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Tools for high throughput computing

High troughput computing (HTC) means running lots of jobs automatically using scripts or workflows. Workflow automation saves human time and reduces manual errors. Workflows can be very specific and if you can't find one that suits your needs out-of-the-box, they may need a lot of work before they bring benefit. However, the simplest ones are easy to use. This section introduces some tools available at CSC, but you can of course develop or install your own.

Simple general tools that run multiple jobs with one script

  • Array jobs are a native Slurm tool to submit several independent jobs with one command
  • GREASY runs multiple job steps in a larger allocation, and allows simple dependencies
  • DIY gnuparallel tutorial shows how to efficiently run a very large number of serial jobs without bloating the Slurm log

Science specific workflow tools

  • Nextflow singularity container based bioinformatics pipelines on Puhti
  • TBC