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Schrodinger

Schrodinger

Schrodinger [2] 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.

Important Notes

  • 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 Schrodinger, please contact  to discuss about getting the permission, to talk about the restrictions or if you need to use more than 2 tokens. Also, see the section "License Management" below.
  • It is a visual intensive Software and you are recommended to use X2Go or NX client (visit HPC GUI Access for instructions)
  • 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.
  • We recommend running Schrodinger job REMOTELY (see Remote section below) to avoid job being halted by broken X-connection.

Installed Versions

All the available versions of SCHRODINGER for use can be viewed by issuing the following command. This applies for other applications as well.
module avail schrodinger
output:
---------------------- /usr/local/share/modulefiles/Core -------------------------
schrodinger/2017-3 (D)

The default version is identified by "(D)" behind the module name and can be loaded as:
module load schrodinger

The other versions of SCHRODINGER (when available) can be loaded as:
module load schrodinger/<version>

Running Schrodinger in HPC

Interactive Job

Serial:
Access compute node via NX Client (visit HPC GUI Access for instructions). In the terminla type the following to get the compute node:
srun --x11 -N 1 -n 1 --time=10:00:00 --pty /bin/bash
You may want to request the time other than the default time of 10 hrs (--time=10:00:00) if your job takes longer to complete.

Load the module 
module load schrodinger

Run schrodinger's interface program:
maestro &

Parallel:
In Schrodinger, parallel jobs may be distributed over multiple cpus according to task division, or by data division. Task division applies for glide and for jaguar. Data division is the approach to run ligprep in parallel. Please search the Schrodinger documentation to determine how other packages within Schrodinger achieve parallel computation.

For task parallel jobs, allocate multiple tasks with -n <n>, where n is the number of processors. In this example, 4 processors (-n 4) are requested.
srun --x11 -N 1 -n 4 --time=10:00:00 --mem=5gb --pty /bin/bash
You may want to assign enough memory (--mem=5gb) for your job to avoid unexpected termination due to "out of memory".

For data parallel jobs, allocate one task (-n 1) and then multiple processors using --cpus-per-task=<num cpus>. 
srun --x11 -N 1 -n 1 --cpus-per-task=4 --time=10:00:00 --mem=5gb --pty /bin/bash

An example command for ligprep follows as created in a shell script [credit S. Kahremany]:
"${SCHRODINGER}"/utilities/para_ligprep -inp ligprep_test.inp -LOCAL -HOST "localhost:4" -NJOBS 20

Load the module and run maestro as in serial section above.

License Management

Remote Schrodinger from PC

It allows you to run schrodinger from your PC using the Schrodigner license managed in HPC. Note that if your PC is linked to your own schrodinger license, you may want to disable it before using HPC schrodinger license.

Download Schrodinger (use version 2017-3 or earlier for compatibility)

Download Schrodinger from http://www.schrodinger.com/ -> Resources & Downloads -> Download. You may be asked to create a free account if you don't have it already. Choose the one that matches your platform (Linux/Windows/MAC). Also, make sure that you are downloading the version NOT newer than whatever is installed in HPC in case you want to use HPC Schrodinger license.

Install and configure Schrodinger

Note that the information on installation and configuration of schrodinger in  this link may contain stale information. So, always check the most recent environment variables for schrodinger by typing:
module display schrodinger
output: 
------------------------------------------------------------------------------------------
   /usr/local/share/modulefiles/Core/schrodinger/2017-3.lua:
------------------------------------------------------------------------------------------
whatis("Name: schrodinger")
whatis("Version 2017-3")
whatis("Category: library, software")
whatis("Description: Schrodinger Suite for Drug  Diiscovery")
pushenv("SCHRODINGER","/usr/local/schrodinger/2017-3")
pushenv("SCHRODINGER_THIRDPARTY","/usr/local/schrodinger/2017-3/thirdparty")
pushenv("SCHRODINGER_SQLITE_TEMP_STORE_DIRECTORY","/scratch/pbsjobs/schrodinger")
pushenv("MAESTRO_TEMP","/scratch/pbsjobs/schrodinger")
pushenv("MAESTRO_TEMP_LOCATION","/scratch/pbsjobs/schrodinger")
pushenv("SCHRODINGER_TEMP_PROJECT","/scratch/pbsjobs/schrodinger")
pushenv("SCHROD_LICENSE_FILE","27008@hpcmaster.case.edu")
pushenv("SCHROD_LIC","/usr/local/schrodinger/2017-3/mmshare-v3.9/bin/Linux-x86_64/lmutil lmstat -a -c 27008@hpcmaster")
prepend_path("LD_LIBRARY_PATH","/usr/local/schrodinger/2017-3/maestro-v11.3/lib/Linux-x86_64/gl")
prepend_path("PATH","/usr/local/schrodinger/2017-3")

Note the Schrodinger Path as /usr/local/schrodinger/2017-3 and license path as 27008@hpcmaster.case.edu.

Older Info:
Please follow instructions on the following handouts for Windows, and Linux/Mac

For more insight, some of the steps are outlined here too but look out for outdated information.
  • Download the software 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 may need to have OpenGL installed if you use Linux. OpenGL is already installed in Windows.

  • Please refer to HPC Software License Status.

  • Set the ssh-without-password from to the cluster. You can use Putty or SSH setup
    • You should have already run the sshpass command to generate an ssh key, allowing your account to ssh between cluster nodes without entering a password.
    • Follow this Schrodinger KnowledgeBase article as an aid to using the already existing cluster key to set up password-less remote login through the Schrodinger client.

  • Add the cluster information in the schrodinger.hosts file. This will add the cluster as an option to run your Schrodinger jobs. Examples of this file for both Windows and Linux/Mac are 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


Desmond

The desmond package is installed in the Rider (SLURM) cluster.

module load schrodinger
which desmond
output:
/usr/local/schrodinger/2017-3/desmond

This Desmond Guide can be helpful.

Troubleshooting

For more troubleshooting info refer to Schrodinger KB [3].

Problem: When attempting to edit the schrodinger.hosts file for remote host, I received the message "Access denied."
Solution: change the permission so that you have the edit permission. In Linix/Mac, use chmod 644 schrodinger.hosts and in windows, right click on the schrodinger.hosts file, and you'll see 'properties' at the bottom of the pop-up. Select that, and you should be able to change the permissions to allow your user account to write in that file.

References:

[1] Schrodinger FAQ: https://www.schrodinger.com/supportfaq/18/
[2] Schrodinger website: https://www.schrodinger.com/