turn off monitor jobs for JEDIATMVAR, adjust JEDIATM resources, fix pynorm error (NOAA-EMC#2294)

Author: RussTreadon-NOAA

parm/config/gfs/config.base.emc.dyn

@@ -396,4 +396,11 @@ export FITSARC="YES"
 export FHMAX_FITS=132
 [[ "${FHMAX_FITS}" -gt "${FHMAX_GFS}" ]] && export FHMAX_FITS=${FHMAX_GFS}
 
+# The monitor jobs are not yet supported for JEDIATMVAR
+if [[ ${DO_JEDIATMVAR} = "NO" ]]; then
+   export DO_VERFOZN="NO"     # Ozone data assimilation monitoring
+   export DO_VERFRAD="NO"     # Radiance data assimilation monitoring
+   export DO_VMINMON="NO"     # GSI minimization monitoring
+fi
+
 echo "END: config.base"

parm/config/gfs/config.resources

@@ -91,7 +91,7 @@ case ${step} in
     ;;
 
   "prepatmiodaobs")
-    export wtime_prepatmiodaobs="00:10:00"
+    export wtime_prepatmiodaobs="00:30:00"
     export npe_prepatmiodaobs=1
     export nth_prepatmiodaobs=1
     export npe_node_prepatmiodaobs=$(( npe_node_max / nth_prepatmiodaobs ))
@@ -196,8 +196,8 @@ case ${step} in
 
   "atmanlinit")
     # make below case dependent later
-    export layout_x=1
-    export layout_y=1
+    export layout_x=8
+    export layout_y=8
 
     export layout_gsib_x=$(( layout_x * 3 ))
     export layout_gsib_y=$(( layout_y * 2 ))
@@ -212,15 +212,16 @@ case ${step} in
 
   "atmanlrun")
     # make below case dependent later
-    export layout_x=1
-    export layout_y=1
+    export layout_x=8
+    export layout_y=8
 
     export wtime_atmanlrun="00:30:00"
     export npe_atmanlrun=$(( layout_x * layout_y * 6 ))
     export npe_atmanlrun_gfs=$(( layout_x * layout_y * 6 ))
     export nth_atmanlrun=1
     export nth_atmanlrun_gfs=${nth_atmanlrun}
     export npe_node_atmanlrun=$(( npe_node_max / nth_atmanlrun ))
+    export memory_atmanlrun="96GB"
     export is_exclusive=True
     ;;
 
@@ -833,8 +834,8 @@ case ${step} in
 
   "atmensanlinit")
     # make below case dependent later
-    export layout_x=1
-    export layout_y=1
+    export layout_x=8
+    export layout_y=8
 
     export wtime_atmensanlinit="00:10:00"
     export npe_atmensanlinit=1
@@ -845,15 +846,16 @@ case ${step} in
 
   "atmensanlrun")
     # make below case dependent later
-    export layout_x=1
-    export layout_y=1
+    export layout_x=8
+    export layout_y=8
 
     export wtime_atmensanlrun="00:30:00"
     export npe_atmensanlrun=$(( layout_x * layout_y * 6 ))
     export npe_atmensanlrun_gfs=$(( layout_x * layout_y * 6 ))
     export nth_atmensanlrun=1
     export nth_atmensanlrun_gfs=${nth_atmensanlrun}
     export npe_node_atmensanlrun=$(( npe_node_max / nth_atmensanlrun ))
+    export memory_atmensanlrun="96GB"
     export is_exclusive=True
     ;;
 

workflow/setup_expt.py

@@ -219,7 +219,7 @@ def link_files_from_src_to_dst(src_dir, dst_dir):
     src_dir = os.path.join(inputs.icsdir, current_cycle_dir, src_atm_anl_dir)
     dst_dir = os.path.join(rotdir, current_cycle_dir, dst_atm_anl_dir)
     makedirs_if_missing(dst_dir)
-    for ftype in ['abias', 'abias_pc', 'abias_air', 'radstat', 'atms_n20.satbias.nc4', 'atms_n20.satbias_cov.nc4', 'atms_n20.tlapse.txt' ]:
+    for ftype in ['abias', 'abias_pc', 'abias_air', 'radstat', 'atms_n20.satbias.nc4', 'atms_n20.satbias_cov.nc4', 'atms_n20.tlapse.txt']:
         fname = f'{inputs.cdump}.t{idatestr[8:]}z.{ftype}'
         src_file = os.path.join(src_dir, fname)
         if os.path.exists(src_file):