Adding refine runjob » History » Revision 5
Revision 4 (Christopher Irving, 08/02/2011 11:22 AM) → Revision 5/17 (Amber Herold, 07/21/2014 11:59 AM)
h1. Adding refine job
h3. 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:
<pre>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</pre>
*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:
# Job object: this can be a *genericJob* which does not require a specialized job file, or a job class based on *refineJob*,
h3. 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.
# Add the name of the module you created to the import statements at the top of the file.
# In the method _createJobInst_ add the new refinment job type to the condition statements.
<pre>
Ex.
elif "newJobType" == jobType:
jobInstance = newModuleName.NewRefinementClass(command)
</pre>
!Agent_class_diag.png!