3D-FSC crashing

Post Processing
1

My ThreeDFSC jobs crashes with this error message. Any clues of what is going on?

[CPU:  166.6 MB  Avail: 250.46 GB]
Job J237 Started
[CPU:  166.6 MB  Avail: 250.46 GB]
Master running v4.1.2, worker running v4.1.2
[CPU:  166.6 MB  Avail: 250.46 GB]
Working in directory: /home/larsson/cryosparc_projects/P100/J237
[CPU:  166.6 MB  Avail: 250.46 GB]
Running on lane Ampere
[CPU:  166.6 MB  Avail: 250.46 GB]
Resources allocated: 
[CPU:  166.6 MB  Avail: 250.46 GB]
  Worker:  Ampere
[CPU:  166.6 MB  Avail: 250.46 GB]
  CPU   :  [0]
[CPU:  166.6 MB  Avail: 250.46 GB]
  GPU   :  [0]
[CPU:  166.6 MB  Avail: 250.46 GB]
  RAM   :  [0]
[CPU:  166.6 MB  Avail: 250.46 GB]
  SSD   :  False
[CPU:  166.6 MB  Avail: 250.46 GB]
--------------------------------------------------------------
[CPU:  166.6 MB  Avail: 250.46 GB]
Importing job module for job type fsc3D...
[CPU:  168.0 MB  Avail: 250.45 GB]
Job ready to run
[CPU:  168.0 MB  Avail: 250.45 GB]
***************************************************************
[CPU:  168.7 MB  Avail: 250.44 GB]
Loading input volumes...
[CPU:   1.78 GB  Avail: 248.81 GB]
Input volumes loaded
[CPU:   2.31 GB  Avail: 248.27 GB]
Resampling mask to box size 520
[CPU:   3.93 GB  Avail: 246.66 GB]
Generating 3DFSC
[CPU:  26.15 GB  Avail: 224.38 GB]
Averaging on shells - 100.00% complete in 6253.07 seconds
[CPU:  29.97 GB  Avail: 216.57 GB]
Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 96, in cryosparc_compute.run.main
  File "/home/cryosparcuser/cryosparc/cryosparc_worker/cryosparc_compute/jobs/fsc3D/run.py", line 80, in run_fsc3D
    results = compute.generate_3dfsc(map_half_A, map_half_B, apix, dthetaInDegrees)
  File "/home/cryosparcuser/cryosparc/cryosparc_worker/cryosparc_compute/jobs/fsc3D/compute.py", line 858, in generate_3dfsc
    NormalizeShells(nx,ny,nz,kXofR,kYofR,kZofR,inc,retofROutR, retofROutI, n1ofROut,n2ofROut, NumAtEachR, RMax);
IndexError: index 8 is out of bounds for axis 0 with size 8
2

I have this same error. Running on 4.1.2 with v100 GPUs. It used to work on this instance.

1 Like
3

Same problem here! Anybody looking into this?

4

Hey @Pielhaas, @simonbrown and @daniel.s.d.larsson, it seems to be a bug within the 3DFSC code itself, and I’m not sure why it’s only showing up now. But we will fix it on our end in a future patch :slight_smile:

5

Dear kwang,

Don’t mean to be a pest but do you have an approximate ‘ETA’ for your next patch? I have a collection of refinements I’m trying to compare in a reasonably quantitative manner rather than trusting my eyes!

Thanks!

6

Hi,

FWIW, if it’s urgent, you could consider submitting your analyses to the public 3DFSC webserver or installing and running the standalone version outside of cryoSPARC.

Cheers,
Yang

7

Hey @Pielhaas @simonbrown @daniel.s.d.larsson @scottbcohen, the fix is out in the latest patch! Let us know if there are any additional issues.

2 Likes
8

Works for us. Thanks!