Patch motion correction failed in processing

Motion Correction
1

Hello.
When I performed the patch motion correction, it failed.
I met some errors as follows, but I don’t know how to deal with them.
1)

*Processing ...*
Traceback (most recent call last):
  File "/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/jobs/runcommon.py", line 1722, in run_with_except_hook
    run_old(*args, **kw)
  File "/home/yu/cryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/threading.py", line 870, in run
    self._target(*self._args, **self._kwargs)
  File "/home/yu/cryoSPARC/cryosparc_worker/cryosparc_compute/jobs/pipeline.py", line 164, in thread_work
    work = processor.process(item)
  File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_patch.py", line 190, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
  File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_patch.py", line 193, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
  File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_patch.py", line 195, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
  File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/patchmotion.py", line 251, in cryosparc_compute.jobs.motioncorrection.patchmotion.unbend_motion_correction
  File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/patchmotion.py", line 368, in cryosparc_compute.jobs.motioncorrection.patchmotion.unbend_motion_correction
  File "cryosparc_worker/cryosparc_compute/engine/newgfourier.py", line 22, in cryosparc_compute.engine.newgfourier.get_plan_R2C_2D
  File "/home/yu/cryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/skcuda/fft.py", line 102, in __init__
    capability = misc.get_compute_capability(misc.get_current_device())
  File "/home/yu/cryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/skcuda/misc.py", line 254, in get_current_device
    return drv.Device(cuda.cudaGetDevice())
  File "/home/yu/cryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/skcuda/cudart.py", line 767, in cudaGetDevice
    cudaCheckStatus(status)
  File "/home/yu/cryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/skcuda/cudart.py", line 565, in cudaCheckStatus
    raise e
skcuda.cudart.cudaErrorInsufficientDriver

*Outputting partial results now...*
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/motioncorrection/run_patch.py", line 402, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi
AssertionError: Child process with PID 103683 has terminated unexpectedly!

Any information is appreciated.
Thank you!

2

Hi @yuhx0914,

This indicates you may need to update your NVIDIA Driver.
Please see this article for more information:
https://guide.cryosparc.com/setup-configuration-and-management/troubleshooting#cudaerrorinsufficientdriver

The second traceback is a byproduct of the first traceback, so you can ignore it.

3

Stephan:

Thanks for your prompt reply.
After the update of my NVIDIA Driver, and restart the cryoSPARC.
It seems like the 1st error I posted disappeared, and only the 2nd error still remained.

[CPU: 221.4 MB] 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/motioncorrection/run_patch.py”, line 402, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi AssertionError: Child process with PID 2086 has terminated unexpectedly!

best,
Yu

4

When I checked the GPU by “cryosparcw gpulist”
It shows as follows, but I can see my gpulist before the update the NVIDIA driver.

Traceback (most recent call last):
File “”, line 1, in
File “/home/yu/cryoSPARC/cryosparc_worker/bin/connect.py”, line 25, in print_gpu_list
cudrv.init()
pycuda._driver.LogicError: cuInit failed: system has unsupported display driver / cuda driver combination

5

Hi, @stephan:

After the error system has unsupported display driver / cuda driver combination, I checked GPU by nvidia-smi, it still feeds me an error: Failed to initialize NVML: Driver/library version mismatch.
And I adopted the advice: https://comzyh.com/blog/archives/967/
Finally, the patch motion correction completed successfully!

Thanks for your kindness!

Yu