Installation problems about Cryosparc2.11

I face the problem about installation of Cryosparc2.11. Look at the following:

[fanhc@Purple cryosparc2_master]$ ./ --standalone --license $LICENSE_ID --worker_path /home/fanhc/cryosparc/cryosparc2_worker/ --cudapath /usr/local/cuda-8.0 --initial_email xxxx --initial_password xxxx--initial_name xxxx --nossd 
************ CRYOSPARC SYSTEM: MASTER INSTALLER **************

 Installation Settings:
   License ID              : xxxx
   Root Directory          : /home/fanhc/cryosparc/cryosparc2_master
   Master Hostname         : Purple
   Database Directory      : /home/fanhc/cryosparc/cryosparc2_database
   Base HTTP Port Number   : 39000
   Developer Install       : false
   Operating System        : Linux
   Insecure Install        : false
   Standalone Install      : true
   Worker Root Directory   : /home/fanhc/cryosparc/cryosparc2_worker/
   Initial User Email      : xxxx
   Initial User Password   : xxxx
   Initial User Name       : xxxx
   CUDA Path               : /usr/local/cuda-8.0
   SSD                     : false
   Version                 : v2.11.0


The cryoSPARC System master installation will host a database, 
web application, and command layer for cryoSPARC, but will not 
perform processing jobs. 

Please read and confirm the above settings. The cryoSPARC database
will be stored at the database directory which is relative to the
root directory, unless provided as an absolute path.
You can change the database directory now by passing the --dbapth
parameter to this installer, or later via the command line.

Are the above settings correct?
1) Yes
2) No
#? 1


 Setting up hard-coded environment variables


 Installing all dependencies.

  Checking dependencies... 
  Dependencies for python have not changed.
  Currently checking hash for mongodb
  Dependencies for mongodb have not changed.
  Completed dependency check. 


 CryoSPARC System master has now been installed. 
 Add bin directory to your ~/.bashrc ?
1) Yes
2) No
#? 1

 The following lines were appended to your ~/.bashrc:
  export PATH=/home/fanhc/cryosparc/cryosparc2_master/bin:$PATH


  The installer will now download, install and connect the worker
  package on this machine. The worker package will allow cryoSPARC
  to run compute jobs.


 Starting cryoSPARC...

Starting cryoSPARC System master process..
CryoSPARC is already running.
If you would like to restart, use cryosparcm restart


 Creating the initial cryoSPARC user...

Creating user xxxx with email: xxxx password: xxxx
*** command (http://Purple:39002/api) did not reply within timeout of 300 seconds, attempt 1 of 3
*** command (http://Purple:39002/api) did not reply within timeout of 300 seconds, attempt 2 of 3
*** command (http://Purple:39002/api) did not reply within timeout of 300 seconds, attempt 3 of 3
Traceback (most recent call last):
  File "/home/fanhc/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/fanhc/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/", line 72, in _run_code
    exec code in run_globals
  File "/home/fanhc/cryosparc/cryosparc2_master/cryosparc2_compute/", line 82, in <module>
    cli = CommandClient(host, int(port))
  File "/home/fanhc/cryosparc/cryosparc2_master/cryosparc2_compute/", line 33, in __init__
  File "/home/fanhc/cryosparc/cryosparc2_master/cryosparc2_compute/", line 61, in _reload
    system = self._get_callable('system.describe')()
  File "/home/fanhc/cryosparc/cryosparc2_master/cryosparc2_compute/", line 49, in func
    r =, data = json.dumps(data, cls=NumpyEncoder), headers = header, timeout=self.timeout)
  File "/home/fanhc/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/", line 116, in post
    return request('post', url, data=data, json=json, **kwargs)
  File "/home/fanhc/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/", line 60, in request
    return session.request(method=method, url=url, **kwargs)
  File "/home/fanhc/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/", line 533, in request
    resp = self.send(prep, **send_kwargs)
  File "/home/fanhc/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/", line 646, in send
    r = adapter.send(request, **kwargs)
  File "/home/fanhc/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/", line 516, in send
    raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPConnectionPool(host='purple', port=39002): Max retries exceeded with url: /api (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f65a3491990>: Failed to establish a new connection: [Errno 111] Connection refused',))
[fanhc@Purple cryosparc2_master]$

How to solve it? Thank you

Hi @Peter,

Is this a brand new install, or an update?

This is a reinstall in my workstation. I deleted the earlier verion cryosparc 2.05 including cryosparc2_master, cryosparc2_worker and cryosparc2_database. Then I download the latest version in the website and reinstalled according to the mannual. I guess maybe it’s due to the web port is still be used? If it’s this, How to release port?

Hi @Peter,

You have to make sure cryoSPARC is fully turned off by killing any related processes.

cryosparcm stop

ps -ax | grep “supervisord” (kill only the process that is running from your cryosparc2 install)
ps -ax | grep “cryosparc2_command” (kill all the matching processes related to your cryosparc2 instance)
ps -ax | grep “mongod” (kill only the process running your cryosparc2 database)

e.g. kill 82681 

Thank you so much! The problem has been fixed according to your advice.:smiley: