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