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

Schrödinger software can be configured to run jobs on remote Linux machines. Running jobs remotely on Windows or Mac machines is not supported, but you can submit jobs from Windows or Mac machines to a remote Linux machine.

We recommend you use a queueing system on the remote machine to manage its resources. Schrödinger software can be configured to work with several popular queueing systems: Grid Engine (SGE), LSF, PBS Pro, Torque, and SLURM.

A summary of the process is given below. Chapter 6 of the Installation Guide (Chapter 7 prior to the 2015-3 release) provides detailed configuration instructions for remote job submission, including submission to queueing systems on remote hosts. Most of the configuration tasks can be performed with the Configure Schrodinger Software application, as of the 2015-4 release — see section 6.1 of the Installation Guide.

First, you will need to set up the remote host:

  1. Install one of the recommended queueing systems, and set up the queues you will need. Verify that the queueing system is working properly, using the vendor's (or supplier's) instructions.
  2. Ensure that the SSH service is running.
  3. Ensure that all the nodes can access the head node via passwordless ssh.
  4. Ensure that TCP/IP socket connections between the head node and the compute nodes on the cluster are allowed on ports above 1024. If you are not using a queueing system, you must also do this between the remote host and the machines from which jobs are launched.
  5. Install Schrödinger software. The installation of the Schrödinger software must reside in the same path on every node of a 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.

See the section "Configuring Clusters" in the Installation Guide for more details.

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.

From the 2015-4 release, this file can be created or edited in the Configure Schrodinger Software application, which you can start as follows:

  • Mac: Applications → SchrodingerSuites2015-4 →
  • Windows: Start → All Programs → Schrodinger-2015-4 → Configure Software
  • Linux: $SCHRODINGER/utilities/configure

For earlier releases, and for detailed information about the hosts file, see the sections "The Hosts File" and "Preparing for Batch Queue Submission" in chapter 6 (or 7) of the Installation Guide. 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.

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. You can perform this task from the 2015-4 release with the Configure Schrodinger Software application, which is also available from Maestro under Help → Configure Licensing and Hosts. For earlier releases, see the relevant section of the Installation Guide for instructions.

Once you have finished these tasks, you can check that everything is set up correctly, by using the Configure Schrodinger Software application (as of the 2015-4 release). For any release 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 Configure Schrodinger Software application and the Diagnostics panel run 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.

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.

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.

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