CryoSPARC Guide
  • About CryoSPARC
  • Current Version
  • Licensing
    • Non-commercial license agreement
  • Setup, Configuration and Management
    • CryoSPARC Architecture and System Requirements
    • CryoSPARC Installation Prerequisites
    • How to Download, Install and Configure
      • Obtaining A License ID
      • Downloading and Installing CryoSPARC
      • CryoSPARC Cluster Integration Script Examples
      • Accessing the CryoSPARC User Interface
    • Deploying CryoSPARC on AWS
      • Performance Benchmarks
    • Using CryoSPARC with Cluster Management Software
    • Software Updates and Patches
    • Management and Monitoring
      • Environment variables
      • (Optional) Hosting CryoSPARC Through a Reverse Proxy
      • cryosparcm reference
      • cryosparcm cli reference
      • cryosparcw reference
    • Software System Guides
      • Guide: Updating to CryoSPARC v4
      • Guide: Installation Testing with cryosparcm test
      • Guide: Verify CryoSPARC Installation with the Extensive Validation Job (v4.3+)
      • Guide: Verify CryoSPARC Installation with the Extensive Workflow (≤v4.2)
      • Guide: Performance Benchmarking (v4.3+)
      • Guide: Download Error Reports
      • Guide: Maintenance Mode and Configurable User Facing Messages
      • Guide: User Management
      • Guide: Multi-user Unix Permissions and Data Access Control
      • Guide: Lane Assignments and Restrictions
      • Guide: Queuing Directly to a GPU
      • Guide: Priority Job Queuing
      • Guide: Configuring Custom Variables for Cluster Job Submission Scripts
      • Guide: SSD Particle Caching in CryoSPARC
      • Guide: Data Management in CryoSPARC (v4.0+)
      • Guide: Data Cleanup (v4.3+)
      • Guide: Reduce Database Size (v4.3+)
      • Guide: Data Management in CryoSPARC (≤v3.3)
      • Guide: CryoSPARC Live Session Data Management
      • Guide: Manipulating .cs Files Created By CryoSPARC
      • Guide: Migrating your CryoSPARC Instance
      • Guide: EMDB-friendly XML file for FSC plots
    • Troubleshooting
  • Application Guide (v4.0+)
    • A Tour of the CryoSPARC Interface
    • Browsing the CryoSPARC Instance
    • Projects, Workspaces and Live Sessions
    • Jobs
    • Job Views: Cards, Tree, and Table
    • Creating and Running Jobs
    • Low Level Results Interface
    • Filters and Sorting
    • View Options
    • Tags
    • Flat vs Hierarchical Navigation
    • File Browser
    • Blueprints
    • Workflows
    • Inspecting Data
    • Managing Jobs
    • Interactive Jobs
    • Upload Local Files
    • Managing Data
    • Downloading and Exporting Data
    • Instance Management
    • Admin Panel
  • Cryo-EM Foundations
    • Image Formation
      • Contrast in Cryo-EM
      • Waves as Vectors
      • Aliasing
  • Expectation Maximization in Cryo-EM
  • Processing Data in cryoSPARC
    • Get Started with CryoSPARC: Introductory Tutorial (v4.0+)
    • Tutorial Videos
    • All Job Types in CryoSPARC
      • Import
        • Job: Import Movies
        • Job: Import Micrographs
        • Job: Import Particle Stack
        • Job: Import 3D Volumes
        • Job: Import Templates
        • Job: Import Result Group
        • Job: Import Beam Shift
      • Motion Correction
        • Job: Patch Motion Correction
        • Job: Full-Frame Motion Correction
        • Job: Local Motion Correction
        • Job: MotionCor2 (Wrapper) (BETA)
        • Job: Reference Based Motion Correction (BETA)
      • CTF Estimation
        • Job: Patch CTF Estimation
        • Job: Patch CTF Extraction
        • Job: CTFFIND4 (Wrapper)
        • Job: Gctf (Wrapper) (Legacy)
      • Exposure Curation
        • Job: Micrograph Denoiser (BETA)
        • Job: Micrograph Junk Detector (BETA)
        • Interactive Job: Manually Curate Exposures
      • Particle Picking
        • Interactive Job: Manual Picker
        • Job: Blob Picker
        • Job: Template Picker
        • Job: Filament Tracer
        • Job: Blob Picker Tuner
        • Interactive Job: Inspect Particle Picks
        • Job: Create Templates
      • Extraction
        • Job: Extract from Micrographs
        • Job: Downsample Particles
        • Job: Restack Particles
      • Deep Picking
        • Guideline for Supervised Particle Picking using Deep Learning Models
        • Deep Network Particle Picker
          • T20S Proteasome: Deep Particle Picking Tutorial
          • Job: Deep Picker Train and Job: Deep Picker Inference
        • Topaz (Bepler, et al)
          • T20S Proteasome: Topaz Particle Picking Tutorial
          • T20S Proteasome: Topaz Micrograph Denoising Tutorial
          • Job: Topaz Train and Job: Topaz Cross Validation
          • Job: Topaz Extract
          • Job: Topaz Denoise
      • Particle Curation
        • Job: 2D Classification
        • Interactive Job: Select 2D Classes
        • Job: Reference Based Auto Select 2D (BETA)
        • Job: Reconstruct 2D Classes
        • Job: Rebalance 2D Classes
        • Job: Class Probability Filter (Legacy)
        • Job: Rebalance Orientations
        • Job: Subset Particles by Statistic
      • 3D Reconstruction
        • Job: Ab-Initio Reconstruction
      • 3D Refinement
        • Job: Homogeneous Refinement
        • Job: Heterogeneous Refinement
        • Job: Non-Uniform Refinement
        • Job: Homogeneous Reconstruction Only
        • Job: Heterogeneous Reconstruction Only
        • Job: Homogeneous Refinement (Legacy)
        • Job: Non-uniform Refinement (Legacy)
      • CTF Refinement
        • Job: Global CTF Refinement
        • Job: Local CTF Refinement
        • Job: Exposure Group Utilities
      • Conformational Variability
        • Job: 3D Variability
        • Job: 3D Variability Display
        • Job: 3D Classification
        • Job: Regroup 3D Classes
        • Job: Reference Based Auto Select 3D (BETA)
        • Job: 3D Flexible Refinement (3DFlex) (BETA)
      • Postprocessing
        • Job: Sharpening Tools
        • Job: DeepEMhancer (Wrapper)
        • Job: Validation (FSC)
        • Job: Local Resolution Estimation
        • Job: Local Filtering
        • Job: ResLog Analysis
        • Job: ThreeDFSC (Wrapper) (Legacy)
      • Local Refinement
        • Job: Local Refinement
        • Job: Particle Subtraction
        • Job: Local Refinement (Legacy)
      • Helical Reconstruction
        • Helical symmetry in CryoSPARC
        • Job: Helical Refinement
        • Job: Symmetry search utility
        • Job: Average Power Spectra
      • Utilities
        • Job: Exposure Sets Tool
        • Job: Exposure Tools
        • Job: Generate Micrograph Thumbnails
        • Job: Cache Particles on SSD
        • Job: Check for Corrupt Particles
        • Job: Particle Sets Tool
        • Job: Reassign Particles to Micrographs
        • Job: Remove Duplicate Particles
        • Job: Symmetry Expansion
        • Job: Volume Tools
        • Job: Volume Alignment Tools
        • Job: Align 3D maps
        • Job: Split Volumes Group
        • Job: Orientation Diagnostics
      • Simulations
        • Job: Simulate Data (GPU)
        • Job: Simulate Data (Legacy)
    • CryoSPARC Tools
    • Data Processing Tutorials
      • Case study: End-to-end processing of a ligand-bound GPCR (EMPIAR-10853)
      • Case Study: DkTx-bound TRPV1 (EMPIAR-10059)
      • Case Study: Pseudosymmetry in TRPV5 and Calmodulin (EMPIAR-10256)
      • Case Study: End-to-end processing of an inactive GPCR (EMPIAR-10668)
      • Case Study: End-to-end processing of encapsulated ferritin (EMPIAR-10716)
      • Case Study: Exploratory data processing by Oliver Clarke
      • Tutorial: Tips for Membrane Protein Structures
      • Tutorial: Common CryoSPARC Plots
      • Tutorial: Negative Stain Data
      • Tutorial: Phase Plate Data
      • Tutorial: EER File Support
      • Tutorial: EPU AFIS Beam Shift Import
      • Tutorial: Patch Motion and Patch CTF
      • Tutorial: Float16 Support
      • Tutorial: Particle Picking Calibration
      • Tutorial: Blob Picker Tuner
      • Tutorial: Helical Processing using EMPIAR-10031 (MAVS)
      • Tutorial: Maximum Box Sizes for Refinement
      • Tutorial: CTF Refinement
      • Tutorial: Ewald Sphere Correction
      • Tutorial: Symmetry Relaxation
      • Tutorial: Orientation Diagnostics
      • Tutorial: BILD files in CryoSPARC v4.4+
      • Tutorial: Mask Creation
      • Case Study: Yeast U4/U6.U5 tri-snRNP
      • Tutorial: 3D Classification
      • Tutorial: 3D Variability Analysis (Part One)
      • Tutorial: 3D Variability Analysis (Part Two)
      • Tutorial: 3D Flexible Refinement
        • Installing 3DFlex Dependencies (v4.1–v4.3)
      • Tutorial: 3D Flex Mesh Preparation
    • Webinar Recordings
  • Real-time processing in cryoSPARC Live
    • About CryoSPARC Live
    • Prerequisites and Compute Resources Setup
    • How to Access cryoSPARC Live
    • UI Overview
    • New Live Session: Start to Finish Guide
    • CryoSPARC Live Tutorial Videos
    • Live Jobs and Session-Level Functions
    • Performance Metrics
    • Managing a CryoSPARC Live Session from the CLI
    • FAQs and Troubleshooting
  • Guides for v3
    • v3 User Interface Guide
      • Dashboard
      • Project and Workspace Management
      • Create and Build Jobs
      • Queue Job, Inspect Job and Other Job Actions
      • View and Download Results
      • Job Relationships
      • Resource Manager
      • User Management
    • Tutorial: Job Builder
    • Get Started with CryoSPARC: Introductory Tutorial (v3)
    • Tutorial: Manually Curate Exposures (v3)
  • Resources
    • Questions and Support
Powered by GitBook
On this page
  • Introduction
  • Benchmarking vs. Testing
  • Datasets Available
  • Prerequisites
  • Creating and Running the Extensive Validation Job
  • Troubleshooting Failed Jobs
  • Additional Extensive Testing
  • Expected Results
  1. Setup, Configuration and Management
  2. Software System Guides

Guide: Verify CryoSPARC Installation with the Extensive Validation Job (v4.3+)

PreviousGuide: Installation Testing with cryosparcm testNextGuide: Verify CryoSPARC Installation with the Extensive Workflow (≤v4.2)

Last updated 1 year ago

The "Extensive Workflow" job has been renamed to "Extensive Validation" in CryoSPARC v4.3.0+. For the version of this guide applicable to CryoSPARC versions ≤v4.2, please see:

Introduction

CryoSPARC's "Extensive Validation" job orchestrates a full 3D target reconstruction for two datasets:

  • T20S Proteasome () from a small subset of movies (~8GB)

  • Tobacco Mosaic Virus ()

CryoSPARC's engineering team uses this job to automatically test and benchmark CryoSPARC between releases.

System Administrators may use the Extensive Validation job to verify that CryoSPARC is correctly configured following a fresh installation or an update.

Benchmarking vs. Testing

The Extensive Validation job has two modes: Benchmark mode and Testing mode.

In Benchmark mode, jobs with pre-defined parameters run sequentially on the worker node in order. Each job accesses available system resources independently of other jobs to collect accurate runtime statistics. Benchmark mode is useful for evaluating the overall performance of a worker node.

In Testing mode, jobs run in parallel when possible. Multiple parameter combinations of each job are dispatched. Testing mode is useful for ensuring that a CryoSPARC instance is installed correctly.

Both Benchmark and Testing modes verify the following system requirements:

  • CryoSPARC system and license installation

  • Worker/Cluster configuration

  • GPU and CUDA driver installation

  • SSD caching

Datasets Available

CryoSPARC downloads the selected dataset into the project directory when the Extensive Validation job first runs in the current project.

  • Number of movies: 20

  • Frames per movie: 38

  • Movie size: 7420 × 7676 (K2 Super Resolution)

  • Pixel size: 0.86 Å

  • Particles processed: 10,000

  • Particle box size (pixels): 448

Jobs run in Benchmark Mode

  1. Import Movies

  2. Patch Motion Correction

  3. Patch CTF Estimation

  4. Curate Exposures

  5. Blob Picker

  6. Inspect Picks

  7. Extract From Micrographs

  8. 2D Classification

  9. Select 2D

  10. Template Picker

  11. Inspect Picks

  12. Extract From Micrographs

  13. 2D Classification (50 Class)

  14. 2D Classification (100 Class) (All Job Types Enabled)

  15. 2D Classification (200 Class) (All Job Types Enabled)

  16. Select 2D

  17. Particle Sets Tools

  18. Ab-Initio Reconstruction

  19. Ab-Initio Reconstruction (3 Class) (All Job Types Enabled)

  20. Homogeneous Refinement

  21. Non-Uniform Refinement

  22. Homogeneous Refinement Legacy (All Job Types Enabled)

  23. Non-Uniform Refinement Legacy (All Job Types Enabled)

  24. 3D Classification

  25. 3D Variability (3 Mode)

  26. 3D Variability (6 Mode) (All Job Types Enabled)

Jobs run in Testing Mode

  1. Import Movies

  2. Patch Motion Correction

  3. Full-Frame Motion Correction

  4. Patch CTF Estimation

  5. CTFFIND4

  6. Curate Exposures (Stream A)

  7. Curate Exposures (Stream B)

  8. Blob Picker (Stream A)

  9. Blob Picker (Stream B)

  10. Inspect Picks (Stream A)

  11. Inspect Picks (Stream B)

  12. Extract From Micrographs (Stream A)

  13. Local Motion Correction (Stream B)

  14. 2D Classification (Stream A) # all jobs past this point are in Stream A

  15. Select 2D

  16. Template Picker

  17. Inspect Picks

  18. Extract From Micrographs

  19. 2D Classification (50 Class)

  20. 2D Classification (100 Class)

  21. 2D Classification (200 Class)

  22. Select 2D

  23. Particle Sets Tools

  24. Ab-Initio Reconstruction

  25. Ab-Initio Reconstruction (3 Class)

  26. Homogeneous Refinement

  27. Non-Uniform Refinement

  28. Homogeneous Refinement (Legacy)

  29. Non-Uniform Refinement (Legacy)

  30. Heterogeneous Refinement (3 Class)

  31. Heterogeneous Refinement (6 Class)

  32. 3D Classification (Simple mode)

  33. 3D Classification (PCA mode)

  34. 3D Variability (3 mode)

  35. 3D Variability (6 mode)

  36. Sharpening Tools

  37. Validation (FSC)

  38. Global CTF Refinement

  39. Local CTF Refinement

  40. 3D Variability Display

  • Number of movies: 62

  • Frames per movie: 20

  • Movie size: 7420 × 7676 (K2 Super Resolution)

  • Pixel size: 0.32 Å

  • Particles processed: ~30,000

  • Particle box size (pixels): 512

Jobs run in Benchmark Mode

  1. Import Movies

  2. Patch Motion Correction

  3. Patch CTF Estimation

  4. Curate Exposures

  5. Blob Picker

  6. Inspect Picks

  7. Extract From Micrographs

  8. 2D Classification

  9. Select 2D

  10. Template Picker

  11. Inspect Picks

  12. Extract From Micrographs

  13. 2D Classification

  14. Select 2D

  15. Particle Sets Tools

  16. Ab-Initio Reconstruction

  17. Homogeneous Refinement

  18. Non-Uniform Refinement

  19. 3D Classification

  20. 3D Variability

Jobs run in Testing Mode

  1. Import Movies

  2. Patch Motion Correction

  3. Patch CTF Estimation

  4. Filament Tracer

  5. Inspect Picks

  6. Extract From Micrographs

  7. 2D Classification

  8. Select 2D

  9. Helical Refinement

  10. Local CTF Refinement

  11. Global CTF Refinement

  12. Symmetry Expansion

  13. Homogeneous Reconstruct Only

Prerequisites

Creating and Running the Extensive Validation Job

  1. Open the CryoSPARC web interface

  2. In the dashboard, create a new Project from the navigation bar and create an initial workspace.

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

Best practices: Create a new workspace and run the Extensive Validation 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 v4.3.0, name the workspace "v4.3.0 Benchmark and Validation"

4. Select the Job Builder from the sidebar and select the "Extensive Validation" job (under the Validation category).

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

6. Select the node or cluster that the Extensive Validation jobs should run on.

Queue the job from the Job Builder sidebar. Open the job's Event log (either click/tap the Job card header or select the Job card and press the Space key) to monitor its progress. The Validation job logs each spawned job as it is queued and logs how long it takes to complete.

Close the Job modal with the × button. This shows the workspace overview with CryoSPARC jobs spawned by the Extensive Validation job

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

Troubleshooting Failed Jobs

Extensive Validation will fails if any spawned job fails.

Scroll through the workspace to find jobs with the "Failed" status. Open the failed job's Event Log.

Scroll to the bottom to see why the job failed.

Common failure reasons include

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

Additional Extensive Testing

For an even more extensive system test, the Extensive Validation job provides the parameter "Run Advanced Jobs"

With "Run Advanced Jobs" enabled, additional validation jobs run in parallel. Use this to verify multi-GPU performance on a single node. Advanced jobs available for each dataset are listed in the "Datasets Available" section above.

Expected Results

To compare the results of Extensive Validation runs, use "Benchmark" mode. This locks in the parameters and runs each job serially to ensure all system resources are available independently. The benchmark results may be viewed in the "Manage" panel, under the "Benchmarks" tab.

There are several reference benchmarks available for comparison with your CryoSPARC installation, including benchmarks completed on AWS EC2 instances. Select one or more benchmark rows and click "Compare" to compare benchmarks.

or license key entered incorrectly

EMPIAR-10025
EMPIAR-10305
How to Download, Install and Configure
Cannot verify license
Incorrect filesystem permissions
CUDA not set up correctly
SSD cache full or not set up correctly
Worker registration issue
Not enough GPU memory available
Extensive Workflow
EMPIAR-10025
EMPIAR-10305
Table view of a workspace with an Extensive Validation run
Switch the Extensive Workflow job from "Testing" mode to "Benchmark" mode using the drop-down menu.
Example Import Movies failure because the Gain Reference was not found
Turn on the "Run Advanced Jobs" radio button to run the full workflow.