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Doppio in BEAR Portal

Note

Information on running Doppio assumes you already have knowledge and experience using RELION

Launching Doppio in BEAR Portal

From the menu bar at the top of the page, select the 'Interactive Apps' menu and then select 'Doppio'. (If you cannot see the 'Interactive Apps' menu when you log in to the BEAR Portal this means that you need to follow the steps listed in the Access to BEAR Portal section.)

portal-home-interactive-menu-with-Doppio

This will open a page for you to specify options for your job, such as:

  • Doppio version (currently only 1.2.1 is available).
  • Duration for which you want to run the interactive app.
  • Number of cores to use in your job.
  • BEAR project to allocate the session against.
  • QOS to run the job against. If you want to access RELION's GPU features then choose an appropriate QOS, e.g. bbgpu.
  • RELION version to load when running Doppio GUI.
  • Base directory where your RELION project files are located.

You can also tick the checkbox for creating a Doppio job submission script in your home directory. First-time users of Doppio on BlueBEAR are advised to check this option.

portal-Doppio

Once you are happy with the selected options, click the 'Launch' button at the bottom of the page. When you have done this a BlueBEAR job will be submitted to the cluster.

Note

The length of time you will have to wait for this job to start will depend on the resources you have requested - Doppio only allows a maximium of 10 cores as it is only used to visualise and submit jobs.

Once the resource is available you'll see a 'Connect to Doppio' button appear on the page. Clicking this will take you to the Doppio GUI instance. When you have finished your work please click the 'Delete' button to stop the job and release the compute resources.

Doppio in BEAR Portal

Info

To see information relating to your BEAR Portal jobs please refer to the Portal Job Output page.

Doppio interface: directory setup

Launching Doppio GUI will open a webpage as shown below:

Doppio GUI Project Info

If the project info isn't visible in the 'Info' tab, please select the appropriate directory by clicking the pencil icon next to the 'Projects' field.

Doppio Edit Project name

If the directory isn't available in the menu, click the plus icon to add a new directory.

Doppio Add Project Directory

Doppio interface: walk-through

The GUI has multiple tabs on the left-hand side and sub-tabs on the right-hand side. The GUI opens with 'Project' tab's 'Info' sub-tab. Navigating to the 'Workflow' sub-tab under the 'Project' tab shows the visualisation of the jobs and their inter-dependence in the current project directory.

Doppio Workflow Tab

Selecting the 'Jobs' tab shows a list of executed jobs in the current project directory. Selecting a job from the list then shows the job details on the right-hand side.

Doppio Jobs Tab

The 'Nodes' tab shows the list of output images available after running the jobs.

Doppio Nodes Tab

Navigate to the 'New Job' tab to create a new job. The 'New Job' tab has multiple sub-tabs for different job types. Selecting a job type will show the relevant parameters to set for that job type on the right-hand side.

Doppio New Job Tab

Enter following parameters when submitting a new job:

  • Number of MPI procs: Select as per your requirements. This reserves the specified number of nodes for your job.
  • Number of threads: Select as per your requirements. This reserves the specified number of CPU cores on each node.
  • Submit to queue: Select 'Yes'
  • Queue name: Enter a GPU QOS for RELION jobs.
  • Queue submit command: Leave as default 'sbatch'.
  • Standard submission script: Leave as default.
  • Minimum dedicated cores per node: Select as per your requirements. This reserves the specified number of CPU cores on each node.
  • Job time limit: Select as per your requirements.
  • Slurm Account/Project code: Select the BEAR project to allocate your job against.
  • GPU: Select the number of GPUs required for your job.

Known issues and advice

  • Doppio is built to run with GPU versions of RELION and as such you must you a GPU QOS and those RELION versions.
  • The 'Import' job type in the 'New Job' tab of the Doppio doesn't work and the import step must be done in RELION.
  • Refer to Doppio official documentation by CCP-EM for further info on how to use the Doppio GUI.
  • The RELION Single Particle Tutorial is a good example to learn how to navigate Doppio.
  • Refer to Doppio Tutorial for refining a model using Doppio.