Appion

xmipp single-model refinement, after prepping, cannot be submitted from web gui. Typically, we click "run refinement", this gives an error, and then I copy the runjob.py command, and run on terminal. An example of runjob.py command is below:

runJob.py --jobtype=xmipprecon --endIter=10 --outerMaskRadius=189 --innerAlignRadius=1 --outerAlignRadius=189 --angSampRate=4x10:2x5:2x3:2x2 --maxAngularChange=4x1000:2x20:2x9:2x6 --maxChangeOffset=1000 --search5DShift=4x5:0 --search5DStep=2 --symmetry=C1 --percentDiscard=10 --reconMethod=fourier --ARTLambda=0.15 --fourierMaxFrequencyOfInterest=0.25 --DoComputeResolution --modelnames=initmodel0003.spi --stackname=partlist.sel --apix=10.48 --boxsize=40 --totalpart=65060 --cs=2.7 --kv=300 --description="Redo Rd 1" --runname=xmipp_recon4 --rundir=/data2/log-l/appion/15jun02c/recon/xmipp_recon4 --nodes=2 --ppn=20 --rpn=20 --walltime=9999 --cput=9999 --remoterundir=/data2/log-l/appion/15jun02c/recon/xmipp_recon4 --projectid=7 --expid=14126 --jobid=1401

A related issue: runjob.py launches a python process, BUT the process is not killed. Python processes have to be killed subsequently by hand