2D Error- Nan problem

Troubleshooting
1

Dear Cryosparc developer,

I am new to the cryosparc. Below is the error message, while running the 2D classification. Could you please help.
I am using the latest version 4.6.

Traceback (most recent call last):
File “/home/cryosparc_user/software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 2304, in run_with_except_hook
run_old(*args, **kw)
File “cryosparc_master/cryosparc_compute/gpu/gpucore.py”, line 135, in cryosparc_master.cryosparc_compute.gpu.gpucore.GPUThread.run
File “cryosparc_master/cryosparc_compute/gpu/gpucore.py”, line 136, in cryosparc_master.cryosparc_compute.gpu.gpucore.GPUThread.run
File “cryosparc_master/cryosparc_compute/jobs/class2D/newrun.py”, line 640, in cryosparc_master.cryosparc_compute.jobs.class2D.newrun.class2D_engine_run.work
File “cryosparc_master/cryosparc_compute/engine/newengine.py”, line 1534, in cryosparc_master.cryosparc_compute.engine.newengine.EngineThread.compute_error
ValueError: Detected NaN values in newengine.compute_error. 198450 NaNs in total, 1 particles with NaNs.

I tried running the following command.
cryosparcm eventlog pxx jxxx | tail n -30

[Thu, 26 Sep 2024 18:58:47 GMT] [CPU RAM used: 91 MB] --------------------------------------------------------------
[Thu, 26 Sep 2024 18:58:47 GMT] [CPU RAM used: 91 MB] Importing job module for job type class_2D_new…
[Thu, 26 Sep 2024 18:58:51 GMT] [CPU RAM used: 275 MB] Job ready to run
[Thu, 26 Sep 2024 18:58:51 GMT] [CPU RAM used: 275 MB] ***************************************************************
[Thu, 26 Sep 2024 18:59:10 GMT] [CPU RAM used: 2467 MB] Using random seed of 1351769025
[Thu, 26 Sep 2024 18:59:10 GMT] [CPU RAM used: 2467 MB] Using pixel size from location/micrograph_psize_A for duplicate removal
[Thu, 26 Sep 2024 18:59:10 GMT] [CPU RAM used: 2467 MB] Loading a ParticleStack with 3489279 items…
[Thu, 26 Sep 2024 18:59:46 GMT] [CPU RAM used: 4158 MB] Done.
[Thu, 26 Sep 2024 18:59:46 GMT] [CPU RAM used: 4158 MB] Windowing particles
[Thu, 26 Sep 2024 18:59:46 GMT] [CPU RAM used: 4159 MB] Done.
[Thu, 26 Sep 2024 18:59:46 GMT] [CPU RAM used: 4412 MB] Using 50 classes.
[Thu, 26 Sep 2024 18:59:46 GMT] [CPU RAM used: 4412 MB] Computing 2D class averages:
[Thu, 26 Sep 2024 18:59:46 GMT] [CPU RAM used: 4412 MB] Volume Size: 128 (voxel size 1.85A)
[Thu, 26 Sep 2024 18:59:46 GMT] [CPU RAM used: 4412 MB] Zeropadded Volume Size: 256
[Thu, 26 Sep 2024 18:59:46 GMT] [CPU RAM used: 4412 MB] Data Size: 324 (pixel size 0.73A)
[Thu, 26 Sep 2024 18:59:46 GMT] [CPU RAM used: 4412 MB] Using Reconstruction Resolution: 6.00A (39.0 radius)
[Thu, 26 Sep 2024 18:59:46 GMT] [CPU RAM used: 4412 MB] Using Alignment Resolution: 6.00A (39.0 radius)
[Thu, 26 Sep 2024 18:59:46 GMT] [CPU RAM used: 4412 MB] Windowing only corners of 2D classes at each iteration.
[Thu, 26 Sep 2024 18:59:46 GMT] [CPU RAM used: 4412 MB] Using random seed for initialization of 1351769025
[Thu, 26 Sep 2024 18:59:47 GMT] [CPU RAM used: 4414 MB] Done in 0.477s.
[Thu, 26 Sep 2024 18:59:51 GMT] [CPU RAM used: 4560 MB] Start of Iteration 0
[Thu, 26 Sep 2024 18:59:51 GMT] [CPU RAM used: 4560 MB]
[Thu, 26 Sep 2024 18:59:58 GMT] [CPU RAM used: 7800 MB] Traceback (most recent call last):
File “/home/cryosparc_user/software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 2304, in run_with_except_hook
run_old(*args, **kw)
File “cryosparc_master/cryosparc_compute/gpu/gpucore.py”, line 135, in cryosparc_master.cryosparc_compute.gpu.gpucore.GPUThread.run
File “cryosparc_master/cryosparc_compute/gpu/gpucore.py”, line 136, in cryosparc_master.cryosparc_compute.gpu.gpucore.GPUThread.run
File “cryosparc_master/cryosparc_compute/jobs/class2D/newrun.py”, line 640, in cryosparc_master.cryosparc_compute.jobs.class2D.newrun.class2D_engine_run.work
File “cryosparc_master/cryosparc_compute/engine/newengine.py”, line 1534, in cryosparc_master.cryosparc_compute.engine.newengine.EngineThread.compute_error
ValueError: Detected NaN values in newengine.compute_error. 198450 NaNs in total, 1 particles with NaNs.

2

Welcome to the forum @Akmp .

Please can you send the failed job’s error report to us.

I will let you know a suitable email address via a private message.

3

Thanks @wtempel

I sent you an email.

4

Error report received. Thanks.

5

Hello, I have encountered the same problem. How did you solve it?

1 Like
6

Hi,

I am waiting for the reply from the cryosparc team.

7

Hi both, I had this issue recently - it was some corrupt particles in the stack (NaN values cause divisions by zero). I ran “Check for corrupt particles” job which fixed the issue. :slight_smile:

1 Like
8

Hi @Akmp, @martic and @gilyarod,

CryoSPARC v4.6.1, released today, now contains a few changes to help resolve NaN issues. We’ve added more detailed diagnostics to the NaN checks to help us find the source of the NaNs. Additionally, the Check for Corrupt Particles Job now checks for NaN values by default and fails if any corrupt files are detected. The job can then be marked as completed or re-run with the “Fail if corruption is detected” parameter turned off in order to use the output in which corrupt files have been filtered out.

–Katherine

1 Like