Homogeneous refinement fails after several iterations

3D Refinement
1

Hi,

I am running cryosparc v2.4.0 trying to perform homogeneous refinements.
After 4-5 iterations jobs keep crashing with the following similar error messages.
The messages differ in the IOError values between runs.

We did some python updates recently, but these were of the system python.

Are there any system dependencies that we should make sure to have?

Best,

Ron

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_worker/cryosparc2_compute/jobs/refine/run.py”, line 507, in cryosparc2_compute.jobs.refine.run.run_homo_refine
File “cryosparc2_compute/dataset.py”, line 363, in to_file
n.save(file, outdata, allow_pickle=False)
File “/data/cryosparc2/cryosparc2_master/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/numpy/lib/npyio.py”, line 491, in save
pickle_kwargs=pickle_kwargs)
File “/data/cryosparc2/cryosparc2_master/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/numpy/lib/format.py”, line 584, in write_array
array.tofile(fp)
IOError: 37249 requested and 13 written

2

Hi @RD_Cryo,

Is it possible if you can share more information? You can use this post as a guide. Also, can you double check if you have enough space on the drives where these files are?

3

Problem solved!

Indeed, we runout of disk space.
Working through the Webapp and not through the terminal makes you less aware of the available resources on the computer.
Adding an available disk space gauge to the webapp could be very useful.
Thanks,
Ron

4

Hey @RD_Cryo,

Glad to hear!
Thank you for your input. We’ve recorded the request and will update you when it’s released in a future version of cryoSPARC :smile: