Guide: Verify CryoSPARC Installation with the Extensive Workflow (≤v4.2)
For the version of this guide applicable to CryoSPARC versions v4.3.0+, please see: Extensive Validation
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.
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
pageHow to Download, Install and ConfigureCreating and Running the Extensive Workflow
Open the CryoSPARC web interface
In the dashboard, create a new Project from the navigation bar
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.
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)
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"
After queuing, a modal opens with an overview of the workflow job progress. The job status should shortly change to "Running".
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.
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".
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.
Example Import Movies failure because the Gain Reference was not found
Common failure reasons include
Cannot verify license or license key entered incorrectly
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.
Additional Extensive Testing
For an even more extensive test of robustness, the Extensive Workflow job provides an advanced option called "Run all job types"
Enable advanced mode near the top of the job builder
Enable to "Run all job types" switch
With this option enabled, the job runs additional child jobs in parallel. Use this to verify multi-GPU performance on a single node.
The following additional job types are included:
Full-frame motion correction
Global CTF estimation
Local motion correction
Multi-class ab-initio reconstruction
Heterogeneous and non-uniform refinement
3D Variability
Expected Results
Below are the results from our tests with CryoSPARC v3.1 on a 4GPU machine with the T20S subset.
On a machine with the recommended system configuration, the Extensive Workflow takes ~1 hour with the default settings and ~1 hour 30 minutes with all job types enabled (note that some jobs run in parallel when enough GPUs are available).
Job Type | Approximate Run Time (seconds) |
Import Movies | 92 |
Patch Motion Correction (Multi) | 220 |
Full Frame Motion Correction (Multi) | 75 |
Patch CTF Estimation (Multi) | 66 |
Curate Exposures | 1.1 |
Blob Picker | 12 |
Template Picker | 13 |
Inspect Picks | 12 |
Extract from Micrographs (CPU) | 39 |
Extract from Micrographs (GPU) | 43 |
Local Motion Correction | 180 |
2D Classification | 280 |
Select 2D Classes | 7.5 |
Ab-Initio Reconstruction (1 class) | 450 |
Ab-Initio Reconstruction (3 class) | 800 |
Homogenous Refinement | 1940 |
Heterogeneous Refinement (3 class) | 3000 |
Non-Uniform Refinement | 4300 |
Sharpen | 32 |
Validation | 94 |
Global CTF Refinement | 41 |
Local CTF Refinement | 46 |
3D Variability | 560 |
3D Variability Display | 140 |
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