Update JEDI-T2O to work with JCB

[RussTreadon-NOAA]

GDASApp PR #1033 and g-w PR #2477 bring the JEDI Configuration Builder (JCB) tool into develop of both repositories. As such the configuration for GDAS-validation needs to be updated to work with JCB. This issue is opened to make these changes.

[RussTreadon-NOAA]

Work for this issue will be done in RussTreadon-NOAA:/feature/jcb.

[RussTreadon-NOAA]

Orion test

Install GDAS-validation

1. cd /work2/noaa/da/rtreadon/git/jedi-t2o
2. mkdir test
3. cd test
4. git clone https://github.com/RussTreadon-NOAA/JEDI-T2O.git .
5. git checkout feature/jcb
6. cd GDAS-validation
7. ./setup_workspace.sh -c
8. ./setup_workspace.sh -b
9. ./setup_workspace.sh -s

Output from the -s step is shown below

Orion-login-3:/work2/noaa/da/rtreadon/git/jedi-t2o/test/GDAS-validation$ ./setup_workspace.sh -s
Staging configuration files
+ ./setup_expt.py gfs cycled --idate 2021080100 --edate 2021080200 --app ATM --start warm --gfs_cyc 0 --resdetatmos 768 --nens 0 --cdump gdas --pslot gdas_eval_satwind_GSI --configdir /work2/noaa/da/rtreadon/gdas-validation/gdas_config --comroot /work2/noaa/da/rtreadon/gdas-validation/comroot --expdir /work2/noaa/da/rtreadon/gdas-validation/expdir --yaml /work2/noaa/da/rtreadon/gdas-validation/gdas_config/config_gsi.yaml --icsdir /work2/noaa/da/cmartin/UFO_eval/data/para/output_ufo_eval_aug2021/2021080100
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_GSI/config.base as per user input.
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_GSI/config.atmanl as per user input.
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_GSI/config.atmensanl as per user input.
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_GSI/config.aeroanl as per user input.
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_GSI/config.snowanl as per user input.
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_GSI/config.ocnanal as per user input.
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_GSI/config.prepoceanobs as per user input.
****************************************************************************************************
EXPDIR: /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_GSI
ROTDIR: /work2/noaa/da/rtreadon/gdas-validation/comroot/gdas_eval_satwind_GSI
****************************************************************************************************
+ ./setup_expt.py gfs cycled --idate 2021080100 --edate 2021080200 --app ATM --start warm --gfs_cyc 0 --resdetatmos 768 --nens 0 --cdump gdas --pslot gdas_eval_satwind_JEDI --configdir /work2/noaa/da/rtreadon/gdas-validation/gdas_config --comroot /work2/noaa/da/rtreadon/gdas-validation/comroot --expdir /work2/noaa/da/rtreadon/gdas-validation/expdir --yaml /work2/noaa/da/rtreadon/gdas-validation/gdas_config/config_jedi.yaml --icsdir /work2/noaa/da/cmartin/UFO_eval/data/para/output_ufo_eval_aug2021/2021080100
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_JEDI/config.base as per user input.
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_JEDI/config.atmanl as per user input.
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_JEDI/config.atmensanl as per user input.
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_JEDI/config.aeroanl as per user input.
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_JEDI/config.snowanl as per user input.
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_JEDI/config.ocnanal as per user input.
EDITED:  /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_JEDI/config.prepoceanobs as per user input.
****************************************************************************************************
EXPDIR: /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_JEDI
ROTDIR: /work2/noaa/da/rtreadon/gdas-validation/comroot/gdas_eval_satwind_JEDI
****************************************************************************************************
+ set +x
Finalizing initialize
sourcing config.prep
sourcing config.anal
sourcing config.analdiag
sourcing config.sfcanl
sourcing config.analcalc
sourcing config.fcst
sourcing config.upp
sourcing config.atmos_products
sourcing config.arch
sourcing config.cleanup
sourcing config.fit2obs
sourcing config.verfozn
sourcing config.verfrad
sourcing config.vminmon
sourcing config.tracker
sourcing config.genesis
sourcing config.genesis_fsu
sourcing config.gempak
sourcing config.postsnd
sourcing config.awips
Finalizing initialize
sourcing config.prep
sourcing config.prepatmiodaobs
sourcing config.atmanlinit
sourcing config.atmanlvar
sourcing config.atmanlfv3inc
sourcing config.atmanlfinal
sourcing config.sfcanl
sourcing config.analcalc
sourcing config.fcst
sourcing config.upp
sourcing config.atmos_products
sourcing config.arch
sourcing config.cleanup
sourcing config.fit2obs
sourcing config.tracker
sourcing config.genesis
sourcing config.genesis_fsu
sourcing config.gempak
sourcing config.postsnd
sourcing config.awips
Linking backgrounds to /work2/noaa/da/rtreadon/gdas-validation/comroot/gdas_eval_satwind_GSI/
Orion-login-3:/work2/noaa/da/rtreadon/git/jedi-t2o/test/GDAS-validation$

Test GSI validation

1. cd /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_GSI
2. rocotoboot -d gdas_eval_satwind_GSI.db -w gdas_eval_satwind_GSI.xml -c 202108010000 -t gdasprep
   • enter y when asked if you want to activate the cycle
3. boot gdasanal after prep completes
4. boot gdasanaldiag after anal completes

Output is in /work2/noaa/da/rtreadon/gdas-validation/comroot/gdas_eval_satwind_GSI

Test JEDI validation

1. cd /work2/noaa/da/rtreadon/gdas-validation/expdir/gdas_eval_satwind_JEDI
2. rocotoboot -d gdas_eval_satwind_JEDI.db -w gdas_eval_satwind_JEDI.xml -c 202108010000 -t gdasprep
   • enter y when asked if you want to activate the cycle
3. boot gdasprepatmiodaobs after prep completes
4. boot gdasatmanlinit after prepatmiodaobs
5. boot gdasatmanlvar after atmanlinit
6. boot gdasatmanlfinal after atmanlvar
   • note that we skip over gdasatmanlfv3inc. The yaml used to run atmanlvar is configured to not write an analysis increment file. Thus, gdasatmanlfv3inc will fail if booted

Output is in /work2/noaa/da/rtreadon/gdas-validation/comroot/gdas_eval_satwind_GSI