numpy.linalg.LinAlgError: Array must not contain infs or NaNs from 3D Variability of v3.1.0

Troubleshooting
1

Hi All,

I searched the following error but no solution so I posted it as a separate topic. Any suggestion? Thanks.

[CPU: 14.90 GB] Start iteration 6 of 20
[CPU: 14.90 GB] batch 3567 of 3567
[CPU: 14.89 GB] Done. Solving…
[CPU: 15.83 GB] diagnostic: min-ev nan
[CPU: 15.40 GB] Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 84, in cryosparc_compute.run.main
File “cryosparc_worker/cryosparc_compute/jobs/var3D/run.py”, line 524, in cryosparc_compute.jobs.var3D.run.run
File “cryosparc_worker/cryosparc_compute/jobs/var3D/run.py”, line 436, in cryosparc_compute.jobs.var3D.run.run.M_step
File “<array_function internals>”, line 6, in eigvals
File “/data/donghua/cryosparc/cryosparc2_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/numpy/linalg/linalg.py”, line 1063, in eigvals
_assert_finite(a)
File “/data/donghua/cryosparc/cryosparc2_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/numpy/linalg/linalg.py”, line 209, in _assert_finite
raise LinAlgError(“Array must not contain infs or NaNs”)
numpy.linalg.LinAlgError: Array must not contain infs or NaNs

2

Dear @donghuachen, can you please see if this post helps? 3DVar must not contain infs or NaN

3

@spunjani, Thanks. I am re-running the same job with another GPU on the same computer.

4

@spunjani, I re-run the same job on another GPU of the same computer and succeeded.

1 Like