Fail to update worker node v3.1.0 to v3.2.0

Install, Configure and Update
1

Hi,

When running the automatic update to v3.2.0 it seemed like the update was only applied to the master node as I was not asked for a password half way through, like when updating another of our machines. After updating to v3.2.0, our cryosparc startup ends at:

Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
command_core: started
    command_core connection succeeded

I followed instructions here to update the worker node by copying cryosparc_worker.tar.gz into both cryosparc_worker and cryosparc2_worker directories, and in both cases running the command bin/cryosparcw update gave the output:

Updating… checking versions

Current version v3.1.0 - New version v3.1.0

Already up to date

The new version should surely be v3.2.0 ??

I should add that when I run cryosparcm update --version v.3.1.0 the update runs as expected and I can start cryosparc as normal, and use the web app.

Thanks
Max

2

Hi Max, this looks like the correct cryosparc_worker.tar.gz package failed to download. Try the update again with the override flag to force-reinstall the latest version:

cryosparcm update --override

If this doesn’t work, send me the output of that command.

3

Hi Nick,
Seems as if the same issues persists. Initially both the master and worker updates download:

>  Downloading master update...
>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
>                                  Dload  Upload   Total   Spent    Left  Speed
>   0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
> 100  785M  100  785M    0     0  21.6M      0  0:00:36  0:00:36 --:--:-- 37.0M
>   Downloading worker update...
>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
>                                  Dload  Upload   Total   Spent    Left  Speed
>   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
> 100 1807M  100 1807M    0     0  21.1M      0  0:01:25  0:01:25 --:--:-- 32.7M
>   Done.

Then the master node seems to update successfully:

Successfully updated master to version v3.2.0.

Then it appears as if cryoSPARC starts, and then the update ends - nothing happens to the worker node:

> Starting cryoSPARC System master process..
> CryoSPARC is not already running.
> database: started
> command_core: started
>     command_core connection succeeded
> command_vis: started
> command_rtp: started
>     command_rtp connection succeeded
> webapp: started
> app: started
> liveapp: started
> -----------------------------------------------------
> 
> CryoSPARC master started. 
>  From this machine, access cryoSPARC at
>     http://localhost:39000
>  and access cryoSPARC Live at
>     http://localhost:39006
>  please note the legacy cryoSPARC Live application is running at
>     http://localhost:39007
> 
>  From other machines on the network, access cryoSPARC at
>     http://hlowsrv2.bc.ic.ac.uk:39000
>  and access cryoSPARC Live at
>     http://hlowsrv2.bc.ic.ac.uk:39006
> 
> 
> Startup can take several minutes. Point your browser to the address
> and refresh until you see the cryoSPARC web interface.
> CryoSPARC is running.
> Stopping cryoSPARC 
> app: stopped
> command_core: stopped
> command_rtp: stopped
> command_vis: stopped
> liveapp: stopped
> webapp: stopped
> database: stopped
> Shut down
> Starting cryoSPARC System master process..
> CryoSPARC is not already running.
> database: started
> command_core: started
>     command_core connection succeeded

I have also tried using the override flag with the bin/cryosparcw update command in the worker node directories. I guess this doesn’t work for the same reason as before - incorrect download of the cryosparc_worker.tar.gz package.

Thanks
Max

4

@nfrasser do you have any further suggestions, I have not been able to sort this out.
Hoping to avoid reinstalltion if possible…
Thanks
Max

5

Hi @maxm, apologies for the delay.

Now that the master installation has worked, try copying cryosparc_worker.tar.gz from the cryosparc_master directory into the cryosparc_worker directory. Then navigate into the cryosparc_worker directory on the worker node via terminal and run the following:

bin/cryosparcw update --override

What output do you get?

6

Hi Nick,

I actually tried this again this morning and successfully updated the worker node, don’t know why this did not work before. If I go to the cryosparc_worker folder now and look at the version files it says v3.2.0…

However, I still cannot start cryoSPARC properly.

Startup appears to end prematurely:

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

No further outputs are given after this

Any idea?

Thanks
Max

7

I have not seen this before, it looks like one of cryoSPARC’s components is having trouble starting. Can you try running the following commands?

cryosparcm stop
eval $(cryosparcm env)
lsof -i :$CRYOSPARC_HTTP_PORT
lsof -i :$CRYOSPARC_HTTP_RTP_PORT
lsof -i :$CRYOSPARC_COMMAND_RTP_PORT
lsof -i :$CRYOSPARC_COMMAND_VIS_PORT
cryosparcm start
cryosparcm status
cryosparcm start command_rtp
cryosparcm start command_vis
cryosparcm start webapp
cryosparcm start app

Send me the full output (omit the CRYOSPARC_LICENSE_ID line from the output of cryosparcm status) then try accessing cryoSPARC’s web interface.

8

Output of cryosparcm status:

CryoSPARC System master node installed at
/data/cryosparc/cryosparc_master
Current cryoSPARC version: v3.2.0

CryoSPARC process status:

app STOPPED Not started
app_dev STOPPED Not started
command_core RUNNING pid 169150, uptime 0:00:15
command_rtp STOPPED Not started
command_vis STOPPED Not started
database RUNNING pid 169075, uptime 0:00:17
liveapp STOPPED Not started
liveapp_dev STOPPED Not started
webapp STOPPED Not started
webapp_dev STOPPED Not started

global config variables:

export CRYOSPARC_LICENSE_ID=“xxx”
export CRYOSPARC_MASTER_HOSTNAME=“hlowsrv2.bc.ic.ac.uk”
export CRYOSPARC_DB_PATH="/data/cryosparc/cryosparc_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=true
export CRYOSPARC_CLICK_WRAP=true

However, if I start up command_rtp etc. separately as you instructed, I am able to access cryosparc via the web interface…

Thanks
Max

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