Wrong generation counter error during particle extraction

Particle Picking
1

The user extracts From the Micrographs job with the following error


Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 93, in cryosparc_compute.run.main
  File "/Share/app/cryosparc/cryosparc2_worker/cryosparc_compute/jobs/extract/run.py", line 552, in run_extract_micrographs_multi
    retval = retqueue.get()
  File "/Share/app/cryosparc/cryosparc2_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/multiprocessing/queues.py", line 113, in get
    return _ForkingPickler.loads(res)
  File "/Share/app/cryosparc/cryosparc2_worker/cryosparc_tools/cryosparc/dataset.py", line 761, in __setstate__
    self.__init__(data, row_class=row_class)
  File "/Share/app/cryosparc/cryosparc2_worker/cryosparc_tools/cryosparc/dataset.py", line 638, in __init__
    self.add_fields([entry[0] for entry in populate])
  File "/Share/app/cryosparc/cryosparc2_worker/cryosparc_tools/cryosparc/dataset.py", line 933, in add_fields
    ), f"Could not add {field} with dtype {dt}"
AssertionError: Could not add ('uid', '<u8') with dtype uint64

log content in metadata

================= CRYOSPARCW =======  2022-12-20 16:18:23.937633  =========
Project P892 Job J255
Master alogin03 Port 39002
===========================================================================
========= monitor process now starting main process
MAINPROCESS PID 377245
========= monitor process now waiting for main process
MAIN PID 377245
extract.run cryosparc_compute.jobs.jobregister
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
***************************************************************
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
uid: invalid handle 562949953454080, wrong generation counter (given 1, expected 5) (errno 1: Operation not permitted)
add column: invalid handle 562949953454080, wrong generation counter (given 1, expected 5) (errno 1: Operation not permitted)
min: 157546.564789 max: 159822.435211
min: 10591.249069 max: 11006.555618
**** handle exception rc
set status to failed
========= main process now complete.
========= monitor process now complete.
2

@zhenyuanliu Does the job complete when the user attempts to restart the job?

3

Rerun cannot run successfully

4

A post was split to a new topic: “0 Particles” shown in UI for 2D classification job

5

How many micrographs did you connect to the particle extraction job?

6

Patch 221221 for CryoSPARC v4.1.1 addresses the “wrong generation counter” issue. Please see the guide for patch instructions.

7

Thank you. I’ve upgraded to the latest version and will let users test if the task works.