Preparing for Batch Queue Submission

Schrödinger supplies support for the PBS Pro, Grid Engine family (Son of Grid Engine, Open Grid Scheduler, and Univa Grid Engine), LSF, Slurm, and Torque queuing systems in the standard software installation. Below are links to information about these queuing systems:

• PBS Pro: https://www.altair.com/pbs-works/
• Grid Engine (SGE): http://sourceforge.net/projects/gridscheduler, http://gridengine.org, http://www.univa.com/products/grid-engine.php
• LSF: https://www.ibm.com/products/hpc-workload-management
• Slurm: https://slurm.schedmd.com/
• Torque: http://www.adaptivecomputing.com/products/open-source/torque/

Enabling batch queue submissions to a supported queuing system for simple job submission only requires the addition of a few lines to the schrodinger.hosts file and the specification of the queuing system and the queue name in a configuration file. These additions are described in the next subsections. For distributed or threaded jobs, you can set up license checking to ensure that licenses are available when a job is executed. Desmond jobs can make use of GPUs, and for Quantum ESPRESSO jobs, OpenMPI can be used for parallel execution.

The topics listed below describe the general setup procedures and provide information on settings common to all queuing systems, and give details for each queuing system.