Greetings,
I’m having trouble setting up CryoSPARC using a database from a previous setup. My goal is to transfer the projects and database from our previous CryoSPARC setup to this new setup
We received a desktop with CryoSPARC v5.0.6 installed. The previous CryoSPARC setup we have uses v4.2.1 and has a separate LICENSE_ID from the desktop. I copied over our old database to this desktop and set it to use this database. I started CryoSPARC using “cryosparcm start” but have been getting various error messages related to the database and MongoDB
I’m not sure how to proceed. I’ve been following the instructions here:
Changing CRYOSPARC_BASE_PORT from 61000 to 39000 fixed one issue but currently I’m not able to get CryoSPARC to run. Here are some of the errors I’m getting; any help would be appreciated:
cryosparc_user@sn4622129907:~/software/cryosparc/cryosparc_master$ cryosparcm start
Starting CryoSPARC master services…
CryoSPARC is not already running.
Configuring database… OK
database: started
Checking database… OK
cache: started
✓ cache connection succeeded
✕ CSModelException: Failed to validate lane with name highmem-slurm-lane
cryosparc_user@sn4622129907:~/software/cryosparc/cryosparc_master$ cryosparcm status
────────────────────────────────────────────────────────────────────────────────────────────────
CryoSPARC System master node installed at
/home/cryosparc_user/software/cryosparc/cryosparc_master
Current CryoSPARC version: v5.0.6
────────────────────────────────────────────────────────────────────────────────────────────────
CryoSPARC process status:
api:0 STOPPED Not started
api:1 STOPPED Not started
api:2 STOPPED Not started
app STOPPED Not started
app_api STOPPED Not started
cache RUNNING pid 23002, uptime 0:00:05
command_vis STOPPED Not started
database RUNNING pid 22942, uptime 0:00:07
scheduler STOPPED Not started
────────────────────────────────────────────────────────────────────────────────────────────────
✓ License is valid
────────────────────────────────────────────────────────────────────────────────────────────────
global config variables:
export CRYOSPARC_LICENSE_ID=“ff0e28c8-4280-11f1-b3f0-87bc7c4d33fd”
export CRYOSPARC_MASTER_HOSTNAME=“sn4622129907”
export CRYOSPARC_DB_PATH=“/home/cryosparc_user/software/cryosparc/cryosparc_database”
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DB_CONNECTION_TIMEOUT_MS=20000
export CRYOSPARC_INSECURE=false
export CRYOSPARC_DB_ENABLE_AUTH=true
export CRYOSPARC_PROJECT_DIR_PREFIX=‘CS-’
export CRYOSPARC_CLICK_WRAP=true
cryosparc_user@sn4622129907:~/software/cryosparc/cryosparc_master$ cryosparcm start
Starting CryoSPARC master services…
CryoSPARC is not already running.
Configuring database… OK
database: started
Checking database… OK
cache: started
✓ cache connection succeeded
✕ CSModelException: Failed to validate lane with name highmem-slurm-lane
cryosparc_user@sn4622129907:~/software/cryosparc/cryosparc_master$ cryosparcm cli “get_scheduler_targets()”
/home/cryosparc_user/software/cryosparc/cryosparc_master/tools/cryosparc/api.py:195: UserWarning: *** API client GET /openapi.json failed due to [Errno 111] Connection refused (attempt 1/3)
warnings.warn(
/home/cryosparc_user/software/cryosparc/cryosparc_master/tools/cryosparc/api.py:195: UserWarning: *** API client GET /openapi.json failed due to [Errno 111] Connection refused (attempt 2/3)
warnings.warn(
/home/cryosparc_user/software/cryosparc/cryosparc_master/tools/cryosparc/api.py:195: UserWarning: *** API client GET /openapi.json failed due to [Errno 111] Connection refused (attempt 3/3)
warnings.warn(
Traceback (most recent call last):
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpx/_transports/default.py”, line 101, in map_httpcore_exceptions
yield
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpx/_transports/default.py”, line 250, in handle_request
resp = self._pool.handle_request(req)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpcore/_sync/connection_pool.py”, line 256, in handle_request
raise exc from None
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpcore/_sync/connection_pool.py”, line 236, in handle_request
response = connection.handle_request(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpcore/_sync/connection.py”, line 101, in handle_request
raise exc
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpcore/_sync/connection.py”, line 78, in handle_request
stream = self._connect(request)
^^^^^^^^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpcore/_sync/connection.py”, line 124, in _connect
stream = self._network_backend.connect_tcp(**kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpcore/_backends/sync.py”, line 207, in connect_tcp
with map_exceptions(exc_map):
^^^^^^^^^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/contextlib.py”, line 158, in exit
self.gen.throw(value)
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpcore/_exceptions.py”, line 14, in map_exceptions
raise to_exc(exc) from exc
httpcore.ConnectError: [Errno 111] Connection refused
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File “”, line 198, in _run_module_as_main
File “”, line 88, in _run_code
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/cli/setup_client.py”, line 16, in
api = APIClient(
^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/tools/cryosparc/api.py”, line 266, in init
self(auth=auth) # query the OpenAPI server and populate endpoint functions
^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/tools/cryosparc/api.py”, line 280, in call
with self._request(“get”, “/openapi.json”) as res:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/contextlib.py”, line 137, in enter
return next(self.gen)
^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/tools/cryosparc/api.py”, line 191, in _request
request = self._client.request(method, url, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpx/_client.py”, line 825, in request
return self.send(request, auth=auth, follow_redirects=follow_redirects)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpx/_client.py”, line 914, in send
response = self._send_handling_auth(
^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpx/_client.py”, line 942, in _send_handling_auth
response = self._send_handling_redirects(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpx/_client.py”, line 979, in _send_handling_redirects
response = self._send_single_request(request)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpx/_client.py”, line 1014, in _send_single_request
response = transport.handle_request(request)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpx/_transports/default.py”, line 249, in handle_request
with map_httpcore_exceptions():
^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/contextlib.py”, line 158, in exit
self.gen.throw(value)
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpx/_transports/default.py”, line 118, in map_httpcore_exceptions
raise mapped_exc(message) from exc
httpx.ConnectError: [Errno 111] Connection refused
cryosparc_user@sn4622129907:~/software/cryosparc/cryosparc_master$