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Edit the local hosts file
Next, you will need to create a hosts file that identifies the remote hosts and queues. You will need to add entries to your hosts file that point to the cluster, and indicate which queue to use, where tmpdir should go, and where the software is installed on the cluster. This file must be available in the Schrödinger software installation on the machines from which users will submit jobs. For detailed information about the hosts file, see The Hosts File and Preparing for Batch Queue Submission. For applications that can use MPI for parallel execution (Desmond; Jaguar prior to the 2015-4 release), special entries in the hosts file are needed to make use of MPI.
Example schrodinger.hosts files are available through these links to text files.
- when the local host has a Windows OS & file system
- when the local host has a linux OS & file system
The next step is to set up access to the remote hosts via passwordless ssh. This must be done by each user who wants to submit jobs, as it requires their own ssh keys. See Setting Up Access to Remote Hosts for instructions.
Once you have finished these tasks, you can check that everything is set up correctly. You can run tests of the configuration either by using the Diagnostics panel, or by executing the following command (in a terminal window on Linux or Mac, or a Schrodinger Command Prompt on Windows):
installation_check -testall
The Diagnostics panel runs this command for you. The command runs some tests, prints a summary with advice, and also creates an archive .zip file (.tarball prior to 2014-3) containing the results.
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If the tests on the remote hosts fail, and you need help to fix the problem, go to the Support page to request support, and upload the archive to the web form.
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Jobs can be submitted to a cluster or remote host directly from Maestro. Instructions for running jobs from the command line are contained in the user manuals. General information on running jobs with Schrödinger software can be found in the Job Control Guide.
Troubleshooting
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[1] Schrodinger FAQ: https://www.schrodinger.com/supportfaq/18/
[2] Schrodinger website: https://www.schrodinger.com/
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