Port obs-monitor to wcoss2 (#34)

This release allows obs-monitor to run on wcoss2. The strategy is to split the model level yaml plot file into lots of pieces and submitted as a single serial job with one node per piece (plot job). Satellite plots (rad and ozn) are broken down by instrument, for iasi and cris down to instrument/plot_type. The minimization and conventional plots are submitted as two plot jobs without breaking them down further. There are some caveats: - Surface pressure plots are not working on either wcoss2 or hera. This is a problem in eva (`mon_data_space.py`), and issue [#194](JCSDA-internal/eva#194) has been opened to address it. - `Logos `and `tight layout` options have been temporarily commented out of the yaml plot tempates. These features fail on wcoss2 and seem to be issues in emcpy. Issue [#142](NOAA-EMC/emcpy#142) has been opened to address the problem. - Some of the plots in `parm/gfs/gfs_plots.yaml` have been commented out owing to what seems to be file corruption issues in my test data suite (probably hera stmp space issues). Testing has been conducted on wcoss2 and hera, and all plots work on both machines within the stated caveats.
NOAA-EMC · Jun 26, 2024 · 4a414a4 · 4a414a4
1 parent 67c1cde
commit 4a414a4
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diff --git a/driver/runObsMon.sh b/driver/runObsMon.sh
@@ -86,13 +86,13 @@ export COMOUT=${COMOUT}/${NET}
 #-------------------------
 #  Set up & submit j-job
 #
-jobname="PlotObsMon"
+jobname="PlotObsMon_setup"
 jobfile="${JOBSobsmon}/JMON_PLOT_OBS"
 
 logdir="${OM_LOGS}/${MODEL}"
 if [[ ! -d ${logdir} ]]; then mkdir -p ${logdir}; fi
 
-logfile="${OM_LOGS}/${MODEL}/OM_log"
+logfile="${logdir}/OM_setup.log"
 if [[ -e ${logfile} ]]; then rm ${logfile}; fi
 
 case ${MACHINE_ID} in
@@ -101,9 +101,13 @@ case ${MACHINE_ID} in
              -J ${jobname} --partition service -o ${logfile} ${jobfile}
       ;;
 
-   wcoss2)	# NOTE:  this has not been tested; eva doesn't yet run on wcoss2
-      $SUB -q $JOB_QUEUE -A $ACCOUNT -o ${logfile} -e ${logfile} \
-           -V -l select=1:mem=500M -l walltime=0:05:00 -N ${jobname} ${jobfile}
+   wcoss2)	
+      $SUB -q ${JOB_QUEUE} -A ${ACCOUNT} -o ${logfile} -e ${logfile} \
+	   -v "PYTHONPATH=${PYTHONPATH}, PATH=${PATH}, HOMEobsmon=${HOMEobsmon}, COMOUT=${COMOUT}, \
+	       MODEL=${MODEL}, PDY=${PDY}, cyc=${cyc}, DATAROOT=${DATAROOT}, APRUN_PY=${APRUN_PY}, \
+	       MACHINE_ID=${MACHINE_ID}, ACCOUNT=${ACCOUNT}, JOB_QUEUE=${JOB_QUEUE}, SUB=${SUB},
+	       OM_LOGS=${OM_LOGS}" \
+           -l select=1:mem=500mb -l walltime=0:05:00 -N ${jobname} ${jobfile}
       ;;
 esac
 

diff --git a/jobs/JMON_PLOT_OBS b/jobs/JMON_PLOT_OBS
@@ -26,7 +26,7 @@ mkdir -m 775 -p $COMOUTplots
 # Create $DATA for temp workspace
 ###################################
 export DATA=${DATA:-${DATAROOT}/${NET}/${MODEL}/Plot}
-if [[ -d ${DATA} ]]; then rm -rf ${DATA}; fi
+if [[ -d ${DATAROOT}/${NET} ]]; then rm -rf ${DATAROOT}/${NET}; fi
 
 mkdir -p ${DATA}
 cd ${DATA}
@@ -51,5 +51,3 @@ fi
 KEEPDATA=${KEEPDATA:-"NO"}
 cd ${DATAROOT}
 [[ ${KEEPDATA} = "NO" ]] && rm -rf ${DATA}
-
-report-mem
diff --git a/parm/OM_config b/parm/OM_config
@@ -7,7 +7,7 @@ export JOBSobsmon=${om_dir_root}/jobs
 # Export job submission vars per MACHINE_ID
 #
 source ${om_dir_root}/ush/detect_machine.sh
-MACHINE_ID=`echo "${MACHINE_ID%%.*}"`
+export MACHINE_ID=`echo "${MACHINE_ID%%.*}"`
 
 case ${MACHINE_ID} in
 
@@ -31,7 +31,7 @@ case ${MACHINE_ID} in
       queue="dev"
       project="GDAS-DEV"
       account="GFS-DEV"
-      aprun_py="python"
+      aprun_py=`which python`
       ;;
 esac
 

diff --git a/parm/gfs/conTime.yaml b/parm/gfs/conTime.yaml
@@ -460,13 +460,13 @@ graphics:
       figure:
         layout: [4,1]
         figure size: [20,18]
-        tight layout:
+#       tight layout:
         title: "Valid: {{ PDATE | to_YMDH }} \n ${datatype}, Global, All Levels"
         output name: line_plots/con/time/${datatype}_count.{{ PDATE | to_YMDH }}.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper left'
-          subplot_orientation: 'last'
+#       plot logo:
+#         which: 'noaa/nws'
+#         loc: 'upper left'
+#         subplot_orientation: 'last'
 
       plots:
         - add_xlabel: 'Assimilated'
@@ -584,13 +584,13 @@ graphics:
       figure:
         layout: [6,1]
         figure size: [20,18]
-        tight layout:
+#       tight layout:
         title: "Valid: {{ PDATE | to_YMDH }}\n ${datatype}, Global, All Levels"
         output name: line_plots/con/time/${datatype}_bias.{{ PDATE | to_YMDH }}.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper left'
-          subplot_orientation: 'last'
+#       plot logo:
+#         which: 'noaa/nws'
+#         loc: 'upper left'
+#         subplot_orientation: 'last'
 
       plots:
         - add_xlabel: 'Obs-Ges Assimilated'

diff --git a/parm/gfs/conVert.yaml b/parm/gfs/conVert.yaml
@@ -67,13 +67,13 @@ graphics:
       figure:
         layout: [2,2]
         figure size: [20,18]
-        tight layout:
+#       tight layout:
         title: "Valid: {{ PDATE | to_YMDH }} \n ${datatype}, Global"
         output name: line_plots/con/vert/${datatype}.vert.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper left'
-          subplot_orientation: 'first'
+#       plot logo:
+#         which: 'noaa/nws'
+#         loc: 'upper left'
+#         subplot_orientation: 'first'
 
       plots:
         - add_xlabel: 'Assimilated'

diff --git a/parm/gfs/gfs_plots.yaml b/parm/gfs/gfs_plots.yaml
@@ -174,7 +174,7 @@ satellites:
             times: 121
             channels: 'all'
             component: ges
-#     file corruption here?
+#     test data file corruption here?
 #          - plot: rad angle
 #            times: 121
 #            channels: 'all'
@@ -321,7 +321,7 @@ satellites:
             channels: 'all'
             component: ges
 
-#  file corruption? 
+#  test data file corruption here 
 #  - name: n19
 #    instruments:
 #      - name: amsua

diff --git a/parm/gfs/minGnormFourCycle.yaml b/parm/gfs/minGnormFourCycle.yaml
@@ -94,12 +94,12 @@ graphics:
     - figure:
         layout: [1,1]
         figure size: [20,18]
-        tight layout:
+#        tight layout:
         title: "Valid: {{ PDATE | to_YMDH }}"
         output name: line_plots/min/{{MODEL}}_{{RUN}}.4cycle.gnorms.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper center'
+          #        plot logo:
+          #          which: 'noaa/nws'
+          #          loc: 'upper center'
 
       plots:
         - add_xlabel: 'Iteration Number'

diff --git a/parm/gfs/minGnormOneCycle.yaml b/parm/gfs/minGnormOneCycle.yaml
@@ -68,12 +68,12 @@ graphics:
     - figure:
         layout: [1,1]
         figure size: [20,18]
-        tight layout:
+#        tight layout:
         title: "Valid: {{ PDATE | to_YMDH }}"
         output name: line_plots/min/{{MODEL}}_{{RUN}}.{{ PDATE | to_YMDH }}.gnorms.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper right'
+          #        plot logo:
+          #          which: 'noaa/nws'
+          #          loc: 'upper right'
 
       plots:
         - add_xlabel: 'Iteration Number'
@@ -106,12 +106,12 @@ graphics:
     - figure:
         layout: [1,1]
         figure size: [20,18]
-        tight layout:
+#        tight layout:
         title: "Valid: {{ PDATE | to_YMDH }}"
         output name: line_plots/min/{{MODEL}}_{{RUN}}.{{ PDATE | to_YMDH }}.reduction.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper right'
+#        plot logo:
+#          which: 'noaa/nws'
+#          loc: 'upper right'
 
       plots:
         - add_xlabel: 'Iteration Number'

diff --git a/parm/gfs/minSummary.yaml b/parm/gfs/minSummary.yaml
@@ -37,13 +37,13 @@ graphics:
     - figure:
         layout: [3,1]
         figure size: [20,18]
-        tight layout:
+          #        tight layout:
         title: "Valid: {{ PDATE | to_YMDH }}"
         output name: line_plots/min/{{MODEL}}_{{RUN}}.summary.gnorms.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper left'
-          subplot_orientation: 'first'
+          #        plot logo:
+          #which: 'noaa/nws'
+          #loc: 'upper left'
+          #subplot_orientation: 'first'
 
       plots:
         - add_xlabel: 'Cycle Time'

diff --git a/parm/gfs/oznSummary.yaml b/parm/gfs/oznSummary.yaml
@@ -295,13 +295,13 @@ graphics:
     - figure:
         layout: [3,1]
         figure size: [20,18]
-        tight layout:
+#       tight layout:
         title: "Summary Plot {{SENSOR}}_{{SAT}} \n Valid: {{ PDATE | to_YMDH }}"
         output name: line_plots/ozn/summary/{{SENSOR}}_{{SAT}}.summary.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper left'
-          subplot_orientation: 'first'
+#       plot logo:
+#         which: 'noaa/nws'
+#         loc: 'upper left'
+#         subplot_orientation: 'first'
       plots:
         # Obs counts, last 4 cycles
         # -------------------------

diff --git a/parm/gfs/oznTime.yaml b/parm/gfs/oznTime.yaml
@@ -164,12 +164,12 @@ graphics:
       figure:
         layout: [1,1]
         figure size: [20,18]
-        tight layout:
+#       tight layout:
         title: "${variable}, {{SENSOR}}_{{SAT}} level ${level}  \n Valid: {{ PDATE | to_YMDH }}"
         output name: line_plots/ozn/time/{{SENSOR}}_{{SAT}}.${level}.${variable}.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper right'
+#       plot logo:
+#         which: 'noaa/nws'
+#         loc: 'upper right'
 
       plots:
         - add_xlabel: 'Cycle'
@@ -198,12 +198,12 @@ graphics:
       figure:
         layout: [2,1]
         figure size: [20,18]
-        tight layout:
+#       tight layout:
         title: "obs-{{COMPONENT}} {{SENSOR}}_{{SAT}} level ${level}  \n Valid: {{ PDATE | to_YMDH }}"
         output name: line_plots/ozn/time/{{SENSOR}}_{{SAT}}.${level}.omg.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper right'
+#       plot logo:
+#         which: 'noaa/nws'
+#         loc: 'upper right'
 
       plots:
         - add_xlabel: 'Cycle'

diff --git a/parm/gfs/radAngle.yaml b/parm/gfs/radAngle.yaml
@@ -255,9 +255,9 @@ graphics:
         figure size: [20,18]
         title: "${variable}, {{SENSOR}}_{{SAT}} channel ${channel}  \n Valid: {{ PDATE | to_YMDH }}"
         output name: line_plots/rad/angle/angle.{{SENSOR}}_{{SAT}}.${channel}.${variable}.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper left'
+#       plot logo:
+#         which: 'noaa/nws'
+#         loc: 'upper left'
 
       plots:
 
@@ -317,9 +317,9 @@ graphics:
         figure size: [20,18]
         title: "${variable}, {{SENSOR}}_{{SAT}} channel ${channel}  \n Valid: {{ PDATE | to_YMDH }}"
         output name: line_plots/rad/angle/angle.{{SENSOR}}_{{SAT}}.${channel}.${variable}.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper left'
+#       plot logo:
+#         which: 'noaa/nws'
+#         loc: 'upper left'
 
       plots:
         - add_xlabel: 'Scan Position'

diff --git a/parm/gfs/radBcoef.yaml b/parm/gfs/radBcoef.yaml
@@ -177,12 +177,12 @@ graphics:
       figure:
         layout: [1,1]
         figure size: [20,18]
-        tight layout:
+#       tight layout:
         title: "${variable}, {{SENSOR}}_{{SAT}} channel ${channel}  \n Valid: {{ PDATE | to_YMDH }}"
         output name: line_plots/rad/bcoef/bcoef.{{SENSOR}}_{{SAT}}.${channel}.${variable}.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper right'
+#       plot logo:
+#         which: 'noaa/nws'
+#         loc: 'upper right'
 
       plots:
         - add_xlabel: 'Cycle'

diff --git a/parm/gfs/radTime.yaml b/parm/gfs/radTime.yaml
@@ -328,12 +328,12 @@ graphics:
       figure:
         layout: [1,1]
         figure size: [20,18]
-        tight layout:
+#       tight layout:
         title: "${variable}, {{SENSOR}}_{{SAT}} channel ${channel}  \n Valid: {{ PDATE | to_YMDH }}"
         output name: line_plots/rad/time/time.{{SENSOR}}_{{SAT}}.${channel}.${variable}.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper right'
+#       plot logo:
+#         which: 'noaa/nws'
+#         loc: 'upper right'
 
       plots:
         - add_xlabel: 'Cycle'
@@ -356,12 +356,12 @@ graphics:
       figure:
         layout: [1,1]
         figure size: [20,18]
-        tight layout:
+#       tight layout:
         title: "${variable}, {{SENSOR}}_{{SAT}} channel ${channel}  \n Valid: {{ PDATE | to_YMDH }}"
         output name: line_plots/rad/time/time.{{SENSOR}}_{{SAT}}.${channel}.${variable}.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper right'
+#       plot logo:
+#         which: 'noaa/nws'
+#         loc: 'upper right'
 
       plots:
         - add_xlabel: 'Cycle'
@@ -378,13 +378,13 @@ graphics:
     - figure:
         layout: [4,1]
         figure size: [20,18]
-        tight layout:
+#       tight layout:
         title: "Summary Plot {{SENSOR}}_{{SAT}} \n Valid: {{ PDATE | to_YMDH }}"
         output name: line_plots/rad/summary/summary.{{SENSOR}}_{{SAT}}.png
-        plot logo:
-          which: 'noaa/nws'
-          loc: 'upper center'
-          subplot_orientation: 'first'
+#       plot logo:
+#         which: 'noaa/nws'
+#         loc: 'upper center'
+#         subplot_orientation: 'first'
       plots:
         # Obs counts, last 4 cycles
         # -------------------------