Database spawn error under other user accounts


(YH) #1

I successfully installed cryosparc v2 with user for example user1. Everything is ok. When I log in with another user account and launch the cryosparcm, I got the error message:

$cryosparcm start
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: ERROR (spawn error)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/opt/bioSoft/cryosparc-2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/", line 1149, in database_names
  File "/opt/bioSoft/cryosparc-2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/", line 491, in command
    with client._socket_for_reads(read_preference) as (sock_info, slave_ok):
  File "/opt/bioSoft/cryosparc-2/cryosparc2_master/deps/anaconda/lib/python2.7/", line 17, in __enter__
  File "/opt/bioSoft/cryosparc-2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/", line 859, in _socket_for_reads
    with self._get_socket(read_preference) as sock_info:
  File "/opt/bioSoft/cryosparc-2/cryosparc2_master/deps/anaconda/lib/python2.7/", line 17, in __enter__
  File "/opt/bioSoft/cryosparc-2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/", line 823, in _get_socket
    server = self._get_topology().select_server(selector)
  File "/opt/bioSoft/cryosparc-2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/", line 214, in select_server
  File "/opt/bioSoft/cryosparc-2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/", line 189, in select_servers
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: [Errno 111] Connection refused

I checked the cryosparcm status:
$ cryosparcm status
CryoSPARC System master node installed at
Current cryoSPARC version: v2.0.27

cryosparcm process status:

command_core                     STOPPED   Not started
command_proxy                    STOPPED   Not started
command_vis                      STOPPED   Not started
database                         FATAL     Exited too quickly (process log may have details)
watchdog_dev                     STOPPED   Not started
webapp                           STOPPED   Not started
webapp_dev                       STOPPED   Not started

I also found some text in database.log file
[initandlisten] WiredTiger error (1) [1535011333:146083][19076:0x7fcc1ad5fd40], file:WiredTiger.wt, connection: /opt/bioSoft/cryosparc-2.0/cryosparc2_database/WiredTiger.wt: handle-open: open: Operation not permitted

It seems that there is a permissions issue with the WiredTiger.wt file. But I have already set all of the subfolders and files in the cryosparc-2 folder owned/writable by everyone.

I cannot find any solution what is wrong with it.

Thanks a lot.

Database: ERROR (spawn error) during update
(Yong Zi Tan) #2

Dear Soyvia,

I have been having the same issue. Any luck in solving your problem? Thank you.

(Antoine Koehl) #3

I’m having the same issue with my install. Has anyone been able to resolve this issue? Any help is greatly appreciated!

(Stephan Arulthasan) #4

Hi @soyvia,

This seems like it’s happening because you installed cryosparc with one user, but turned it on with another. Make sure cryosparc is turned off on all accounts/machines, delete the lock file, and reinstall it with the user you want cryosparc to run on.

(YH) #5

Thanks so much for the reply. I will reinstall it following your suggestion, but how about more than one users use the same workstation and everyone must log on the workstation with his own account?
Thanks again.

(Stephan Arulthasan) #6

Hi @soyvia,

If you take a look at the overall setup description here:

It mentions that only one UNIX user needs to run cryoSPARC. You can access cryoSPARC through the user interface (the address will be displayed to you upon first installation). If you keep following the installation instructions, it’ll explain how you can create multiple user accounts that can access the UI.

(Maarten Tuijtel) #7

Hi sarulthasan,
you wrote:
Make sure cryosparc is turned off on all accounts/machines, delete the lock file, and reinstall it with the user you want cryosparc to run on.

How can I do this? I’m not sure to which lock file you are referring to.
Many thanks

(Stephan Arulthasan) #8

Hi @maarten.tuijtel,

In this case of this issue, I instructed OP to delete the .lock file because a previous user maintained a lock on the database. This is not always the solution because deleting the lock file can corrupt the database. Is is possible if you can start a new post with your specific problem and I can help you there?