CryoSPARC Fails to start: CommandClient could not get license verification status

Troubleshooting
1

I installed stand-alone cryosparc and after running “cryosparcm start” it stops at “command_core: started” and stays like that for at least 1 hour. I tried cryosparcm status and if the connection is ok and the license and can’t figure out where is the problem. Below is the output.

[ ]$ cryosparcm status

CryoSPARC System master node installed at
//cryoSPARC/cryosparc_master
Current cryoSPARC version: v4.2.0

CryoSPARC process status:

app STOPPED Not started
app_api STOPPED Not started
app_api_dev STOPPED Not started
app_legacy STOPPED Not started
app_legacy_dev STOPPED Not started
command_core STARTING
command_rtp STOPPED Not started
command_vis STOPPED Not started
database RUNNING pid 3443280, uptime 0:02:44

*** CommandClient: (http://“login-node.bullx”:<port_number>/api) URL Error [Errno 111] Connection refused
An error ocurred while checking license status
Could not get license verification status. Are all CryoSPARC processes RUNNING?

[]$ curl https://get.cryosparc.com/checklicenseexists/$LICENSE_ID
{“success”: true}

[]$ curl https://get.cryosparc.com
{“message”:“Missing Authentication Token”}

2

Welcome to the forum @zlpl.
What are the outputs of the following commands (on the CryoSPARC master host):

host login-node.bullx
curl login-node.bullx:<port_number>
curl 127.0.0.1:<port_number>
3

Hi @wtempel . Thank you.

The outputs are:

[]$ host my-login-node.bullx
my-login-node.bullx has address xx.xx.xx.xx

[]$ curl xx.xx.xx.xx:<port_number>
curl: (7) Failed to connect to xx.xx.xx.xx port <port_number>: Connection refused

[]$ curl my-login-node.bullx:<port_number>
curl: (7) Failed to connect to my-login-node.bullx port <port_number>: Connection refused

I run this from my login node which I accessed with ssh.

4

Please also let us know the output of
curl 127.0.0.1:<port_number>
and the offset (“0”, “+1” or “+2”, etc.) of <port_number> from CRYOSPARC_BASE_PORT (the port number in the url of the CryoSPARC web interface).

5

@wtempel

[]$ curl 127.0.0.1:40600
curl: (7) Failed to connect to 127.0.0.1 port 40600: Connection refused

[]$ curl 127.0.0.1:40601
curl: (7) Failed to connect to 127.0.0.1 port 40601: Connection refused

[]$ curl 127.0.0.1:40602
curl: (7) Failed to connect to 127.0.0.1 port 40602: Connection refused

[]$ curl 127.0.0.1:40603
curl: (7) Failed to connect to 127.0.0.1 port 40603: Connection refused

[]$ curl 127.0.0.1:40604
curl: (7) Failed to connect to 127.0.0.1 port 40604: Connection refused

[]$ curl 127.0.0.1:40605
curl: (7) Failed to connect to 127.0.0.1 port 40605: Connection refused

[]$ curl 127.0.0.1:40606
It looks like you are trying to access MongoDB over HTTP on the native driver port.

[]$ curl 127.0.0.1:40607
Forbidden.

[]$ curl 127.0.0.1:40608
curl: (7) Failed to connect to 127.0.0.1 port 40608: Connection refused

[]$ curl 127.0.0.1:40609
curl: (7) Failed to connect to 127.0.0.1 port 40609: Connection refused

[]$ curl 127.0.0.1:40610
curl: (7) Failed to connect to 127.0.0.1 port 40610: Connection refused

6

Was it your intention to access the CryoSPARC web interface at
http://<hostname>:46000 or http://<hostname>:46005?
What is the output of (execute under the Linux account that runs the CryoSPARC instance)

ps x | grep -e cryosparc -e mongo

?

7

During installation I used 40605 port number. And after that I can’t even start cryosparc to create the first user.

$ ps x | grep -e cryosparc -e mongo
2120488 pts/40   S+     0:00 bash //cryoSPARC/cryosparc_master/bin/cryosparcm start
2123549 ?        Ss     0:00 python //cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c //cryoSPARC/cryosparc_master/supervisord.conf
2124510 ?        Sl     0:01 mongod --auth --dbpath //cryoSPARC_database/ --port 40606 --oplogSize 64 --replSet meteor --nojournal --wiredTigerCacheSizeGB 4 --bind_ip_all
2141636 ?        R      0:00 python -c import cryosparc_command.command_core as serv; serv.start(port=40607)
2141661 pts/415  S+     0:00 grep --color=auto -e cryosparc -e mongo
8

Given the installation with port 40605, the expected output should be:

$ curl 127.0.0.1:40607
Hello World from cryosparc command core.

Please eliminate the following potential impediments:

  1. The command_core process encountered an error. Please inspect the output of
    cryosparcm log command_core for errors.
  2. Another process is using port 40607. What is the output of:
    sudo ss -nap | grep 40607
  3. (Unlikely, given the 127.0.0.1 address) A firewall is blocking access to port 40607.
9

Hi. Thank you for the help @wtempel . I solved the issue. It was to do with access permissions and forwarding to the supercomputer where I installed cryoSPARC.

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