Feature #219
closed
Create Frealign web interface
Added by Neil Voss over 14 years ago.
Updated over 14 years ago.
Description
Create Frealign web interface. There are many steps involved:
Current state:
- Prepare Frealign (interface)
- Click Frealign Refinement from the menu
- Select Model and Stack
- Set Frealign parameters
- Launch prepFrealign.py script
- Prepare Frealign (background)
- Create shell script for each node
- Package tar file for transfer to garibaldi
- Create entry into ApFrealignPrepareData
- Lanuch Frealign Job (interface)
- Menu shows frealign jobs are prepare (from ApFrealignPrepareData query)
- Click on menu shows list of prepared jobs
- Select a prepared job and use this job
- Set Wall and CPU time, cluster directory and click show job file
- Review job file, (copy files to DMF?), and click submit job to cluster
- Job runs on Garibaldi
Needed:
- Method to review progress of job
- Method to flag prepared job as running and/or complere
- Method to (copy data from DMF? and) launch uploadFrealign jobs
- Method to flag prepared job as running and/or complere
We could do a query, because the garibaldi job in ApClusterJobData and the prepared frealign job in ApFrealignPrepareData share the same path. So, prepared jobs that share a path with a cluster job of type runfrealign are no longer prepared.
I went with a much simpler method, looking at the job types in ApClusterJobData. One drawback is that the number can get out of whack. But it makes it much simpler.
Prepared = prepfrealign(done) - runfrealign(all)
Run (Ready to Upload) = runfrealign(done) - uploadfrealign(all)
Uploaded = uploadfrealign(done)
The prepareFrealign script will use the method from note 1 to determine if a specific prepared job has already been run.
Neil Voss wrote:
- Method to flag prepared job as running and/or complere
We could do a query, because the garibaldi job in ApClusterJobData and the prepared frealign job in ApFrealignPrepareData share the same path. So, prepared jobs that share a path with a cluster job of type runfrealign are no longer prepared.
- % Done changed from 20 to 50
upload frealign and check frealign status are mostly done.
DMF still untouch.
uploadfrealign.py not started.
- Status changed from Assigned to Closed
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