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Can Glide be run in parallel — for example on a cluster?

Glide docking jobs can be distributed over multiple processors. This is done by partitioning the ligands into sets and running each set on a separate processor. This is more efficient than MPI parallel processing, which Glide is not set up for.

Beginning with Maestro 8.0, you can set up distributed docking jobs over multiple processors on multiple hosts in the Start dialog box. Simply specify the number of subjobs, select the hosts, and specify the number of processors on each host.

You can also run distributed jobs from the command line with $SCHRODINGER/glide. The job can be set up in Maestro, and the input files written by clicking Write rather than Start. See the Glide User Manual for more information on the glide command.

Note that each subjob requires a license. The number of processors chosen is therefore the maximum number of licenses that will be used.

For instructions on configuring your Schrödinger installation for remote and batch queue submission, please see the "Preparing for Job Submission" chapter of the Installation Guide.

Keywords: Glide, parallel, distributed, MPI

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