Verify cryoSPARC installation with the Extensive Workflow (Sysadmin Guide)

Last Updated: March 11, 2020

Introduction

CryoSPARC provides a job called "Extensive Workflow for T20S", which performs a full 3D reconstruction of the T20S Proteasome (EMPIAR-10025) from a small (~8GB) subset of movies. The cryoSPARC engineering team uses this job to automatically test and benchmark cryoSPARC between releases.

System Administrators may use the extensive workflow job to verify that cryoSPARC is correctly configured following a fresh installation or an update.

Result of a successful extensive workflow run

The Extensive Workflow covers the full T20S tutorial, including the following workflow jobs:

  • Import Micrographs
  • Motion Correction
  • CTF Estimation
  • Particle Picking and Extraction
  • 2D Classification
  • Ab-initio reconstruction
  • Homogeneous Refinement

The following system requirements are verified:

  • cryoSPARC system and license installation
  • Worker/Cluster configuration
  • GPU and CUDA driver installation
  • SSD caching

The sample data has the following characteristics:

  • Number of images: 20
  • Frames per image: 38
  • Image size: 7420 × 7676 (K2 Super Resolution)
  • Pixel size: 0.66 Å

Once started, the workflow should take no more than an hour to complete.

Prerequisites

Creating and Running the Extensive Workflow

  1. Open the cryoSPARC web interface

  2. In the dashboard, create a new Project from the navigation bar

    Follow steps to create a new project Fill out new project details

    Specify a descriptive title such as "Extensive Workflow Testing" and directory for the project to store its data

  3. Create a new workspace for that project.

    Select the "Add Workspace" button Fill out new workspace details

    Best practices: Create a new workspace and run the Extensive Workflow in that workspace each time cryoSPARC updates and restarts. Name each workspace with the latest installed version of cryoSPARC that the job runs on. For example, when testing cryoSPARC v2.15.0, name the workspace "v2.15.0 Benchmark & Validation"

  4. Select the Job Builder from the sidebar and select the "Extensive Workflow for T20S (BENCH) (BETA)" job (under Workflows)

    Select "Extensive Workflow" from the Job Builder

  5. (Optional) If desired, change the workflow parameters.

    Specifying a valid "Movies data path" and "Gain reference path" is NOT required; if the path does not exist on the system, cryoSPARC automatically downloads a ~8GB subset of the T20S dataset and deletes the download when the job finishes.

  6. Select "Queue" and choose a worker lane for the job, then select "Create"

    Queue the job Select a job lane

After queuing, a modal opens with an overview of the workflow job progress. The job status should shortly change to "Running".

Extensive Workflow job in "Running" status

Close the modal with the × button. This shows a workspace overview with the child jobs that the Extensive Workflow job spawns to carry out T20S processing.

Workspace with running Extensive Workflow

Once all child jobs successfully complete, the Extensive Workflow job status changes to "Completed". This means the installation was successful. Users may now be notified to start or resume processing!

Troubleshooting Failed Jobs

If any child jobs fails, the extensive workflow times-out and its status is set to "Failed".

Example of failed Extensive Workflow workspace

Scroll through the workspace to find other jobs with the "Failed" status. Open the job overview either by selecting the job number next to the status indicator (e.g., J4) , or by selecting the Job card and pressing the Space key.

Scroll to the bottom to see why the job failed.

Extensive Workflow: Failed import job due to missing gain reference

Example Import Movies failure because the Gain Reference was not found

Common failure reasons include

Once the configuration issue is resolved, restart the Extensive Workflow job: Either create a new workspace and job as already noted, or clear the existing Extensive Workflow job and re-queue.

Clear a selected job

Requeue the selected job on a worker ndoe

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