I used bin2 on my particle set for local refinement (otherwise the job crashes), but I am a bit confused on how to get the full resolution density. I tried to do a non-uniform refinement using the volume and particle outputs from the local refinement- changing the particle blobs to the full resolution ones from a previous extraction job, but this job crashed as well. Any advice would be greatly appreciated!
Hi @merandamasse, in order to diagnose why it crashed, can you please provide the error message?
And were the particles downsampled from full (using the downsample job) or re-extracted at bin2 w/ fourier cropping?
Hey @olibclarke, I used the downsample job to downsample them from full. The error message I received was “Job is unresponsive - no heartbeat received in 30 seconds.” after iteration 2.
The local refinement jobs work just fine when I use the downsampled particles, but I’m wondering how I get them back to unbinned particles so that I can add the densities together in Chimera. I figured I’d try doing a local refinement at full resolution but it just seems my GPU capacity can’t handle it.
What is the original box size? yes sounds like running into a computational bottleneck
It was 512. It actually looks like all of my jobs are crashing now so I’m looking into the log files and will probably make a new post soon
One thing I would say is that sometimes the “no heartbeat” error doesn’t mean the job has actually died - even though it is marked as failed, in some instances it will still be ticking away
It’s crashing my entire program, like I can’t get to the UI without restarting it and none of the other jobs have continued on. I tried to increase the heartbeat but no such luck.
Sometimes that’s happened to me because of unrelated server instability (ex. I’ve had network outages that have made the UI inaccessible and made all my jobs truly fail with the “no heartbeat” error).