Compute Roadmap

This pages describes plans to make Compute even better.

NB: the features below have still to be put on a release schedule!

Finish creation of tests for all important configurations

• local, pbs, grid
• impute, align

Make it easier to insert additional step/remove a step

• requires seperation between 'per protocol input/output parameters' and 'workflow links'
• should not be extra work; could do automatic mapping?
• should be solved in the workflow.csv (instead of control flow, do data flow, i.e. create list of output-input edges)

Auto generate the list of parameters that you need

• could automatigically be filled from templates or, if we have it, the data flow?

Better error reporting on input

• doesn't list which variable is missing
• templates are missing
• syntax checking of CSV files

Monitoring of progress

• how far is the analysis
• succesfully or wrongly, during running (could be done with #end macro)
• add a job at the end that creates report of results (for commandline)
  • Also do this for database version to have this info incase of database problems.

Monitoring of success and resource usage

• have harmonized method to report 'success' or 'error', incl message + runtime
• include also stuff like max, min etc.

Make transparant/unimportant for the user which backend is actually used

• system decides where it (can) run: cluster, pbs, grid, local
• needs flexible file manager that can 'stage' data for any backend
• like to restart on other backend

Transparent server to stage data

• to easily move pipeline to other storage.

Restart from specific step

• Remove files for the step from which to restart as well as for all steps that depend on that one.
• Reduce problem by using *tmp file and and only 'mv' if step is successful (as automatically determined by compute)
• However, this doesn't work if we want to restart from a step that was successful as automatically determined by compute, but has failed as manually determined by a user.
• Could use folders per step, so you could more easily delete all output from a specific step onwards
• Can be solved by good practice -> Compute should assist users as much as possible to standardize good practice and make it as easy as possible.

Store pilot job id in the task in the database

• I need to know which pilot jobs have died, and which tasks were associated with it
• Then I can re-release tasks to they can be done by another pilot
• Alternative: jobs are sending heart-bits to the server every 5-10 minutes and the actual analysis is running in the background

Like to have a 'heartbeat' for jobs

• so I can be sure a (pilot) job is still alive
• could us a 'background' process that pings back to database
• could also be used for pbs jobs

Add putFile -force to manual

Enable easy merging of workflows, merging of parameters

• Easily combine protocols from multiple workflows
• wants less parameter files
• meanwhile allow multiple worksheets

Get rid of parameters.csv and instead create worksheet

• so parameter names on first row
• hasOne using naming scheme A_B, means B has one A
• conclusion: use multiple headers.
• allow -parameters and -tparameter

Cleanup backend specific protocols

• e.g. 'touch' commands

Visualization framework for analyses runs

Rearchitecture the components

• one interface, multiple implementations
• unit tests
• Can we do something with unit tests per protocol?

Stable JPA

Make submit.sh uses 'lock' file so the jobs can only end when all is submitted

• Problem is that first jobs fails quickly, many dependent jobs are not yet submitted, and get orphaned
• so dependent jobs can be submitted and never have issue (alex feature)
• at this in the #end macro so jobs can never finish until complete workflow is submitted
• After all jobs are submitted lock file will be removed

Seperate protocols from code

• yes, seperate github repo
• should enable to combine multiple protocol folders, multiple parameter filse
• should indicate at which compute version it works

Users for runs, priorities?

• needed if we want 'priority queue' for pilot jobs

Publish!

Approach

• Clean start = yes
• Separate development of v5 from v4
• Bug fixes for v4 = yes
• Database, commandline or both = both
• Release schedule -> roadmap
• Backwards compatibility = no