An Open OnDemand (OOD) Batch Connect application that launches a PhenoTypic GUI server on the UCR HPCC cluster for colony phenotyping and image analysis.
This app provides a web-based interface to submit a Slurm job that runs the phenotypic-gui server. Once the job starts, users connect to the GUI directly from their browser through OOD, or via an SSH tunnel from a local machine.
| File | Purpose |
|---|---|
manifest.yml |
App metadata (name, category, role) |
form.yml |
Job submission form fields (cores, memory, runtime, queue, working directory) |
submit.yml.erb |
Translates form values into Slurm sbatch arguments |
view.html.erb |
Connection panel shown after the job starts |
template/before.sh.erb |
Pre-launch setup: finds an available port, exports the module function |
template/script.sh.erb |
Main job script: loads the phenotypic module and starts phenotypic-gui |
template/after.sh |
Post-launch check: waits up to 60 seconds for the server port to open |
| Field | Default | Description |
|---|---|---|
| Working Directory | $HOME |
Project directory passed to phenotypic-gui --root |
| Number of Cores | 4 | Slurm -c value |
| Memory (GB) | 8 | Slurm --mem value |
| Job Runtime | 2-00:00:00 |
Slurm -t value (DD-HH:MM:SS) |
| Queue | — | Slurm partition (auto_queues) |
| Additional Slurm Arguments | — | Any extra sbatch flags (e.g. --gres=gpu:1) |
- Open the app from the OOD Interactive Apps panel on the HPCC portal.
- Fill in the form and click Launch.
- Once the job is running, click Connect to PhenoTypic to open the GUI in your browser.
To connect from a local machine instead:
ssh -NL <port>:localhost:<port> <username>@cluster.hpcc.ucr.eduThen open http://localhost:<port>/ in your local browser.
- Access to the UCR HPCC cluster via Open OnDemand
- The
phenotypic/environment module available on the cluster