5.0.6: ab-initio reconstruction loop

3D Reconstruction
1

Hi

Since the upgrade to Cryosparc V5 some users are complaining that ab initio reconstruction jobs occasionally go into a loop where they keep running but never produce any output.

This issue appears to occur when an ab initio reconstruction job is missing a class.
I’d say this problem of endless running always coincides with this appearance that a class from the workspace-tile remains empty/dark. I have the feeling that it is stuck somewhere before finishing the first iteration. But what exactly causes what, I cannot see as the log doesn’t update anymore (last two lines from a job that is stuck since yesterday):

[2026-06-22 22:56:16.15] ----------- Iteration 0 (epoch 0.000). radwn 10.00 resolution 33.28A minisize 90 beta 0.10

[2026-06-22 22:56:18.40] Estimating noise model to meet target of 98.17 poses.. Current ESS R is 1116.56 poses.. Current sigma is 0.10 New sigma is 0.10

These jobs are fresh and not copied from jobs generated in v4

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image857×549 124 KB

Any idea?

2

Usually in my experience this happens because users have unintentionally set minimum alignment resolution (highpass) rather than initial resolution - this parameter name should be changed, I think

3

Thanks. The job has these metadata:

    "abinit_min_res": {
      "type": "number",
      "value": null,
      "title": "Minimum alignment resolution (Angstroms)",
      "desc": "High-pass filter for the purpose of alignment",
      "order": 6,
      "section": "abinit",
      "advanced": true,
      "hidden": false
    }
    "abinit_init_res": {
      "type": "number",
      "value": 35,
      "title": "Initial resolution (Angstroms)",
      "desc": "Starting frequency to consider",
      "order": 7,
      "section": "abinit",
      "advanced": false,
      "hidden": false
    }

As far as i can see both values are set. So it would be better to remove the highpass value?

4

Hmmm no this seems like a different issue then, because the minimum alignment res here is set to “null”, meaning it shouldn’t be applied..

5

I got now the info that sometimes it helps to clone the job again and run it. Strange.

6

Looks like somehow one of the initial volumes is ending up empty. Cloning changes the random seed which would explain why that helps, but it shouldn’t initialize from an empty volume to begin with, that is odd

7

@biocit Thanks for your initial post and the additional information. What is the THP setting on the worker node, viewable via the following command:

cat /sys/kernel/mm/transparent_hugepage/enabled
8 
cat /sys/kernel/mm/transparent_hugepage/enabled
always madvise [never]
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