MiGA Manual
AboutCodebaseMiGA Online
main
main
  • Introduction
  • Part I: What is MiGA?
    • How can MiGA help me?
    • Who is using MiGA?
    • Who is behind MiGA?
    • Definitions
  • Part II: Getting started
    • Requirements
      • Using Homebrew
      • Using apt-get
      • Using Conda
      • Installing from source
      • MyTaxa Utils
    • Installation
    • MiGA types
    • Input data
    • Distances
    • Clustering
  • Part III: Interfaces
    • MiGA API
    • MiGA CLI
    • MiGA Web
  • Part IV: Deploying examples
    • RefSeq in MiGA
    • Build a clade collection
    • Launching daemons
    • Setting up MiGA in a cluster
  • Part V: Additional details
    • Advanced configuration
    • MiGA workflow
    • Metadata
    • External Software
  • Part VI: Workflows
    • Quality
    • Dereplicate
    • Classify
    • Preprocess
    • Index
    • Summaries
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  1. Part IV: Deploying examples

Setting up MiGA in a cluster

PreviousLaunching daemonsNextPart V: Additional details

Last updated 4 years ago

MiGA is developed to run on clusters with a TORQUE scheduler. The administrator should install the and on a networked file system.

When you first initialize MiGA, the program will prompt the user for the type of daemon. For a cluster with TORQUE, the user can choose a qsub daemon. During the initialization, MiGA will also ask for the number of jobs to submit and the number of CPUs per job.

After you have setup a MiGA project, you can create a job script to start daemon. The daemon requires to be alive until all the jobs for the have finished, so you should add a long-enough walltime. If you didn't give enough walltime for your job, the MiGA daemon will get killed by the system. In this case, you can restart the daemon again to finish processing the project.

Example job script:

#PBS -N MiGADaemon
#PBS -l mem=2gb
#PBS -l nodes=1:ppn2
#PBS -l walltime=48:00:00

cd $HOME/Path-to-project/
miga daemon start -P .
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