Run Locally#

The Run console drives a single CLI invocation as a subprocess of the GUI. Stdout streams into a 5000-line ring buffer and onto disk under <output_dir>/.gui_log/stdout.log; once the dashboard is written, an iframe panel shows the live progress dashboard.

Open the run console#

Click the Run tab (or navigate to /run/):

Run console form.

The form has three pickers (Pipeline JSON, Input directory, Output directory), a Local/SLURM mode radio, two short-flag checkboxes (Dry-run, Resume), an Advanced collapse for the long-tail flags (--sample, --nrows, --ncols, --image-type, Workers → --njobs), and a SLURM config collapse covered on the next page. The Log level field in Advanced is reserved — the GUI accepts a value but the CLI does not currently expose --log-level, so the field is a no-op until that flag lands. The right pane shows the dashboard preview slot and the log tail.

Pick the pipeline and dataset#

You can fill in the pickers two ways:

From the sidebar (hand-off). Click pipeline.json in the sidebar; the hand-off banner above the form activates with Set as pipeline. Click it — the picker label updates. Then click plates/ and use Set as input dir, and finally choose a fresh output folder and use Set as output dir.

From the inline modal browser. Click any Browse… button. A modal opens rooted at the sandbox:

Input directory picker modal.

Click into the directory you want and use Use this directory. The modal respects the same hidden-files / external-symlinks toggles as the sidebar.

Validate before running#

Validate (dry-run) spawns python -m phenotypic --mode full <args> --dry-run. The CLI parses the pipeline JSON, lists the images it would process, then exits without writing any output. The log tail shows the dry-run output. Use this whenever you’re not sure the form values match what the CLI expects — the dry-run takes seconds, a bad real run can waste minutes.

Run#

Clicking Run spawns python -m phenotypic --mode full <args> (no --dry-run). While the subprocess is alive:

  • The log tail polls the ring buffer on a short interval. Lines arrive in order with stderr merged in.

  • Once the CLI writes <output_dir>/deliverables/dashboard.html, the iframe panel points at /runs/<rel>/deliverables/dashboard.html and the live dashboard renders inside the run console — same dashboard you’d open standalone, just iframed.

  • Only one local run can be active at a time; the Run button stays disabled until the current run exits or you click Cancel (which sends SIGTERM, then SIGKILL after a 10-second grace period).

Recent Runs#

The Recent Runs panel below the form lists every run associated with this sandbox — both runs from the current session and historical runs rehydrated from the sandbox at boot time. The screenshot below shows the panel populated with the synthetic dataset’s run:

Recent Runs panel after one local completion.

Each row carries the output directory, mode (local or slurm-<job-id>), status (rendered uppercase by CSS, stored lowercase as one of running, complete, failed, cancelled, unknown), and a Dashboard indicator. Clicking a row re-points the iframe at that run’s dashboard so you can re-visit historical results without leaving the page.

The status comes from <output_dir>/progress/manifest.json; the dashboard indicator is true when deliverables/dashboard.html is present. The hub registers a /runs/<rel>/<file> route on the shell’s Flask server so the iframe URLs work regardless of which tab is currently active.

For SLURM submissions, see Run on SLURM.