Adding refine job¶

How a cluster job file is built and launched¶

To run a cluster job, the user runs a command on the head node of the cluster that looks like this:

runJob.py --jobtype=frealignrecon --outerMaskRadius=65 --innerMaskRadius=0 --symmetry="D7 (z)" --endIter=10 --percentDiscard=15 --wgh=0.07 --hp=300 --lp=10 --ffilt --psi --theta --phi --x --y --modelnames=initmodel0001.mrc --stackname=start.mrc --apix=1.63 --boxsize=120 --totalpart=300 --cs=2 --kv=120 --description="test frealign get preset" --runname=frealign_recon69 --rundir=/ami/data17/appion/zz07jul25b/recon/frealign_recon69 --nodes=2 --ppn=4 --rpn=8 --walltime=240 --cput=2400 --localhost=guppy.scripps.edu --remoterundir=/ami/data15/appion/zz07jul25b/recon/frealign_recon69 --projectid=303 --expid=8556

runJob.py is a python script that passes all the command parameters to a python class called apAgent.
The apAgent object instantiates 2 more classes:

1. Job object: this can be a genericJob which does not require a specialized job file, or a job class based on refineJob,

Add job type to Agent.¶

After you have added a new refinement job class it needs to be added to the job running agent by editing the file apAgent.py in appionlib.

1. Add the name of the module you created to the import statements at the top of the file.
2. In the method createJobInst add the new refinment job type to the condition statements.
   

     Ex.
     elif "newJobType" == jobType:
               jobInstance = newModuleName.NewRefinementClass(command)