Checklists

Running a Processed Setup

Prepackaged runs are common for testing SCHISM on a new system or rerunning a model from another user delivered as a bundle. In this case the user will have obtained a complete set up as a “tarball” (tar.gz) file or copies the run using the rsync command (don’t use copy command cp). See Linux hints.

The steps are:

☐ Set up the environment and compile schism

☐ Untar the archived run

☐ If the atmospheric files are packaged separately, reestablish the linkage using the instructions in the readme file.

☐ Compile the model using instructions on the VIMS website or precompliled binaries for Windows*

☐ Most clusters use a job manager and you submit to queue. Usually you need to adapt

☐ schism.sh to point to executable and load dependencies

☐ launch files such as launch.pbs (user name, number of cores and cpus per core, name of run)

☐ Create a directory called outputs

☐ Take care of any ‘gotchas’ such as making sure there is a directory named ‘outputs’ and that stack limits are disabled.

* Windows is good for learning but not typical for full Delta runs

Simple Hindcast Runs

☐ Choose run dates

See hotstart section on this topic

☐ Apply template to existing mesh

☐ Clone BayDeltaSCHISM from GitHub. Get a fresh copy or git stash any changes.

☐ Note the git hash code or tag in a readme.

☐ Copy BayDeltaSCHISM/templates/bay_delta to study preprocessing directory mystudy/bay_delta

☐ Obtain an SMS .2dm or SCHISM hgrid.gr3 file (e.g. bay_delta_111_prop605.2dm and add it to bay_delta folder)

☐ Change main_bay_delta.yaml by pointing the mesh_inputfile to the name of the mesh

☐ Make sure your flow transect file (flow_station_xsect.yaml) contains output you want

☐ Invoke the preprocessor with the command: $ prepare_schism main_bay_delta.yaml

☐ Copy the prepared items (.in, ,gr3, .ll, .prop, .nml) to the launch place.

☐ Collect time series inputs

☐ These steps are the two steps in BayDeltaSCHISM/bdschism/bdschism elev2d.bat, which you would adapt

☐ download NOAA files for coastal stations at SF, Point Reyes, Monterey using download_noaa

☐ validate that the datum shown in the file is NAVD88 as this has been somewhat unpredictable

☐ run the genelev2D, a utility that installs with schimpy. For details try genelev2D –help

☐ Adapt and run the multi_clip.py example in BayDeltaSCHISM/bdschism/bdschism to subset boundary/source data for your period.

☐ Hotstart (can be concurrent with barotropic)

☐ Nudging (can be concurrent with barotropic)

☐ Barotropic warmup

☐ interpolate_variables7 (or later) script to create uv3D.th.

☐ move the uv3D.th to the study directory

☐ delete all the files outputs/* or move /outputs to /outputs.tropic and create an empty /outputs

☐ Baroclinic simulation

☐ finalize your station.in output request