Patch 210216 available for v3.1.0 - Fixes CPU extraction bug and Patch CTF bug

Install, Configure and Update
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February 16, 2021: Patch 210216 is out for v3.1.0.

Release notes:

To apply this patch, please follow the instructions available here: Apply Patches

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Hi all, I am still having what I think is the same issue with patch ctf after applying the patch per your instructions. I am using super-resolution images from a K3 camera. Am I just exhausting gpu memory or something?
Thanks,
Eric Gibbs

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Hi @edg42,
Can you please copy+paste the full text of the traceback? It’s cut off in the screenshot. Thanks!

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[CPU: 241.5 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/ctf_estimation/run.py”, line 256, in cryosparc_compute.jobs.ctf_estimation.run.run
AssertionError: Child process with PID 147843 has terminated unexpectedly!

[CPU: 819.4 MB] Traceback (most recent call last):
File “/home/edg42/bin/cryosparc6/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 1726, in run_with_except_hook
run_old(*args, **kw)
File “/home/edg42/bin/cryosparc6/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/edg42/bin/cryosparc6/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 186, in thread_work
work = processor.exec(item)
File “/home/edg42/bin/cryosparc6/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 43, in exec
return self.process(item)
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py”, line 209, in cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
AssertionError: Job is not in running state - worker thread with PID 147842 terminating self.

[CPU: 823.3 MB] Traceback (most recent call last):
File “/home/edg42/bin/cryosparc6/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 1726, in run_with_except_hook
run_old(*args, **kw)
File “/home/edg42/bin/cryosparc6/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/edg42/bin/cryosparc6/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 186, in thread_work
work = processor.exec(item)
File “/home/edg42/bin/cryosparc6/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 43, in exec
return self.process(item)
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py”, line 209, in cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
AssertionError: Job is not in running state - worker thread with PID 147844 terminating self.

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Hi @edg42,

I imagine you’ve tried this by now (sorry for the slow reply!) but you should be able to circumvent this issue just by clearing the job and running it again. if it crashes again, please post the job log so we can take a look at why its crashing.

–Harris