Batch Connect - OSC Schrodinger
Overview
OSC Schrodinger is an interactive app designed for OSC OnDemand that launches Schrodinger in an XFCE desktop. Schrodinger is designed for researchers running molecular modeling.
Screenshots
Features
- Launches Schrodinger via interactive desktop (TurboVNC + XFCE) on compute nodes
- Configurable cores, memory, wall time, and node type via the launch form
Requirements
Compute Node Software
- Schrodinger 2020.1+
- Lmod 6.0.1+ or any other
module purge and module load based CLI used to load appropriate environments within the batch job before launching the Jupyter server.
- Xfce Desktop 4+
For VNC server support:
For hardware rendering support:
Open OnDemand
- Open OnDemand 2.x+ (Batch Connect support required)
- Scheduler: Slurm
App Installation
1. Clone the repository into your Open OnDemand apps directory:
cd /var/www/ood/apps/sys
git clone https://github.com/OSC/bc_osc_schrodinger.git
cd bc_osc_schrodinger
# Pin to a release (recommended)
git checkout v0.6.0
You will not need to do anything beyond this as all necessary assets are
installed. You will also not need to restart this app as it isn't a Passenger app.
To update the app you would:
cd bc_osc_schrodinger
git fetch
git checkout
Again, you do not need to restart the app as it isn't a Passenger app.
Edit form.yml and update these values for your cluster:
| Attribute |
Default |
Change to |
cluster |
cardinal |
Your cluster name(s) |
schrodinger_version |
2024.3, 2023.2 |
Schrodinger versions on your system via schrodinger/ module |
node_type |
OSC-specific node types |
Node types available on your cluster |
3. Verify
No OOD restart is needed (Batch Connect apps are detected automatically). Visit your OOD dashboard and look for Schrodinger under Interactive Apps > GUIs.
Configuration
| Attribute |
Description |
Default |
cluster |
Target cluster ID |
cardinal |
schrodinger_version |
Schrodinger version to launch via schrodinger/ module |
2024.3 |
bc_num_hours |
Maximum wall time (hours) |
1 |
bc_num_slots |
Number of scheduler slots requested (number of nodes) |
1 |
num_cores |
Number of CPU cores (1--96, varies by node type/cluster) |
1 |
node_type |
Compute node type (any, vis, hugemem) |
any |
licenses |
String with specified licenses for macromodel, glide, ligprep, qikprep, or epik features. |
|
bc_vnc_resolution |
Resolution of VNC desktop session |
1228 x 691 |
Environment variables
| Variable |
Required |
Description |
| SCHRODINGER |
Yes |
Path to Schrodinger installation root |
| LM_LICENSE_FILE |
Yes |
License server or file for Schrodinger |
| VGL_DISPLAY |
No |
VirtualGL display for GPU rendering |
Troubleshooting
Job starts but app doesn't appear (Batch Connect)
- Check the job's
output.log in ~/ondemand/data/sys/bc_osc_schrodinger/
- Verify the module loads correctly:
module load schrodinger/
- Verify the window manager is installed:
which xfwm4
- Verify websockify is installed and accessible
"Module not found" error
The module name in form.yml doesn't match your system. Run module spider software to find the correct name and update the modules attribute.
Connection timeout
The app may need more time to start. Increase the connection timeout or check that the compute node can open the required port.
Testing
| Site |
OOD Version |
Scheduler |
Status |
| Ohio Supercomputer Center |
4.1.4 |
Slurm |
Production |
Known Limitations
- Licensing for Schrodinger features must be correctly configured and requested
Contributing
- Fork this repository
- Create a feature branch (
git checkout -b feature/my-improvement)
- Submit a pull request with a description of your changes
For bugs or feature requests, open an issue.
This app is part of the OOD Appverse. Join the Appverse Affinity Group to connect with other contributors.
References
License
- Documentation, website content, and logo is licensed under
CC-BY-4.0
- Code is licensed under MIT (see LICENSE.txt)
- The Schrodinger logo is a trademark of Schrodinger.
Acknowledgements
This app is built on Open OnDemand, developed and maintained by the Ohio Supercomputer Center (OSC).
Open OnDemand is supported by the National Science Foundation under awards NSF SI2-SSE-1534949 and NSF CSSI-Frameworks-1835725.