOAA WalterKolczynski-NOAA approved these changes

@aerorahul aerorahul aerorahul approved these changes

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Create an obs component in preparation for coupled DA
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@lgannoaa @WalterKolczynski-NOAA @aerorahul @RussTreadon-NOAA