Problem launching cryosparc on cluster with several users


I am using cryosparc on a cluster with multiple users. I created a new bulk directory using cryosparc configure bulk add and it is successful. But when I launched the cryosparc website using firefox and created a new account I see someone elses bulk directories and not mine. Attached is a screenshot of the launch error after inputing what my bulk directory should be. Any suggestions as to what the problem is or what I can try? Is there a launch command that would specifically the cryosparc I want? Thanks in advance for any help.

Hi @Dominique,

Do you have one single cryoSPARC instance that is running, for multiple users in a cluster? In this case, the single instance will only have one set of bulk dirs (i.e. they are not per-user) so you would see all the bulk directories no matter what cryoSPARC user you log in as.

If you are running multiple cryosparc instances as different unix users on the cluster, they must be run on different nodes. Then each instance will have its own bulk directories and you will be able to only see the bulk dirs that you configure in that instance via the command line.

Right now however it looks like the error you’re showing is saying that the path you’ve entered when you configured your dataset is not within your bulk directories. Can you show what the configuration of the dataset is? The paths should be relative (i.e. something like local_hdd/somefolder/ where local_hdd is one of the names for a bulk dir you’ve added.


Hi @Dominique,

If the multiple instances are using the same node, you need to change the instances to use different port numbers for HTTP and the internal database. This can be done by editing the file in the cryosparc installation directory. You need to change the lines:


You can change the two ports to something different, like 39000 and 39001. Then the modified instance (after cryosparc stop && cryosparc start) will be at http://node004:39000

Hello Ali,

I get these errors when I try to launch after changing the port:

Traceback (most recent call last):
File “”, line 1, in
File “/home/amedee/bin/cryoSPARC/anaconda2/lib/python2.7/site-packages/pymongo/”, line 1088, in database_names
File “/home/amedee/bin/cryoSPARC/anaconda2/lib/python2.7/site-packages/pymongo/”, line 478, in command
with client._socket_for_reads(read_preference) as (sock_info, slave_ok):
File “/home/amedee/bin/cryoSPARC/anaconda2/lib/python2.7/”, line 17, in enter
File “/home/amedee/bin/cryoSPARC/anaconda2/lib/python2.7/site-packages/pymongo/”, line 798, in _socket_for_reads
with self._get_socket(read_preference) as sock_info:
File “/home/amedee/bin/cryoSPARC/anaconda2/lib/python2.7/”, line 17, in enter
File “/home/amedee/bin/cryoSPARC/anaconda2/lib/python2.7/site-packages/pymongo/”, line 762, in _get_socket
server = self._get_topology().select_server(selector)
File “/home/amedee/bin/cryoSPARC/anaconda2/lib/python2.7/site-packages/pymongo/”, line 210, in select_server
File “/home/amedee/bin/cryoSPARC/anaconda2/lib/python2.7/site-packages/pymongo/”, line 186, in select_servers
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: [Errno 111] Connection refused