Knowledge Base

Article ID: 128 - Last Modified: August 15, 2014

Could you tell me about running Schrödinger applications on a remote host or cluster? What is required?

Chapter 7 of the Installation Guide provides detailed configuration instructions for remote job submission, including submission to clusters. Briefly, you will need to perform the following tasks, in addition to installing the software on the cluster itself.

  1. Configure passwordless SSH (section 7.2)
  2. Configure the hosts file, schrodinger.hosts, with information about the remote host or cluster (section 7.1, section 7.3)

For applications requiring MPI (e.g. Desmond, parallel Jaguar), be sure to read through section 7.3.3, as these applications require special entries in the hosts file.

The installation of the Schrödinger software must reside in the same path on every node of the cluster, including the head node. The easiest way to accomplish this is to install the software once, and then share the installation to all the other nodes using NFS or some other shared filesystem. You must also make sure that all the nodes can access the head node via passwordless ssh, and that the head node can make TCP/IP socket connections to the compute nodes on ports above 1024. The compute nodes must also be able to make TCP/IP socket connections to the head node. Schrodinger officially supports PBS, LSF, SGE, Slurm, and Torque queueing systems.

Once you have installed and configured the software, you can check your installation, 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, which you can upload to the support page if further assistance is needed.

Jobs can be submitted to a cluster 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.

Keywords: queue

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