NaN error during ab-initio

3D Reconstruction
1

Hi all,

I’m encountering a recurring issue during ab-initio reconstruction.

> Apr 3, 2026, 2:06:36 PM

Traceback (most recent call last):
File “cli/run.py”, line 105, in cli.run.run_job
File “cli/run.py”, line 210, in cli.run.run_job_function
File “compute/jobs/abinit/run.py”, line 436, in compute.jobs.abinit.run.run_homo_abinit
File “compute/engine/engine.py”, line 1204, in compute.engine.engine.process
File “compute/engine/engine.py”, line 1205, in compute.engine.engine.process
File “compute/engine/engine.py”, line 1146, in compute.engine.engine.process.work
File “compute/engine/engine.py”, line 431, in compute.engine.engine.EngineThread.compute_error
ValueError: Detected NaN values in engine.compute_error. 979776000 NaNs in total, 500 particles with NaNs.

The error does not occur at a fixed iteration:

  • In some runs, it appears around iteration ~43

  • In others, it happens much later (e.g., ~1900 iterations)

  • Before crashing, the reconstruction often becomes abnormal

  • image
    image1062×285 128 KB

2

Dear @pey123456 ,

Apologies for the delay. We would appreciate if you could answer the following questions:

  • Can you confirm whether this is a single-class ab-initio job, multi-class ab-initio job, or an ab-initio refinement job?
  • Have there been any successful runs using this particle stack, or have all of them resulted in these errors at some point in the job’s execution?
  • Has this error been observed across multiple particle stacks, or is it specific to this one?
  • In the failing runs, do any intermediate iterations produce intact results that appear normal looking, or are they consistently abnormal from the start of the job?
  • Could you provide the values of all non-default parameters used in these runs?

Let me know if you are also willing to share full event logs of the jobs with us to help us understand the failure, and I can provide upload instructions.

Michael