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Schrodinger


Schrodinger is a suite that is aimed to help the drug screening process (energy minimization, ligand-protein docking, building fragments, molecular dynamics, and so on). It is a widely-used application in the drug industries and in biomedical schools.
Version: Schrodinger-2010, Schrodinger-2011, Schrodinger-2012
License: Schrodinger's license is based on tokens which are reserved when you run jobs with multiple sub jobs. If you are planning to use it, please contact
 to discuss about getting the permission, to talk about the restrictions or if you need to use more than 2 tokens.


General information:
To run Schrodinger jobs from the compute nodes, you are importing the graphic environment of Schrodinger to your local terminal. Since this requires a lot of connection bandwidth, please use wired campus connection for best usage.

To run serial Schrodinger Job in the cluster:
  • access compute node with the following command
       qsub -I -X

  • load the module schrodinger
       module load schrodinger or check module avail followed by the appropriate module load schrodinger/<version>

  • run schrodinger's interface program:
       maestro

To run interactive maestro in the cluster:

If you need to do extensive molecular manipulation using maestro, you might want to use hpcviz.case.edu and NX access to run interactive maestro. The response time would be much faster than running maestro on the compute node. Since the hpcviz node is a common access node, please refrain from using this node for more than 1-2 hours.
 

NOTE: We recommend running Schrodinger job REMOTELY to avoid job being halted by broken X-connection.

To run Multiprocessor Schrodinger Job in the cluster:

Scenario: You are specifying 8 processors in maestro

You have to modify your qsub -I -X to request 8 processors.

         qsub -l nodes=1:ppn=8 -X -I

In short, just change the value of ppn according to the number of processors you are specifying.

( Important Note: Keep in mind that you will also be checking out licenses equivalent to the number of requested processors so do not exceed your quota; you can monitor the licenses using the commands, /usr/local/matlab/matlabR2009b/etc/lmstat -a -c /usr/local/schrodinger/schrodinger-2010/license )

Run Schrodinger remotely from your local desktop: 

Click on the appropriate links for descriptive instructions:

Please follow instructions on the following handouts for Windows, and Linux

Some of the steps are outlined here too:
  • You have to download the software first from hpclogin: /usr/local/doc/schrodinger/... (the appropriate version for your desktop); use of the utilities explained here or you can use Globus Online. You can also download it directly from Schrodinger website (schrodinger.com). Please download all the tools that you need.

  • Install the software on your local desktop: Run the executable that you downloaded.

  • You need to have OpenGL installed if you use Linux. OpenGL is already installed in Windows.

  • Set SCHROD_LICENSE_FILE to 27008@hpcmaster.case.edu
    • In the Windows environment (Right click on My Computer -> Properties -> Advanced tab -> Environment Variables button at the bottom -> Edit user variable -> Save/OK. (thanks Matthew Kalp)
    • or put EXPORT SCHROD_LICENSE_FILE=27008@hpcmaster.case.edu in the .bashrc on your desktop in Linux

  • Set the ssh-without-password from to the cluster. You can use Putty or SSH setup
    • Reference for terminal: http://www.thegeekstuff.com/2008/11/3-steps-to-perform-ssh-login-without-password-using-ssh-keygen-ssh-copy-id/
    • Reference for Putty: http://www.tonido.com/blog/index.php/2009/02/20/ssh-without-password-using-putty/ 

  • Add the cluster information in the schrodinger.hosts file. This will add the cluster as an option to run your Schrodinger jobs.
    An example of this file is given in this link

  • Open Maestro (use "maestro -SGL" in Linux to link to the OpenGL library)

  • Pick the cluster option (HPC) to run your job in the HPC environment
Please follow instructions on the following handouts for Windows, and Linux

Maestro Tutorial (Remote PC)

  • Open Maestro Window: Start->All Programs->Schrodinger2010->maestro 9.1
  • Open the tutorial: Help->Manual Index and find Maestro Tutorial under Section Maestro 9.1