Local refinement fails at iteration 0 Running local cross validation for A

Local Refinement
1

Hello,

I have been trying to run local refinement to mask out one subunit of an icosahedral virus. However, the jobs always fail at the Running local cross validation for A … step for iteration 0. The job only gives the error job process terminated abnormally.

This happens for both full particles and subtracted particles which have been symmetry expanded following a homogeneous refinement job.

The parameters of the job have been left as default.

Screenshot 2022-11-15 at 23.02.21
Screenshot 2022-11-15 at 23.02.212118×1594 355 KB

Screenshot 2022-11-15 at 23.02.37
Screenshot 2022-11-15 at 23.02.371920×1423 180 KB

Screenshot 2022-11-15 at 23.02.46
Screenshot 2022-11-15 at 23.02.462138×1432 214 KB

Screenshot 2022-11-15 at 23.02.53
Screenshot 2022-11-15 at 23.02.532122×850 129 KB

I have no idea about where to start to fix this issue, so any ideas are appreciated.

2

What GPU do you have? I’ve noticed this as well an RTX 2080, but re-launching on a machine with an RTX 2080 Ti successfully completes the refinement. I was wondering if it was a cryptic memory issue or something

3

We have a RTX 3080 ti. However, the box size is large 768. I will try downsampling the particles and see if this helps (if it is indeed a memory issue).

4

Both downsampling and reducing the number of particles has not helped.

5

Please can you post job.json and job.log from the failed job’s directory.
What are the

  • reduced box size
  • number of particles

?

6

It eventually worked when I reduced the particle number further. Now I have 700,000 particles and a box size of 384