Cluster Setup for Schrödinger Jobs (DEPRECATED)

This document summarizes the steps needed to set up a cluster for running Schrödinger jobs via a queueing system and ensuring user access. It is assumed that the manager node (head node) is the node on which the queue commands will be run. For more information, see the appropriate sections of Preparing for Remote Job Submission (DEPRECATED).

  1. Install the software in a location that is accessible to the manager node and the compute nodes.

    This location will be referred to as cluster-installation. Installation on a common file system in the cluster is recommended. The same version of the software must be available to the user’s computers (at user-installation); it need not be in the same location as the cluster installation.

  2. Install and configure a supported queueing system, if not already installed (Preparing for Batch Queue Submission).

  3. Edit the file cluster-installation/queues/type/config on all queue submission hosts to set the location of the queue binaries (Setting Up Access to a Queueing System). Here, type is the queueing system type, e.g. SGE.

  4. Add entries to user-installation/schrodinger.hosts in the user-accessible software installation for the cluster queues (The Hosts File and Setting Up the Hosts File for Batch Queues).

  5. Ensure that the manager node has a static host name that is resolvable from any cluster node and is always associated with the same physical host.

    Communications addressed to that host name must not be redirected to another physical host.

  6. Enable the manager node and the compute nodes to open socket connections to the FlexLM license server.

  7. Enable the job submission hosts (users' workstations) and the compute nodes to open socket connections to the manager node on ports above 1024 (Cluster Configuration Requirements).

  8. Configure passwordless SSH for each user (Setting Up Access to Remote Hosts):

    • between all cluster nodes
    • between the users' workstations and the manager node

  9. Test the installation with the following command (Linux):

    $SCHRODINGER/run installation_check -testall

These steps are sufficient for serial jobs and for distributed jobs. If you want to run MPI parallel applications such as Quantum Espresso, you should also do the following:

  1. Add entries to user-installation/schrodinger.hosts that are specifically set up for MPI parallel appplications (Setting Up Queuing Systems for Open MPI Parallel Execution).

  2. If using the Torque queueing system, install the OpenMPI plugins (OpenMPI Configuration for Torque).

You might also want to configure license checking if it is supported by your queueing system (Setting Up License Checking for Queueing Systems (DEPRECATED)).