High-Throughput Computing

Last updated on 2024-08-13 | Edit this page

Estimated time: 15 minutes

Overview

Questions

  • What is the difference between high-throughput computing and cluster computing?

Objectives

  • Learn what types of jobs run well on HTC systems.
  • Understand how to submit jobs using OSG.

High-Throughput Computing

A typical HPC system today is a cluster computer made of one or more head nodes and many compute nodes tied together with a common file server and having a batch scheduler to control where jobs run. Some of the largest supercomputers in the world are similar conceptually to a cluster computer but have more custom designed circuit boards as nodes and may be packaged up and racked in a different manner than cluster systems that use more off-the-shelf components.

A High-Throughput Computer (HTC) system is designed to run very large numbers of small jobs and is often made up of many HPC systems separated geographically. In the U.S. the main example is the Open Science Grid (OSG) which is open for use to anyone associated with a U.S. university or national laboratory. Time is given away freely on a first-come first-served basis and computer resources are donated by various institutions. Since HTC is geared toward running large numbers of smaller jobs, the jobs fit well into the spare nooks and crannies of most HPC systems and these systems are set up to kill any OSG job when the host institute needs those resources back. In this way the HTC jobs run invisibly on the over 100 HPC sites spread across the U.S. offering free computing to any who need to run small jobs while greatly enhancing the usage of each HPC system by using the spare CPU cycles that would otherwise go wasted.

Large numbers of small jobs

One of the first examples of HTC was the SETI program where individual PC users could donate their CPU cycles to the project to search through large quantities of data to try to find signals that might come from intelligent life. This problem is ideal for HTC since it can be broken up into large numbers of small jobs, and any job that did not return an answer in a given period was just thrown away and rerun on another system.

OSG has the ability to run a wide variety of jobs including large memory and GPU runs, but it is much more difficult than running the simple small jobs that it was designed for. The OSG guidelines for the typical job are 1-8 cores, up to 40 GB memory and 10 GB IO, and up to 20 hours run-time.

The most important aspect of working with HTC systems is that the jobs be self-contained as much as possible, and be able to run on any operating system and use mainstream modules. This is essential since each job may be run on a wide range of HPC environments. Executables that are dynamically linked can work if you request the matching resources by specifying things like acceptable CPU architectures. Statically linked executables will always work. Containers take more effort to set up but are ideal for HTC since all executables, modules, and environmental variables are set within the container. Running on multiple nodes using MPI is possible but difficult usually requiring containers with the MPI connections specified externally.

Using OSG

Users may submit jobs to the OSG queue through their institute’s portal if one exists or through the OSG Connect submission service at the link below. If using the OSG Connect portal you will need to request access and arrange for a short Zoom meeting with one of their support staff. There are links to the OSG Consortium and support documentation at the end of this lesson.

Working with the HTCondor scheduler

Submitting jobs to HTCondor for scheduling on any of the hundreds of remote systems available is similar to using any scheduler, except for the notes above on the job not relying on modules and libraries that may not be available or labeled the same everywhere. Below is an example job script to run the stand-alone executable namd2. Note that the X64_64 CPU architecture is specified. The script requests 1 GB of disk for this job and directs that all files from the directory input_files be transferred along with the job at the start, and all files in output be transferred back at the end. The queue 1 command then specifies the number of these jobs to submit. If multiple jobs are submitted then the environmental variable $(Process) will be used in the script to differentiate each with that being between zero and the number of jobs specified minus one.

BASH 

#!/bin/bash -l
 
output = osg.namd.out
error = osg.namd.error
log = osg.namd.log
 
# Requested resources
request_cpus = 8
request_memory = 8 GB
request_disk = 1 GB
requirements = Arch == "X86_64" && HAS_MODULES == True
 
transfer_input_files = input_files/         # Slash means all files in that directory
executable = namd2
arguments = +p8 test.0.namd
transfer_output_files = output
queue 1

Most systems will have support for modules, but the HAS_MODULES == True requirement can mean some systems are not supported. Most systems use RHEL7, so specifying that may also rule out use of RHEL6 and RHEL8 systems. In general, if you use a mainstream operating system and modules then you should be fine. Otherwise you likely will need to use a container.

Once you have the script you can submit, monitor, and control the job using commands like those below.

BASH 

> condor_submit htc_job.sh                   # Submit the condor script to the queue
> condor_q                                   # Check on the status while in the queue
> condor_q netid                             # Check status of currently running jobs
> condor_q 121763                            # Check status of a particular job
> condor_history 121763                      # Check status of a job that is completed
> condor_history -long 121763                # Same but report more info
> condor_rm 121763                           # Remove the job number specified
> condor_rm daveturner                       # Remove all jobs for the given username

HTC Outside the U.S.

Need to add info about non-US HTC systems

Optional Homework: Get an OSG account and submit a test job.

If you are in the U.S. and want a big challenge, request an OSG account and try submitting some small jobs.

Summary

High-Throughput Computing is free in the U.S. using the Open Science Grid. It is great for running large numbers of small jobs. Using it for GPU jobs or when large memory or IO is needed is possible but much more challenging. Aside from that it is similar to running jobs using any other scheduler.

Key Points

  • Explore the basics of HTC computing.