Queue Job, Inspect Job and Other Job Actions
Last updated
Last updated
Once you have built a job and are ready to run the job, click 'Queue' on the Job Builder. This will bring up the Queue Modal.
1. Select the lane where the job should run. By default, new jobs you create will run in the current active workspace. If you wish to run the job and link it into a different workspace, you can also specify this under 'Run Job in'.
2. Optionally, you can set the Job Priority. See: Priority Queuing.
3. Click 'Create' to run the job.
You can queue up a chain of jobs, which will each commence as soon as their respective required inputs (i.e., the outputs from jobs earlier in the series) become available.
For example, while an Import Movies job is running, open the job card, and drag and drop the imported-movies output into a new Patch Motion Correction job in the Job Builder. Queue the Patch Motion Correction job and it will appear in "Queued - waiting because inputs are not ready" state until the imported movies become available, at which point it will start running automatically.
See also, Management and Monitoring if you wish to create and launch jobs through the command line interface.
You can easily determine the status of jobs within the workspace view looking at the coloured dots on the job card. Purple = building, teal = queued, gray = started, blue = running, green = completed, orange = killed and red = failed. Hovering over a job's status circle will indicate the status as a tool tip.
Once the job starts to run, you can view its progress and intermediate outputs at any time from the inspect view.
To open the inspect view, click on the job number (at the top right of the job card), or select the job and press SPACEBAR.
The job inspect view has several tabs, including an 'Overview' or stream log, 'Inputs and Parameters', 'Outputs' and 'Metadata'. To navigate easily through the stream log without having to scroll, select a checkpoint from the top, or use the filters. Clicking on "Follow latest" will cause the streamlog to tail the end of the job's output as it runs in real time. You can also filter by image, plots, etc.
Press SPACEBAR again or use the x on the top right of the inspect view, to close it.
To quickly view which parameters you adjusted for a given job, open the inspect view and click on the 'Inputs and Parameters' tab. Parameters which were unchanged from their default values display with a blue D. Parameters you specified are outlined in green and display with a green S.
Each output in cryoSPARC jobs contains "low level" result groups that may be useful for advanced processing strategies. For a detailed overview of outputs and passthrough results, please see: Inputs and Outputs in cryoSPARC
To avoid redundant processing, it's possible to link jobs in multiple workspaces to continue processing in a new or existing workspace. Select a job and click on 'Link Job' the Job Details panel to select another Workspace in the same Project where you would like to link the job.
Any changes you make to the job in one workspace will be reflected in the other, as both workspaces will be displaying the exact same job. If a linked job is deleted from any workspace, all other instances of it in other workspaces will also be deleted. You can also unlink a job from a workspace if needed.
When re-organizing your workspaces, you may find it necessary to move a job from one workspace to another. To do so, select the job and navigate to the 'Details' tab. Here, you can click the Move Job dropdown to select which workspace you would like to move the job to. The job will disappear from its original workspace and move to the new one.
You can kill a job while it is running. A pop-up message will allow you to confirm. Killed jobs will display as orange and will remain part of the workspace unless you delete them. Killed jobs will not have their intermediate results expunged until they are cleared.
When a job has been killed, has failed, or has been completed, it can be cleared, meaning that its results and outputs are all erased from the file system, but its connections to other jobs and parameters are retained. This makes it easy to correct a mistakenly set parameter, or to re-run a failed job. Clearing also removes queued jobs from the queue and resets jobs to Building status.
Unused intermediate results can be cleared from iterative jobs to save space. This action can be executed at a job level (by clicking the "Clear Intermediate Results" button on the Job Details panel) or at a project level for every job (by clicking the "Clear Intermediate Results" button on the Project Details panel). This function will remove all unused outputs created by iterative jobs that save raw data at every iteration. Final results for every result slot will be retained, whether they have been used elsewhere or not.
Any individual job can be exported, for sharing, manipulation, or archiving. Jobs must be exported manually in order to create a "consolidated" exported-job directory which is then importable. For more details, please see: Exporting a job
Cloning is particularly useful when you wish to process subsequent jobs in a new workspace for better organization of your experiment, or if you wish to quickly replicate a job (to try another setting of parameters) without dragging and dropping inputs into the Job Builder. Select the job you wish to clone, and from the 'Details' tab, click 'Clone job'. By default, the job will be cloned in the current workspace. Click 'Queue' to launch the job. A modal will appear asking whether you wish to run the job in the current workspace or in a new workspace, and you can select as appropriate. Note that you can always edit the parameters of a new cloned job before Queuing. You can also change inputs by removing connected inputs and dragging in new inputs.
This option allows you to mark failed or killed jobs in cryoSPARC as completed in order to allow their latest outputs to be used for further processing. For more details, please see: Data Management in cryoSPARC
While selected, you can delete a job from the 'Details' tab. A pop-up message will ask you to confirm the delete. Once deleted, the job will disappear from the workspace (except in the tree view, if it has children that need to be displayed). Note that job numbers within a workspace are unique, so a new job in the same workspace will not be assigned the same number as a previously run or previously deleted job. Deleted jobs are first cleared before deleting, meaning that their intermediate and final results are erased from disk.
