Child process with PID 29978 terminated unexpectedly with exit code 1

Install, Configure and Update
1

Hi I am new to linux and cryosparc and i was trying to run patch motion correction and ran into this error. I tried restarting cryosparc but do not seem to fix it. May i ask how to fix the error. The log message is shown below

[CPU: 258.3 MB Avail: 96.40 GB]
Child process with PID 30685 terminated unexpectedly with exit code 1.

[CPU: 259.0 MB Avail: 96.40 GB]
[‘uid’, ‘movie_blob/path’, ‘movie_blob/shape’, ‘movie_blob/psize_A’, ‘movie_blob/is_gain_corrected’, ‘movie_blob/format’, ‘movie_blob/has_defect_file’, ‘movie_blob/import_sig’, ‘micrograph_blob/path’, ‘micrograph_blob/idx’, ‘micrograph_blob/shape’, ‘micrograph_blob/psize_A’, ‘micrograph_blob/format’, ‘micrograph_blob/is_background_subtracted’, ‘micrograph_blob/vmin’, ‘micrograph_blob/vmax’, ‘micrograph_blob/import_sig’, ‘micrograph_blob_non_dw/path’, ‘micrograph_blob_non_dw/idx’, ‘micrograph_blob_non_dw/shape’, ‘micrograph_blob_non_dw/psize_A’, ‘micrograph_blob_non_dw/format’, ‘micrograph_blob_non_dw/is_background_subtracted’, ‘micrograph_blob_non_dw/vmin’, ‘micrograph_blob_non_dw/vmax’, ‘micrograph_blob_non_dw/import_sig’, ‘micrograph_blob_non_dw_AB/path’, ‘micrograph_blob_non_dw_AB/idx’, ‘micrograph_blob_non_dw_AB/shape’, ‘micrograph_blob_non_dw_AB/psize_A’, ‘micrograph_blob_non_dw_AB/format’, ‘micrograph_blob_non_dw_AB/is_background_subtracted’, ‘micrograph_blob_non_dw_AB/vmin’, ‘micrograph_blob_non_dw_AB/vmax’, ‘micrograph_blob_non_dw_AB/import_sig’, ‘micrograph_thumbnail_blob_1x/path’, ‘micrograph_thumbnail_blob_1x/idx’, ‘micrograph_thumbnail_blob_1x/shape’, ‘micrograph_thumbnail_blob_1x/format’, ‘micrograph_thumbnail_blob_1x/binfactor’, ‘micrograph_thumbnail_blob_1x/micrograph_path’, ‘micrograph_thumbnail_blob_1x/vmin’, ‘micrograph_thumbnail_blob_1x/vmax’, ‘micrograph_thumbnail_blob_2x/path’, ‘micrograph_thumbnail_blob_2x/idx’, ‘micrograph_thumbnail_blob_2x/shape’, ‘micrograph_thumbnail_blob_2x/format’, ‘micrograph_thumbnail_blob_2x/binfactor’, ‘micrograph_thumbnail_blob_2x/micrograph_path’, ‘micrograph_thumbnail_blob_2x/vmin’, ‘micrograph_thumbnail_blob_2x/vmax’, ‘background_blob/path’, ‘background_blob/idx’, ‘background_blob/binfactor’, ‘background_blob/shape’, ‘background_blob/psize_A’, ‘rigid_motion/type’, ‘rigid_motion/path’, ‘rigid_motion/idx’, ‘rigid_motion/frame_start’, ‘rigid_motion/frame_end’, ‘rigid_motion/zero_shift_frame’, ‘rigid_motion/psize_A’, ‘spline_motion/type’, ‘spline_motion/path’, ‘spline_motion/idx’, ‘spline_motion/frame_start’, ‘spline_motion/frame_end’, ‘spline_motion/zero_shift_frame’, ‘spline_motion/psize_A’]

2

Below is the job log if helpful

================= CRYOSPARCW ======= 2025-01-14 14:56:09.033942 =========
Project P2 Job J13
Master DESKTOP-TUBG805.localdomain Port 61002

MAIN PROCESS PID 30656
========= now starting main process at 2025-01-14 14:56:09.034274
motioncorrection.run_patch cryosparc_compute.jobs.jobregister
MONITOR PROCESS PID 30658
========= monitor process now waiting for main process
========= sending heartbeat at 2025-01-14 14:56:10.023354

Transparent hugepages setting: [always] madvise never

Running job on hostname %s DESKTOP-TUBG805.localdomain
Allocated Resources : {‘fixed’: {‘SSD’: False}, ‘hostname’: ‘DESKTOP-TUBG805.localdomain’, ‘lane’: ‘default’, ‘lane_type’: ‘node’, ‘license’: True, ‘licenses_acquired’: 1, ‘slots’: {‘CPU’: [0, 1, 2, 3, 4, 5], ‘GPU’: [0], ‘RAM’: [0, 1]}, ‘target’: {‘cache_path’: ‘/home/daredrylab/cryosparc_cache’, ‘cache_quota_mb’: None, ‘cache_reserve_mb’: 10000, ‘desc’: None, ‘gpus’: [{‘id’: 0, ‘mem’: 10736762880, ‘name’: ‘NVIDIA GeForce RTX 3080’}], ‘hostname’: ‘DESKTOP-TUBG805.localdomain’, ‘lane’: ‘default’, ‘monitor_port’: None, ‘name’: ‘DESKTOP-TUBG805.localdomain’, ‘resource_fixed’: {‘SSD’: True}, ‘resource_slots’: {‘CPU’: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35], ‘GPU’: [0], ‘RAM’: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]}, ‘ssh_str’: ‘daredrylab@DESKTOP-TUBG805.localdomain’, ‘title’: ‘Worker node DESKTOP-TUBG805.localdomain’, ‘type’: ‘node’, ‘worker_bin_path’: ‘/home/daredrylab/CryoSPARC/cryosparc_worker/bin/cryosparcw’}}
Process Process-1:
Traceback (most recent call last):
File “/home/daredrylab/CryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/multiprocessing/process.py”, line 314, in _bootstrap
self.run()
File “/home/daredrylab/CryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/multiprocessing/process.py”, line 108, in run
self._target(*self._args, **self._kwargs)
File “/home/daredrylab/CryoSPARC/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 199, in process_work_simple
process_setup(proc_idx) # do any setup you want on a per-process basis
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/run_patch.py”, line 116, in cryosparc_master.cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.process_setup
File “cryosparc_master/cryosparc_compute/gpu/gpucore.py”, line 30, in init cryosparc_master.cryosparc_compute.gpu.gpucore
File “/home/daredrylab/CryoSPARC/cryosparc_worker/cryosparc_compute/gpu/gpuarray.py”, line 18, in
from . import cryosparc_gpu
ImportError: /home/daredrylab/CryoSPARC/cryosparc_worker/cryosparc_compute/gpu/cryosparc_gpu.so: undefined symbol: cuMemFreeAsync
========= sending heartbeat at 2025-01-14 14:56:20.038091
========= sending heartbeat at 2025-01-14 14:56:30.053219
========= sending heartbeat at 2025-01-14 14:56:40.068098
/home/daredrylab/CryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3474: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
/home/daredrylab/CryoSPARC/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
========= sending heartbeat at 2025-01-14 14:56:50.082449
========= heartbeat failed at 2025-01-14 14:56:50.086559:
========= sending heartbeat at 2025-01-14 14:57:00.096775
========= heartbeat failed at 2025-01-14 14:57:00.100751:
========= sending heartbeat at 2025-01-14 14:57:10.110934
========= heartbeat failed at 2025-01-14 14:57:10.114991:
************* Connection to cryosparc command lost. Heartbeat failed 3 consecutive times at 2025-01-14 14:57:10.115074.
/home/daredrylab/CryoSPARC/cryosparc_worker/bin/cryosparcw: line 153: 30656 Killed python -c “import cryosparc_compute.run as run; run.run()” “$@”

3

Can you provide some more information about your system, and how you’re running CryoSPARC? because

looks like it’s a Windows PC.
But then

Looks like Linux.
Are you running in WSL2?
But the reason it’s failing is it’s losing the command process for some reason.

WSL2 doesn’t stay running if you log out, for example.
But I may be way off base here…

4

Hi, I am running on a windows PC but running using WSL2 on MobaXterm for CryoSPARC.
I am not sure if this below is part of the error as well?
ImportError: /home/daredrylab/CryoSPARC/cryosparc_worker/cryosparc_compute/gpu/cryosparc_gpu.so: undefined symbol: cuMemFreeAsync

5

CryoSPARC is not supported on WSL. Baremetal Linux only. A few people have tried to get it working on WSL(2),at different times and releases and with mixed success, but it’s basically a mix of “good luck” and “here be dragons” with no guarantees. A 10GB GPU is almost certainly going to struggle, as Windows itself occupies a fair chunk of VRAM sitting there doing nothing.

See also the following: