Can anyone give me some suggestions on what might cause the first exhaustive 3D classification to run extremely slowly under Relion 2.2? Specifically, I've got ~50,000 particles (box size 128) from ~280 micrographs, an initiial model low pass filtered to 5 nm, and am trying to classify into 4 classes using 25 iterations, as in the 2.2 tutorial. I'm running on a Linux cluster, with a dedicated single node (32 real cores, 32 hyper-threaded) using 3 MPI process and 20 threads per process. The first iteration only took about 20 minutes. The 2nd took about 90 minutes, and the 3d took 27 hours. At this rate, there's no telling how long all 25 iterations might take. I should add that there's no sign of thrashing or anything abnormal on the node running this job. Top output looks normal, and over the day and half it's been running so far, I've used up 1070 hours of cup time... i.e. about 40X wall time, which is about what I'd expect.
On a related note, what's the best way to proceed if in the middle of a single particle analysis I decide to remove certain particles or micrographs after picking / extraction / sorting have already been done? Obviously, I can manually edit files, but it seem likely there's a better way through the gui?
Thanks!
-jh-
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