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Merge branch 'develop' into feature/jstassi/#345/runjob_and_checkinput_updates
2 parents 3fd2553 + 8e56741 commit d57bc94

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‎components.yaml‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -28,14 +28,14 @@ crtm:
2828
NCEP_Shared:
2929
local: ./src/Shared/@NCEP_Shared
3030
remote: ../NCEP_Shared.git
31-
tag: v1.3.0
31+
tag: v5.42.3
3232
sparse: ./config/NCEP_Shared.sparse
3333
develop: main
3434

3535
GMAO_Shared:
3636
local: ./src/Shared/@GMAO_Shared
3737
remote: ../GMAO_Shared.git
38-
tag: g5.42.0
38+
tag: v5.42.2
3939
sparse: ./config/GMAO_Shared.sparse
4040
develop: main
4141

@@ -61,7 +61,7 @@ GEOS_Util:
6161
GMAO_perllib:
6262
local: ./src/Shared/@GMAO_Shared/@GMAO_perllib
6363
remote: ../GMAO_perllib.git
64-
tag: g1.0.1
64+
tag: v1.1.0
6565
develop: main
6666

6767
# When updating the MAPL version, also update the MAPL version in the
@@ -75,7 +75,7 @@ MAPL:
7575
GEOSldas_GridComp:
7676
local: ./src/Components/@GEOSldas_GridComp
7777
remote: ../GEOSldas_GridComp.git
78-
tag: v1.0.2
78+
tag: v2.0.0
7979

8080
FMS:
8181
local: ./src/Shared/@FMS
@@ -86,13 +86,13 @@ FMS:
8686
GEOSana_GridComp:
8787
local: ./src/Components/@GEOSana_GridComp
8888
remote: ../GEOSana_GridComp.git
89-
tag: v5.42.0
89+
tag: v5.42.4
9090
develop: develop
9191

9292
mksi:
9393
local: ./src/Components/@GEOSana_GridComp/GEOSaana_GridComp/GSI_GridComp/@mksi
9494
remote: ../GEOS_mksi.git
95-
tag: v5.42.0
95+
tag: v5.42.3
9696
develop: develop
9797

9898
GEOSgcm_GridComp:
@@ -251,7 +251,7 @@ umwm:
251251
GEOSgcm_App:
252252
local: ./src/Applications/@GEOSgcm_App
253253
remote: ../GEOSgcm_App.git
254-
tag: g2.3.8.1
254+
tag: g2.3.8.2
255255
develop: develop
256256

257257
Ocean-LETKF:

‎src/Applications/GEOSdas_App/AGCMrc.pm‎

100644100755
Lines changed: 15 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -17,6 +17,7 @@ package AGCMrc;
1717
# 03May2010 Todling Add reference to CARMA rst
1818
# 19Aug2010 Todling turb_internal_rst is needed for reproduc/ble fcst
1919
# 09Oct2013 Todling Add logics to handle precip-forcing option
20+
# 07Jan2024 Stassi No longer need '#' in front of key in %uncomment hash
2021
#
2122
#########################################################################
2223
use strict;
@@ -35,6 +36,7 @@ my ($gocart_tracers, $carma_tracers, $iau, $pcp_forced, $lsmodel_flag);
3536
my ($fvhome, $fvroot);
3637
my ($coupled);
3738
my ($envvars_set, $flags_set, %subst);
39+
my ($ldas_flag);
3840

3941
#----------------------------------
4042
# GCM Restart files
@@ -123,7 +125,6 @@ my %list = (rs5_core => \@rs5_core,
123125
stratchem_internal_rst
124126
stratchem_import_rst );
125127

126-
127128
#=======================================================================
128129
# name - set_AGCM_envvars
129130
# purpose - set global variables: $fvhome and $fvroot
@@ -144,7 +145,6 @@ sub set_AGCM_envvars {
144145
@rs5_notused = (@rs5_notused, @rs5_coupled);
145146
@rs5_files = (@rs5_core, @rs5_boot, @rs5_others);
146147
}
147-
148148
}
149149

150150
#=======================================================================
@@ -160,6 +160,7 @@ sub set_AGCM_flags {
160160
$lsmodel_flag = hashextract("lsmodel_flag", %flags);
161161
$iau = hashextract("iau", %flags);
162162
$pcp_forced = hashextract("pcp_forced", %flags);
163+
$ldas_flag = hashextract("ldas_flag", %flags);
163164
$flags_set = 1;
164165
}
165166

@@ -290,6 +291,10 @@ sub ed_g5agcm_rc {
290291
if ( $gocart_tracers ) { $comment{"GOCART.data_INTERNAL"} = 1 }
291292
else { $comment{"GOCART_INTERNAL"} = 1 }
292293

294+
# uncomment ldas increment flag
295+
#------------------------------
296+
if ($ldas_flag == 1) { $uncomment{"LDAS_INCR"} = 1 }
297+
293298
# comment unused catch or catchCN restart
294299
#----------------------------------------
295300
if ($lsmodel_flag == 1) {
@@ -310,8 +315,8 @@ sub ed_g5agcm_rc {
310315
# uncomment precipation force except when specified
311316
# -------------------------------------------------
312317
if ( $pcp_forced ) {
313-
$uncomment{"#PRECIP_FILE"} = 1;
314-
$uncomment{"#USE_PP_TAPER"} = 1;
318+
$uncomment{"PRECIP_FILE"} = 1;
319+
$uncomment{"USE_PP_TAPER"} = 1;
315320
}
316321

317322
# edit and output AGCM.rc.tmpl
@@ -350,6 +355,7 @@ sub outputAGCM {
350355
my ($outfile, $ox_friendlies);
351356
my ($rcd, $label, $key, $rst);
352357
my (@DEFAULT_TYPE_FOUND);
358+
my ($space, $pound);
353359

354360
$tmpl = shift @_;
355361
$outfl = shift @_;
@@ -409,8 +415,11 @@ sub outputAGCM {
409415
# uncomment specified lines if key is in first non-blank position
410416
#----------------------------------------------------------------
411417
foreach $key ( keys %uncomment ) {
412-
if ($rcd =~ /^(\s*)$key/) {
413-
if ( $uncomment{"$key"} ) {$rcd = substr $rcd, 1;};
418+
$key =~ s/^\#//; # no longer need '#' in front of key
419+
if ($rcd =~ /^(\s*)(\#*)\s*$key/) {
420+
$space = $1;
421+
$pound = $2;
422+
$rcd =~ s/^$space$pound/$space/;
414423
}
415424
}
416425
print(LUN2 "$rcd\n");

‎src/Applications/GEOSdas_App/CMakeLists.txt‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,5 @@
11
add_subdirectory(testsuites)
2+
add_subdirectory(jedi)
23

34
set(dasscripts
45
FixUnblocked.csh

‎src/Applications/GEOSdas_App/GEOSdas.csm‎

Lines changed: 50 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -154,6 +154,7 @@
154154
if ( !($?RADCOR) ) setenv RADCOR 0
155155
if ( !($?SHORTFCST) ) setenv SHORTFCST 0
156156
if ( !($?SKIPANA) ) setenv SKIPANA 0
157+
if ( !($?SKIPGSI) ) setenv SKIPGSI 0
157158
if ( !($?SKIP_PSAS) ) setenv SKIP_PSAS 0
158159
if ( !($?SPLITEXE) ) setenv SPLITEXE 0
159160
if ( !($?STRICT) ) setenv STRICT 0
@@ -1610,11 +1611,42 @@ exit 1
16101611
Sub CreateIAUincrement4Fcst_()
16111612
# -------------------------------------
16121613
if ( $?ECHO___ ) set echo
1614+
if ( $SKIPGSI && ! -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) exit 0
16131615

16141616
if ( ! $DO4DIAU ) then
16151617
if ( -e agcm_import_rst ) exit 0 # no need to regenerate IAU increment if already available
16161618
endif
16171619

1620+
# check for presence of jedi tarball holding IAU term
1621+
set fnymdb = $GcmBegDate
1622+
set fnhmsb = $GcmBegTime
1623+
set fhhb = `echo $fnhmsb | cut -c1-2`
1624+
set iamhere = `pwd`
1625+
set arstlst = `ls $FVHOME/fcst/*.jedi_agcmrst.${fnymdb}_${fhhb}z.tar`
1626+
if ( ! $status ) then
1627+
cd $FVWORK
1628+
/bin/mv $arstlst .
1629+
set rstlst = `ls *.jedi_agcmrst.${fnymdb}_${fhhb}z.tar`
1630+
set vexpid = `echo $rstlst | cut -d. -f1`
1631+
set this = `echo $rstlst | cut -d. -f3`
1632+
if (! -d agcmRSTinput_${this} ) mkdir agcmRSTinput_$this
1633+
cd agcmRSTinput_$this
1634+
tar xvf ../$rstlst
1635+
if ( "$EXPID" != "$vexpid" ) then
1636+
foreach fn ( `ls *agcm_internal_rst*` )
1637+
set sfx = `echo $fn | cut -d. -f2-`
1638+
/bin/mv $vexpid.$sfx $EXPID.$sfx
1639+
end
1640+
endif
1641+
# keep only (bin) restart files
1642+
/bin/mv *agcm_import_rst* $fcstage/stage/
1643+
cd -
1644+
/bin/rm -r agcmRSTinput_${this}
1645+
/bin/rm $rstlst
1646+
cd $iamhere
1647+
ln -sf $fcstage/stage/*agcm_import_rst.${fnymdb}_${fhhb}* agcm_import_rst
1648+
endif
1649+
16181650
set agcmfn = `echorc.x -template $EXPID $dtg iau_tendency_filename`
16191651
if ( -e $fcstage/stage/$agcmfn ) then
16201652
ln -sf $fcstage/stage/$agcmfn agcm_import_rst
@@ -2526,6 +2558,8 @@ exit 1
25262558
if ( $?ECHO___ ) set echo
25272559
set qsub_acquire = 0
25282560

2561+
# if ( $SKIPGSI && ! -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) exit 0
2562+
25292563
set ecode = 0
25302564
set acq_status = 0
25312565
set acq_status2 = 0
@@ -2879,6 +2913,8 @@ exit 1
28792913
# -------------------------
28802914
if ( $?ECHO___ ) set echo
28812915

2916+
if ( $SKIPGSI && ! -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) exit 0
2917+
28822918
# Get info about pre-qc files to be combined for QC
28832919
# ------------------------------------------------------
28842920

@@ -2974,6 +3010,7 @@ endif
29743010

29753011
if ( ! $PREPQC ) exit 0
29763012
if ( $SKIPANA ) exit 0
3013+
if ( $SKIPGSI && ! -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) exit 0
29773014

29783015
# Combine pre-qc files...
29793016
# ------------------------
@@ -3139,6 +3176,7 @@ endif
31393176
Sub AnalysisRun_( Viter_, Final_ )
31403177
# ----------------------------------
31413178
if ( $?ECHO___ ) set echo
3179+
if ( $SKIPGSI && ! -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) exit 0
31423180

31433181
if ( $DO4DVAR && $Final_ ) exit 0
31443182

@@ -3264,15 +3302,18 @@ endif
32643302
#
32653303

32663304
if ( ! -d $FVHOME/run/jedi ) exit (0)
3305+
if ( -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) exit (0) # only run from second cycle of experiment onwards
32673306

32683307
@ idummy = $VAROFFSET * 60
32693308
set ana_datetime = ( `tick $gcm_nymd0 $gcm_nhms0 $idummy` )
32703309

32713310
set this_hh0 = `echo $gcm_nhms0 | cut -c1-2`
32723311
set this_hha = `echo $ana_datetime[2] | cut -c1-2`
32733312

3274-
set this_log = $EXPID.ana_jo.log.${ana_datetime[1]}_${this_hha}z.txt
3275-
obimp_summary.pl -rc $FVROOT/etc/odsstats4jedi.rc -type diag -josummary -o $this_log $ana_datetime[1] $ana_datetime[2]
3313+
if ( ! $SKIPGSI && ! -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) then
3314+
set this_log = $EXPID.ana_jo.log.${ana_datetime[1]}_${this_hha}z.txt
3315+
obimp_summary.pl -rc $FVROOT/etc/odsstats4jedi.rc -type diag -josummary -o $this_log $ana_datetime[1] $ana_datetime[2]
3316+
endif
32763317

32773318

32783319
jedi_driver.csh $gcm_nymd0 $gcm_nhms0 $ana_datetime[1] $ana_datetime[2] |& tee -a $FVWORK/$EXPID.jedi_drv.log.${gcm_nymd0}_${this_hh0}z.txt
@@ -3424,6 +3465,7 @@ endif
34243465
Sub CoupleAnaToGcm_( Viter_, Final_ )
34253466
# ------------------------------
34263467
if ( $?ECHO___ ) set echo
3468+
if ( $SKIPGSI && ! -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) exit 0
34273469

34283470
set updrst0 =
34293471
if ( "$MPIRUN_UPRST" != "/dev/null" ) then
@@ -6047,6 +6089,10 @@ endif
60476089
/bin/mv $momoutdir/MOM.res_${fn}.nc $FVHOME/recycle/hold/$EXPID.mom${fn}_rst.${momtag}.nc4
60486090
end
60496091
endif
6092+
set lstbkglfo = `ls $FVWORK/$EXPID.bkg.lfo*.$NCSUFFIX`
6093+
if ( ${%lstbkglfo} ) then
6094+
tar cvf $FVWORK/$EXPID.bkglforst.${rtag}.tar $EXPID.bkg.lfo*.$NCSUFFIX
6095+
endif
60506096
cd $FVHOME/recycle/hold
60516097
tar cvf $FVWORK/$EXPID.rst.${rtag}.tar $EXPID.*
60526098
/bin/mv $FVWORK/$EXPID.xinc*$NCSUFFIX .
@@ -6082,9 +6128,8 @@ endif
60826128
#------------------------------------
60836129

60846130
if ( $LDAS_ANA ) then
6085-
mkdir -p $FVHOME/recycle/holdpredout
6086-
/bin/mv -f $FVWORK/*lfo_Nx+-* $FVHOME/recycle/holdpredout/.
6087-
/bin/cp $FVHOME/recycle/holdpredout/*lfo_Nx+-* $LDHOME/input/met_forcing/.
6131+
/bin/rm -f $FVHOME/recycle/holdpredout/*lfo*
6132+
/bin/cp $FVWORK/*bkg.lfo*.nc4 $FVHOME/recycle/holdpredout/.
60886133
endif
60896134

60906135
exit 0

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