Hi all,
I am having an issue with NU refinement. Firstly I imported my polishing shiny.star file from relion using the Import Particle Stack job and then performed NU refinement, I got an error like this:
License is valid.
Launching job on lane default target localhost ...
Running job on master node hostname localhost
[CPU: 68.3 MB] Project P12 Job J42 Started
[CPU: 68.3 MB] Master running v3.3.2, worker running v3.3.2
[CPU: 68.6 MB] Working in directory: /home/ZDQ/data2/cryosparc/P12/J42
[CPU: 68.6 MB] Running on lane default
[CPU: 68.6 MB] Resources allocated:
[CPU: 68.6 MB] Worker: localhost
[CPU: 68.6 MB] CPU : [0, 1, 2, 3]
[CPU: 68.6 MB] GPU : [2]
[CPU: 68.6 MB] RAM : [0, 1, 2]
[CPU: 68.8 MB] SSD : True
[CPU: 68.8 MB] --------------------------------------------------------------
[CPU: 68.8 MB] Importing job module for job type nonuniform_refine_new...
[CPU: 232.9 MB] Job ready to run
[CPU: 232.9 MB] ***************************************************************
[CPU: 553.9 MB] Traceback (most recent call last):
File "cryosparc_worker/cryosparc_compute/run.py", line 85, in cryosparc_compute.run.main
File "cryosparc_worker/cryosparc_compute/jobs/refine/newrun.py", line 114, in cryosparc_compute.jobs.refine.newrun.run_homo_refine
File "/home/ZDQ/Documents/cryosparc_worker/cryosparc_compute/particles.py", line 58, in init
assert n.all(self.data['blob/shape'][:,0] == self.N_input), "All particles must have the same box size."
AssertionError: All particles must have the same box size.
So I tried to extract my particles in pixel size of 0.93 in relion and then imported particles to cryosparc. When I performed NU refinement again, it came up that:
[CPU: 1.78 GB] Traceback (most recent call last):
File "/home/ZDQ/Documents/cryosparc_worker/cryosparc_compute/jobs/runcommon.py", line 1844, in run_with_except_hook
run_old(*args, **kw)
File "cryosparc_worker/cryosparc_compute/engine/cuda_core.py", line 131, in cryosparc_compute.engine.cuda_core.GPUThread.run
File "cryosparc_worker/cryosparc_compute/engine/cuda_core.py", line 132, in cryosparc_compute.engine.cuda_core.GPUThread.run
File "cryosparc_worker/cryosparc_compute/engine/engine.py", line 1028, in cryosparc_compute.engine.engine.process.work
File "cryosparc_worker/cryosparc_compute/engine/engine.py", line 87, in cryosparc_compute.engine.engine.EngineThread.load_image_data_gpu
File "/home/ZDQ/Documents/cryosparc_worker/cryosparc_compute/particles.py", line 22, in get_original_real_data
return self.blob.view().copy()
File "/home/ZDQ/Documents/cryosparc_worker/cryosparc_compute/blobio/mrc.py", line 127, in view
return self.get()
File "/home/ZDQ/Documents/cryosparc_worker/cryosparc_compute/blobio/mrc.py", line 122, in get
_, data, total_time = prefetch.synchronous_native_read(self.fname, idx_start = self.page, idx_limit = self.page+1)
File "cryosparc_worker/cryosparc_compute/blobio/prefetch.py", line 69, in cryosparc_compute.blobio.prefetch.synchronous_native_read
RuntimeError: mrc_readmic (1) 481
Please report this as a bug.: Invalid argument
[arguments] /data2/cryosparc/instance_localhost:39001/imports/home/ZDQ/data2/20230412_XM/Extract/job067/movies/FoilHole_12293355_Data_12234370_12234372_20230413_090351_EER.mrcs, 0, 0, 57, 58, 2, 40
I try to restart cyrosparc now but keep getting this error. I don’t know what is happening and how to fix it?
My cryosparc version is v3.3.2
Any help is appreciated.