[Production/AQMv7] merge the changes related to EE2 with conflicts re…

…solved to production/AQMv7 (#1075) * Bring in EE2 resolutions. * Update .readthedocs.yaml for older doc directory --------- Co-authored-by: Brian Curtis <[email protected]>
ufs-community · Apr 22, 2024 · 8f3296c · 8f3296c
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -17,7 +17,7 @@ build:
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/UsersGuide/source/conf.py
+   configuration: doc/UsersGuide/source/conf.py
 
 # If using Sphinx, optionally build your docs in additional formats such as PDF
 # formats:
@@ -26,7 +26,7 @@ sphinx:
 # Optionally declare the Python requirements required to build your docs
 python:
    install:
-   - requirements: docs/UsersGuide/requirements.txt
+   - requirements: doc/UsersGuide/requirements.txt
 
 submodules:
    include:

diff --git a/ecf/scripts/cycle_end.ecf → ecf/cycle_end.ecf b/ecf/scripts/cycle_end.ecf → ecf/cycle_end.ecf
diff --git a/ecf/defs/aqm_cycled.def b/ecf/defs/aqm_cycled.def
@@ -14,11 +14,11 @@ suite nco_aqm
     family 00
       edit CYC '00'
       task cycle_end
-        edit ECF_FILES '%PACKAGEHOME%/ecf/scripts'
+        edit ECF_FILES '%PACKAGEHOME%/ecf'
         cron 23:00
       family aqm
         family v1.0
-          edit ECF_FILES '%PACKAGEHOME%/ecf/scripts'
+          edit ECF_FILES '%PACKAGEHOME%/ecf'
           family nexus
             task jaqm_nexus_emission_00
               edit NSPT '00'
@@ -113,11 +113,11 @@ suite nco_aqm
     family 06
       edit CYC '06'
       task cycle_end
-        edit ECF_FILES '%PACKAGEHOME%/ecf/scripts'
+        edit ECF_FILES '%PACKAGEHOME%/ecf'
         cron 05:00
       family aqm
         family v1.0
-          edit ECF_FILES '%PACKAGEHOME%/ecf/scripts'
+          edit ECF_FILES '%PACKAGEHOME%/ecf'
           family nexus
             task jaqm_nexus_emission_00
               edit NSPT '00'
@@ -486,11 +486,11 @@ suite nco_aqm
     family 12
       edit CYC '12'
       task cycle_end
-        edit ECF_FILES '%PACKAGEHOME%/ecf/scripts'
+        edit ECF_FILES '%PACKAGEHOME%/ecf'
         cron 11:00
       family aqm
         family v1.0
-          edit ECF_FILES '%PACKAGEHOME%/ecf/scripts'
+          edit ECF_FILES '%PACKAGEHOME%/ecf'
           family nexus
             task jaqm_nexus_emission_00
               edit NSPT '00'
@@ -859,11 +859,11 @@ suite nco_aqm
     family 18
       edit CYC '18'
       task cycle_end
-        edit ECF_FILES '%PACKAGEHOME%/ecf/scripts'
+        edit ECF_FILES '%PACKAGEHOME%/ecf'
         cron 17:00
       family aqm
         family v1.0
-          edit ECF_FILES '%PACKAGEHOME%/ecf/scripts'
+          edit ECF_FILES '%PACKAGEHOME%/ecf'
           family nexus
             task jaqm_nexus_emission_00
               edit NSPT '00'

diff --git a/ecf/scripts/forecast/jaqm_forecast.ecf → ecf/forecast/jaqm_forecast.ecf b/ecf/scripts/forecast/jaqm_forecast.ecf → ecf/forecast/jaqm_forecast.ecf
@@ -3,9 +3,8 @@
 #PBS -S /bin/bash
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
-#PBS -l walltime=03:15:00
-#PBS -l select=14:mpiprocs=128:ompthreads=1:ncpus=128
-#PBS -l place=vscatter:exclhost
+#PBS -l walltime=%WALLTIME:03:15:00%
+#PBS -l place=vscatter:exclhost,select=14:mpiprocs=128:ompthreads=1:ncpus=128
 #PBS -l debug=true
 
 model=aqm

diff --git a/...cripts/forecast/jaqm_forecast_manager.ecf → ecf/forecast/jaqm_forecast_manager.ecf b/...cripts/forecast/jaqm_forecast_manager.ecf → ecf/forecast/jaqm_forecast_manager.ecf
@@ -3,8 +3,8 @@
 #PBS -S /bin/bash
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
-#PBS -l walltime=03:15:00
-#PBS -l select=1:mpiprocs=1:ncpus=1:mem=150G:prepost=true
+#PBS -l walltime=%WALLTIME:03:15:00%
+#PBS -l place=shared,select=1:mpiprocs=1:ncpus=1:mem=150G:prepost=true
 #PBS -l debug=true
 
 model=aqm

diff --git a/...ipts/nexus/jaqm_nexus_emission_master.ecf → ecf/nexus/jaqm_nexus_emission_master.ecf b/...ipts/nexus/jaqm_nexus_emission_master.ecf → ecf/nexus/jaqm_nexus_emission_master.ecf
@@ -3,7 +3,7 @@
 #PBS -S /bin/bash
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
-#PBS -l walltime=01:00:00
+#PBS -l walltime=00:25:00
 #PBS -l select=4:mpiprocs=64:ompthreads=2:ncpus=128
 #PBS -l place=vscatter:exclhost
 #PBS -l debug=true

diff --git a/ecf/scripts/nexus/jaqm_nexus_post_split.ecf → ecf/nexus/jaqm_nexus_post_split.ecf b/ecf/scripts/nexus/jaqm_nexus_post_split.ecf → ecf/nexus/jaqm_nexus_post_split.ecf
diff --git a/ecf/scripts/post/jaqm_post_master.ecf → ecf/post/jaqm_post_master.ecf b/ecf/scripts/post/jaqm_post_master.ecf → ecf/post/jaqm_post_master.ecf
@@ -4,7 +4,7 @@
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
 #PBS -l walltime=00:10:00
-#PBS -l select=1:mpiprocs=48:ncpus=48:mem=16G
+#PBS -l select=1:mpiprocs=48:ncpus=48:mem=192G
 #PBS -l place=vscatter
 #PBS -l debug=true
 

diff --git a/ecf/scripts/prep/jaqm_ics.ecf → ecf/prep/jaqm_ics.ecf b/ecf/scripts/prep/jaqm_ics.ecf → ecf/prep/jaqm_ics.ecf
@@ -4,11 +4,12 @@
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
 #PBS -l walltime=00:10:00
-#PBS -l select=1:mpiprocs=1:ncpus=1:mem=48G:prepost=true
+#PBS -l select=1:mpiprocs=1:ncpus=1:mem=64G:prepost=true
 #PBS -l debug=true
 
 model=aqm
 export cyc="%CYC%"
+export COLDSTART=%COLDSTART:NO%
 %include <head.h>
 %include <envir-p1.h>
 

diff --git a/ecf/scripts/prep/jaqm_lbcs.ecf → ecf/prep/jaqm_lbcs.ecf b/ecf/scripts/prep/jaqm_lbcs.ecf → ecf/prep/jaqm_lbcs.ecf
diff --git a/ecf/scripts/prep/jaqm_make_ics.ecf → ecf/prep/jaqm_make_ics.ecf b/ecf/scripts/prep/jaqm_make_ics.ecf → ecf/prep/jaqm_make_ics.ecf
diff --git a/ecf/scripts/prep/jaqm_make_lbcs.ecf → ecf/prep/jaqm_make_lbcs.ecf b/ecf/scripts/prep/jaqm_make_lbcs.ecf → ecf/prep/jaqm_make_lbcs.ecf
diff --git a/...ripts/product/jaqm_bias_correction_o3.ecf → ecf/product/jaqm_bias_correction_o3.ecf b/...ripts/product/jaqm_bias_correction_o3.ecf → ecf/product/jaqm_bias_correction_o3.ecf
diff --git a/...pts/product/jaqm_bias_correction_pm25.ecf → ecf/product/jaqm_bias_correction_pm25.ecf b/...pts/product/jaqm_bias_correction_pm25.ecf → ecf/product/jaqm_bias_correction_pm25.ecf
diff --git a/ecf/scripts/product/jaqm_post_stat_o3.ecf → ecf/product/jaqm_post_stat_o3.ecf b/ecf/scripts/product/jaqm_post_stat_o3.ecf → ecf/product/jaqm_post_stat_o3.ecf
diff --git a/ecf/scripts/product/jaqm_post_stat_pm25.ecf → ecf/product/jaqm_post_stat_pm25.ecf b/ecf/scripts/product/jaqm_post_stat_pm25.ecf → ecf/product/jaqm_post_stat_pm25.ecf
diff --git a/ecf/scripts/product/jaqm_pre_post_stat.ecf → ecf/product/jaqm_pre_post_stat.ecf b/ecf/scripts/product/jaqm_pre_post_stat.ecf → ecf/product/jaqm_pre_post_stat.ecf
@@ -4,7 +4,7 @@
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
 #PBS -l walltime=00:10:00
-#PBS -l select=1:mpiprocs=1:ncpus=1:mem=4G
+#PBS -l select=1:mpiprocs=1:ncpus=1:mem=8G
 #PBS -l debug=true
 
 model=aqm

diff --git a/...ipts/pts_fire_emis/jaqm_fire_emission.ecf → ecf/pts_fire_emis/jaqm_fire_emission.ecf b/...ipts/pts_fire_emis/jaqm_fire_emission.ecf → ecf/pts_fire_emis/jaqm_fire_emission.ecf
diff --git a/...ripts/pts_fire_emis/jaqm_point_source.ecf → ecf/pts_fire_emis/jaqm_point_source.ecf b/...ripts/pts_fire_emis/jaqm_point_source.ecf → ecf/pts_fire_emis/jaqm_point_source.ecf
@@ -3,7 +3,7 @@
 #PBS -S /bin/bash
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
-#PBS -l walltime=00:10:00
+#PBS -l walltime=00:15:00
 #PBS -l select=1:mpiprocs=1:ncpus=1:mem=8G
 #PBS -l debug=true
 

diff --git a/ecf/setup_ecf_links.sh b/ecf/setup_ecf_links.sh
@@ -30,12 +30,12 @@ function link_master_to_cyc_3d(){
 }
 
 # AQM post
-cd $ECF_DIR/scripts/post
+cd $ECF_DIR/post
 echo "Linking AQM post ..."
 cyc=$(seq 0 72)
 link_master_to_cyc_3d "jaqm_post" "$cyc"
 # AQM nexus_emission
-cd $ECF_DIR/scripts/nexus
+cd $ECF_DIR/nexus
 echo "Linking AQM nexus_emission ..."
 cyc=$(seq 0 5)
 link_master_to_cyc_2d "jaqm_nexus_emission" "$cyc"
diff --git a/jobs/JAQM_BIAS_CORRECTION_O3 b/jobs/JAQM_BIAS_CORRECTION_O3
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 date
-export PS4=' $SECONDS + '
+export PS4='+ $SECONDS + '
 set -xue
 
 #-----------------------------------------------------------------------
@@ -55,7 +55,7 @@ scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 
-env
+#env
 #-----------------------------------------------------------------------
 # Print message indicating entry into script.
 #-----------------------------------------------------------------------

diff --git a/jobs/JAQM_BIAS_CORRECTION_PM25 b/jobs/JAQM_BIAS_CORRECTION_PM25
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 date
-export PS4=' $SECONDS + '
+export PS4='+ $SECONDS + '
 set -xue
 
 #-----------------------------------------------------------------------
@@ -85,7 +85,7 @@ export PARMaqm_utils="${PARMaqm_utils:-${HOMEaqm}/parm/aqm_utils}"
 TMP_STDAY=`${NDATE} -8760 ${PDY}${cyc} | cut -c1-8`  # 1 year back
 export BC_STDAY=${BC_STDAY:-${TMP_STDAY}}
 
-env
+#env
 #-----------------------------------------------------------------------
 # Call the ex-script for this J-job and pass to it the necessary varia-
 # bles.

diff --git a/jobs/JAQM_FIRE_EMISSION b/jobs/JAQM_FIRE_EMISSION
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 date
-export PS4=' $SECONDS + '
+export PS4='+ $SECONDS + '
 set -xue
 
 #-----------------------------------------------------------------------
@@ -33,7 +33,6 @@ export PARMaqm=${PARMaqm:-${HOMEaqm}/parm}
 export FIXaqm=${FIXaqm:-${HOMEaqm}/fix}
 export FIXaqmfire="${FIXaqmfire:-${HOMEaqm}/fix/fire}"
 
-export DCOMROOT=${DCOMROOT:-/lfs/h1/ops/prod/dcom}
 export DCOMINfire="${DCOMINfire:-${DCOMROOT}/${PDY}/rave}"
 
 export COMINgfs="${COMINgfs:-$(compath.py gfs/${gfs_ver})}"
@@ -50,7 +49,7 @@ scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 
-env
+#env
 #-----------------------------------------------------------------------
 # Print message indicating entry into script.
 #-----------------------------------------------------------------------

diff --git a/jobs/JAQM_FORECAST b/jobs/JAQM_FORECAST
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 date
-export PS4=' $SECONDS + '
+export PS4='+ $SECONDS + '
 set -xue
 
 #-----------------------------------------------------------------------
@@ -58,7 +58,7 @@ scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 
-env
+#env
 #-----------------------------------------------------------------------
 # Print message indicating entry into script.
 #-----------------------------------------------------------------------

diff --git a/jobs/JAQM_FORECAST_MANAGER b/jobs/JAQM_FORECAST_MANAGER
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 date
-export PS4=' $SECONDS + '
+export PS4='+ $SECONDS + '
 set -xue
 
 #-----------------------------------------------------------------------
@@ -52,7 +52,7 @@ scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 
-env
+#env
 #-----------------------------------------------------------------------
 # Print message indicating entry into script.
 #-----------------------------------------------------------------------

diff --git a/jobs/JAQM_ICS b/jobs/JAQM_ICS
@@ -1,13 +1,14 @@
 #!/bin/bash
 
 date
-export PS4=' $SECONDS + '
+export PS4='+ $SECONDS + '
 set -xue
 
 #-----------------------------------------------------------------------
 export USHaqm=${EXECaqm:-${HOMEaqm}/ush}
 export PARMaqm=${PARMaqm:-${HOMEaqm}/parm}
 
+export CSMI=${COLDSTART:-"NO"}
 export subcyc='00'
 export SLASH_ENSMEM_SUBDIR=''
 export ENSMEM_INDX='##'
@@ -49,7 +50,7 @@ scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 
-env
+#env
 #-----------------------------------------------------------------------
 # Print message indicating entry into script.
 #-----------------------------------------------------------------------

diff --git a/jobs/JAQM_LBCS b/jobs/JAQM_LBCS
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 date
-export PS4=' $SECONDS + '
+export PS4='+ $SECONDS + '
 set -xue
 
 #-----------------------------------------------------------------------
@@ -52,7 +52,7 @@ scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 
-env
+#env
 #-----------------------------------------------------------------------
 # Print message indicating entry into script.
 #-----------------------------------------------------------------------

diff --git a/jobs/JAQM_MAKE_ICS b/jobs/JAQM_MAKE_ICS
@@ -1,7 +1,7 @@
 #!/bin/bash 
 
 date
-export PS4=' $SECONDS + '
+export PS4='+ $SECONDS + '
 set -xue
 
 #-----------------------------------------------------------------------
@@ -50,7 +50,7 @@ scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 
-env
+#env
 #-----------------------------------------------------------------------
 # Print message indicating entry into script.
 #-----------------------------------------------------------------------

diff --git a/jobs/JAQM_MAKE_LBCS b/jobs/JAQM_MAKE_LBCS
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 date
-export PS4=' $SECONDS + '
+export PS4='+ $SECONDS + '
 set -xue
 
 #-----------------------------------------------------------------------
@@ -50,7 +50,7 @@ scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 
-env
+#env
 #-----------------------------------------------------------------------
 # Print message indicating entry into script.
 #-----------------------------------------------------------------------

diff --git a/jobs/JAQM_NEXUS_EMISSION b/jobs/JAQM_NEXUS_EMISSION
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 date
-export PS4=' $SECONDS + '
+export PS4='+ $SECONDS + '
 set -xue
 
 #-----------------------------------------------------------------------

diff --git a/jobs/JAQM_NEXUS_POST_SPLIT b/jobs/JAQM_NEXUS_POST_SPLIT
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 date
-export PS4=' $SECONDS + '
+export PS4='+ $SECONDS + '
 set -xue
 
 #-----------------------------------------------------------------------
@@ -56,7 +56,7 @@ scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 
-env
+#env
 #-----------------------------------------------------------------------
 # Print message indicating entry into script.
 #-----------------------------------------------------------------------

diff --git a/jobs/JAQM_POINT_SOURCE b/jobs/JAQM_POINT_SOURCE
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 date
-export PS4=' $SECONDS + '
+export PS4='+ $SECONDS + '
 set -xue
 
 #-----------------------------------------------------------------------
@@ -47,7 +47,7 @@ scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 
-env
+#env
 #-----------------------------------------------------------------------
 # Print message indicating entry into script.
 #-----------------------------------------------------------------------