Port obs-mon to orion and hercules, add lua module files to create ob…

…s-mon python ve (NOAA-EMC#42)

This PR includes:

- Port Obs-Monitor to orion & hercules. 
- Addition of lua module files to create an obs-mon python virtual
environment. Note that I have the ve components temporarily installed in
my own noscrub space. I know this isn't suitable for a permanent
solution but thought it would be an acceptable placeholder.
- Correct use of CFP on wcoss2.  Really this time I've got it.  Honest.
- Removed file cleanup at finish. This needs to be done as a separate
job submission which runs after the plot job finishes. I'll open a new
issue to get that done.

Lastly, as describe in the discussion in NOAA-EMC#41 hercules is now having what
looks like communications issues when it runs eva. Execution hangs when
trying to resolve a url request from cartopy. That may be a system
issue, or it might be a permissions issue from the ve components which I
parked in my noscrub space. Though that location works fine on orion
(and wcoss2). I'm not quite sure how much to make of that.



Closes NOAA-EMC#41

driver/runObsMon.sh

@@ -106,7 +106,7 @@ logfile="${logdir}/OM_setup.log"
 if [[ -e ${logfile} ]]; then rm ${logfile}; fi
 
 case ${MACHINE_ID} in
-   hera)
+   hera|orion|hercules)
       ${SUB} --account ${ACCOUNT}  --ntasks=1 --mem=400M --time=0:05:00 \
              -J ${jobname} --partition service -o ${logfile} ${jobfile}
       ;;
@@ -116,7 +116,7 @@ case ${MACHINE_ID} in
 	   -v "PYTHONPATH=${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=${OM_LOGS}, YAML_FILE=${YAML_FILE}" \
+	       OM_LOGS=${OM_LOGS}, YAML_FILE=${YAML_FILE}, CARTOPY_DATA_DIR=${CARTOPY_DATA_DIR}" \
            -l select=1:mem=500mb -l walltime=0:05:00 -N ${jobname} ${jobfile}
       ;;
 esac

jobs/JMON_PLOT_OBS

@@ -31,6 +31,11 @@ if [[ -d ${DATAROOT}/${NET} ]]; then rm -rf ${DATAROOT}/${NET}; fi
 mkdir -p ${DATA}
 cd ${DATA}
 
+##################################
+# Remove workspace when finished
+##################################
+KEEPDATA=${KEEPDATA:-"NO"}
+
 ################
 # Run exscript
 ################
@@ -46,8 +51,6 @@ if [[ -e "${pgmout}" ]] ; then
 fi
 
 ####################
-# Remove workspace
+# Remove workspace -- this will have to be a separate job that runs
+# after the OM_plot job is complete.
 ####################
-KEEPDATA=${KEEPDATA:-"NO"}
-cd ${DATAROOT}
-[[ ${KEEPDATA} = "NO" ]] && rm -rf ${DATA}

modulefiles/obs-monitor/hera.lua

@@ -0,0 +1,39 @@
+help([[
+Load python virtual environment for obs-monitor
+]])
+
+local pkgName    = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+conflict(pkgName)
+
+
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/modulefiles/Core")
+
+load ("stack-intel/2021.5.0")
+load ("python/3.10.13")
+
+local pyenvpath = "/scratch1/NCEPDEV/da/Edward.Safford/noscrub/python/envs/"
+local pyenvname = "obs-mon"
+
+local pyenvactivate = pathJoin(pyenvpath, pyenvname, "bin/activate")
+
+if (mode() == "load") then
+  local activate_cmd = "source "..pyenvactivate
+  execute{cmd=activate_cmd, modeA={"load"}}
+  prepend_path("PATH", "/scratch1/NCEPDEV/da/Edward.Safford/noscrub/python/envs/obs-mon/bin")
+  prepend_path("PYTHONPATH", "/scratch1/NCEPDEV/da/Edward.Safford/noscrub/python/envs/obs-mon")
+
+else
+  if (mode() == "unload") then
+    local deactivate_cmd = "deactivate"
+    execute{cmd=deactivate_cmd, modeA={"unload"}}
+  end
+end
+
+whatis("Name: ".. pkgName)
+whatis("Version: ".. pkgVersion)
+whatis("Category: Obs-monitor")
+whatis("Description: Load all libraries needed for obs-monitor")
+

modulefiles/obs-monitor/hercules.lua

@@ -0,0 +1,39 @@
+help([[
+Load python virtual environment for obs-monitor
+]])
+
+local pkgName    = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+conflict(pkgName)
+
+
+prepend_path("MODULEPATH", " /work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.6.0/envs/unified-env-intel-2023.2.4/install/modulefiles/Core")
+
+load ("stack-intel/2021.10.0")
+load ("python/3.10.8")
+
+local pyenvpath = "/work/noaa/da/esafford/noscrub/python/envs/"
+local pyenvname = "obs-mon"
+
+local pyenvactivate = pathJoin(pyenvpath, pyenvname, "bin/activate")
+
+if (mode() == "load") then
+  local activate_cmd = "source "..pyenvactivate
+  execute{cmd=activate_cmd, modeA={"load"}}
+  prepend_path("PATH", "/work/noaa/da/esafford/noscrub/python/envs/obs-mon/bin")
+  prepend_path("PYTHONPATH", "/work/noaa/da/esafford/noscrub/python/envs/obs-mon")
+
+else
+  if (mode() == "unload") then
+    local deactivate_cmd = "deactivate"
+    execute{cmd=deactivate_cmd, modeA={"unload"}}
+  end
+end
+
+whatis("Name: ".. pkgName)
+whatis("Version: ".. pkgVersion)
+whatis("Category: Obs-monitor")
+whatis("Description: Load all libraries needed for obs-monitor")
+

modulefiles/obs-monitor/orion.lua

@@ -0,0 +1,39 @@
+help([[
+Load python virtual environment for obs-monitor
+]])
+
+local pkgName    = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+conflict(pkgName)
+
+
+prepend_path("MODULEPATH", " /work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.6.0/envs/unified-env-rocky9/install/modulefiles/Core")
+
+load ("stack-intel/2021.9.0")
+load ("python/3.10.8")
+
+local pyenvpath = "/work/noaa/da/esafford/noscrub/python/envs/"
+local pyenvname = "obs-mon"
+
+local pyenvactivate = pathJoin(pyenvpath, pyenvname, "bin/activate")
+
+if (mode() == "load") then
+  local activate_cmd = "source "..pyenvactivate
+  execute{cmd=activate_cmd, modeA={"load"}}
+  prepend_path("PATH", "/work/noaa/da/esafford/noscrub/python/envs/obs-mon/bin")
+  prepend_path("PYTHONPATH", "/work/noaa/da/esafford/noscrub/python/envs/obs-mon")
+
+else
+  if (mode() == "unload") then
+    local deactivate_cmd = "deactivate"
+    execute{cmd=deactivate_cmd, modeA={"unload"}}
+  end
+end
+
+whatis("Name: ".. pkgName)
+whatis("Version: ".. pkgVersion)
+whatis("Category: Obs-monitor")
+whatis("Description: Load all libraries needed for obs-monitor")
+

modulefiles/obs-monitor/wcoss2.lua

@@ -0,0 +1,36 @@
+help([[
+Load python virtual environment for obs-monitor
+]])
+
+local pkgName    = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+conflict(pkgName)
+
+
+load ("python/3.10.4")
+
+local pyenvpath = "/lfs/h2/emc/da/noscrub/edward.safford/python/envs/"
+local pyenvname = "obs-mon"
+
+local pyenvactivate = pathJoin(pyenvpath, pyenvname, "bin/activate")
+
+if (mode() == "load") then
+  local activate_cmd = "source "..pyenvactivate
+  execute{cmd=activate_cmd, modeA={"load"}}
+  prepend_path("PATH", "/lfs/h2/emc/da/noscrub/edward.safford/python/envs/obs-mon/bin")
+  prepend_path("PYTHONPATH", "/lfs/h2/emc/da/noscrub/edward.safford/python/envs/obs-mon")
+
+else
+  if (mode() == "unload") then
+    local deactivate_cmd = "deactivate"
+    execute{cmd=deactivate_cmd, modeA={"unload"}}
+  end
+end
+
+whatis("Name: ".. pkgName)
+whatis("Version: ".. pkgVersion)
+whatis("Category: Obs-monitor")
+whatis("Description: Load all libraries needed for obs-monitor")
+

parm/OM_config

@@ -9,37 +9,65 @@ export JOBSobsmon=${om_dir_root}/jobs
 source ${om_dir_root}/ush/detect_machine.sh
 export MACHINE_ID=`echo "${MACHINE_ID%%.*}"`
 
+module use ${HOMEobsmon}/modulefiles
+
 case ${MACHINE_ID} in
 
    hera)
       export SUB="sbatch"
       export SERVICE_PARTITION="service"
+      export CARTOPY_DATA_DIR="/scratch1/NCEPDEV/da/Edward.Safford/noscrub/python/envs/obs-mon/share/cartopy"
 
-      ptmp="/scratch2/NCEPDEV/stmp3/$USER"
-      stmp="/scratch2/NCEPDEV/stmp1/$USER"
+      ptmp="/scratch2/NCEPDEV/stmp3/${USER}"
+      stmp="/scratch2/NCEPDEV/stmp1/${USER}"
       queue=""
       project=""
       account="da-cpu"
-      aprun_py="python"
       ;;
 
    wcoss2)
       export SUB="qsub"
+      export CARTOPY_DATA_DIR="/lfs/h2/emc/da/noscrub/edward.safford/python/envs/obs-mon/share/cartopy"
 
-      ptmp="/lfs/h2/emc/ptmp/$USER"
-      stmp="/lfs/h2/emc/stmp/$USER"
+      ptmp="/lfs/h2/emc/ptmp/${USER}"
+      stmp="/lfs/h2/emc/stmp/${USER}"
       queue="dev"
       project="GDAS-DEV"
       account="GFS-DEV"
-      aprun_py=`which python`
+      ;;
+
+   orion)
+      export SUB="sbatch"
+      export CARTOPY_DATA_DIR="/work/noaa/da/esafford/noscrub/python/envs/obs-mon/share/cartopy"
+
+      ptmp="/work2/noaa/stmp/${USER}"
+      stmp="/work/noaa/stmp/${USER}" 
+
+      queue=""
+      project=""
+      account="da-cpu"
+      ;;
+
+   hercules)
+      export SUB="sbatch"
+      export CARTOPY_DATA_DIR="/work/noaa/da/esafford/noscrub/python/envs/obs-mon/share/cartopy"
+
+      ptmp="/work2/noaa/stmp/${USER}"
+      stmp="/work/noaa/stmp/${USER}" 
+
+      queue=""
+      project=""
+      account="da-cpu"
       ;;
 esac
 
+module load obs-monitor/${MACHINE_ID}
+export APRUN_PY=`which python`
+
 export ACCOUNT=${ACCOUNT:-$account}
 export PROJECT=${PROJECT:-$project}
 export JOB_QUEUE=${JOB_QUEUE:-$queue}
 
 export OM_LOGS="${ptmp}/logs/OM_logs"
 export DATAROOT=${DATAROOT:-${stmp}}
 export COMOUT=${COMOUT:-${ptmp}}
-export APRUN_PY=${APRUN_PY:-${aprun_py}}