Total size of new array must be unchanged


(Elena Zehr) #1


I am trying to run 2D classification and encountering the following error. Has anyone had a similar problem.


Using random seed of 558330554

Loading a ParticleStack with 1553134 items…

SSD cache : cache successfuly synced in_use

SSD cache : cache successfuly synced, found 539185.52MB of files on SSD.

SSD cache : cache successfuly requested to check 2533 files.

SSD cache : cache requires 319.04MB more on the SSD for files to be downloaded.

SSD cache : cache has enough available space.

Transferring J37/imported/17sep06c_G9-3_00039gr_00002sq_v02_00005hl4_00004ed-a-DW_particle.mrcs (155MB)
Complete : 164MB
Total : 412619MB
Speed : 500.85MB/s

SSD cache : complete, all requested files are available on SSD.


Windowing particles


Using 100 classes.

Computing 2D class averages:

Volume Size: 128 (voxel size 2.37A)

Zeropadded Volume Size: 256

Data Size: 264 (pixel size 1.15A)

Using Resolution: 6.00A (50.0 radius)

Windowing only corners of 2D classes at each iteration.

Using random seed for initialization of 1121242163

Done in 0.819s.

Start of Iteration 0

– DEV 0 THR 0 NUM 500 TOTAL 8.5584180 ELAPSED 9.4281439 –

Traceback (most recent call last):
File “cryosparc2_compute/jobs/”, line 738, in run_with_except_hook
run_old(*args, **kw)
File “cryosparc2_worker/cryosparc2_compute/engine/”, line 92, in
File “cryosparc2_worker/cryosparc2_compute/engine/”, line 93, in
File “cryosparc2_worker/cryosparc2_compute/engine/”, line 980, in
File “cryosparc2_worker/cryosparc2_compute/engine/”, line 88, in cryosparc2_compute.engine.engine.EngineThread.load_image_data_gpu
File “cryosparc2_compute/”, line 109, in get_original_real_data
return self.blob.view().copy() # TODO!!! All the particle code assumes x is slow axis! WRONG!
File “cryosparc2_compute/blobio/”, line 101, in view
return self.get()
File “cryosparc2_compute/blobio/”, line 98, in get
data = n.fromfile(file_obj, dtype=self.dtype, count=
ValueError: total size of new array must be unchanged

(Ali Haydaroglu) #2

Hi Elena,

This error may indicate that there is something unexpected with the .mrc file containing the raw particle images. Where did your particles come from? Were they outputs of a different job?

Ali H.

(Elena Zehr) #3

Hi Ali,

Thank you for your response.
My particles came from collaborators / from cryosparc (presumably v1).
No error is given when I import particle stacks into cryosparc v2. I examined box size for each stack and did not find any problems, otherwise I do not know how else I can quickly check these stacks.

Many thanks,

(Jacque Faylo) #4

Has anyone been able to resolve this? I am getting the same error with 2D classification.

Sometimes the error occurs on iteration 3, sometimes it gets all the way to 10 iterations, sometimes it fails right away. Therefore I don’t know how it could be an issue with the raw input files.