Hello,
We have been having periodic job failures with ServerSelectTimeOutError recently. I have been working with our IT staff, but they have not been able to identify the cause.
Our CryoSPARC (4.7.1) is running on an HPC (Red Hat Linux 9.4).
The following error is from a 2D classification job, but the error has occurred on many job types. Any help troubleshooting this error would be greatly appreciated.
[2025-08-26 13:20:54.27]
[CPU: 5.08 GB]
Traceback (most recent call last):
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/cryosparc_compute/jobs/runcommon.py", line 2306, in run_with_except_hook
run_old(*args, **kw)
File "cryosparc_master/cryosparc_compute/gpu/gpucore.py", line 136, in cryosparc_master.cryosparc_compute.gpu.gpucore.GPUThread.run
File "cryosparc_master/cryosparc_compute/gpu/gpucore.py", line 137, in cryosparc_master.cryosparc_compute.gpu.gpucore.GPUThread.run
File "cryosparc_master/cryosparc_compute/jobs/class2D/newrun.py", line 670, in cryosparc_master.cryosparc_compute.jobs.class2D.newrun.class2D_engine_run.work
File "cryosparc_master/cryosparc_compute/jobs/class2D/newrun.py", line 232, in cryosparc_master.cryosparc_compute.jobs.class2D.newrun.run_class_2D.progress
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/cryosparc_compute/jobs/runcommon.py", line 1826, in update_event_text
db['events'].update_one({'_id':event_id},
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/collection.py", line 1077, in update_one
self._update_retryable(
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/collection.py", line 872, in _update_retryable
return self.__database.client._retryable_write(
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/mongo_client.py", line 1575, in _retryable_write
return self._retry_with_session(retryable, func, s, bulk, operation, operation_id)
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/mongo_client.py", line 1461, in _retry_with_session
return self._retry_internal(
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/_csot.py", line 108, in csot_wrapper
return func(self, *args, **kwargs)
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/mongo_client.py", line 1507, in _retry_internal
).run()
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/mongo_client.py", line 2353, in run
return self._read() if self._is_read else self._write()
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/mongo_client.py", line 2456, in _write
self._server = self._get_server()
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/mongo_client.py", line 2439, in _get_server
return self._client._select_server(
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/mongo_client.py", line 1322, in _select_server
server = topology.select_server(
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/topology.py", line 368, in select_server
server = self._select_server(
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/topology.py", line 346, in _select_server
servers = self.select_servers(
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/topology.py", line 253, in select_servers
server_descriptions = self._select_servers_loop(
File "/home/exacloud/gscratch/reichowlab/local/cryosparc/reichow-cs2.ohsu.edu/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/pymongo/topology.py", line 303, in _select_servers_loop
raise ServerSelectionTimeoutError(
pymongo.errors.ServerSelectionTimeoutError: reichow-cs2.ohsu.edu:61001: timed out (configured timeouts: socketTimeoutMS: 20000.0ms, connectTimeoutMS: 20000.0ms), Timeout: 30.0s, Topology Description: <TopologyDescription id: 68ae13dc5334b0f9ab8a00bb, topology_type: Single, servers: [<ServerDescription ('reichow-cs2.ohsu.edu', 61001) server_type: Unknown, rtt: None, error=NetworkTimeout('reichow-cs2.ohsu.edu:61001: timed out (configured timeouts: socketTimeoutMS: 20000.0ms, connectTimeoutMS: 20000.0ms)')>]>