HTCondor @ Danforth Center User's Guide

This document is a user's guide for using HTCondor on the Danforth Center Bioinformatics cluster. The guide will be updated as guidelines are developed, and questions/problems arise.

HTCondor is a workload management system. It handles job batching and queuing, resource matching, usage accounting, and more. The documentation is extensive, read more here.

Basic infrastructure concepts

  • Central manager server. This server is the central brain of HTCondor. It is the interface between job scheduling machines and job execution machines. Users do not interact with this server (basestar in our case) directly.
  • Scheduler server. This server submits jobs to the HTCondor system. Multiple servers can run the job scheduling service. Currently the Danforth Center infrastructure runs the scheduler on stargate.
  • Execution server. These are the servers where jobs are run. Jobs submitted from apollo are analyzed by the central manager (basestar) to determine which execution servers can support the job (based on resource requests), whether or not resources are free currently, and what the job priority (rank in the queue) is.


  • Job priority. HTCondor uses a fair share model to assign jobs a priority. This means jobs are executed in an order that preserves resource allocation shares as much as possible (as opposed to a first-come, first-serve model).
  • Slots. HTCondor matches jobs to resource "slots." For the Bioinformatics cluster, each server is configured as a single resources slot (all the CPUs and RAM in one slot). Each slot is configured to be partitionable, so a job requesting less than 100% of all the resources in a slot will cause the slot to be divided so that the remaining resources can be matched to another job.
  • Universe. HTCondor provides different "universes" for executing jobs. Each universe has different properties. For now we will primarily use the vanilla universe.
  • Vanilla: Essentially the same as running any basic program with one or more processors.
  • Java: Java applications can be run in this special environment (although they can often be run in vanilla).
  • Docker: Run jobs in isolated environments (containers).
  • Accounting group. The system usage activity of each user is logged but accounting is done at the group level. This is managed using the CONDOR_GROUP environmental variable. Accounting group is set for you automatically. If you belong to more than one group, make sure your active group is set to the group you want to log the activity for.