Enable diagnostics package, add surface field plotter and live dashboard

- Enable useDIAGNOSTICS=.TRUE. in data.pkg, diag_mnc=.TRUE. for NetCDF output
- Configure daily snapshots of prognostic fields (THETA, SALT, UVEL, VVEL, ETAN, WVEL)
  via diagnostics package; disable dumpFreq to avoid MNC OOM
- Add plot_surface_fields.py: watches MNC diagnostics output, stitches tiles,
  renders SST/SSS/SSH/KE surface plots to PNG
- Add monitor_dashboard.py: live-updating dashboard with Chart.js, SLURM info,
  throughput estimate, CFL panels, and surface field viewer with variable
  selector, time slider (5 most recent), and archive page
- Add plot_surface_fields.sh workflow to run plotter alongside simulation
- Update run.sh for local disk staging and 3-day walltime
- Set deltaT=360s after testing (600s blows up, 120s stable but slow)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: fluidnumericsJoe

simulations/glorysv12-curvilinear/code/EXF_OPTIONS.h

@@ -40,7 +40,7 @@ C read evaporation from file
 
 
 C ** Interpolation / Vector rotation behavior ** 
-#define USE_EXF_INTERPOLATION
-#define EXF_INTERP_USE_DYNALLOC
+#undef USE_EXF_INTERPOLATION
+#undef EXF_INTERP_USE_DYNALLOC
 
 #endif

simulations/glorysv12-curvilinear/etc/config.yaml

@@ -37,10 +37,10 @@ atmosphere:
     - era_name: "surface_thermal_radiation_downwards"
       mitgcm_name: "lwdown"
       scale_factor: 2.7778E-04
-    - era_name: "mean_surface_downward_short_wave_radiation_flux"
-      mitgcm_name: "mswdown"
-    - era_name: "mean_surface_downward_long_wave_radiation_flux"
-      mitgcm_name: "mlwdown"
+        #    - era_name: "mean_surface_downward_short_wave_radiation_flux"
+        #      mitgcm_name: "mswdown"
+        #    - era_name: "mean_surface_downward_long_wave_radiation_flux"
+        #      mitgcm_name: "mlwdown"
     - era_name: "mean_sea_level_pressure"
       mitgcm_name: "pressure"
     - era_name: "runoff"

simulations/glorysv12-curvilinear/input/data

@@ -42,13 +42,13 @@
  &PARM03
  nIter0=0,
  baseTime=0.0,
-# End at end of day 365
+# 1-year run (365 days)
  endTime=31536000.0,
- deltaT=120.0,
+ deltaT=360.0,
  abEps=0.01,
- pChkptFreq=31536000.0, 
- chkptFreq=3153600.0,
- dumpFreq=120.0,
+ pChkptFreq=15768000.0,
+ chkptFreq=2592000.0,
+ dumpFreq=0.0,
  monitorSelect=2,
  monitorFreq=3600.0,
 # Daily forced

simulations/glorysv12-curvilinear/input/data.diagnostics

@@ -7,26 +7,29 @@
 #  frequency(n):< 0 : write snap-shot output every |frequency| seconds
 #               > 0 : write time-average output every frequency seconds
 #  timePhase(n)     : write at time = timePhase + multiple of |frequency|
-#    averagingFreq  : frequency (in s) for periodic averaging interval
-#    averagingPhase : phase     (in s) for periodic averaging interval
-#    repeatCycle    : number of averaging intervals in 1 cycle
 #  levels(:,n) : list of levels to write to file (Notes: declared as REAL)
 #                when this entry is missing, select all common levels of this list
 #  fields(:,n) : list of selected diagnostics fields (8.c) in outp.stream n
 #                (see "available_diagnostics.log" file for the full list of diags)
-#  missing_value(n) : missing value for real-type fields in output file "n"
-#  fileFlags(n)     : specific code (8c string) for output file "n"
 #--------------------
  &DIAGNOSTICS_LIST
-  diag_mnc     = .FALSE.,
-  fields(1:2,1) ='CH_QNET','CH_EmP',
-  fileName(1) = 'Cheapaml',
-  frequency(1) = -43200.0,
-  timePhase(1) = 0.0,
-  fields(1:5,2) ='TFLUX','SFLUX','oceFWflx','oceSflux','oceQnet',
-  fileName(2) = 'Thermo',
-  frequency(2) = -43200.0,
-  timePhase(2) = 0.0,
+  diag_mnc     = .TRUE.,
+
+# Stream 1: Daily snapshots of prognostic variables (3D)
+  fields(1:4,1) = 'THETA   ','SALT    ','UVEL    ','VVEL    ',
+  fileName(1) = 'state3D',
+  frequency(1) = -86400.0,
+
+# Stream 2: Daily snapshots of 2D prognostic fields
+  fields(1:2,2) = 'ETAN    ','WVEL    ',
+  fileName(2) = 'state2D',
+  frequency(2) = -86400.0,
+
+# Stream 3: Daily snapshots of surface fluxes
+  fields(1:5,3) = 'TFLUX   ','SFLUX   ','oceFWflx','oceSflux','oceQnet ',
+  fileName(3) = 'Thermo',
+  frequency(3) = -86400.0,
+
  &end
  &DIAG_STATIS_PARMS
  &end

simulations/glorysv12-curvilinear/input/data.pkg

@@ -4,7 +4,7 @@
  useKPP=.TRUE.,
  useCHEAPAML=.FALSE.,
  useMNC=.TRUE.,
- useDIAGNOSTICS=.FALSE.,
+ useDIAGNOSTICS=.TRUE.,
  useCAL=.TRUE.,
  useEXF=.TRUE,
  &end

simulations/glorysv12-curvilinear/workflows/env.sh

@@ -2,5 +2,6 @@
 
 # Path where downloaded data is stored
 export HOST_DATADIR=/mnt/beegfs/spectre-150-ensembles/simulations/glorysv12-curvilinear/downloads
+export SIMULATION_INPUT_DIR=/mnt/raid/joe/glorys12-curvilinear/input
 export SPECTRE_UTILS_IMG="docker://ghcr.io#ocean-spectre/spectre-ensembles/spectre-utils:main"
 export MITGCM_BASE_IMG="docker://ghcr.io#fluidnumerics/mitgcm-containers/gcc-openmpi:latest"

simulations/glorysv12-curvilinear/workflows/plot_surface_fields.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+#SBATCH -n1
+#SBATCH -c4
+#SBATCH --time=3-00:00:00
+#SBATCH --job-name=spectre_plot
+#SBATCH --output=./spectre_plot.out
+#SBATCH --error=./spectre_plot.out
+
+if [ -n "${SLURM_JOB_ID:-}" ]; then
+    SCRIPT_PATH=$(scontrol show job "$SLURM_JOB_ID" --json | jq -r '.jobs[0].command' )
+    SCRIPT_DIR=$(dirname "$(readlink -f "$SCRIPT_PATH")")
+    SIMULATION_DIR=$(dirname $SCRIPT_DIR)
+else
+    SCRIPT_DIR=$(dirname "$(readlink -f "$0")")
+fi
+
+source $SCRIPT_DIR/env.sh
+
+RUN_DIR="${RUN_DIR:-test-run-03252026/}"
+
+srun --container-image=$SPECTRE_UTILS_IMG \
+     --container-mounts=${HOME}:${HOME},${SCRIPT_DIR}/../:/workspace,${HOST_DATADIR}:/data \
+     python /opt/spectre_utils/plot_surface_fields.py \
+       /workspace/${RUN_DIR} \
+       --plots-dir /workspace/${RUN_DIR}/plots \
+       --poll 120 \
+       --start-date 2002-07-01 \
+       --dt 360.0

simulations/glorysv12-curvilinear/workflows/run.sh

@@ -1,11 +1,12 @@
 #!/bin/bash
 #SBATCH -n64
 #SBATCH -c1
+#SBATCH --time=3-00:00:00
 #SBATCH --job-name=spectre_glorysv12_run
 #SBATCH --output=%x-%A.out
 #SBATCH --error=%x-%A.out
 
-export RUN_DIR="new/"
+export RUN_DIR="test-run-03252026/"
 
 if [ -n "${SLURM_JOB_ID:-}" ]; then
     SCRIPT_PATH=$(scontrol show job "$SLURM_JOB_ID" --json | jq -r '.jobs[0].command' )
@@ -36,7 +37,7 @@ if [[ ! -d "$RUN_DIR" ]]; then
   srun --ntasks=1 \
        --mpi=pmix \
        --container-image=$MITGCM_BASE_IMG \
-       --container-mounts=$SIMULATION_DIR:/workspace:rw \
+       --container-mounts=$SIMULATION_INPUT_DIR:/input:ro,$SIMULATION_DIR:/workspace:rw \
        --container-env=RUN_DIR \
        /bin/bash -c /workspace/workflows/run_setup.sh
   echo ""