Article ID: 128 - Last Modified: February 28, 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.
- Configure passwordless SSH (section 7.2)
- 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 schrodinger.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 queuing systems.
Once you have installed and configured the software, you can check your installation, by executing the following command (on a Linux host):
This command runs some tests, prints a summary with advice, and also creates a .tarball file containing the zipped results that you can send to 'email@example.com' for further assistance if 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, installation
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