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Merge branch 'develop' into feature/jstassi/local-acquire-gaas_obs
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so that I can issue a PR with my changes back to 'develop'.
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@gmao-jstassi
gmao-jstassi committed Aug 23, 2022
2 parents 90516bd + 0d99b65 commit f4902f5
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Showing 45 changed files with 1,612 additions and 232 deletions.
10 changes: 5 additions & 5 deletions components.yaml
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Expand Up @@ -28,13 +28,13 @@ NCEP_Shared:
GMAO_Shared:
local: ./src/Shared/@GMAO_Shared
remote: ../GMAO_Shared.git
tag: rt1_4_10_geosit
tag: rt1_4_10_geosit4
develop: main

MAPL:
local: ./src/Shared/@MAPL
remote: ../MAPL.git
tag: v2.8.0.7
tag: v2.8.0.9
develop: develop

FMS:
Expand All @@ -46,7 +46,7 @@ FMS:
GEOSana_GridComp:
local: ./src/Components/@GEOSana_GridComp
remote: ../GEOSana_GridComp.git
tag: v1.5.4.2
tag: v1.5.4.4
develop: develop

GEOSgcm_GridComp:
Expand Down Expand Up @@ -101,7 +101,7 @@ geos-chem:
GOCART:
local: ./src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/@GEOSchem_GridComp/@GOCART
remote: ../GOCART.git
tag: rt1.0.1_geosit
tag: rt1.0.1_geosit2
sparse: ./config/GOCART.sparse
develop: develop

Expand All @@ -121,7 +121,7 @@ mom6:
GEOSgcm_App:
local: ./src/Applications/@GEOSgcm_App
remote: ../GEOSgcm_App.git
tag: rt1.5.6_geosit_hist2
tag: rt1.5.6_geosit_hist4
develop: develop

UMD_Etc:
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2 changes: 1 addition & 1 deletion src/Applications/GAAS_App/patmosx_l2a.py
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Expand Up @@ -43,7 +43,7 @@ def patmosx_has_obs(fname):
"""
Returns true if PATMOSX reflectance file has something in it.
"""
return 'latitude' in load(fname).keys()
return 'latitude' in load(fname,allow_pickle=True).keys()

#---------------------------------------------------------------------

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44 changes: 27 additions & 17 deletions src/Applications/GEOSdas_App/GEOSdas.csm
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Expand Up @@ -1953,9 +1953,11 @@ exit 1
endif
endif

set ars_list = ( satbias satbang )
set ars_list = ( satbias )
if ($NEWRADBC || $ANGLEBC) then
set ars_list = ( $ars_list satbiaspc )
else if ( ! $ANGLEBC ) then
set ars_list = ( $ars_list satbang )
endif
if ($ACFTBIAS) then
set ars_list = ( $ars_list acftbias )
Expand Down Expand Up @@ -2949,27 +2951,35 @@ endif
/bin/rm -f input_combfr.txt
touch input_combfr.txt
foreach qcpat ( `cat pre-qc.acq | sort | uniq`)
echorc.x -template dummy $nymdb $nhmsb -fill $qcpat >> input_combfr.txt
# echorc.x -template dummy $nymdb $nhmsb -fill $qcpat >> input_combfr.txt
set fn = `echorc.x -template dummy $nymdb $nhmsb -fill $qcpat`
if ( -e $fn && ! -z $fn ) echo $fn >> input_combfr.txt
end
combfrd.x -d $pbdtg $pbname < input_combfr.txt
scanbuf0.x $pbname >! data_types.log

if ( `grep PROFLR data_types.log | wc -l `) then
setenv PROFQC 1
if ( -z input_combfr.txt) then
# if no files to combine then no input for prepqc, so try setting prepqc 0
if ($PREPQC) setenv PREPQC 0
else
setenv PROFQC 0
endif
combfrd.x -d $pbdtg $pbname < input_combfr.txt
scanbuf0.x $pbname >! data_types.log

if ( `grep AIRCFT data_types.log | wc -l`) then
setenv ACFTQC 1
else
setenv ACFTQC 0
endif
if ( `grep PROFLR data_types.log | wc -l `) then
setenv PROFQC 1
else
setenv PROFQC 0
endif

if ( `grep AIRCAR data_types.log | wc -l`) then
setenv ACARSQC 1
else
setenv ACARSQC 0
if ( `grep AIRCFT data_types.log | wc -l`) then
setenv ACFTQC 1
else
setenv ACFTQC 0
endif

if ( `grep AIRCAR data_types.log | wc -l`) then
setenv ACARSQC 1
else
setenv ACARSQC 0
endif
endif
endif
endif
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26 changes: 16 additions & 10 deletions src/Applications/GEOSdas_App/fvsetup
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Expand Up @@ -392,7 +392,7 @@ my ($sysfile, $nodeflg);
my (@rmTilde);
my ($merra2, $acftbias, $doRcorr, $nrt, $rstype);
my ($hyb_ens, $do4diau, $newradbc, $siglevs, $vres, $aensupa);
my ($geosit, $r21c);
my ($geosit, $r21c,$bcopt);

system clear;
get_runtime_values();
Expand Down Expand Up @@ -1776,9 +1776,9 @@ sub ed_ncep_rc {
}

if ( $siglevs <= 72 ) {
if($rcd =~ /\@NLEV_EXT/) {$rcd=~ s/\@NLEV_EXT/15/g; }
if($rcd =~ /\@NLEV_EXT/) {$rcd=~ s/\@NLEV_EXT/18/g; }
} elsif ( $siglevs > 72 & $siglevs <= 132 ) {
if($rcd =~ /\@NLEV_EXT/) {$rcd=~ s/\@NLEV_EXT/17/g; }
if($rcd =~ /\@NLEV_EXT/) {$rcd=~ s/\@NLEV_EXT/21/g; }
} elsif ( $siglevs > 132 ) {
if($rcd =~ /\@NLEV_EXT/) {$rcd=~ s/\@NLEV_EXT/27/g; }
}
Expand Down Expand Up @@ -3062,7 +3062,7 @@ sub get_nodeflg {
elsif ($ans == 3) { $nodeflg = "ivy"; $ncpus_per_node = 20 }
elsif ($ans == 4) { $nodeflg = "hasw"; $ncpus_per_node = 24 }
elsif ($ans == 5) { $nodeflg = "sky"; $ncpus_per_node = 36 }
elsif ($ans == 6) { $nodeflg = "cas"; $ncpus_per_node = 46 }
elsif ($ans == 6) { $nodeflg = "cas"; $ncpus_per_node = 45 }
# currently not applicable at nccs
#---------------------------------
Expand Down Expand Up @@ -3110,7 +3110,7 @@ sub get_times {
# # ----
if ($res eq "C48") { $nx = 4; $ny = 24 } # (b) 96
elsif ($res eq "C90") { $nx = 4; $ny = 24 } # (c) 96
elsif ($res eq "C180") { $nx = 8; $ny = 30 } # (d) 240
elsif ($res eq "C180") { $nx = 15; $ny = 36 } # (d) 360
elsif ($res eq "C360") { $nx = 8; $ny = 48 } # (e) 384
else { $nx = 28; $ny = 48 } # (f+) 1344
}
Expand Down Expand Up @@ -5007,6 +5007,9 @@ EOF
$ana_im_ens = $ana_im;
$ana_jm_ens = $ana_jm;
} elsif ( "$res" eq "C180" ) { # Cubed-sphere
if ($geosit) {
$o_servers = 0; # 10; this does not payoff for C180 resolution
}
$cubed = 1;
# $ios_nds = 2;
$specres = "254";
Expand Down Expand Up @@ -7484,6 +7487,8 @@ sub build_lnbcs {
$bcopt = "-merra2" ;
}elsif ( $r21c ) {
$bcopt = "-r21c";
}elsif ($geosit) {
$bcopt = "-geosit";
}
if ( $cubed ) {
$cmd = "$fvbin/gen_lnbcs.pl -fvhome $fvhome -o lnbcs $bcopt -cubed $agcm_im $agcm_jm $ogcm $landbcs";
Expand Down Expand Up @@ -8058,7 +8063,7 @@ print SCRIPT <<"EOF";
setenv RUN_OPT_BLEND "esma_mpirun -np \$NCPUS \$HDF2RSX"
if (\$G5GCM ) then
if ( \$O_SERVERS > 0 ) then
setenv RUN_OPT_BEGIN "mpirun -np \$NCPUSX \$GCMX --npes_model \$NCUPS --nodes_output_server \$O_SERVERS --oserver_type multigroup --npes_backend_pernode \$O_SERVERS"
setenv RUN_OPT_BEGIN "mpirun -np \$NCPUSX \$GCMX --npes_model \$NCPUS --nodes_output_server \$O_SERVERS --oserver_type multigroup --npes_backend_pernode \$O_SERVERS"
else
setenv RUN_OPT_BEGIN "esma_mpirun -np \$NCPUS \$GCMX"
endif
Expand Down Expand Up @@ -8331,9 +8336,9 @@ print SCRIPT <<"EOF";
cd \$FVWORK
if (`uname -n` =~ borg*) then
cat \$PBS_NODEFILE | head -1 > \$FVWORK/OIQC_list
cat \$PBS_NODEFILE | tail +2 > \$FVWORK/GCM_list
cat \$PBS_NODEFILE > \$FVWORK/ANA_list
cat \$PBS_NODEFILE | head -1 > \$FVWORK/OIQC_list
cat \$PBS_NODEFILE | tail -n +2 > \$FVWORK/GCM_list
cat \$PBS_NODEFILE > \$FVWORK/ANA_list
subset_nodefile.pl \$NCPUS_IDF -f \$PBS_NODEFILE -o \$FVWORK/IDF_list
subset_nodefile.pl \$NCPUS_IAU -f \$PBS_NODEFILE -o \$FVWORK/IAU_list
endif
Expand Down Expand Up @@ -8610,6 +8615,7 @@ EOF
endif
echo2 ""
echo2 "setenv FVHOME \$FVHOME"
echo2 "setenv ARCHIVE \$FVARCH"
echo2 "set Bin = \$Bin"
echo2 "set output = \$lname2"
echo2 ""
Expand Down Expand Up @@ -9248,7 +9254,7 @@ print SCRIPT <<"EOF";
setenv RUN_OPT_BLEND "esma_mpirun -np \$NCPUS \$HDF2RSX"
if (\$G5GCM ) then
if ( \$O_SERVERS > 0 ) then
setenv RUN_OPT_BEGIN "mpirun -np \$NCPUSX \$GCMX --npes_model \$NCUPS --nodes_output_server \$O_SERVERS --oserver_type multigroup --npes_backend_pernode \$O_SERVERS"
setenv RUN_OPT_BEGIN "mpirun -np \$NCPUSX \$GCMX --npes_model \$NCPUS --nodes_output_server \$O_SERVERS --oserver_type multigroup --npes_backend_pernode \$O_SERVERS"
else
setenv RUN_OPT_BEGIN "esma_mpirun -np \$NCPUS \$GCMX"
endif
Expand Down
14 changes: 11 additions & 3 deletions src/Applications/GEOSdas_App/gen_lnbcs.pl
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Expand Up @@ -33,6 +33,7 @@
"cubed",
"merra2",
"r21c",
"geosit",
"h" );

usage() if $opt_h;
Expand Down Expand Up @@ -139,9 +140,15 @@ sub init {
} else {
$BCSTAG = "$lndbcs/Icarus_Ostia";
}
$fvrtbcs = "g5gcm/bcs/realtime/OSTIA_REYNOLDS";
$sstfile = "dataoceanfile_OSTIA_REYNOLDS_SST.$ogrid.\$year.data";
$icefile = "dataoceanfile_OSTIA_REYNOLDS_ICE.$ogrid.\$year.data";
if ($opt_r21c or $opt_geosit){
$fvrtbcs = "g5gcm/bcs/realtime/OSTIA_REYNOLDS_ITR21C";
$sstfile = "dataoceanfile_OSTIA_REYNOLDS_ITR21C_SST.$ogrid.\$year.data";
$icefile = "dataoceanfile_OSTIA_REYNOLDS_ITR21C_ICE.$ogrid.\$year.data";
} else {
$fvrtbcs = "g5gcm/bcs/realtime/OSTIA_REYNOLDS";
$sstfile = "dataoceanfile_OSTIA_REYNOLDS_SST.$ogrid.\$year.data";
$icefile = "dataoceanfile_OSTIA_REYNOLDS_ICE.$ogrid.\$year.data";
}
}
elsif ($ogcm eq "T") { # Coupled-Tripolar-Ocean
$coupled = 1;
Expand Down Expand Up @@ -429,6 +436,7 @@ sub usage {
-cubed needed for cubed GCM
-merra2 specify to set related BCs
-r21c specify to set related BCs
-geosit specify to set related BCs
-h prints this usage notice
EXAMPLE COMMAND LINE
Expand Down
1 change: 1 addition & 0 deletions src/Applications/GEOSdas_App/gen_silo_arc.pl
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Expand Up @@ -342,6 +342,7 @@ sub append_other_info {
\${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.ana.obs.%y4%m2%d2_%h2z.ods
\${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.prepbufr.%y4%m2%d2.t%h2z.blk
\${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.acft_profl.%y4%m2%d2.t%h2z.bfr
\${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.gmao_global_convinfo.%y4%m2%d2_%h2z.txt
\${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.gmao_global_satinfo.%y4%m2%d2_%h2z.txt
\${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.gmao_global_ozinfo.%y4%m2%d2_%h2z.txt
\${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.sac.nl.%y4%m2%d2_%h2z.txt
Expand Down
4 changes: 2 additions & 2 deletions src/Applications/GEOSdas_App/testsuites/C180RPY.input
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Expand Up @@ -2,9 +2,9 @@
# C180RPY.input
#------------

codeID: b3a880f
codeID: 523f29e
description: C180RPY__GEOSadas-5_29_3__agrid_C180__ogrid_C
fvsetupID: f7d8d041c9
fvsetupID: f7aaa973c7

---ENDHEADERS---

Expand Down
4 changes: 2 additions & 2 deletions src/Applications/GEOSdas_App/testsuites/C180T14RPY.input
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Expand Up @@ -2,9 +2,9 @@
# C180T14RPY.input
#------------

codeID: b3a880f
codeID: 523f29e
description: C180T14RPY__GEOSadas-5_29_3__agrid_C180__ogrid_T14
fvsetupID: f7d8d041c9
fvsetupID: f7aaa973c7

---ENDHEADERS---

Expand Down
4 changes: 2 additions & 2 deletions src/Applications/GEOSdas_App/testsuites/C360L181_replay.input
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Expand Up @@ -2,9 +2,9 @@
# C360L181_replay.input
#------------

codeID: b3a880f
codeID: 523f29e
description: C360L181_replay__GEOSadas-5_29_3__agrid_C360__ogrid_C
fvsetupID: f7d8d041c9
fvsetupID: f7aaa973c7

---ENDHEADERS---

Expand Down
4 changes: 2 additions & 2 deletions src/Applications/GEOSdas_App/testsuites/C360L91_replay.input
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Expand Up @@ -2,9 +2,9 @@
# C360L91_replay.input
#------------

codeID: b3a880f
codeID: 523f29e
description: C360L91_replay__GEOSadas-5_29_3__agrid_C360__ogrid_C
fvsetupID: f7d8d041c9
fvsetupID: f7aaa973c7

---ENDHEADERS---

Expand Down
4 changes: 2 additions & 2 deletions src/Applications/GEOSdas_App/testsuites/C48f.input
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Expand Up @@ -2,9 +2,9 @@
# C48f.input
#-----------

codeID: b3a880f
codeID: 523f29e
description: C48f__GEOSadas-5_29_3__agrid_C48__ogrid_f34
fvsetupID: f7d8d041c9
fvsetupID: f7aaa973c7
fvsetupflags: -sensdeg 1

---ENDHEADERS---
Expand Down
4 changes: 2 additions & 2 deletions src/Applications/GEOSdas_App/testsuites/C90C.input
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Expand Up @@ -2,9 +2,9 @@
# C90C.input
#-----------

codeID: b3a880f
codeID: 523f29e
description: C90C__GEOSadas-5_29_3__agrid_C90__ogrid_CS
fvsetupID: f7d8d041c9
fvsetupID: f7aaa973c7

---ENDHEADERS---

Expand Down
4 changes: 2 additions & 2 deletions src/Applications/GEOSdas_App/testsuites/C90C_ens.input
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Expand Up @@ -2,9 +2,9 @@
# C90C_ens.input
#---------------

codeID: b3a880f
codeID: 523f29e
description: C90C_ens__GEOSadas-5_29_3__agrid_C90__ogrid_C
fvsetupID: f7d8d041c9
fvsetupID: f7aaa973c7

---ENDHEADERS---

Expand Down
4 changes: 2 additions & 2 deletions src/Applications/GEOSdas_App/testsuites/C90C_replay.input
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Expand Up @@ -2,9 +2,9 @@
# C90C_replay.input
#---------------

codeID: b3a880f
codeID: 523f29e
description: C90C_replay__86f27c6__agrid_C90__ogrid_C
fvsetupID: f7d8d041c9
fvsetupID: f7aaa973c7

---ENDHEADERS---

Expand Down
4 changes: 2 additions & 2 deletions src/Applications/GEOSdas_App/testsuites/fpp.input
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Expand Up @@ -2,9 +2,9 @@
# fpp.input
#------------

codeID: b3a880f
codeID: 523f29e
description: fpp__GEOSadas-5_29_3__agrid_C720__ogrid_C
fvsetupID: f7d8d041c9
fvsetupID: f7aaa973c7

---ENDHEADERS---

Expand Down
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