'List index out of range' during Import Particles - v2.12.4

Troubleshooting
1

Dear Cryosparc developers,

I have installed cryosparc V2.12.4 on a brand new workstation running scientific linux with kernel 3.10.0-1062.4.1.el7.x86_64. Although the installation procedure seems normal, when I tried to import particles I got the error of ‘list index out of range’. This is very strange because the same set of particles and star file works perfectly fine on another workstation. Does anyone have any clue of what is going on?

Thanks a lot for your inputs!

2

Hi @chenzhao,

Can you provide us with job logs? cryosparcm joblog <project_uid> <job_uid> Also, do you happen to be importing Relion 3.1 .star files?

3

Hi @stephan,

Thank you for your reply. I am using relion 3.0.8 star file which works fine on another machine. Unfortunately, the job did not even run when showing this error (meaning it is still queued), so there is no job.log to display.

I know this is very strange problem and I have no clue of how to even troubleshot…

BTW, I have reinstalled it several times, and another lab member also tried to install using his own account, but the same problem happens to both of us…

Thanks a lot,
Chen

4

Hi @chenzhao,

Can you please provide the output of the command_core when this error happens? cryosparcm log command_core Can you also confirm where you installed cryoSPARC? Is it in your home directory?

5

Hi @stephan,

Thank you for your suggestion. This time I did get something informative, and the error I got is the following (I erased the IP address for security purpose):

---------- Scheduler running ---------------
Jobs Queued: [u’J1’, u’J1’, u’J1’]
Licenses currently active : 0
Now trying to schedule J1
Need slots : {}
Need fixed : {}
Master direct : True
Scheduling directly onto master node XXX.XX.XX.XXX
Traceback (most recent call last):
File “cryosparc2_command/command_core/init.py”, line 187, in background_worker
scheduler_run_core() # sets last run time
File “cryosparc2_command/command_core/init.py”, line 1514, in scheduler_run_core
‘lane’ : lanes[0][‘name’],
IndexError: list index out of range
****** Scheduler Failed ****

Any ideas?

Thanks a lot,
Chen

6

Hi @chenzhao,

Can you report the output of the command:
cryosparcm cli "get_scheduler_lanes()"

7

Hi, when I imported some mrcs movies and got this the error of ‘list index out of range’ too. Not sure what is the problem. The machine is running CentOS Linux release 7.7.1908 and CryoSPARC v2.13.2. Please help. Thanks.

8

When I type the command:
cryosparcm cli “get_scheduler_lanes()”

I got:
[ ]

Any idea about the error of ‘list index out of range’ ? Thanks.

9

Hi, just found on the “Change Log” page of Firefox browser for “localhost:39000”, there is “Invalid date” for cryoSPARC. Not sure why not show the normal one “Jan 30, 2020”. Is this related to the error “list index out of range”?

10

Hi @donghuachen,

The invalid date showing in some browsers is unrelated, although it has been corrected.

You’re encountering an issue because a worker node has not been set up, therefore cryoSPARC doesn’t have a target to run a job. Please follow the instructions outlined here: https://cryosparc.com/docs/reference/install/#worker

Regards,
Suhail

11

Hi @stephan and @sdawood and @donghuachen,

I am sorry that I have not got a chance to follow up on this issue for a while. I also got [] from cryosparcm cli “get_scheduler_lanes()”. Then I followed the instructions and connected the worker now the problem is solved. In older versions if the worker is not connected it gave a different error message like “job cannot run because resource is not available” or whatever. But anyway thank you so much for your help and I now learned how to identify and solve this problem.

12

Thanks. To follow the installation for “Standalone worker” worked.

1 Like
13

Hi team - I’m following up on the above comment. I am getting the same issue when trying to create a project in v2.14.2

What is the fix/workaround for this? I can’t find any other threads on the topic.

14

Hi @Michael_L,

Can you please upload a screenshot of the issue? I’m not sure what the invalid date in the change log has to do with creating a project…

Thanks,
Suhail

15

Hi,

Upon further investigation, this may have been a consequence of trying to specify a path that cryosparc user did not have access permissions for. Trying a path with read/write permissions gives the same invalid date message (the folder is empty) but it is possible to create a project and once the folder has been populated the invalid date message goes away.

Thanks