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Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor.

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High-throughput computing (HTC) offers a scalable solution for computationally intensive research in biology and environmental science. This approach distributes tasks across multiple computers, overcoming limitations of traditional methods.

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Area of Science:

  • Computational biology
  • Environmental science
  • Data science

Background:

  • Modern biological and environmental research involves complex computational tasks like geospatial data processing, omics analysis, and large-scale simulations.
  • Conventional desktop computing and sometimes high-performance computing (HPC) are insufficient or inappropriate for these demanding problems.

Purpose of the Study:

  • To introduce high-throughput computing (HTC) as a viable alternative for computationally intensive research in biology and environmental science.
  • To demonstrate the application of HTC using the open-source HTCondor system with practical examples.

Main Methods:

  • High-throughput computing (HTC) distributes computational tasks across numerous distributed resources (e.g., desktop computers, servers, cloud).
  • Contrasts HTC with high-performance computing (HPC), highlighting HTC's distributed nature versus HPC's single supercomputer approach.
  • Utilizes HTCondor, an open-source HTC system, for practical examples in biology and environmental science.

Main Results:

  • HTC provides a flexible and accessible method for tackling large-scale computational challenges in scientific research.
  • Availability of HTC through academic/government facilities, consortia (e.g., Open Science Grid), and commercial cloud solutions facilitates adoption.
  • HTCondor serves as an effective open-source tool for implementing HTC strategies.

Conclusions:

  • HTC is a powerful and accessible computing paradigm for biologists and environmental scientists facing significant computational demands.
  • Researchers can leverage existing infrastructure or readily available solutions to implement HTC for their studies.
  • The adoption of HTC, exemplified by HTCondor, empowers scientific discovery through efficient data processing and simulation.