Cryosparc V2 hangs during startup

closed

#1

I am trying to install cryosparc v2 as a single workstation following the instructions provided. After installing the master without issues, when I first try to start it it hangs as follows:

cryosparc_user@bs-zorro01:~/cryosparc2_master$ cryosparcm start
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
command_core: started

And nothing happens after that for… ever. if I hit Ctrl+C and try to proceed with the installation instructions (create user), I get this error:

Traceback (most recent call last):
  File "/home/cryosparc_user/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/cryosparc_user/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/cryosparc_user/cryosparc2_master/cryosparc2_compute/client.py", line 56, in <module>
    cli = CommandClient(host, int(port))
  File "/home/cryosparc_user/cryosparc2_master/cryosparc2_compute/client.py", line 17, in __init__
    self._reload()
  File "/home/cryosparc_user/cryosparc2_master/cryosparc2_compute/client.py", line 35, in _reload
    system = self._get_callable('system.describe')()
  File "/home/cryosparc_user/cryosparc2_master/cryosparc2_compute/client.py", line 28, in func
    r = requests.post(self.url, json = data, headers = header, timeout=self.timeout)
  File "/home/cryosparc_user/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/api.py", line 112, in post
    return request('post', url, data=data, json=json, **kwargs)
  File "/home/cryosparc_user/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/api.py", line 58, in request
    return session.request(method=method, url=url, **kwargs)
  File "/home/cryosparc_user/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/sessions.py", line 508, in request
    resp = self.send(prep, **send_kwargs)
  File "/home/cryosparc_user/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/sessions.py", line 618, in send
    r = adapter.send(request, **kwargs)
  File "/home/cryosparc_user/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/adapters.py", line 508, in send
    raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPConnectionPool(host='bs-zorro01', port=39002): Max retries exceeded with url: /api (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f5eb7a70050>: Failed to establish a new connection: [Errno 111] Connection refused',))

The OS is Ubuntu 16.04.2 LTS. How can I get cryosparc V2 to start?

Thank you!


#3

I encountered similar problem as rdrighetto. After installing the master program, when I first start it it hangs after it started command_core. Then I hit Ctrl+C and proceed with the next step and got the error message:

If this is incorrect, you should re-run this command with the flag --sshstr <ssh string>
 ---------------------------------------------------------------
Traceback (most recent call last):
  File "bin/connect.py", line 57, in <module>
    cli = client.CommandClient(host=master_hostname, port=command_core_port)
  File "/opt/bioSoft/cryosparc-2.0/cryosparc2_worker/cryosparc2_compute/client.py", line 17, in __init__
    self._reload()
  File "/opt/bioSoft/cryosparc-2.0/cryosparc2_worker/cryosparc2_compute/client.py", line 35, in _reload
    system = self._get_callable('system.describe')()
  File "/opt/bioSoft/cryosparc-2.0/cryosparc2_worker/cryosparc2_compute/client.py", line 28, in func
    r = requests.post(self.url, json = data, headers = header, timeout=self.timeout)
  File "/opt/bioSoft/cryosparc-2.0/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 "/opt/bioSoft/cryosparc-2.0/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 "/opt/bioSoft/cryosparc-2.0/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/requests/sessions.py", line 508, in request
    resp = self.send(prep, **send_kwargs)
  File "/opt/bioSoft/cryosparc-2.0/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/requests/sessions.py", line 618, in send
    r = adapter.send(request, **kwargs)
  File "/opt/bioSoft/cryosparc-2.0/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/requests/adapters.py", line 508, in send
    raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPConnectionPool(host='earth', port=39002): Max retries exceeded with url: /api (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f18cad00910>: Failed to establish a new connection: [Errno -2] Name or service not known',))

I also checked the cryosparm status:
$ cryosparcm status
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/opt/bioSoft/cryosparc-2.0/cryosparc2_master
Current cryoSPARC version: v2.0.27
----------------------------------------------------------------------------

cryosparcm process status:

command_core                     RUNNING   pid 14193, uptime 0:06:18
command_proxy                    STOPPED   Not started
command_vis                      STOPPED   Not started
database                         RUNNING   pid 14113, uptime 0:06:21
watchdog_dev                     STOPPED   Not started
webapp                           STOPPED   Not started
webapp_dev                       STOPPED   Not started

The OS is Centos 7.3. What is wrong with the installation? Thanks a lot.


#4

I got now the same problem. My computer died while cryosparc was running. However after restart I get almost exactly the same problem.

cryosparcm start
Starting cryoSPARC System master process…
CryoSPARC is not already running.
database: started
command_core: started

and there it hangs. However if I Ctrl+C I get no more output.

cryosparcm process status:

command_core RUNNING pid 4587, uptime 0:02:07
command_proxy STOPPED Not started
command_vis STOPPED Not started
database RUNNING pid 4510, uptime 0:02:09
watchdog_dev STOPPED Not started
webapp STOPPED Not started
webapp_dev STOPPED Not started

Any idea what could be the problem?

Best,

David


#5

I found the solution for me. The master node did not reach itself. due to network issues. Now it works again.


#6

It looks like I am having a very similar problem.
Could you please elaborate further about they way you solved it?
Thanks,
Ron


#7

I tried to reach all the nodes including the master node via the ssh string that I had given in the installation. and noticed that the masternode itself was not reachable anymore due to renaming of hostnames by our IT department. So I suggest to check whether you could ssh everywhere you specified.


#8

Hey,

I get the same error as rdrighetto. I try to set-up cryosparc 2.5 on a workstation, following the ’ Quick Install: Single workstation’ . How this error can be solved? Has anyone found a solution? I think the answer from david.haselbach does not apply for a single workstation, am I right?

Thanks for all hints,

Andrzej


#9

Hi @andrzej,

Can you paste the contents of the file cryosparc2_master/config.sh (please ensure to censor your license ID).


#10

Here is my config file

export CRYOSPARC_LICENSE_ID="XX"
export CRYOSPARC_MASTER_HOSTNAME="XX"
export CRYOSPARC_DB_PATH="/usr/local/cryosparc/cryosparc2_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false

Andrzej


#11

Hi @andrzej,

Are you running cryoSPARC on CentOS? Can you post the output of cryosparcm log command_core?


#12

Hi,

Here the command output:

$ cryosparcm log command_core
COMMAND CORE STARTED ===  2019-03-04 07:01:34.472665  ==========================
*** BG WORKER START
*** LINK WORKER START
COMMAND CORE STARTED ===  2019-03-04 07:44:11.702255  ==========================
*** BG WORKER START
*** LINK WORKER START

Linux distro:

$ lsb_release -d
Description:	CentOS Linux release 7.5.1804 (Core)

Thanks,

Andrzej