Drop "nowcast-dev" run from automation workflow and configuration

config/nowcast.yaml

@@ -292,14 +292,10 @@ run types:
     land processor elimination: bathymetry_202108.csv
     duration: 1  # day
     restart from: nowcast-green
+  ### retained because plots for nowcast-dev haven't been removed from
+  ### make_plots.make_plots() yet
   nowcast-dev:
-    config name: SalishSeaCast_Blue
-    coordinates: coordinates_seagrid_SalishSea201702.nc
-    bathymetry: bathymetry_201702.nc
     mesh mask: mesh_mask201702.nc
-    land processor elimination: bathymetry_201702.csv
-    duration: 1  # day
-    restart from: nowcast-dev
   nowcast-green:
     config name:  SalishSeaCast
     coordinates: coordinates_seagrid_SalishSea201702.nc
@@ -340,6 +336,9 @@ results archive:
   # Values are directories on results server where run results are stored
   # in ddmmmyy/ directories.
   nowcast: /results/SalishSea/nowcast-blue.202111/
+  ### retained until make_plots is refactored to remove nowcast-dev
+  ### that refactoring needs to come after compare_venus_ctd fig module is updated
+  ### to handle ONC API v3
   nowcast-dev: /results/SalishSea/nowcast-dev.201905/
   forecast: /results/SalishSea/forecast.202111/
   forecast2: /results/SalishSea/forecast2.202111/
@@ -623,34 +622,13 @@ run:
         weather dir: /nemoShare/MEOPAR/GEM2.5/ops/NEMO-atmos/
 
     salish-nowcast:
-      shared storage: True
-      make forcing links: True
+      ### retained because workers.test_upload_forcing.TestConfig.test_ssh_keys() needs
+      ### to find this item for every enabled host
       ssh key: SalishSeaNEMO-nowcast_id_rsa
-      envvars: /SalishSeaCast/nowcast-env/etc/conda/activate.d/envvars.sh
-      python: /SalishSeaCast/nowcast-env/bin/python3
-      config file: /SalishSeaCast/SalishSeaNowcast/config/nowcast.yaml
-      run prep dir: /SalishSeaCast/runs/
+      ### retained because next_workers needs to know until salish is fully removed
+      shared storage: True
+      ### retained because make_*_runoff_file workers use this to get grid files
       grid dir: /SalishSeaCast/grid/
-      salishsea_cmd: /SalishSeaCast/nowcast-env/bin/salishsea
-      job exec cmd: qsub
-      # Optional email address to which to send notifications of the beginning
-      # and end of execution of the run, as well as notification of abnormal
-      # abort messages.
-      email: [email protected]
-      run types:
-        nowcast-dev:
-          run sets dir: /SalishSeaCast/SS-run-sets/v201905/nowcast-dev/
-          mpi decomposition: 1x7
-          walltime: 23:30:00
-          results: /results/SalishSea/nowcast-dev.201905/
-        nowcast-green:
-          results: /results2/SalishSea/nowcast-green.201905/
-      forcing:
-        ssh dir: /results/forcing/sshNeahBay/
-        bc dir: /results/forcing/LiveOcean/boundary_conditions/
-        rivers dir: /results/forcing/rivers/
-        bottom friction mask: /SalishSeaCast/grid/jetty_mask_bathy201702.nc
-        weather dir: /results/forcing/atmospheric/continental2.5/nemo_forcing/
 
     orcinus-nowcast-agrif:
       ssh key: SalishSeaNEMO-nowcast_id_rsa
@@ -1372,8 +1350,6 @@ message registry:
       failure nowcast: nowcast NEMO run failed
       success nowcast-green: nowcast-green NEMO run started
       failure nowcast-green: nowcast-green NEMO run failed
-      success nowcast-dev: nowcast-dev NEMO run started
-      failure nowcast-dev: nowcast-dev NEMO run failed
       success forecast: forecast NEMO run started
       failure forecast: forecast NEMO run failed
       success forecast2: forecast2 NEMO run started
@@ -1399,8 +1375,6 @@ message registry:
       failure nowcast: nowcast watch_NEMO failed
       success nowcast-green: nowcast-green NEMO run ended
       failure nowcast-green: nowcast-green watch_NEMO failed
-      success nowcast-dev: nowcast-dev NEMO run ended
-      failure nowcast-dev: nowcast-dev watch_NEMO failed
       success forecast: forecast NEMO run ended
       failure forecast: forecast watch_NEMO failed
       success forecast2: forecast2 NEMO run ended

docs/deployment/index.rst

@@ -23,7 +23,7 @@ Nowcast Production Deployments
 ******************************
 
 In October 2016 the production deployment of the nowcast system was changed to use the :ref:`SalishSeaNowcast-repo` package that is based on the `NEMO_Nowcast framework`_ framework.
-The production deployment uses 3 systems:
+The production deployment uses 2 systems:
 
 .. _NEMO_Nowcast framework: https://nemo-nowcast.readthedocs.io/en/latest/
 
@@ -32,14 +32,6 @@ The production deployment uses 3 systems:
    :py:mod:`nemo_nowcast.log_aggregator`,
    most of the pre- and post-processing workers run on the :ref:`SalishSeaModelResultsServer`, :kbd:`skookum`, where the deployment is in the :file:`/SalishSeaCast/` directory tree.
 
-#. The development compute server,
-   :kbd:`salish`,
-   is used to run the daily development model run,
-   :kbd:`nowcast-dev` NEMO-3.6 model run.
-   :kbd:`salish` and :kbd:`skookum` share storage via NFS mounts,
-   so,
-   :kbd:`salish` uses the same deployment in the :file:`/SalishSeaCast/` directory tree.
-
 #. The daily
    :kbd:`forecast2`
    (preliminary forecast),
@@ -73,13 +65,13 @@ The production deployment uses 3 systems:
    .. _arbutus.cloud: https://docs.alliancecan.ca/wiki/Cloud_resources#Arbutus_cloud
    .. _Ceph object storage: https://en.wikipedia.org/wiki/Ceph_(software)
 
-These sections describe the setup of the nowcast system on :kbd:`skookum`/:kbd:`salish` and :kbd:`arbutus.cloud`,
-and it operation.
+These sections describe the setup of the nowcast system on :kbd:`skookum` and :kbd:`arbutus.cloud`,
+and their operation.
 
 .. toctree::
    :maxdepth: 2
 
-   skookum_salish
+   skookum
    arbutus_cloud
    operations
 
@@ -106,3 +98,10 @@ The setup on :kbd:`optimum` is described in:
 See also the `#optimum-cluster`_ Slack channel.
 
 .. _#optimum-cluster: https://salishseacast.slack.com/?redir=%2Farchives%2FC011S7BCWGK
+
+With the update of the production to run the V21-11 model version in January 2024,
+we decided to end the daily :kbd:`nowcast-dev` development model runs on :kbd:`salish`.
+Development is now generally done in research runs on :kbd:`graham`.
+:kbd:`salish` is now mostly used for analysis tasks, post-processing of NEMO model results files
+to produce day-average and month-average dataset files,
+and Lagrangian particle tracking analysis with :program:`ariane` and :program:`OceanParcels`.

docs/deployment/skookum_salish.rst → docs/deployment/skookum.rst

@@ -16,11 +16,11 @@
 .. SPDX-License-Identifier: Apache-2.0
 
 
-.. _SkookumSalishDeployment:
+.. _SkookumDeployment:
 
-***************************************
-:kbd:`skookum`/:kbd:`salish` Deployment
-***************************************
+************************
+:kbd:`skookum`Deployment
+************************
 
 Git Repositories
 ================
@@ -47,42 +47,6 @@ Clone the following repos into :file:`/SalishSeaCast/`:
     $ git clone [email protected]:SalishSeaCast/tracers.git
     $ git clone [email protected]:mdunphy/FVCOM-VHFR-config.git
     $ git clone [email protected]:douglatornell/OPPTools.git
-    $ git clone [email protected]:SalishSeaCast/NEMO-3.6-code.git
-    $ git clone [email protected]:SalishSeaCast/XIOS-ARCH.git
-    $ git clone [email protected]:SalishSeaCast/XIOS-2.git
-
-
-Build XIOS-2
-============
-
-Symlink the XIOS-2 build configuration files for :kbd:`salish` from the
-:file:`XIOS-ARCH` repo clone into the :file:`XIOS-2/arch/` directory:
-
-.. code-block:: bash
-
-    $ cd /SalishSeaCast/XIOS-2/arch
-    $ ln -s ../../XIOS-ARCH/UBC-EOAS/arch-GCC_SALISH.fcm
-    $ ln -s ../../XIOS-ARCH/UBC-EOAS/arch-GCC_SALISH.path
-
-:command:`ssh` to :kbd:`salish` and build XIOS-2 with:
-
-.. code-block:: bash
-
-    $ cd /SalishSeaCast/XIOS-2
-    $ ./make_xios --arch GCC_SALISH --netcdf_lib netcdf4_seq --job 8
-
-
-Build NEMO-3.6
-==============
-
-Build NEMO-3.6 and :program:`rebuild_nemo.exe`:
-
-.. code-block:: bash
-
-    $ cd /SalishSeaCast/NEMO-3.6-code/NEMOGCM/CONFIG
-    $ XIOS_HOME=/SalishSeaCast/XIOS-2 ./makenemo -m GCC_SALISH -n SalishSeaCast_Blue -j8
-    $ cd /SalishSeaCast/NEMO-3.6-code/NEMOGCM/TOOLS/
-    $ XIOS_HOME=/SalishSeaCast/XIOS-2 ./maketools -m GCC_SALISH -n REBUILD_NEMO
 
 
 Python Packages
@@ -264,9 +228,6 @@ On the hosts where the nowcast system NEMO runs will be executed create a
 
 The hosts and their :file:`runs` directories presently in use are:
 
-* :kbd:`salish`
-    :file:`/SalishSeaCast/runs/`
-
 * :kbd:`arbutus.cloud`
     See :ref:`ArbutusCloudNEMORunsDirectory`
 

nowcast/next_workers.py

@@ -667,19 +667,17 @@ def after_make_forcing_links(msg, config, checklist):
         "failure nowcast+": [],
         "failure nowcast-green": [],
         "failure nowcast-agrif": [],
-        "failure nowcast-dev": [],
         "failure forecast2": [],
         "failure ssh": [],
         "success nowcast+": [],
         "success nowcast-green": [],
         "success nowcast-agrif": [],
-        "success nowcast-dev": [],
         "success forecast2": [],
         "success ssh": [],
     }
     if msg.type.startswith("success"):
         run_types = {
-            "nowcast+": ("nowcast", "nowcast-dev"),
+            "nowcast+": ("nowcast",),
             "nowcast-green": ("nowcast-green",),
             "nowcast-agrif": ("nowcast-agrif",),
             "ssh": ("forecast",),
@@ -738,12 +736,10 @@ def after_run_NEMO(msg, config, checklist):
         "crash": [],
         "failure nowcast": [],
         "failure nowcast-green": [],
-        "failure nowcast-dev": [],
         "failure forecast": [],
         "failure forecast2": [],
         "success nowcast": [],
         "success nowcast-green": [],
-        "success nowcast-dev": [],
         "success forecast": [],
         "success forecast2": [],
     }
@@ -777,12 +773,10 @@ def after_watch_NEMO(msg, config, checklist):
         "crash": [],
         "failure nowcast": [],
         "failure nowcast-green": [],
-        "failure nowcast-dev": [],
         "failure forecast": [],
         "failure forecast2": [],
         "success nowcast": [],
         "success nowcast-green": [],
-        "success nowcast-dev": [],
         "success forecast": [],
         "success forecast2": [],
     }
@@ -849,16 +843,6 @@ def after_watch_NEMO(msg, config, checklist):
                             ],
                         )
                     )
-        if run_type == "nowcast-green":
-            for host in config["run"]["enabled hosts"]:
-                run_types = config["run"]["enabled hosts"][host]["run types"]
-                if "nowcast-dev" in run_types:
-                    next_workers[msg.type].append(
-                        NextWorker(
-                            "nowcast.workers.make_forcing_links",
-                            args=[host, "nowcast+", "--shared-storage"],
-                        )
-                    )
         if run_type == "forecast2":
             host_name = config["wave forecasts"]["host"]
             run_date = arrow.get(msg.payload[run_type]["run date"]).shift(days=+1)

nowcast/workers/run_NEMO.py

@@ -12,10 +12,8 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-"""SalishSeaCast worker that prepares the YAML run
-description file and bash run script for a nowcast, nowcast-green, nowcast-dev,
-forecast or forecast2 run on the ONC cloud or salish,
-and launches the run.
+"""SalishSeaCast worker that prepares the YAML run description file and bash run script
+for a nowcast, nowcast-green, forecast or forecast2 run on the ONC cloud, and launches the run.
 """
 import logging
 import os
@@ -49,12 +47,11 @@ def main():
     worker.cli.add_argument("host_name", help="Name of the host to execute the run on")
     worker.cli.add_argument(
         "run_type",
-        choices={"nowcast", "nowcast-green", "nowcast-dev", "forecast", "forecast2"},
+        choices={"nowcast", "nowcast-green", "forecast", "forecast2"},
         help="""
         Type of run to execute:
         'nowcast' means nowcast physics run,
         'nowcast-green' means nowcast green ocean run,
-        'nowcast-dev' means nowcast physics run with in-development features,
         'forecast' means updated forecast run,
         'forecast2' means preliminary forecast run,
         """,
@@ -145,7 +142,6 @@ def _create_run_desc_file(run_date, run_type, host_name, config):
     run_days = {
         "nowcast": run_date,
         "nowcast-green": run_date,
-        "nowcast-dev": run_date,
         "forecast": run_date.shift(days=1),
         "forecast2": run_date.shift(days=2),
     }
@@ -170,7 +166,6 @@ def _update_time_namelist(run_date, run_type, run_duration, host_config, run_pre
         # run-type: based-on run-type, date offset
         "nowcast": ("nowcast", -1),
         "nowcast-green": ("nowcast-green", -1),
-        "nowcast-dev": ("nowcast-dev", -1),
         "forecast": ("nowcast", 0),
         "forecast2": ("forecast", 0),
     }
@@ -207,7 +202,6 @@ def _calc_new_namelist_lines(
     run_date_offset = {
         "nowcast": 0,
         "nowcast-green": 0,
-        "nowcast-dev": 0,
         "forecast": 1,
         "forecast2": 2,
     }
@@ -246,7 +240,6 @@ def _run_description(run_date, run_type, run_id, restart_timestep, host_name, co
         # run-type: previous run's ddmmmyy results directory name
         "nowcast": run_date.shift(days=-1).format("DDMMMYY").lower(),
         "nowcast-green": run_date.shift(days=-1).format("DDMMMYY").lower(),
-        "nowcast-dev": run_date.shift(days=-1).format("DDMMMYY").lower(),
         "forecast": run_date.shift(days=-1).format("DDMMMYY").lower(),
         "forecast2": run_date.shift(days=-2).format("DDMMMYY").lower(),
     }
@@ -346,9 +339,7 @@ def _run_description(run_date, run_type, run_id, restart_timestep, host_name, co
         grid_dir / config["run types"][run_type]["bathymetry"]
     )
     lpe_filename = config["run types"][run_type]["land processor elimination"]
-    run_desc["grid"]["land processor elimination"] = (
-        False if host_name == "salish-nowcast" else os.fspath(grid_dir / lpe_filename)
-    )
+    run_desc["grid"]["land processor elimination"] = os.fspath(grid_dir / lpe_filename)
     run_desc["restart"] = restart_filepaths
     run_desc["output"].update(
         {

nowcast/workers/watch_NEMO.py

@@ -44,7 +44,7 @@ def main():
     worker.cli.add_argument("host_name", help="Name of the host to monitor the run on")
     worker.cli.add_argument(
         "run_type",
-        choices={"nowcast", "nowcast-green", "nowcast-dev", "forecast", "forecast2"},
+        choices={"nowcast", "nowcast-green", "forecast", "forecast2"},
         help="""
         Type of run to monitor:
         'nowcast' means nowcast physics run,