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Schrödinger#

Schrödinger licensing change

Starting in January 2025, Schrödinger's license mechanism changed. Please note that versions prior to 2024-2 are no longer be supported.

Schrödinger is licensed by the Department of Biochemistry and available to all MCW investigators.

Users interested in contributing funds or discussing Schrödinger licensing at MCW should contact Dawn Wenzel and Brian Smith.

The Schrödinger Small-Molecule Drug Discovery Suite includes a GUI client that you can run on your Windows, Mac, or Linux desktop/laptop. This client can be configured to send jobs to the HPC Cluster. Example use includes molecular modeling, docking, molecular dynamics simulation, etc. See below for installation.

Requirements#

  • RCC user account

Installation & Configuration#

  1. Download 2024-4 software from https://www.schrodinger.com and run the installer.

  2. Locate the schrodinger.hosts file:

    $INSTALLDIR\Schrodinger 2024-4\schrodinger.hosts

    /opt/schrodinger/suites2024-4/schrodinger.hosts

  3. Download the server schrodinger.hosts file. Add the text from the downloaded file to your schrodinger.hosts file (you located in step #2). Replace NetID with your MCW username and save the file.

  4. If using 2024-2, enable new Schrödinger License Manager (enabled by default on 2024-3 and above):

    Open a Schrödinger Command Prompt or Schrödinger Power Shell and enter:

    feature_flags -e SCHRODINGER_LICENSE_MANAGER

    Open a terminal and enter:

    /opt/schrodinger/suites2024-3/utilities/feature_flags -e SCHRODINGER_LICENSE_MANAGER

  5. Add the license server on your computer:

    Open the Configure Software tool and select Server Identifiers. Enter the hostname and port found in licensing info and select Install License.

    Open the Configuration tool and select Server Identifiers. Enter the hostname and port found in licensing info and select Install License.

  6. Setup remote connection to the cluster:

    Open the Remote Login Configuration tool. Select Generate Keys. Select Initialize Host Access. Enter the host IP Address (this is in your schrodinger.hosts file) and your MCW username. Select Initialize.

    Configure password-less SSH for remote login. Open a terminal and follow this guide.

  7. Launch the Maestro application.

Upgrading#

To upgrade your Schrödinger installation, first uninstall the current version. The uninstall process should leave your configuration intact. Then install the upgraded version of Schrödinger and remember to update your schrodinger.hosts file as it appears above. If you have issues upgrading, please contact help-rcc@mcw.edu.

Remote Job Submission#

Included in your install are configurations for the remote server connection to HPC Cluster. This allows you to send large or computationally intensive workloads to the cluster from your desktop. The cluster will run the job and return the results.

server_cpu - HPC Cluster connection for Schrödinger CPU jobs

server_gpu - HPC Cluster connection for Schrödinger GPU jobs

When running Schrödinger jobs, please follow these guidelines:

  • Run all pre-processing jobs on the localhost (your machine).

  • Run docking, MD, etc. jobs with remote connection to HPC Cluster.

Direct Job Submission#

You can also submit jobs directly from the cluster command line. This is helpful for submitting large numbers of jobs, where using the desktop launch interface might be repetitive. All direct jobs are launched from a cluster login node using Schrödinger to submit the job to the SLURM job scheduler. Please follow this syntax using the server_cpu or server_gpu for -HOST as appropriate.

# print the command-line options for Desmond (molecular dynamics package)
/hpc/apps/schrodinger/2024-4/desmond -h

# submit a desmond job to the SLURM job scheduler
/hpc/apps/schrodinger/2024-4/desmond -HOST server_gpu -c x.cfg -in x.cms

Mistakes to avoid

  • Do not run the Schrödinger apps in a job script. Schrödinger will submit the job to SLURM for you.
  • Do not use localhost as the -HOST setting. This will cause the job to run on the login node and/or bypass the license checking. Either case will cause your job and other jobs to fail.

Schrödinger Utility Scripts#

Schrödinger includes additional utility scripts that are not included in the Maestro interface and must be run directly within a job script. See Schrödinger scripts for a complete list and details.

Why are utility scripts submitted via job script?

These utility scripts do not have the advanced job submission options that the Schrödinger apps (Desmond, Epik, etc.) include. Therefore, we have to write a separate SLURM job script for submission.

To see the options for a particular script on the cluster:

# script has no requirements
/hpc/apps/schrodinger/2024-4/run entropy_calc.py -h

Some scripts are dependent on a specific Schrödinger app. Check the Schrödinger scripts page Requires column.

# run a script requiring the Desmond app
/hpc/apps/schrodinger/2024-4/run -FROM desmond trj_center.py -h

To run the script in a job on the cluster, adapt the following job submission script to your specific command:

#!/bin/bash
#SBATCH --job-name=test_job
#SBATCH --ntasks=1
#SBATCH --time=01:00:00
#SBATCH --output=%x-%j.out

/hpc/apps/schrodinger/2024-4/run script.py

Troubleshooting#

Schrödinger can be sensitive to changes in networking. This is often an issue for laptop users. You may see errors such as:

  • Launch failed: no JobId found.
  • WARNING: You did not specify for -maxjob. Remember its default value is 1.

In this case, you should reset your connection to the Schrödinger server using the following steps.

Mac OS X only

This solution works on Mac OS X and assumes that you have installed Schrödinger 2024-4. Modify the version number if you have an older version installed.

On your laptop/desktop:

  • Shutdown Schrödinger.
  • Open terminal and run the following commands:
/opt/schrodinger/suites2024-4/utilities/jserver -shutdown
/opt/schrodinger/suites2024-4/utilities/jserver -cleanall
/opt/schrodinger/suites2024-4/utilities/jserver -proxy -shutdown
/opt/schrodinger/suites2024-4/utilities/jserver -proxy -cleanall

On the cluster:

  • Run the following commands:
/hpc/apps/schrodinger/2024-4/utilities/jserver -shutdown
/hpc/apps/schrodinger/2024-4/utilities/jserver -cleanall
/hpc/apps/schrodinger/2024-4/utilities/jserver -proxy -shutdown
/hpc/apps/schrodinger/2024-4/utilities/jserver -proxy -cleanall

Help#

Having issues installing? Contact help-rcc@mcw.edu to schedule a support session.

For general Schrödinger questions, see https://www.schrodinger.com/kb.

For training opportunities, see https://www.schrodinger.com/seminars/current and https://www.schrodinger.com/training.