Hello!
I am running the latest version V4.1.2. of CryoSparc on the MRC LMB cluster.
Linux hal.lmb.internal 4.18.0-425.3.1.el8.x86_64 #1 SMP Tue Nov 8 14:08:25 EST 2022 x86_64 x86_64 x86_64 GNU/Linux
total used free shared buff/cache available
Mem: 3022 496 998 0 1527 2511
Swap: 3 0 3
Several days ago, I started noticing considerable web interface lags. Some of the functions are available (browsing projects, running queued jobs), but very often new jobs are not showing, I can’t build new ones, and deleted jobs are not being removed. Sometimes, it randomly works, but all actions are very slow.
E.g.:
2023-01-27 14:31:06,247 COMMAND.CORE run INFO | Received task layout_tree with 4 args and 0 kwargs
2023-01-27 14:32:34,381 COMMAND.CORE run INFO | Completed task in 88.13398480415344 seconds
This warning always shows up in :
2023-01-27 13:14:15,092 COMMAND.CORE run WARNING | Insecure mode - no SSL for external requests
Neither an update from 4.1.1 to 4.1.2 nor cryosparcm restart doesn't help.
In addition, 2D classification and Non-Uniform refinement both keep failing. It might be a separate problem.(?) The error messages are:
Traceback (most recent call last):
File "cryosparc_master/cryosparc_compute/run.py", line 96, in cryosparc_compute.run.main
File "cryosparc_master/cryosparc_compute/jobs/refine/newrun.py", line 125, in cryosparc_compute.jobs.refine.newrun.run_homo_refine
File "/lmb/home/agusach/software/cryosparc_worker/cryosparc_compute/particles.py", line 114, in read_blobs
u_blob_paths = cache.download_and_return_cache_paths(u_rel_paths)
File "/lmb/home/agusach/software/cryosparc_worker/cryosparc_compute/jobs/cache.py", line 119, in download_and_return_cache_paths
compressed_keys = rc.cli.cache_request_check(worker_hostname, rc._project_uid, rc._job_uid, com.compress_paths(rel_paths))
File "/lmb/home/agusach/software/cryosparc_worker/cryosparc_tools/cryosparc/command.py", line 104, in func
with make_json_request(self, "/api", data=data) as request:
File "/lmb/home/agusach/software/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/contextlib.py", line 113, in __enter__
return next(self.gen)
File "/lmb/home/agusach/software/cryosparc_worker/cryosparc_tools/cryosparc/command.py", line 165, in make_request
with urlopen(request, timeout=client._timeout) as response:
File "/lmb/home/agusach/software/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/lmb/home/agusach/software/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/lmb/home/agusach/software/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/urllib/request.py", line 542, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/lmb/home/agusach/software/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/urllib/request.py", line 502, in _call_chain
result = func(*args)
File "/lmb/home/agusach/software/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/urllib/request.py", line 1383, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/lmb/home/agusach/software/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/urllib/request.py", line 1358, in do_open
r = h.getresponse()
File "/lmb/home/agusach/software/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/http/client.py", line 1348, in getresponse
response.begin()
File "/lmb/home/agusach/software/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/http/client.py", line 316, in begin
version, status, reason = self._read_status()
File "/lmb/home/agusach/software/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/http/client.py", line 277, in _read_status
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
File "/lmb/home/agusach/software/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/socket.py", line 669, in readinto
return self._sock.recv_into(b)
socket.timeout: timed out
Sorry for so many problems.
Thanks!
Anastasia