Curl command dependency

Install, Configure and Update
1

while trying to run the install.sh it asks for a dependency of curl command, in my remote machine I dont have the access to install the curl command is there a wayaround

2

Can you ask the sysadmin to install it? Out of curiosity, what is the output of the command
cat /etc/*release?

3

I modifies the install.sh and removed that block of code which is asking for “curl” the install process was started untill I encountered could not get databse error

4

after trying again I am getting the following error
Please ensure cryosparc_master/config.sh and cryoparc_worker/config.sh have the same CRYOSPARC_LICENSE_ID entry
or CRYOSPARC_LICENSE_ID is set correctly in the current environment.
See CryoSPARC Architecture and System Requirements | CryoSPARC Guide for more details.

5

CryoSPARC is running.
Stopping cryoSPARC
Shut down
Starting CryoSPARC System master process…
CryoSPARC is not already running.
configuring database…
Warning: Could not get database status (attempt 1/3)
Warning: Could not get database status (attempt 2/3)
Warning: Could not get database status (attempt 3/3)
Traceback (most recent call last):
File “”, line 1, in
File “/local/scratch/v_shourya_aggarwal/cryosparc/cryosparc_master/cryosparc_compute/database_management.py”, line 47, in configure_mongo
initialize_replica_set()
File “/local/scratch/v_shourya_aggarwal/cryosparc/cryosparc_master/cryosparc_compute/database_management.py”, line 84, in initialize_replica_set
admin_db = try_get_pymongo_db(mongo_client)
File “/local/scratch/v_shourya_aggarwal/cryosparc/cryosparc_master/cryosparc_compute/database_management.py”, line 251, in try_get_pymongo_db
admin_db.command(({‘serverStatus’: 1}))
File “/local/scratch/v_shourya_aggarwal/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/_csot.py”, line 108, in csot_wrapper
return func(self, args, kwargs)
File “/local/scratch/v_shourya_aggarwal/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/database.py”, line 893, in command
with self.__client._conn_for_reads(read_preference, session, operation=command_name) as (
File “/local/scratch/v_shourya_aggarwal/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/mongo_client.py”, line 1375, in _conn_for_reads
server = self._select_server(read_preference, session, operation)
File “/local/scratch/v_shourya_aggarwal/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/mongo_client.py”, line 1322, in _select_server
server = topology.select_server(
File “/local/scratch/v_shourya_aggarwal/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/topology.py”, line 368, in select_server
server = self._select_server(
File “/local/scratch/v_shourya_aggarwal/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/topology.py”, line 346, in _select_server
servers = self.select_servers(
File “/local/scratch/v_shourya_aggarwal/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/topology.py”, line 253, in select_servers
server_descriptions = self._select_servers_loop(
File “/local/scratch/v_shourya_aggarwal/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/topology.py”, line 303, in _select_servers_loop
raise ServerSelectionTimeoutError(
pymongo.errors.ServerSelectionTimeoutError: localhost:61001: [Errno 111] Connection refused (configured timeouts: socketTimeoutMS: 20000.0ms, connectTimeoutMS: 20000.0ms), Timeout: 20.0s, Topology Description: <TopologyDescription id: 671bac9e2844e539bae02354, topology_type: Single, servers: [<ServerDescription (‘localhost’, 61001) server_type: Unknown, rtt: None, error=AutoReconnect(‘localhost:61001: [Errno 111] Connection refused (configured timeouts: socketTimeoutMS: 20000.0ms, connectTimeoutMS: 20000.0ms)’)>]>
[2024-10-25T14:36:21+00:00] Error configuring database. Most recent database log lines:
2024-10-25T14:35:07.580+0000 I CONTROL [initandlisten] allocator: tcmalloc
2024-10-25T14:35:07.580+0000 I CONTROL [initandlisten] modules: none
2024-10-25T14:35:07.580+0000 I CONTROL [initandlisten] build environment:
2024-10-25T14:35:07.580+0000 I CONTROL [initandlisten] distarch: x86_64
2024-10-25T14:35:07.580+0000 I CONTROL [initandlisten] target_arch: x86_64
2024-10-25T14:35:07.580+0000 I CONTROL [initandlisten] 506880 MB of memory available to the process out of 515765 MB total system memory
2024-10-25T14:35:07.580+0000 I CONTROL [initandlisten] options: { net: { port: 61001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/local/scratch/v_shourya_aggarwal/cryosparc/cryosparc_database” } }
2024-10-25T14:35:07.580+0000 E NETWORK [initandlisten] Failed to unlink socket file /tmp/mongodb-61001.sock Operation not permitted
2024-10-25T14:35:07.580+0000 F - [initandlisten] Fatal Assertion 40486 at src/mongo/transport/transport_layer_asio.cpp 182
2024-10-25T14:35:07.580+0000 F - [initandlisten] \n\naborting after fassert() failure\n\n

6

Doing so may leave the installed software in a state that is undefined and hard to support.
Please let us know when you have installed the software with an unmodified cryosparc_master/install.sh script.

7

curl is used to download libraries in the installation process as I understand. By removing it, many necessary libraries was not installed.

If you don’t have sudo permission, you can install curl to a non /usr/bin path by " ./configure --prefix=/any/path/you/want". Then add that to you own bin path or make it a lmod module. That’s how I work around it before.

8