I am running a Non Uniform refinement from a re-extracted particles job. I´ve been working with binned particles to sort out and get the best particles. Now, I want to work with the full pixel size to improve the resolution and get the maximun detail.
I am not running a 2D classification because I sorted the particles out already before. However, in order to get the right orientation and poses I run homogeneous refinements jobs and Heterogeneos refinement. Then, I run a NU refinement and it aborts abnormally.
I have a big box size of 882 pixels and pixel size of 1.14. Since I was having problems of space I activated the low memory mode.
I am using the cache particles images on SDD as well, since I am running several refinements at the same time I am afraid that this might afect as well.
@baratachencho Please can you post the output of the command
cryosparcm joblog P99 J199 | tail -n 40
(replacing P99 and J199 with the failed NU refinement job’s actual project and job IDs).
Please can you also post an FSC plot for your best refinement so far and an estimate of the current \frac{\text{box extent (Å)}}{\text{max particle dimension (Å)}} ratio.
Thanks for providing that information, it looks like your node is running out of RAM when you are running NU Refine in Low-Memory mode with a box of 882 pixels. We have a couple of suggestions that you can try:
The FSC curve that you provided, with a resolution of 7.73 Å suggests that you might not need a pixel size as small as 1.14. You could downsample the particles by Fourier-cropping, for example to a box size of 440, and still be able to represent features observable in this resolution range, and not be limited by the Nyquist frequency of the particles.
You mentioned that you are running multiple refinement jobs simultaneously when you observe this error. When refining large box sizes, a larger amount of RAM is required, and so it can help to run just a single NU Refinement on a node at once. This will improve the chances that the job will complete, as it relieves the competing RAM demands coming from other jobs.
You might need to combine both of the above ideas to get your NU Refine job to complete, depending on the box size that you choose.
