A problem with importing particles

Import and Export
1

Hi all,
I seem to be having a problem with importing particles.
I followed the instructions to install cryoSPARC v2 on a single workstation.

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_worker/cryosparc2_compute/jobs/class2D/run.py”, line 64, in cryosparc2_compute.jobs.class2D.run.run_class_2D
File “cryosparc2_compute/particles.py”, line 65, in read_blobs
u_blob_paths = cache.download_and_return_cache_paths(u_rel_paths)
File “cryosparc2_compute/jobs/cache.py”, line 113, in download_and_return_cache_paths
used_mb = sync_hits(worker_hostname, ssd_cache_path, instance_id)
File “cryosparc2_compute/jobs/cache.py”, line 190, in sync_hits
rc.cli.cache_sync_hits(worker_hostname, keys, sizes_mb)
File “cryosparc2_compute/client.py”, line 28, in func
r = requests.post(self.url, json = data, headers = header, timeout=self.timeout)
File “/opt2/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/requests/api.py”, line 112, in post
return request(‘post’, url, data=data, json=json, **kwargs)
File “/opt2/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/requests/api.py”, line 58, in request
return session.request(method=method, url=url, **kwargs)
File “/opt2/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/requests/sessions.py”, line 508, in request
resp = self.send(prep, **send_kwargs)
File “/opt2/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/requests/sessions.py”, line 618, in send
r = adapter.send(request, **kwargs)
File “/opt2/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/requests/adapters.py”, line 521, in send
raise ReadTimeout(e, request=request)
ReadTimeout: HTTPConnectionPool(host=‘gnode1’, port=38002): Read timed out. (read timeout=120)

2

To be specific, an initial joblog check indicated a python package version incompatibility between “requests” and “urllib3”. We then updated them both through pip install, in both master and worker directory. Then it still didn’t work and the only hint was what hello_helios put above. We have tried adding ssh-key, disabling SELinux and firewall, but all failed. We could now only disabling the SSD caching process when submitting jobs, which dramaticallly slowed down all the calculations. Could anyone give us some hint?
Current cryoSPARC version: v2.4.0
export “CRYOSPARC_HTTP_PORT=38000”
export “CRYOSPARC_MASTER_HOSTNAME=gnode1”
export “CRYOSPARC_COMMAND_VIS_PORT=38003”
export “CRYOSPARC_MONGO_PORT=38001”
export “CRYOSPARC_COMMAND_PROXY_PORT=38004”
export “CRYOSPARC_COMMAND_CORE_PORT=38002”
export “CRYOSPARC_BASE_PORT=38000”
export “CRYOSPARC_SUPERVISOR_SOCK_FILE=/tmp/cryosparc-supervisor-b8ec582168ba8950d16946faf36bfa86.sock”