Merge branch 'NOAA-EMC:develop' into feature/fit2obs

.gitignore

@@ -129,6 +129,7 @@ ush/global_chgres.sh
 ush/global_chgres_driver.sh
 ush/global_cycle.sh
 ush/global_cycle_driver.sh
+ush/jediinc2fv3.py
 ush/mkwfsgbl.sh
 ush/ufsda
 ush/wafs_blending.sh

docs/note_fixfield.txt

@@ -4,6 +4,8 @@ They are saved locally on all platforms
 
 Hera: /scratch1/NCEPDEV/global/glopara/fix
 Orion: /work/noaa/global/glopara/fix
+Jet: /mnt/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix
+S4: /data/prod/glopara/fix
 
 ------------------------------------------------------------------------------
 09/28/2018

docs/source/components.rst

@@ -60,6 +60,7 @@ Observation data, also known as dump data, is prepared in production and then ar
 
 * Hera: /scratch1/NCEPDEV/global/glopara/dump
 * Orion: /work/noaa/rstprod/dump
+* Jet: /mnt/lfs4/HFIP/hfv3gfs/glopara/dump
 * WCOSS2: /lfs/h2/emc/global/noscrub/emc.global/dump
 * S4: /data/prod/glopara/dump
 

docs/source/hpc.rst

@@ -22,6 +22,7 @@ HPC helpdesks
 * HPSS: rdhpcs.hpss.help@noaa.gov
 * Gaea: oar.gfdl.help@noaa.gov
 * S4: david.huber@noaa.gov
+* Jet: rdhpcs.jet.help@noaa.gov
 
 ======================
 Restricted data access
@@ -76,6 +77,8 @@ It is advised to use Git v2+ when available. At the time of writing this documen
 +---------+----------+---------------------------------------+
 | Orion   | v1.8.3.1 | **module load git/2.28.0**            |
 +---------+----------+---------------------------------------+
+| Jet     | v2.18.0  | default                               |
++---------+----------+---------------------------------------+
 | WCOSS2  | v2.26.2  | default or **module load git/2.29.0** |
 +---------+----------+---------------------------------------+
 | S4      | v1.8.3.1 | **module load git/2.30.0**            |
@@ -96,9 +99,9 @@ For the manage_externals utility functioning::
    Error: fatal: ssh variant 'simple' does not support setting port
    Fix: git config --global ssh.variant ssh
 
-===================================
-Stacksize on R&Ds (Hera, Orion, S4)
-===================================
+========================================
+Stacksize on R&Ds (Hera, Orion, Jet, S4)
+========================================
 
 Some GFS components, like the UPP, need an unlimited stacksize. Add the following setting into your appropriate .*rc file to support these components:
 

docs/source/init.rst

@@ -190,6 +190,7 @@ Forecast-only P8 prototype initial conditions are made available to users on sup
     WCOSS2: /lfs/h2/emc/global/noscrub/emc.global/IC/COUPLED
     HERA: /scratch1/NCEPDEV/climate/role.ufscpara/IC
     ORION: /work/noaa/global/glopara/data/ICSDIR/prototype_ICs
+    JET: /mnt/lfs4/HFIP/hfv3gfs/glopara/data/ICSDIR/prototype_ICs
     S4: /data/prod/glopara/coupled_ICs
 
 These locations are known within the workflow via paths set in ``parm/config/config.coupled_ic``.
@@ -217,7 +218,7 @@ Not yet supported. See :ref:`Manual Generation<manual-generation>` section below
 ---------------------
 Forecast-only coupled
 ---------------------
-Coupled initial conditions are currently only generated offline and copied prior to the forecast run. Prototype initial conditions will automatically be used when setting up an experiment as an S2SW app, there is no need to do anything additional. Copies of initial conditions from the prototype runs are currently maintained on Hera, Orion, and WCOSS2. The locations used are determined by ``parm/config/config.coupled_ic``. If you need prototype ICs on another machine, please contact Walter (Walter.Kolczynski@noaa.gov).
+Coupled initial conditions are currently only generated offline and copied prior to the forecast run. Prototype initial conditions will automatically be used when setting up an experiment as an S2SW app, there is no need to do anything additional. Copies of initial conditions from the prototype runs are currently maintained on Hera, Orion, Jet, and WCOSS2. The locations used are determined by ``parm/config/config.coupled_ic``. If you need prototype ICs on another machine, please contact Walter (Walter.Kolczynski@noaa.gov).
 
 .. _forecastonly-atmonly:
 

docs/source/setup.rst

@@ -28,6 +28,13 @@ Experiment Setup
 
            module load miniconda/3.8-s4
 
+   * - Jet
+     - ::
+
+           module use /mnt/lfs4/HFIP/hfv3gfs/role.epic/miniconda3/modulefiles
+           module load miniconda3/4.12.0
+           conda activate ufswm
+
 If running with Rocoto make sure to have a Rocoto module loaded before running setup scripts:
 
 .. list-table:: ROCOTO Module Load Commands
@@ -54,6 +61,10 @@ If running with Rocoto make sure to have a Rocoto module loaded before running s
      - ::
 
            module load rocoto/1.3.4
+   * - Jet
+     - ::
+
+           module load rocoto/1.3.3
 
 ^^^^^^^^^^^^^^^^^^^^^^^^
 Forecast-only experiment

env/CONTAINER.env

@@ -4,8 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanalrun atmensanalrun"
-    echo "aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"

env/HERA.env

@@ -4,8 +4,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "atmanalrun atmensanalrun"
-    echo "aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -49,22 +48,16 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
     export wavempexec=${launcher}
     export wave_mpmd=${mpmd_opt}
 
-elif [[ "${step}" = "atmanalrun" ]]; then
+elif [[ "${step}" = "atmanlrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
-    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
+    nth_max=$((npe_node_max / npe_node_atmanlrun))
 
-    nth_max=$((npe_node_max / npe_node_atmanalrun))
-
-    export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
-    [[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
-    export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
+    export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
+    [[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
+    export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"
 
 elif [[ "${step}" = "atmensanalrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
     nth_max=$((npe_node_max / npe_node_atmensanalrun))