Documentation (VF 1.0)
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    • Directory Structure
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    • VirtualFlow Commands
    • Preparing the Workflow
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    • The Completed Workflow
  • Running VirtualFlow in the Cloud
  • Troubleshooting
  • Version History
  • Further Resources
  • VFLP
    • Introduction
    • Features
    • Installation
      • Prerequisities
      • External Packages
    • Background and Principles
      • Directory Structure
      • Input & Output Databases
    • Using VFLP
    • Troubleshooting
    • Version History
  • VFVS
    • Introduction
    • Features
    • Installation
      • External Packages
    • Background and Principles
      • Directory Structure
      • Input & Output Databases
    • Using VFVS
      • Preparing the Workflow
      • Monitoring the Workflow
      • The Completed Workflow
    • Troubleshooting
    • Version History
  • VFTools
    • Introduction
    • Installation
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  • Introduction
  • General Problems/Approaches
  • Increasing the Command-Verbosity
  • Inspecting log files and workflow files
  • Interactive Jobs
  • Specific Problems/Approaches

Troubleshooting

PreviousRunning VirtualFlow in the CloudNextVersion History

Last updated 5 years ago

Introduction

Problems regarding VirtualFlow and approaches to solving them can be classified into two categories:

  1. General problems, where the precise problem is yet to be determined.

  2. Specific problems, where the precise problem could already be determined.

Accordingly, we classify the approaches for troubleshooting into these two categories:

General Problems/Approaches

Overview of general approaches:

    • Logfiles in workflow/output-files/jobs/

    • Logfiles in workflow/output-files/queues/

    • Ligand processing status logs in workflow/ligand-collections/ligand-lists/

Increasing the Command-Verbosity

The verbosity of the VirtualFlow end-user commands (starting with vf_) can be increased by setting the option verbosity_commands in the control file to the value 'debug':

verbosity_commands=debug

Inspecting log files and workflow files

The verbosity of the VirtualFlow logfiles (in the workflow/output-files/ folders) be increased by setting the option verbosity_logfiles in the control file to the value 'debug':

verbosity_logfiles=debug

This will affect the following log files:

  • Logfiles in workflow/output-files/jobs/

  • Logfiles in workflow/output-files/queues/

In addition, the processing status of each ligand and possible errors related to the processing steps can be found int the the subfolders of the workflow/ligand-collections/ligand-lists/ folder.

Interactive Jobs

Interactive jobs can for instance be useful when VirtualFlow starts the workflow and begins using the local storage of the compute nodes, but then crashes and does not manage to copy back the log-files which are stored on the compute nodes. If this case, if one is running VirtualFlow via an interactive job and is logged in to the compute node, one has immediate access to all the workflow files of VirtualFlow on that compute node.

Similarly, one can run non-interactive jobs and then ssh into the the compute node which is used by VirtualFlow. However, this does not always work because if the job crashes and terminates, ssh access is often automatically terminated as well to that compute node (since one may not have any more job running on that node, which is often a requirement for ssh access to a compute node).

Specific Problems/Approaches

[Will be added with feedback from future users.]

General problems/approaches
Specific problems/approaches
Increasing the command-verbosity
Inspecting log files and workflow files
Interactive jobs