Knowledge Base

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. The results are recombined at the end. This is more efficient than MPI parallel processing, which Glide is not set up for.

You can set up distributed docking jobs over multiple processors on multiple hosts in the Job Settings dialog box. Simply specify the number of subjobs, select the hosts, and specify the number of processors on each host. You can split the job into many more subjobs than processors you'll be using. This keeps the subjob execution time reasonable, which helps with load balancing and restartability. Note that each subjob requires a license. The number of processors chosen is therefore the maximum number of licenses that will be used.

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 the arrow next to the Settings (gear) button, and choosing Write. Use the -h option for more information on the glide command.

For instructions on configuring your Schrödinger installation for remote and batch queue submission, see Preparing for Remote Job Submission and Preparing for Batch Queue Submission.

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