User Documentation

This section describes how to install and configure GC3Pie, and how to run The GC3Apps software and The GC3Utils software.

Table of Contents

• Installation of GC3Pie
  • Quick start
  • Non-standard installation options
  • Manual installation
  • Upgrade
  • MacOSX Installation
  • HTML Documentation
• Configuration File
  • Location
  • Configuration file format
  • The DEFAULT section
  • auth sections
    • Authentication types
      • none-type authentication
      • ssh-type authentication
      • ec2-type authentication
  • resource sections
    • Link to [auth/...] sections
    • Configuration keys common to all resource types
    • Configuration keys common to batch-queuing resource types
    • sge resources (all batch systems of the Grid Engine family)
    • pbs resources (TORQUE and PBSPro batch-queueing systems)
    • lsf resources (IBM LSF)
    • slurm resources
    • shellcmd resources
    • ec2+shellcmd resource
    • Example resource sections
  • Enabling/disabling selected resources
• Environment Variables
• GC3Pie usage tutorials
• The GC3Apps software
  • Introduction to session-based scripts
    • Basic command-line usage and options
      • Continuous execution
      • Verbose listing of jobs
      • Maximum number of concurrent jobs
      • Location of output files
    • Job control options
    • Session control options
    • Exit code
  • The ggamess script
    • How to run GAMESS on the Grid
    • Tweaking execution
    • Updating the GAMESS code
  • The ggeotop script
    • Introduction
    • Command-line invocation of ggeotop
    • Output files for ggeotop
    • Example usage
      • Manage a set of jobs from start to end
    • Using GC3Pie utilities
      • gkill: cancel a running job
      • ginfo: accessing low-level details of a job
  • The grosetta and gdocking scripts
    • Introduction
    • Command-line invocation of grosetta
    • Output files for grosetta
    • Output files for gdocking
    • Example usage
      • Manage a set of jobs from start to end
      • Managing a session by repeated grosetta invocation
  • The gcrypto script
    • Introduction
    • Command-line invocation of gcrypto
    • Output files for gcrypto
    • Example usage
      • Manage a set of jobs from start to end
    • Using GC3Pie utilities
      • gkill: cancel a running job
      • ginfo: accessing low-level details of a job
• The GC3Utils software
  • gsession: manage sessions
  • gstat: monitor the status of submitted jobs
  • gtail: peeking at the job output and error report
  • gkill: cancel a running job
  • gget: retrieve the output of finished jobs
  • gclean: remove a completed job from the status list
  • gresub: re-submit a failed job
  • gservers: list available resources
  • ginfo: accessing low-level details of a job
  • gselect: select job ids from from a session
  • gcloud: manage VMs created by the EC2 backend
• Troubleshooting GC3Pie
  • What is a Python traceback?
  • Common errors using GC3Pie
    • AttributeError: module object has no attribute StringIO
    • DistributionNotFound
    • ImportError: No module named pstats
    • NoResources: Could not initialize any computational resource - please check log and configuration file.
    • ValueError: I/O operation on closed file
  • ValueError: Expected version spec in …
• User-visible changes across releases
  • GC3Pie 2.6
    • Important changes
    • Bug fixes
  • GC3Pie 2.5
    • New features
    • Incompatible changes
  • GC3Pie 2.4
    • New features
  • GC3Pie 2.3
    • Incompatible changes
    • New features
    • Important bug fixes
  • GC3Pie 2.2
    • New features
    • Changes to command-line utilities
    • Important bug fixes
  • GC3Pie 2.1
    • New features and incompatible changes
    • Changes to command-line utilities
  • GC3Pie 2.0
    • New features and incompatible changes
    • Configuration file changes
    • Changes to command-line utilities
    • API changes
  • GC3Pie 1.0
    • Configuration file changes
    • Command-line utilities changes
  • GC3Pie 0.10