Schrodinger

Batch Connect - OSC Schrodinger

Overview

An Open OnDemand Batch Connect app that launches a Schrodinger Maestro GUI in an XFCE desktop session on the OSC Cardinal cluster. Schrodinger provides a computational platform for drug discovery and materials science.

This app uses the Batch Connect vnc template with Slurm.

• Upstream project: Schrodinger
• Batch Connect template: vnc
• Scheduler: Slurm

Screenshots

Features

• Launches Schrodinger Maestro GUI in an XFCE VNC desktop session
• Hardware-accelerated 3D visualization on vis nodes via VirtualGL (vglrun maestro -NOSGL)
• Software rendering on non-GPU nodes (maestro -SGL)
• Multiple Schrodinger versions available (schrodinger/2024.3, schrodinger/2023.2)
• Configurable cores, wall time, and node type (any, vis, hugemem) via the launch form
• License management support for Schrodinger features (macromodel, glide, ligprep, qikprep, epik)
• Configurable VNC resolution

Requirements

Compute Node Software

This Batch Connect app requires the following software be installed on the compute nodes that the batch job is intended to run on (NOT the OnDemand node):

• 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:

• TurboVNC 2.1+
• websockify 0.8.0+

For hardware rendering support:

• VirtualGL 2.3+

Open OnDemand

• Tested to work with the latest version of Open OnDemand
• 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

No restart is needed -- Batch Connect apps are not Passenger apps and are detected automatically.

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.

2. Configure for your site

Edit form.yml and update these values for your cluster:

Attribute	Default	Change to
cluster	cardinal	Your cluster name(s)
schrodinger_version	schrodinger/2024.3 (and others)	Schrodinger versions on your system
node_type	OSC-specific node types	Node types available on your cluster
num_cores.max	96	Max cores on your compute nodes

In script.sh.erb, the app loads modules with:

module load 

For GPU/vis nodes, it additionally loads:

module load intel/2021.10.0 virtualgl/3.1.1

Ensure equivalent modules are available on your system.

To Update the App

cd /var/www/ood/apps/sys/bc_osc_schrodinger
git fetch
git checkout 

No restart is needed.

Configuration

form.yml attributes

Attribute	Widget	Description	Default
cluster	select	Target cluster ID(s)	cardinal
schrodinger_version	select	Schrodinger version / module load string	schrodinger/2024.3
bc_num_hours	number	Maximum wall time (hours)	1
bc_num_slots	number	Number of nodes	1
num_cores	number_field	Number of CPU cores (0--96; 0 = full node)	1
node_type	select	Compute node type (any, vis, hugemem)	any
licenses	text	Schrodinger license string (e.g., glide@osc:1)	(empty)
bc_vnc_resolution	text	VNC session resolution	(required)

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)

1. Check the job's output.log in ~/ondemand/data/sys/bc_osc_schrodinger/
2. Verify the module loads correctly: module load schrodinger/
3. Verify the window manager is installed: which xfwm4
4. 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	4.2.2	Slurm	Production

Known Limitations

• Licensing for Schrodinger features must be correctly configured and requested

Contributing

1. Fork this repository
2. Create a feature branch (git checkout -b feature/my-improvement)
3. 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

• Schrodinger — the application launched by this OOD app
• Open OnDemand — the HPC portal framework
• OOD Batch Connect app development docs
• Changelog -- release history for this app

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.